E-coli impact health and environment, writing homework help

User Generated

fgnewbwb

Writing

Description

My assignment about ( E-coli impact health and environment) you have to read the 4 articles I attached in the file you can open it and see them. One of the file I put the highlight you can read it because is related my topic and add. after that, make sure to write 2 pages about the literature review. don't write introduction or conclusion. don't forget the reference and APA style

Unformatted Attachment Preview

Microbes Environ. Vol. 23, No. 2, 101–108, 2008 http://wwwsoc.nii.ac.jp/jsme2/ doi:10.1264/jsme2.23.101 Minireview Escherichia coli in the Environment: Implications for Water Quality and Human Health SATOSHI ISHII1†, and MICHAEL J. SADOWSKY1,2* 1Department of Soil, Water, and Climate, and 2BioTechnology Institute, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA (Received January 30, 2008—Accepted March 5, 2008) Escherichia coli is naturally present in the intestinal tracts of warm-blooded animals. Since E. coli is released into the environment through deposition of fecal material, this bacterium is widely used as an indicator of fecal contamination of waterways. Recently, research efforts have been directed towards the identification of potential sources of fecal contamination impacting waterways and beaches. This is often referred to as microbial source tracking. However, recent studies have reported that E. coli can become “naturalized” to soil, sand, sediments, and algae in tropical, subtropical, and temperate environments. This phenomenon raises issues concerning the continued use of this bacterium as an indicator of fecal contamination. In this review, we discuss the relationship between E. coli and fecal pollution and the use of this bacterium as an indicator of fecal contamination in freshwater systems. We also discuss recent studies showing that E. coli can become an active member of natural microbial communities in the environment, and how this bacterium is being used for microbial source tracking. We also discuss the impact of environmentally-“naturalized” E. coli populations on water quality. Key words: Escherichia coli, water quality, fecal pollution, health risks, “naturalized” population Introduction Contamination of water and food with fecal bacteria is, and remains, a common and persistent problem, impacting public health and local and national economies95). Waterrelated diseases are the major cause of morbidity and mortality worldwide. Among these, diarrheal diseases are estimated to cause 1.8 million deaths each year, mostly in developing countries113). Improved water supplies and proper sanitation can reduce the occurrence of gastrointestinal diseases. However, outbreaks of water- and food-borne diseases still often occur, even in developed countries. In the United States, 76 million cases of foodborne illness occur every year, resulting in 325,000 hospitalizations and 5,000 deaths23). Pathogenic agents causing these diseases include the enteric bacteria (diarrheagenic E. coli, Shigella, Salmonella, and Campylobacter), viruses (norovirus, hepatitis A), and protozoan (Cryptosporidium and Giardia)70). Recently, an outbreak of E. coli O157:H7 was reported in the U.S. and Canada during August and September 2006. The source of E. coli O157:H7 in this outbreak was spinach, which was most likely contaminated by irrigation water in California24). By October 6, 2006, this incident led to 199 infections, 31 cases of hemolytic-uremic syndrome (HUS), and three deaths24). In Japan, a large outbreak of E. coli O157:H7 was recorded in 1996 in elementary schools in Sakai City, Osaka, causing 7,900 hospitalizations, 101 HUS cases, and three deaths71). * Corresponding author. E-mail: sadowsky@umn.edu; Tel: +1–612– 624–2706. † Present address: Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1–1–1 Yayoi, Bunkyo-ku, Tokyo 113– 8657, Japan The source of E. coli O157:H7 for this outbreak was identified as school lunch provided on one particular day. The occurrence of water- and food-borne illnesses has economic and social impacts (medical costs, productivity losses from sick leave, decreasing tourism, etc). The Economic Research Service of the United States Department of Agriculture (USDA-ERS) estimated that in 2001, diseases caused by five major bacterial pathogens in the U.S. resulted in a loss of about $6.9 billion102). Consequently, monitoring levels of fecal contamination and the prevention of disease outbreaks is important from both public health and economic perspectives. Indicators of fecal contamination Drinking water, ground water, and recreational water are mandated to be monitored for levels of fecal indicator bacteria. These bacteria are used to indicate the potential presence of pathogens in the environment, since detection and enumeration of many types of pathogenic organisms is often difficult due to their low numbers and specific growth requirements95). While several bacteria are currently used as indicator organisms for fecal contamination, the ideal indicator bacterium should be: 1) present in intestinal tracts of warm-blooded animals; 2) present when pathogens are there, and absent in uncontaminated samples; 3) present in greater numbers than the pathogen, 4) able to survive similarly to pathogens in the environment; 5) be unable to multiply in the environment; 6) detected and quantified by easy, rapid, and inexpensive methods; and 7) non pathogenic10). Historically, total coliforms, fecal coliforms, enterococci, and E. coli have all been used as fecal indicator organisms5,64,103,104). Coliforms are defined as the lactose-fer- 102 menting, gram-negative, Enterobactericeae, including E. coli, Enterobacter, Klebsiella, and Citrobactor64). Thermotrophic coliforms (also called “fecal coliforms”), which can grow at an elevated temperature (44.5°C), were initially recommended as a more “fecal-specific” indicator103). However, some members of thermotrophic coliforms, such as Klebsiella, can originate from non-fecal sources as well104). In order to determine the best indicator of fecal pollution, the United States Environmental Protection Agency (USEPA) correlated bacterial presence to swimming-associated gastroenteric diseases at beaches on the east coast of the U.S.104). They reported that enterococci and E. coli had the highest correlation to disease incidence at marine and freshwater beaches, respectively. Therefore, enumeration of E. coli was recommended as a means to assess fecal loading in freshwater systems and potential health impacts104). E. coli is also used as an indicator of fecal contamination in the other countries5). Based on the U.S. EPA Ambient Water Quality Criteria for Bacteria104), freshwater beaches should be closed when: (i) E. coli counts of a single sample exceed 235 colonies per 100 ml water, or (ii) the geometric mean of E. coli counts of at least 5 samples, equally spread over a 30-day period, exceeds 126 colonies per 100 ml water. Some freshwater beaches often exceed these limits, and are closed for many days during summer months49). Similar criteria are also used in Japan and other countries for water quality monitoring. ISHII and SADOWSKY Fig. 1. Schematic diagram of the lifecycle of E. coli. Once E. coli is released from their primary host (warm-blooded animals) through fecal droppings, the majority of the released bacteria die due to low nutrients and other environmental factors. Some of them, however, become attached to soil, sand, sediment, or algae surfaces, and survive longer. In some conditions, these E. coli strains can grow and maintain their populations long enough to become adapted or “naturalized” to the environment. The adapted or naturalized E. coli survive and replicated in the environment, and can be reintroduced to animal hosts through contact with water and food. Escherichia coli in the environment E. coli is a rod-shape, gram-negative, gammaproteobacterium in the family Enterobactericeae, and is a member of the fecal coliform group of bacteria. The primary habitat of E. coli is thought to be the lower intestine of warm-blooded animals, including humans88). Greater than one million (106) E. coli cells are generally present in 1 g of colon material, and are often released into the environment (their secondary habitat) through fecal deposition88) (Fig. 1). Until relatively recently, however, E. coli was believed to survive poorly in the environment, and not to grow in secondary habitats, such as water, sediment, and soil116). E. coli faces many stresses in the environment, including low and high temperatures7,48,74,76,93,115), limited moisture8,13,19,20,30,76,93,115), variation in soil texture30,39,76), low organic matter content97,115), high salinity97), solar radiation110), and predation12,14,19,25,93). Recent studies, however, have shown that E. coli can survive for long periods of time in the environment, and potentially replicate, in water, on algae, and in soils in tropical16,19,20,22,37,38), subtropical30,93), and temperate environments9,17,20,48,49,61,99,109). Relatively high concentrations of nutrients and warm temperatures in tropical and subtropical environments are likely factors enabling E. coli to survive and grow outside of the host22,116). The addition of nutrients, such as manure, greatly increased the concentration of E. coli in Ontario soil99), suggesting that E. coli can grow and maintain their population in temperate environments if favorable conditions exist (Fig. 1). Byappanahalli et al.20) reported that E. coli strains were repeatedly isolated from exclosure-protected temperate forest soils in Indiana, and their genetic structure was different Fig. 2. A) Multivariate analysis of variance (MANOVA) of HFERP DNA fingerprints from E. coli strains obtained from soils ( ), deer ( ), and birds [geese ( ), terns ( ), and gulls ( )]. The first two discriminants are represented by the distances along the x and y axes (adapted from Byappanahalli et al.20) B) Conceptual representation of E. coli distribution among humans, animal hosts, and environmental reservoirs. Some level of host specificity can be detected in among E. coli, but some strains can be found in multiple hosts. Environmentallyadapted “naturalized” E. coli strains are unique and different from those found in humans and other animal hosts. Pathogenic E. coli strains can cause human diseases, and can be found in other animal hosts and in the environments. from these bacteria isolated from animals (Fig. 2A). Similarly, Ishii et al.48) reported that genotypically-identical E. coli strains were repeatedly isolated from a temperate soil near Duluth, Minnesota. The soil-borne E. coli strains had DNA fingerprint patterns distinct from animal-borne isolates, suggesting that they were not recently deposited by animals. The presence of E. coli attached to the macroalga Cladophora in Lake Michigan18,21,108) and to periphyton in Lake Superior61), and in beach sand and sediments9,49,106) has also been reported. Na et al.74) showed that E. coli can enter a viable-but-nonculturable (VBNC) state in natural water held at 4°C. Taken together, these results suggest that E. coli can E. coli in the Environment survive, grow, and become “naturalized” members of soil and algal communities. The ability of E. coli to survive and grow in the environment is likely due to its versatility in energy acquisition. E. coli is a heterotrophic bacterium, requiring only simple carbon and nitrogen sources, plus phosphorus, sulfur, and other trace elements for their growth. This bacterium can also degrade various types of aromatic compounds such as phenylacetic acid and benzoic acid, to acquire energy31). In addition, E. coli can grow both under aerobic and anaerobic conditions, which they may face in a variety of fluctuating environments. Furthermore, E. coli can grow over a broad range of temperatures (7.5–49°C), with has a growth optimum of 37°C47,55). The long-term survival of E. coli under freezing temperature has also been reported4,13,39). The ability of E. coli to grow and survive under various conditions likely allows them to become an integrated member of microbial communities in a variety of environments. Pathogenic E. coli Although most E. coli are harmless commensal bacteria, some strains can cause human diseases. Shiga toxin-producing E. coli (STEC), including enterohemorrhagic E. coli (EHEC), can cause bloody diarrhea as well as potentially fatal human diseases, such as hemolytic uremic syndrome (HUS) and hemorrhagic colitis (HC)75). E. coli O157:H7 is among the most recognized serotypes of EHEC, and has caused many large outbreaks of food- and water-borne illness. In addition to STEC and EHEC, at least five additional pathogroups of E. coli have been identified. Enteropathogenic E. coli (EPEC) are one of the major causes of watery diarrhea in infants, especially in developing countries. Enterotoxigenic E. coli (ETEC) are the main cause of traveler’s diarrhea and enteroaggregative E. coli (EAEC) can cause persistent diarrhea, lasting for more than two weeks. Enteroinvasive E. coli (EIEC) are genetically, biochemically, and pathogenically closely related to Shigella75,83). Several, researchers consider Shigella as being a subgroup of E. coli84). While extraintestinal pathogenic E. coli (ExPEC), including uropathogenic and avian pathogenic strains, are thought to be harmless while they are in the intestinal tracts, they can cause neonatal meningitis/sepsis and urinary tract infections if acquired by others107). Extensive reviews are available on the pathogenesis, diagnosis, and sources of pathogenic E. coli56,67,75,80). However, the distribution of pathogenic E. coli in the environment has not been examined in detail. Several studies have shown that EPEC strains can be more frequently detected in the environment than the STEC49,63). Ishii et al.49) and Lauber et al.63) reported the occurrence of potential EPEC strains, but no STEC, at Great Lake beaches. Similarly, Higgins et al.46) reported that the intimin receptor gene tir, an EPEC virulence factor, was more frequently detected than stx genes (STEC virulence factor) in water samples from urban streams. While cattle and other ruminant animals (sheep, goats, and deer) may serve as major reservoirs of STEC50,67,80), EPEC strains might be evenly distributed among diverse human and animal hosts50). The broad distribution of potential EPEC in a large number of animal hosts 103 may, in part, explain the frequent detection of this pathogen in the environment. Diversity of E. coli E. coli is genotypically and phenotypically diverse. Traditional classification of E. coli is made based on reaction of antibodies with three types of antigens: the somatic (O), capsular (K), and flagellar (H) antigens75). Currently, E. coli has been shown to possess 173 O, 103 K, and 56 H antigens, and the number of newly discovered antigens is increasing (The E. coli Index [http://ecoli.bham.ac.uk/]). Diverse E. coli serotypes, which are defined by the combination of O and H antigens, have been identified. For example, E. coli O157:H7 is the most well-known serotype that can cause human disease80). E. coli strains also vary in other phenotypic characteristics, such as carbon utilization patterns, antibiotic resistance profiles, flagellar motility, ability to form biofilms, and the ability to cause diseases3,35,60,79,119). This is probably due to gene mutations and acquisition of new genes via plasmid- or phage-mediated horizontal gene transfer. Genome sequencing has revealed that horizontal gene transfer plays a significant and important role in gene acquisition in E. coli107). In addition, mutation can also contribute to the phenotypic diversity of E. coli. For example, diversity in carbon utilization ability may be caused by mutations and resulting functional failure of the affected genes. Cooper and Lenski28) observed that the several lines of E. coli that were adapted to glucose medium over thousands of generations lost their ability to utilize several other carbon sources. Similarly, auxotrophic mutants (i.e. mutants that cannot synthesize necessary amino acids for growth) were often obtained from biofilm communities29). These studies indicate that some phenotypic variation may be attributed to ecological specialization: thus, E. coli adapted to one environment may lose fitness in another. Diversity of E. coli is observed at the genotype level as well. While more than 650 genotypes were observed among 1,535 unique E. coli strains based on repetitive element palindromic (rep)-PCR DNA fingerprinting, rarefaction analysis revealed that the diversity observed was not saturated53). Similar findings were also reported in other studies3,66,69,119). DNA fingerprint patterns are variable even within the same serotype. For example, pulsed-field gel electrophoresis (PFGE) DNA fingerprint patterns of 1,798 E. coli strains belonging to the O157 serogroup were only 10% similar77). Whole genome PCR scanning analysis revealed that the position and structure of prophages (i.e. viral phage integrated into the bacterial chromosome) were different among 9 representative O157H7 strains77). Comparative genomic analysis done by using microarrays also showed that prophage or prophage-related elements contributed greatly (>85%) to the presence of genes in 12 E. coli O157:H7 and related strains114). These reports indicates that bacteriophage greatly contribute to genotypic diversity. Other factors, such as recombination, can also contribute to genotypic diversity72,111). Recent progress in genome sequencing revealed differences in gene content among E. coli strains. The complete 104 genomes of eight E. coli strains have been published, including nonpathogenic E. coli K12 strains11,73), EHEC O157:H7 strains45,81), uropathogenic strains15,26,107), and an avian pathogenic strain54). Genome sequencing projects of 31 other E. coli strains are currently in progress (http://www.genomesonline.org/). Genome comparisons among E. coli strains, MG1655 (K12), EDL933 (O157:H7), and CFT073 (uropath), revealed that only 40% of the proteins were shared in common107), further indicating that E. coli strains acquired many of their genes by horizontal gene transfer. While E. coli has diverse genotypic and phenotypic characteristics, some characters are shared among strains exposed to similar environments. This is thought to be largely driven by selection pressure. If some of the characteristics among E. coli strains can be grouped by origin of isolation (i.e. host animals), then it is possible to use these phenotypes or genotypes as a tool to determine the source of unknown bacteria. This approach is called microbial source tracking (MST), and is discussed below in more detail. Microbial source tracking Potential sources of fecal contamination in water, soil, and sediments include human sewage, pets, farm animals, wildlife, and waterfowl. Although recreational beaches are routinely monitored for the levels of fecal indicator bacteria, microbial numbers alone cannot determine the potential sources of these bacteria. The identification of potential sources of E. coli and other fecal indicator organisms (such as enterococci and Bacteroides) in the environment is of great interest to the public, government regulatory agencies, beach managers, and operators of sewage treatment facilities. MST data can be used to establish proper risk assessment and abatement procedures96). Several library-dependent and -independent methods have been developed for MST studies (see reviews by Harwood44), Sadowsky et al.86), Santo Domingo et al.87), Scott et al.90), Stewart et al.95), Stoeckel and Harwood96), USEPA105), Yan and Sadowsky118). A library for MST studies contains a dataset of characteristics of the target microorganism from known-source hosts95). Both phenotypic (e.g. antibiotic resistance profile, carbon utilization patterns) and genotypic characteristics (e.g. DNA fingerprint patterns) can be used for library-dependent MST methods60,95,96,118). Among these, repPCR DNA fingerprinting, including horizontal fluorophoreenhanced rep-PCR (HFERP) DNA fingerprinting, has been frequently used as a library-dependent MST method. The technique is reproducible, relatively inexpensive to use, and has relatively high throughput as compared to other molecular methods118). Several studies have shown that the HFERP DNA fingerprint patterns of E. coli strains could be clustered by animal host groups (e.g. Fig. 2A)20,33,48,53). This indicates that some level of host specificity exist in E. coli population (Fig. 2B). However, when E. coli is used as a target organism for MST studies, a large database is necessary to adequately represent diverse genetic and phenotypic characteristics in E. coli populations obtained from multiple hosts51). Moreover, since E. coli is not evenly distributed among host animal species, the distribution of this bacterium in the environment is patchy20,49). The distribution of E. coli is also subject to geo- ISHII and SADOWSKY graphical and temporal variability, thus adequate care must be taken in obtaining representative samples for the construction and analysis of libraries. While these issues need to be taken account in the development of any host-source library95), library-dependent MST methods appear to be useful tools for analysis of fecal contamination in relatively small areas with a limited number of potential input sources. For example, Ishii et al.49) successfully applied HFERP DNA fingerprinting to determine potential sources of E. coli contaminating beaches in Lake Superior. Library-independent MST methods employ host-specific markers, including PCR primers32,52,57–59,62,78,89,91,92) and gene probes43,94), to determine sources of fecal pollution. Host-specific markers, targeting 16S rDNA and other genes, have been identified for E coli43,57,58), methanogens100,101), viruses and coliphage52,59), member of the Bacteriodales32,62,78,89), and metagenomic DNA fragments91,92). However, before use in field studies these host-specific markers need to be validated by estimating the proportion of false-positives and false-negatives in the target population, and for sensitivity in detecting these bacteria that are present in low numbers in complex matrices, such as soil and sediment. In some cases the primers work well when tested with fecal samples, but have sensitivity issues when used with environmental samples, Although only a relatively few field investigations have been done using library-independent approaches52,62,78,89,92), this method appears to be promising for future MST studies86). While E. coli is often used as an organism for both librarydependent and -independent MST studies, and as a metric for fecal contamination, some researchers criticize its use in MST studies postulating that this bacterium may not be distinct enough to be separated into host source-specific groups42,68). Gordon and Lee41) used multilocus enzyme electrophoresis to characterize enteric bacteria and found that only 6% of the genetic diversity in E. coli could be attributed to host animals in Australia. Other studies have shown that while the relationship between E coli genotypes and animal source groups is not perfectly correlated, there is significant clustering of strains by animal or origin33,53). In order to establish a reliable MST method, Malakoff68) suggested that population genetic studies done using more sensitive and discriminative methods are needed to better understand the relationship between diversity and host specificity in E. coli. Health risk implications and MST studies One of the main underlying assumptions of all MST studies is that fecal contamination originating from human sources is indicative of greater health risks for humans than is contamination originating from animals and the environment. This hypothesis, however, has not been adequately tested. Most MST methods are, therefore, designed to correctly and accurately separate fecal indicator organisms from human and other animal sources. Although some pathogens, such as Shigella, may be specifically harbored by humans34), others can be distributed among diverse animals and also be resident in various environments112). For example, birds, including chickens and turkeys, often harbor Salmonella and Campylobacter2,65), and pathogenic E. coli can also be found in non-human animals and in several environments (Fig. 2B). E. coli in the Environment In addition, ruminants, such as cows, sheep, and goats, have been reported to be the major reservoir of STEC50,67,80). Based on these, and other findings, it is obvious that the distribution of pathogenic E. coli and other human pathogens among diverse animal hosts and in the environment is still not well understood. Some pathogenic E. coli, however, appear frequently in specific lineages82). Population genetic studies done by using multilocus enzyme electrophoresis and strains from the E. coli reference (ECOR) collection revealed that E. coli can be divided into four major phylogenetic groups: A, B1, B2, and D27,85). While most STEC strains are found in phylogenetic groups A and B1, ExPEC strains are more frequently identified in phylogenetic group B2 and D27,40). Gordon42) proposed to use virulence factor genes as a MST tool. However, the relationship between phylogenetic groups and host animals is not well understood. Moreover, linking MST studies and potential human health hazards is a challenging but important topic. The construction of microbial risk models is necessary to assess potential human health hazards6). For accurate modeling, however, future studies are needed to clarify the distribution of these pathogens in animals and the environment, and the evolutionary and ecological forces leading to their establishment in humans, animals and environmental niches. Future directions It is clear from results of numerous studies that alternate fecal indicators need to be developed in order to better predict public health risks. Savichtcheva et al.89) reported that a genetic marker for Bacteroides 16S rRNA had a higher predictive value for the occurrence of bacterial enteric pathogens than those based on total and fecal coliforms. Other indicators will likely emerge from ongoing and future epidemiological analyses. Detection and quantification of potentially pathogenic E. coli and other enteric pathogens may be another approach to assess human health hazards. Ahmed et al.1) and Ishii et al.50) surveyed E. coli strains isolated from water samples by using PCR targeting virulence factor genes. The use of colony hybridization using virulence genespecific probes is a promising alternate method since it is reliable and can be applied to high-throughput and largescale studies86,117). The use of robots to pick and array E. coli colonies allows for the simultaneous analysis of up to 20,736 strains, with minimal time and human input117). Another interesting direction for future research is to further investigate the ecology of naturalized E. coli strains. Several questions can be asked about these bacteria, chief of which is why these naturalized strains survive and grow better in the environment than other E. coli. Other questions also remain, such as: What mechanisms enable these bacteria to better survive and grow in soils relative to non-naturalized strains?, What are the unique genetic characteristics of these strains?, Where can we find naturalized E. coli besides soil, sand, and sediments?, and When and how did these strains evolve from a common E. coli ancestral lineage? Genome sequencing of the naturalized E. coli strains may provide us useful information to answer some of these questions. Comparative genomics of naturalized and other E. coli strains 105 (mostly pathogenic strains) is also of interest for ecological perspectives, and the sequencing of some of these environmental strains is currently under way. In situ evolutionary experiments may also provide new insights into adaptive mechanisms that microorganisms use to survive in soil and water environments. Previous laboratory experiments reported that error-prone DNA polymerase was induced under starvation conditions, and produced mutations at a high rate36,98). Since nutrients may limit the growth of E. coli in soil, it is possible that error-prone DNA polymerases may be activated and contributes to the genetic variation observed among soil-naturalized E. coli strains. This implies that mutation rates in E. coli may be different in soil compared to artificial media and the intestinal tract. Other evolutionary mechanisms, such as recombination, plasmid transfer, and the influence of bacteriophage, also need to be studied to understand evolution of E. coli in the environment. Acknowledgements This work was supported, in part, from grants from the Minnesota Sea Grant College Program, supported by the NOAA Office of Sea Grant, United States Department of Commerce, under Grant NA03-OAR4170048, and the University of Minnesota Agricultural Experiment Station (M.J.S.). References 1) Ahmed, W., J. Tucker, K.A. Bettelheim, R. Neller, and M. Katouli. 2007. Detection of virulence genes in Escherichia coli of an existing metabolic fingerprint database to predict the sources of pathogenic E. coli in surface waters. Water Res. 41:3785–3791. 2) Altekruse, S.F., N.J. Stern, P.I. Fields, and D.L. Swerdlow. 1999. Campylobacter jejuni—an emerging foodborne pathogen. Emerg. Infect. Dis. 5:28–35. 3) Anderson, M.A., J.E. Whitlock, and V.J. Harwood. 2006. Diversity and distribution of Escherichia coli genotypes and antibiotic-resistant phenotypes in feces of humans, cattle and horses. Appl. Environ. Microbiol. 72:6914–6922. 4) Ansay, S.E., K.A. Darling, and C.W. Kaspar. 1999. Survival of Escherichia coli O157:H7 in ground-beef patties during storage at 2, −2, 15 and then −2°C, and −20°C. J. Food Prot. 62:1243–1247. 5) Ashbolt, N.J., W.O.K. Grabow, and M. Snozzi. 2001. Indicators of microbial water quality, p. 289–316. In: L. Fewtrell, and J. Bartram (eds.), Water Quality: Guidelines, Standards and Health. IWA Publishing, London. 6) Balbus, J., R. Parkin, A. Makri, L. Ragain, M. Embrey, and F. Hauchman. 2004. Defining susceptibility for microbial risk assessment: results of a workshop. Risk Anal. 24:197–208. 7) Berry, E.D., and P.M. Foegeding. 1997. Cold temperature adaptation and growth of microorganisms. J. Food Prot. 60:1583–1594. 8) Berry, E.D., and D.N. Miller. 2005. Cattle feedlot soil moisture and manure content: II. impact on Escherichia coli O157. J. Environ. Qual. 34:656–663. 9) Beversdorf, L.J., S.M. Bornstein-Forst, and S.L. McLellan. 2007. The potential for beach sand to serve as a reservoir for Escherichia coli and the physical influences on cell die-off. J. Appl. Microbiol. 102:1372–1381. 10) Bitton, G. 2005. Wastewater Microbiology, 3rd ed. Wiley-Liss, Hoboken, NJ. 11) Blattner, F.R., G. Plunkett, III, C.A. Bloch, et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453– 1462. 12) Bogosian, G., L.E. Sammons, P.J. Morris, J.P. O’Neil, M.A. Heitkamp, and D.B. Weber. 1996. Death of the Escherichia coli K-12 strain W3110 in soil and water. Appl. Environ. Microbiol. 62:4114– 4120. 106 13) Bollman, J., A. Ismond, and G. Blank. 2001. Survival of Escherichia coli O157:H7 in frozen foods: impact of the cold shock response. Intl. J. Food Microbiol. 64:127–138. 14) Brettar, I., and M.G. Höfle. 1992. Influence of ecosystematic factors on survival of Escherichia coli after large-scale release into lake water mesocosms. Appl. Environ. Microbiol. 58:2201–2210. 15) Brzuszkiewicz, E., H. Bruggemann, H. Liesegang, et al. 2006. How to become a uropathogen: comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc. Natl. Acad. Sci. USA 103:12879–12884. 16) Byappanahalli, M.N., and R.S. Fujioka. 1998. Evidence that tropical soil environment can support the growth of Escherichia coli. Water Sci. Technol. 38:171–174. 17) Byappanahalli, M., M. Fowler, D. Shively, and R. Whitman. 2003a. Ubiquity and persistence of Escherichia coli in a midwestern coastal stream. Appl. Environ. Microbiol. 69:4549–4555. 18) Byappanahalli, M.N., D.A. Shively, M.B. Nevers, M.J. Sadowsky, and R.L. Whitman. 2003b. Growth and survival of Escherichia coli and enterococci populations in the macro-alga Cladophora (Chlorophyta). FEMS Microbiol. Ecol. 46:203–211. 19) Byappanahalli, M., and R. Fujioka. 2004. Indigenous soil bacteria and low moisture may limit but allo faecal bacteria to multiply and become a minor population in tropical soils. Water Sci. Technol. 50:27–32. 20) Byappanahalli, M.N., R.L. Whitman, D.A. Shively, M.J. Sadowsky, and S. Ishii. 2006. Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed. Environ. Microbiol. 8:504–513. 21) Byappanahalli, M.N., R.L. Whitman, D.A. Shively, J.A. Ferguson, S. Ishii, and M.J. Sadowsky. 2007. Population structure of Cladophora-borne Escherichia coli in nearshore water of Lake Michigan. Water Res. 41:3649–3654. 22) Carrillo, M., E. Estrada, and T.C. Hazen. 1985. Survival and enumeration of the fecal indicators Bifidobacterium adolescentis and Escherichia coli in a tropical rain forest watershed. Appl. Environ. Microbiol. 50:468–476. 23) CDC. 2005. Foodborne illness: Frequently Asked Questions. [Online.] http://www.cdc.gov/ncidod/dbmd/diseaseinfo/files/ foodborne_illness_FAQ.pdf 24) CDC. 2006. Multi-State Outbreak of E. coli O157:H7 Infections From Spinach. [Online.] http://www.cdc.gov/foodborne/ecolispinach/ 25) Chao, W.L., and R.L. Feng. 1990. Survival of genetically engineered Escherichia coli in natural soil and river water. J. Appl. Bacteriol. 68:319–325. 26) Chen, S.L., C.S. Hung, J. Xu, et al. 2006. Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. Proc. Natl. Acad. Sci. USA 103:5977–5982. 27) Clermont, O., S. Bonacorsi, and E. Bingen. 2000. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66:4555–4558. 28) Cooper, V.S., and R.E. Lenski. 2000. The population genetics of ecological specialization in evolving Escherichia coli populations. Nature 407:736–739. 29) Cooper, T.F., H.J.E. Beaumont, and P.B. Rainey. 2005. Biofilm diversity as a test of the insurance hypothesis. Microbiology 151:2815–2816. 30) Desmarais, T.R., H.M. Solo-Gabriele, and C.J. Palmer. 2002. Influence of soil on fecal indicator organisms in a tidally influenced subtropical environment. Appl. Environ. Microbiol. 68:1165–1172. 31) Díaz, E., A. Ferrandez, M.A. Prieto, and J.L. Garcia. 2001. Biodegradation of aromatic compounds by Escherichia coli. Microbiol. Mol. Biol. Rev. 65:523–569. 32) Dick, L.K., A.E. Bernhard, T.J. Brodeur, J.W. Santo Domingo, J.M. Simpson, S.P. Walters, and K.G. Field. 2005. Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Appl. Environ. Microbiol. 71:3184– 3191. 33) Dombek, P.E., L.K. Johnson, S.T. Zimmerley, and M.J. Sadowsky. 2000. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Appl. Environ. Microbiol. 66:2572–2577. 34) DuPont, H.L. 1988. Shigella. Infect. Dis. Clin. N. Am. 2:599–605. ISHII and SADOWSKY 35) Durso, L.M., D. Smith, and R.W. Hutkins. 2004. Measurements of fitness and competition in commensal Escherichia coli and E. coli O157:H7 strains. Appl. Environ. Microbiol. 70:6466–6472. 36) Foster, P.L. 2004. Adaptive mutation in Escherichia coli. J. Bacteriol. 186:4846–4852. 37) Fujioka, R.S. 2001. Monitoring coastal marine waters for sporeforming bacteria of faecal and soil origin to determine point from non-point source pollution. Water Sci. Technol. 44:181–188. 38) Fujioka, R.S., and M.N. Byappanahalli. 2003. Proceedings and Report: Tropical Water Quality Indicator Workshop, SR-2004-01, pp. 1–95. Honolulu, HI, USA: University of Hawaii, Water Resources Research Center. [Online.] http://www.wrrc.hawaii.edu/ tropindworkshop.html 39) Gagliardi, J.V., and J.S. Karns. 2002. Persistence of Escherichia coli O157:H7 in soil and on plant roots. Environ. Microbiol. 4:89–96. 40) Girardeau, J.P., A. Dalmasso, Y. Bertin, C. Ducrot, S. Bord, V. Livrelli, C. Vernozy-Rozand, and C. Martin. 2005. Association of virulence genotype with phylogenetic background in comparison to different seropathotypes of Shiga toxin-producing Escherichia coli isolates. J. Clin. Microbiol. 43:6098–6107. 41) Gordon, D.M., and J. Lee. 1999. The genetic structure of enteric bacteria from Australian mammals. Microbiology 145:2673–2682. 42) Gordon, D.M. 2001. Geographical structure and host specificity in bacteria and the implications for tracing the source of coliform contamination. Microbiology 147:1079–1085. 43) Hamilton, M.J., T. Yan, and M.J. Sadowsky. 2006. Development of goose- and duck-specific DNA markers to determine sources of Escherichia coli in waterways. Appl. Environ. Microbiol. 72:4012– 4019. 44) Harwood, V.J. 2007. Assumptions and limitations associated with microbial source tracking, p. 33–64. In: J.W. Santo Domingo, and M.J. Sadowsky (eds.) Microbial Source Tracking. ASM Press, Washington, D.C. 45) Hayashi, T., K. Makino, M. Ohnishi, et al. 2001. Complete genome sequence of enterohemorrhagic Eschelichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:11– 22. 46) Higgins, J.A., K.T. Belt, J.S. Karns, J. Russell-Anelli, and D.R. Shelton. 2005. tir- and stx-positive Escherichia coli in stream waters in a metropolitan area. Appl. Environ. Microbiol. 71:2511–2519. 47) Ingraham, J.L., and A.G. Marr. 1996. Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd ed. American Society for Microbiology, Washington, DC. 48) Ishii, S., W.B. Ksoll, R.E. Hicks, and M.J. Sadoswky. 2006. Presence and growth of naturalized Escherichia coli in temperate soils from Lake Superior watersheds. Appl. Environ. Microbiol. 72:612– 621. 49) Ishii, S., D.L. Hansen, R.E. Hicks, and M.J. Sadowsky. 2007. Beach sand and sediments are temporal sinks and sources of Escherichia coli in Lake Superior. Environ. Sci. Technol. 41:2203–2209. 50) Ishii, S., K.P. Meyer, and M.J. Sadowsky. 2007. Relationship between phylogenetic groups, genotypic clusters, and virulence gene profiles of Escherichia coli strains from diverse human and animal sources. Appl. Environ. Microbiol. 73:5703–5710. 51) Jenkins, M.B., P.G. Hartel, T.J. Olexa, and J.A. Stuedemann. 2003. Putative temporal variability of Escherichia coli ribotypes from yearling steers. J. Environ. Qual. 32:305–309. 52) Jiang, S.C., W. Chu, and J.-W. He. 2007. Seasonal detection of human viruses and coliphage in Newport Bay, California. Appl. Environ. Microbiol. 73:6468–6474. 53) Johnson, L.K., M.B. Brown, E.A. Carruthers, J.A. Ferguson, P.E. Dombek, and M.J. Sadowsky. 2004. Sample size, library composition, and genotypic diversity among natural populations of Escherichia coli from different animals influence accuracy of determining sources of fecal pollution. Appl. Environ. Microbiol. 70:4478–4485. 54) Johnson, T.J., S. Kariyawasam, Y. Wannemuehler, P. Mangiamele, S.J. Johnson, C. Doetkott, J.A. Skyberg, A.M. Lynne, J.R. Johnson, and L.K. Nolan. 2007. The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J. Bacteriol. 189:3228–3236. 55) Jones, T., C.O. Gill, and L.M. McMullen. 2004. The behaviour of log phase Escherichia coli at temperatures that fluctuate about the minimum for growth. Lett. Appl. Microbiol. 39:296–300. E. coli in the Environment 56) Kaper, J.B., J.P. Nataro, and H.L.T. Mobley. 2004. Pathogenic Escherichia coli. Nat. Rev. Microbiol. 2:123–140. 57) Khatib, L.A., Y.L. Tsai, and B.H. Olson. 2002. A biomarker for the identification of cattle fecal pollution in water using the LTIIa toxin gene from enterotoxigenic Escherichia coli. Appl. Microbiol. Biotechnol. 59:97–104. 58) Khatib, L.A., Y.L. Tsai, and B.H. Olson. 2003. A biomarker for the identification of swine fecal pollution in water, using the STII toxin gene from enterotoxigenic Eschrichia coli. Appl. Microbiol. Biotechnol. 63:231–238. 59) Kirs, M., and D.C. Smith. 2007. Multiplex quantitative real-time reverse transcriptase PCR for F+-specific RNA coliphages: a method for use in microbial source tracking. Appl. Envir. Microbiol. 73:808–814. 60) Krumperman, P.H. 1983. Multiple antibiotic resistance indexing of Escherichia coli to identify high-risk sources of fecal contamination of foods. Appl. Environ. Microbiol. 46:165–170. 61) Ksoll, W.B., S. Ishii, M.J. Sadowsky, and R.E. Hicks. 2007. Presence and sources of fecal coliform bacteria in epilithic periphyton communities. Appl. Environ. Microbiol. 73:3771–3778. 62) Layton, A., L. McKay, D. Williams, V. Garrett, R. Gentry, and G. Sayler. 2006. Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Appl. Environ. Microbiol. 72:4214– 4224. 63) Lauber, C.L., L. Glatzer, and R.L. Sinsabaugh. 2003. Prevalence of pathogenic Escherichia coli in recreational waters. J. Great Lakes Res. 29:301–306. 64) Leclerc, H., D.A.A. Mossel, S.C. Edberg, and C.B. Struijk. 2001. Advances in the bacteriology of the coliform group: their suitability as markers of microbial water safety. Ann. Rev. Microbiol. 55:201– 234. 65) Levesque, B., P. Brousseau, F. Bernier, E. Dewailly, and J. Joly. 2000. Study of the bacterial content of ring-billed gull droppings in relation to recreational water quality. Water Res. 34:1089–1096. 66) Lu, Z., D. Lapen, A. Scott, A. Dang, and E. Topp. 2005. Identifying host sources of fecal pollution: diversity of Escherichia coli in confined dairy and swine production systems. Appl. Environ. Microbiol. 71:5992–5998. 67) Mainil, J.G., and G. Daube. 2005. Verotoxigenic Escherichia coli from animals, humans and foods: who’s who? J. Appl. Microbiol. 98:1332–1344. 68) Malakoff, D. 2002. Microbiologists on the trail of polluting bacteria. Science 295:2352–2353. 69) McLellan, S.L. 2004. Genetic diversity of Escherichia coli isolated from urban rivers and beach water. Appl. Environ. Microbiol. 70:4658–4665. 70) Mead, P.S., and L. Slutsker. 1999. Food-related illness and death in the United States. Emerg. Infect. Dis. 5:607–625. 71) Michino, H., Araki, K., Minami, et al. 1998. Recent outbreaks of infections caused by Escherichia coli O157:H7 in Japan, p. 73–81. In J.B. Kaper, and A.D. O’Brien (eds.) Escherichia coli O157:H7 and Other Shiga Toxin-Producing E. coli Strains. ASM Press, Washington, D.C. 72) Milkman, R., and M. McKane. 1995. DNA sequence variation and recombination in E. coli. In: S. Baumberg, J.P.W. Young, E.M.H. Wellington, and J.R. Saunders (eds.) Population Genetics of Bacteria. Cambridge University Press, Cambridge, United Kingdom. 73) Mori, H., K. Isono, T. Horiuchi, and T. Miki. 2000. Functional genomics of Escherichia coli in Japan. Res. Microbiol. 151:121– 128. 74) Na, S.H., K. Miyanaga, H. Unno, and Y. Tanji. 2006. The survival response of Escherichia coli K12 in a natural environment. Appl. Microbiol. Biotechnol. 72:386–392. 75) Nataro, J.P., and J.B. Kaper. 1998. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11:142–201. 76) Ogden, I.D., D.R. Fenlon, A.J.A. Vinten, and D. Lewis. 2001. The fate of Escherichia coli O157 in soil and its potential to contaminate drinking water. Intl. J. Food Microbiol. 66:111–117. 77) Ohnishi, M., J. Terajima, K. Kurokawa, K. Nakayama, T. Murata, K. Tamura, Y. Ogura, H. Watanabe, and T. Hayashi. 2002. Genomic diversity of enterohemorrhagic Escherichia coli O157 revealed by whole genome PCR scanning. Proc. Natl. Acad. Sci. USA 99:17043–17048. 107 78) Okabe, S., N. Okayama, O. Savichtcheva, and T. Ito. 2007. Quantification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Appl. Microbiol. Biotechnol. 74:890–901. 79) Parveen, S., R.L. Murphree, L. Edmiston, C.W. Kaspar, K.M. Portier, and M.L. Tamplin. 1997. Association of multiple-antibioticresistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay. Appl. Environ. Microbiol. 63:2607–2612. 80) Paton, J.C., and A.W. Paton. 1998. Pathogenesis and diagnosis of Shiga toxin-producing Escherichia coli infections. Clin. Microbiol. Rev. 11:450–479. 81) Perna, N.T., G. Plunkett, V. Burland, et al. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529– 533. 82) Picard, B., J.S. Garcia, S. Gouriou, P. Duriez, N. Brahimi, E. Bingen, J. Elion, and E. Denamur. 1999. The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect. Immun. 67:546–553. 83) Pupo, G.M., D.K. Karaolis, R. Lan, and P.R. Reeves. 1997. Evolutionary relationships among pathogenic and nonpathogenic Escherichia coli strains inferred from multilocus enzyme electrophoresis and mdh sequence studies. Infect. Immun. 65:2685–2692. 84) Pupo, G.M., R. Lan, and P.R. Reeves. 2000. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of any of their characteristics. Proc. Natl. Acad. Sci. USA 97:10567–10572. 85) Reid, S.D., C.J. Herbelin, A.C. Bumbaugh, R.K. Selander, and T.S. Whittam. 2000. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406:64–67. 86) Sadowsky, M.J., D.R. Call, and J.W. Santo Domingo. 2007. The future of microbial source tracking studies, p. 235–277. In: J.W. Santo Domingo and M.J. Sadowsky (eds.) Microbial Source Tracking. ASM Press, Washington, D.C. 87) Santo Domingo, J.W., D.G. Bambic, T.A. Edge, and S. Wuertz. 2007. Quo vadis source tracking? Towards a strategic framework for environmental monitoring of fecal pollution. Water Res. 41:3559– 3552. 88) Savageau, M.A. 1983. Escherichia coli habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122:732–744. 89) Savichtcheva, O., N. Okayama, and S. Okabe. 2007. Relationship between Bacteroides 16S rRNA genetic markes and presence of bacterial enteric pathogens and conventional fecal indicators. Water Res. 41:3615–3628. 90) Scott, T.M., J.B. Rose, T.M. Jenkins, S.R. Farrah, and J. Lukasik. 2002. Microbial source tracking: current methodology and future directions. Appl. Environ. Microbiol. 68:5796–5803. 91) Shanks, O.C., J.W. Santo Domingo, R. Lamendella, C.A. Kelty, and J.E. Graham. 2006. Competitive metagenomic DNA hybridization identifies host-specific microbial genetic markers in cow fecal samples. Appl. Environ. Microbiol. 72:4054–4060. 92) Shanks, O.C., J.W. Santo Domingo, J. Lu, C.A. Kelty, and J.E. Graham. 2007. Identification of bacterial DNA markers for the detection of human fecal pollution in water. Appl. Environ. Microbiol. 73:2416–2422. 93) Solo-Gabriele, H.M., M.A. Wolfert, T.R. Desmarais, and C.J. Palmer. 2000. Sources of Escherichia coli in a coastal subtropical environment. Appl. Environ. Microbiol. 66:230–237. 94) Soule, M., E. Kuhn, F. Loge, J. Gay, and D.R. Call. 2006. Using DNA microarrays to identify library-independent markers for bacterial source tracking. Appl. Environ. Microbiol. 72:1843–1851. 95) Stewart, J., J.W. Santo Domingo, and T.J. Wade. 2007. Fecal pollution, public health, and microbial source tracking, p. 1–32. In: J.W. Santo Domingo and M.J. Sadowsky (eds.) Microbial Source Tracking. ASM Press, Washington, D.C. 96) Stoeckel, D.M., and V.J. Harwood. 2007. Performance, design, and analysis in microbial source tracking studies. Appl. Environ. Microbiol. 73:2405–2415. 97) Tassoula, E.A. 1997. Growth possibilities of E. coli in natural waters. Int. J. Environ. Stud. 52:67–73. 98) Tompkins, J.D., J.L. Nelson, J.C. Hazel, S.L. Leugers, J.D. Stumpf, and P.L. Foster. 2003. Error-prone polymerase, DNA polymerase IV, is responsible for transient hypermutation during adaptive mutation in Escherichia coli J. Bacteriol. 185:3469–3472. 99) Topp, E., M. Welsh, Y.C. Tien, A. Dang, G. Lazarovits, K. Conn, ISHII and SADOWSKY 108 100) 101) 102) 103) 104) 105) 106) 107) 108) and H. Zhu. 2003. Strain-dependent variability in growth and survival of Escherichia coli in agricultural soil. FEMS Microbiol. Ecol. 44:303–308. Ufnar, J.A., D.F. Ufnar, S.Y. Wang, and R.D. Ellender. 2007. Development of a swine-specific fecal pollution marker based on host differences in methanogen mcrA genes. Appl. Environ. Microbiol. 73:5209–5217. Ufnar, J.A., S.Y. Wang, D.F. Ufnar, and R.D. Ellender. 2007. Methanobrevibacter ruminantium as an indicator of domesticated ruminant fecal pollution in surface waters. Appl. Environ. Microbiol. 73:7118–7121. USDA-ERS. 2004. Economics of Foodborne Disease. United States Department of Agriculture Economic Research Service, Washington, DC. [Online.] http://www.ers.usda.gov/briefing/foodbornedisease/ USEPA. 1976. Quality criteria for water. United States Environmental Protection Agency, Washington, D. C. [Online] http:// www.epa.gov/waterscience/criteria/redbook.pdf USEPA. 1986. Ambient water quality criteria for bacteria—1986. United States Environmental Protection Agency, Washington, D.C. [Online] http://www.epa.gov/waterscience/beaches/files/1986crit.pdf USEPA. 2005. Microbial source tracking guide document. United States Environmental Protection Agency, Washington, DC. [Online] http://www.epa.gov/nrmrl/pubs/600r05064/600r05064.pdf Walk, S.T., E.W. Alm, L.M. Calhoun, J.M. Mladonicky, and T.M. Whittam. 2007. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ. Microbiol. 9:2274–2288. Welch, R.A., V. Burland, G. Plunkett, III, et al. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:17020– 17024. Whitman, R.L., D.A. Shively, H. Pawlik, M.B. Nevers, and M.N. Byappanahalli. 2003. Occurrence of Escherichia coli and enterococci in Cladophora (Chlorophyta) in nearshore water and beach sand of Lake Michigan. Appl. Environ. Microbiol. 69:4714–4719. 109) Whitman, R.L., and M.B. Nevers. 2003. Foreshore sand as a source of Escherichia coli in nearshore water of a Lake Michigan beach. Appl. Environ. Microbiol. 69:5555–5562. 110) Whitman, R.L., M.B. Nevers, G.C. Korinek, and M.N. Byappanahalli. 2004. Solar and temporal effects on Escherichia coli concentration at a Lake Michigan swimming beach. Appl. Environ. Microbiol. 70:4276–4285. 111) Whittam, T.S. 1995. Genetic population structure and pathogenicity in enteric bacteria. In: S. Baumberg, J.P.W. Young, E.M.H. Wellington, and J.R. Saunders (eds.) Population Genetics of Bacteria. Cambridge University Press, Cambridge. 112) Whittam, T.S., and T.M. Bergholz. 2007. Molecular subtyping, source tracking, and food safety, p. 93–136. In: J.W. Santo Domingo, and M.J. Sadowsky (eds.) Microbial Source Tracking. ASM Press, Washington, D.C. 113) WHO. 2004. Water, Sanitation and hygiene links to health: facts and figures. World Health Organization. Geneva, Switzerland [Online.] http://www.who.int/water_sanitation_health/factsfigures2005.pdf 114) Wick, L.M., W. Qi, D.W. Lacher, and T.S. Whittam. 2005. Evolution of genomic content in the stepwise emergence of Escherichia coli O157:H7. J. Bacteriol. 187:1783–1791. 115) Williams, A.P., L.M. Avery, K. Killham, and D.L. Jones. 2005. Persistence of Escherichia coli O157 on farm surfaces under different environmental conditions. J. Appl. Microbiol. 98:1075–1083. 116) Winfield, M.D., and E.A. Groisman. 2003. Role of nonhost environments in the lifestyles of Salmonella and Escherichia coli. Appl. Environ. Microbiol. 69:3687–3694. 117) Yan, T., M.J. Hamilton, and M.J. Sadowsky. 2007. High-throughput and quantitative procedure for determining sources of Escherichia coli in waterways by using host-specific DNA marker genes. Appl. Environ. Microbiol. 73:890–896. 118) Yan, T., and M.J. Sadowsky. 2007. Determining sources of fecal bacteria in waterways. Environ. Monit. Assess. 129:97–106. 119) Yang, H.H., R.T. Vinopal, D. Grasso, and B.F. Smets. 2004. High diversity among environmental Escherichia coli isolates from a bovine feedlot. Appl. Environ. Microbiol. 70:1528–1536. REVIEW ARTICLE published: 05 February 2014 doi: 10.3389/fmicb.2014.00023 Potential impact of antimicrobial resistance in wildlife, environment, and human health Hajer Radhouani 1,2,3,4 † , Nuno Silva 3 † , Patrícia Poeta 3,4 , Carmen Torres 5 , Susana Correia 1,2,3,4 and Gilberto Igrejas 1,2 * 1 Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal 3 Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal 4 Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal 5 Biochemistry and Molecular Biology Area, University of La Rioja, Logroño, Spain 2 Edited by: Jose L. Martinez, Centro Nacional de Biotecnología, Spain Reviewed by: Teresa M. Coque, Hospital Universitario Ramón y Cajal, Spain Stefania Stefani, University of Catania, Italy *Correspondence: Gilberto Igrejas, Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology and Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal e-mail: gigrejas@utad.pt Given the significant spatial and temporal heterogeneity in antimicrobial resistance distribution and the factors that affect its evolution, dissemination, and persistence, it is important to highlight that antimicrobial resistance must be viewed as an ecological problem. Monitoring the resistance prevalence of indicator bacteria such as Escherichia coli and enterococci in wild animals makes it possible to show that wildlife has the potential to serve as an environmental reservoir and melting pot of bacterial resistance. These researchers address the issue of antimicrobial-resistant microorganism proliferation in the environment and the related potential human health and environmental impact. Keywords: antimicrobial resistance, Escherichia coli, enterococci, phylogenetic groups, wild animals, virulence factors † Hajer Radhouani and Nuno Silva have contributed equally to this work. INTRODUCTION Microorganisms play an important role in the cycling of elements at a global scale, thus profoundly and directly affecting the environments, in which all of life evolves. While microorganisms affect the environment, the environment in turn also engenders evolutionary pressures on the microorganisms themselves (Reid and Buckley, 2011). Recent advances in DNA sequencing, high-throughput technologies, and genetic manipulation systems have permitted empirical studies that directly characterize the molecular and genomic bases of evolution (Wagner, 2008; Conrad et al., 2011). This launched the challenge of unraveling the genotype-phenotype connection, with implications not only for the investigation of evolution, but also physiology, disease risk, development, and biodiversity (Reid and Buckley, 2011). In microbial populations, evolutionary change is supplied by two sources of new variation: horizontal transfer of genetic material from other, sometimes distantly related species, and mutation. Though, in the short run, mutation is the primary source of new genetic variation driving evolutionary change in microbial populations. In an asexual microbial species, evolutionary changes will happen by the repeated selection of new clones carrying adaptively favorable mutations (Adams, 2004). In fact, firstly, genomic sequencing can determine the complete set of mutations responsible for an advanced phenotype, and has led to the discovery that interactions between these mutations www.frontiersin.org are very usual. Secondly, adaptive mutations commonly target regulatory mechanisms. Thirdly, principles of systems-level optimization cause the genetic changes seen in adaptive evolution, and with a systems-level understanding, these optimization principles can be harnessed for the purposes of metabolic engineering. Fourthly, mutant sub-populations of enhanced fitness invariably arise in growing populations, but their dynamics in the population are complicated due to factors such as natural selection, clonal interference, drift, and frequency-dependent selection (Barrick et al., 2009). Antibiotic-resistant bacteria are extremely important to human health, but the wild reservoirs of resistance determinants are poorly understood. The origins of antimicrobial resistance in the wildlife is important to human health because of the increasing importance of zoonotic diseases as well as the need for predicting emerging resistant pathogens. Wild animals provide a biological mechanism for the spread of antibiotic resistance genes. Antimicrobial-resistant Escherichia coli and Enterococcus spp. isolates originating from wildlife species were reported for the first time from Japanese wild birds (Sato et al., 1978). With the new millennium several studies, in different continents, have described the occurrence of antimicrobial-resistant in these bacteria species in wildlife (Souza et al., 1999; Sherley et al., 2000; Gakuya et al., 2001; Lillehaug et al., 2005; Skurnik et al., 2006; Dolejska et al., 2007; Gaukler et al., 2009; Schierack et al., 2009; Allen et al., 2010; Silva et al., 2010; Marinho et al., 2013; Navarro-Gonzalez et al., February 2014 | Volume 5 | Article 23 | 1 Radhouani et al. 2013; Pesapane et al., 2013; Santos et al., 2013). On the other hand, antimicrobial resistance have been described in others important pathogens, such as Salmonella spp. (Botti et al., 2013) and methicillin-resistant Staphylococcus aureus (MRSA; Porrero et al., 2013) in wild animals. Proximity to human activities influences the antibiotic resistance profiles of the gut bacteria of wild mammals, which live in densely populated microbial habitats in which antibiotics select for resistance. While various bacterial species are important in terms of multiresistance and nosocomial infections in human and veterinary medicine, we consider the Gram-positive vancomycin-resistant enterococci (VRE) and Extended-spectrum Beta-Lactamases producing Gram-negative bacteria like E. coli (ESBL-E. coli) as being key indicator pathogens to trace the evolution of multiresistant bacteria in the environment and wildlife. Enterococcus spp. are Gram-positive facultative anaerobic bacteria, spherical, which occur singly, in pairs or short chains and fit within the general definition of lactic acid bacteria (Ciftci et al., 2009). Most enterococci are not virulent and are considered relatively harmless, with little potential for human infection. However, they have also been identified as nosocomial opportunistic pathogens with increased resistance to antimicrobial approved agents (Chenoweth and Schaberg, 1990). Incidence of VRE among wild animals has been reported in several countries (Mallon et al., 2002; Figueiredo et al., 2009; Ishihara et al., 2013), including in remote areas (Silva et al., 2011a). Escherichia coli is the head of the large bacterial family, Enterobacteriaceae, the enteric bacteria, which are facultatively anaerobic Gram-negative (Sorum and Sunde, 2001). This intestinal bacterium can be easily disseminated in different ecosystems. For this reason, fecal E. coli is considered to be an important indicator for the selective pressure exerted by the use of antimicrobials on intestinal populations of bacteria (van den Bogaard and Stobberingh, 2000). The production of ESBLs by Enterobacteriaceae, specifically by E. coli, has caused a major concern in several countries, being frequently implicated in human infections. Previous reports have described ESBL-containing E. coli strains in healthy wild animals (Pinto et al., 2010; Guenther et al., 2011). The common occurrence of antimicrobial resistance in wildlife has several implications such as: the potential to serve as an environmental reservoir and melting pot of bacterial resistance; the zoonotic potential of enteric bacteria; and the potencial problems of the medical treatment of wildlife. This review aims to summarize the current knowledge on ESBL-E. coli and VRE in wildlife, in turn underlining the need for more large scale research, in particular sentinel studies to monitor the impact of multiresistant bacteria on wildlife. PHYLOGENETIC HISTORY AND GENETIC STRUCTURE The combination of mutation and horizontal transfer has created the overall phylogenetic structure of E. coli and enterococci, resulted to currently recognized four main phylogenetic groups for E. coli and different species for enterococci; and their respective lineages. Thus, an appreciation of mutation and horizontal transfer as important evolutionary processes within bacteria, in Frontiers in Microbiology | Antimicrobials, Resistance and Chemotherapy The genetic and evolutionary frontier of antimicrobial-resistant bacterial general, contributes in understanding of their roles, distribution and mechanistic modes of behavior (Johnson, 2002). A multilocus enzyme electrophoresis (MLEE)-based phenogram using 38 enzymes (Selander et al., 1986; Goullet and Picard, 1989) identified four main phylogenetic groups (A, B1, B2, and D) and two accessory groups (C and E) in E. coli (Selander et al., 1987; Herzer et al., 1990; Tenaillon et al., 2010). These phylogenetic groups were recovered using the 1,878 genes of the Escherichia spp. core genome and the 2.6 million nucleotides of the E. coli chromosomal backbone (Touchon et al., 2009), which permitted a robust phylogeny to be developed; the first split in the E. coli phylogenetic history leads to one branch including the strains of group B2 and a subgroup within D that we called group F75 and another branch containing the rest of the species (Touchon et al., 2009). The remaining strains of group D then appeared from this second branch, followed by group E (Tenaillon et al., 2010). Finally, groups A and B1 are sister groups whereas group B2 is included in an ancestral branch (Jaureguy et al., 2008; Touchon et al., 2009). The B2 group reveals the highest diversity at both the nucleotide and the gene content level (Touchon et al., 2009), supporting its early occurrence in the species lineage and suggesting that it has subspecies status (Lescat et al., 2009). Clermont et al. (2000) described a triplex polymerase chain reaction (PCR) strategy to assign E. coli isolates quickly to one of these phylogroups. It sought three phylogenetic group markers, the chuA and yjaA genes encoding hypothetical proteins and the TSPE4.C2 DNA sequences situated within a gene encoding putative lipase esterase, and groups were assigned based on different combinations of presence and/or absence of the three amplicons (Clermont et al., 2000). Johnson et al. (2001) found that strains from phylogenetic groups B2 and D contained more virulence factors than strains from the phylogenetic groups A and B1. Usually, the extraintestinal pathogenic strains belong to groups B2 and D (Picard et al., 1999; Johnson and Stell, 2000), the commensal strains to groups A and B1 (Bingen et al., 1998), whereas the intestinal pathogenic strains belong to groups A, B1, and D (Pupo et al., 1997). Nowadays, these phylogenetic groups differ in their ecological niches, life-history (Gordon and Cowling, 2003) and some characteristics, such as their ability to exploit different sugar sources, their antimicrobial resistance profiles and their growth rate (Carlos et al., 2010). A recent survey (Walk et al., 2007) demonstrated that the majority of the E. coli strains that are able to persist in the environment belong to the B1 phylogenetic group (Carlos et al., 2010). Various researchers analyzed the distribution of the main phylogenetic groups among E. coli strains isolated from human and animal faces; it was found that the relative abundance of phylogenetic groups among mammals is dependent on the host diet, body mass, and climate (Gordon and Cowling, 2003; Carlos et al., 2010). A study analyzing fecal strains isolated from birds, nonhuman mammals, and humans, observed the prevalence of groups D and B1 in birds, A and B1 in non-human mammals, and A and B2 in humans. These different reports concluded that one of the main forces that shapes the genetic structure of E. coli populations among the hosts is domestication (Escobar-Paramo et al., 2006). Furthermore, other study in the south of French Guiana, February 2014 | Volume 5 | Article 23 | 2 Radhouani et al. human strains very rarely were observed as belonging to B2 phylogroup (3.7%) whereas wild animal strains were characterized by 46.1% belonging to B2 phylogroup (Lescat et al., 2013). Moreover, feces from zoo animals were analyzed and a prevalence of group B1 in herbivorous animals and a prevalence of group A in carnivorous and omnivorous animals were found (Baldy-Chudzik et al., 2008). Furthermore, domesticated animals have a decreased proportion of B2 strains than wild animals (from 30% in wild animals to 14 and 11% in farm and zoo animals, respectively) and an increased proportion of A strains (from 14% in wild animals to 27 and 26% in farm and zoo animals, respectively; Tenaillon et al., 2010). In Portugal, the prevalence of E. coli of groups A and B1 was observed in wild birds as seagulls (Radhouani et al., 2009), birds of prey (Radhouani et al., 2012b), and Passeriformes (Santos et al., 2013), but also in wild mammals as Iberian lynxes (Gonçalves et al., 2012a), red foxes (Radhouani et al., 2013), and in Iberian wolf (Gonçalves et al., 2013a; Figure 1). In addition, a report conducted by Simões et al. (2010) shows that 37% of all ESBL-E. coli isolated from seagulls belong to B2 or D phylogroup, a higher rate than previously reported (27% of all E. coli; Poeta et al., 2008). It is interesting to note that fecal samples from red foxes showed that the E. coli isolates from phylogenetic groups A and D were predominant. Similar results were observed in chickens and swine (Machado et al., 2008), in wild boars (Poeta et al., 2009) and in wild birds (Radhouani et al., 2010a,b) in the same geographical area. With the exception of E. faecium and E. faecalis, the enterococci are infrequently described to be involved in human pathogenesis (Jett et al., 1994; Devriese and Pot, 1995). Though, in some countries association of strains of E. faecalis and E. faecium with human disease has reached proportions of serious concern (Jett et al., 1994; Leclercq, 1997; Fisher and Phillips, 2009). However, these enterococci species can show significant differences in the The genetic and evolutionary frontier of antimicrobial-resistant bacterial incidence of virulence factors and antimicrobial resistance. Generally, E. faecalis appears to harbor more virulence traits while E. faecium strains were generally free of virulence factors (Eaton and Gasson, 2001). In addition, considering the distribution of the antimicrobial resistance according to the species, the E. faecium possessed a higher level of resistance than E. faecalis (Gin and Zhanel, 1996; Franz et al., 2001). Actually, the majority of hospital-derived isolates of E. faecalis cluster in three clonal complexes, CC2, CC9, and CC87, and included the highest proportion of multiresistant isolates. (Ruiz-Garbajosa et al., 2006; van Schaik and Willems, 2010; Weng et al., 2013), while the CC17 is a major group of genetic lineage of E. faecium that has widely spread worldwide and it is associated with hospital outbreaks (Willems et al., 2005; Willems and van Schaik, 2009). Although E. faecalis CC2 and CC9 strains has been detected outside hospitals in farm animals and environment (Freitas et al., 2011; Novais et al., 2013), to our knowledge has not been identified in wild animals. On the other hand, E. faecium CC17 was recovered from seagulls in Portugal (Radhouani et al., 2010c). Recent comparisons of available genome sequences support the concept of a hospital-associated clade that is genetically distinct from most commensal isolates from animals and humans (Willems and van Schaik, 2009; van Schaik and Willems, 2010; Werner et al., 2011; Galloway-Pena et al., 2012). In Portugal, concerning wild animals, E. faecium were found to be the main species in seagulls (Radhouani et al., 2011b); birds of prey (Radhouani et al., 2012b), partridges (Silva et al., 2011b), Iberian wolf (Gonçalves et al., 2013a), red foxes (Radhouani et al., 2013), wild boars (Poeta et al., 2007a), gilthead seabream (Barros et al., 2011), and Echinoderms (Marinho et al., 2013), while E. faecalis was dominant in Passeriformes (Santos et al., 2013) and wild rabbits (Silva et al., 2010). On the other hand, E. hirae was the predominant specie isolated from Iberian lynx (Gonçalves et al., 2013b,c; Figure 2). FIGURE 1 | Phylogenetic group distributions of E. coli in wild animal from Portugal. www.frontiersin.org February 2014 | Volume 5 | Article 23 | 3 Radhouani et al. The genetic and evolutionary frontier of antimicrobial-resistant bacterial FIGURE 2 | Distribution of Enterococcus species in wild animals from Portugal. Along with seagulls and birds of prey in Portugal, migratory Canada geese report showed also the occurrence of E. faecium and E. faecalis species. Furthermore, different reports found that all enterococci isolates detected in wild mammals (Mallon et al., 2002) and also in glaucous gulls (Drobni et al., 2009) were E. faecium species. Another study performed in Brazil, showed the occurrence of E. faecalis in non-human primate (capuchin monkeys and common marmoset) fecal samples (Xavier et al., 2010). In American bison fecal samples, E. casseliflavus was the predominant species recovered with 62.4%, followed by E. faecalis (16%; Anderson et al., 2008). With the arrival of next-generation sequencing (Mardis, 2008), it was quickly possible to investigate hundreds of strains to get a better knowledge at the whole-genome level the evolutionary processes acting in populations (Liti et al., 2009; MacLean et al., 2009; Schacherer et al., 2009), opening the era of “population genomics” (Tenaillon et al., 2010). Certainly further studies using new high throughput technologies are mandatory to completely understand the evolution of predominant clones and species in different hosts and environments (Santagati et al., 2012). overall average genome size than strains from non-hospitalized humans or animals groups (Lebreton et al., 2013). The prevalence of virulence factors genes is variable among commensal populations. On a global scale, the human microbiota is characterized by a higher prevalence of virulence genes than the microbiota of other organisms (Skurnik et al., 2008). In animals, the presence of virulence genes increases with body mass, which reveals the gut complexity of larger animal (Skurnik et al., 2008). Thus, virulence factors and their change in prevalence among hosts may reflect some local adaptation to commensal habitats rather than virulence per se (Tenaillon et al., 2010). INTRA-SPECIES INTERACTIONS Large-scale epidemiological studies provide insight into the diversity and complexity of E. coli and enterococci niches (Tenaillon et al., 2010; Arias and Murray, 2012). Thus, genome plasticity has contributed to the emergence of new virulence traits: some clusters of genes or genomic islands, including pathogenicity islands (PAIs) should be discovered only in a subset of strains and favored in some specific environments. Furthermore, several alternative combinations of genes could promote similar adaptations to a given environment (Tenaillon et al., 2010). Gene gain and loss make fundamental contributions to new habitat adaptation and the emergence of new lineages (Dagan and Martin, 2007). Strains related to hospital infections were found to have significantly larger Interactions between community members are required for community development and maintenance; and can also drive some diversification. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell’s neighbors, or the production of bacteriocins, which harm a cell’s neighbors. To out-compete other clones, the production of colicins can represent a useful strategy in a structured environment (Chao and Levin, 1981). Colicins are the most expansively studied bacteriocins produced by E. coli. This could permit unadapted strains to colonize the gut and, hence, allow numerous clones to coexist in the long term. It may also promote diversification in a clone, as some strains may try to benefit from the production of the colicin but avoid paying the associated cost. However, the secretion of bacteriocins can be defined as a “spiteful” behavior in which are costly for the producer and cause harm to other members of the population (Rankin et al., 2011). Horizontal gene transfer is a key step in the evolution of bacterial pathogens. Chromosomal structures such as PAIs have been shown to extensively contribute to the evolution of bacterial pathogens by providing dynamic changes of the bacterial genome Frontiers in Microbiology | Antimicrobials, Resistance and Chemotherapy February 2014 | Volume 5 | Article 23 | 4 DIVERSITY AND COMPLEXITY OF BACTERIAL NICHES VIRULENCE FACTORS Radhouani et al. composition leading to a bacterial evolution in quantum leaps. Different mechanisms have been proposed for transfer of PAIs across the species border including phage transfer, mobilization by conjugative transposons and plasmids (Schubert et al., 2009). The fact that these microorganisms are less virulent than others is not reassuring, since the acquirement of virulence genes by bacteria is possible (Leclercq, 1997). Further research is required to characterize molecular and cellular interactions between the host and enterococci which lead to intra-species genetic transfer and virulence factors in enterococci species (Giridhara Upadhyaya et al., 2009). ANTIMICROBIAL RESISTANCE Antimicrobial resistance is a worldwide problem in human and veterinary medicine. Commonly, it is usual that the major risk factor for the increase of this situation is an extensive use of antimicrobials that leads to the dissemination of resistant bacteria and resistance genes in animals and humans (van den Bogaard and Stobberingh, 2000). The appearance of multiresistant bacteria of human and veterinary origin is probably accompanied by co-contamination of the environment apparently leading to a great health concern (Grobbel et al., 2007). As in the hospital environment, the agricultural use of antimicrobials agents selects for antibiotic resistance. These antimicrobial drugs from both hospital and agricultural sources can persist in soil and aquatic environments, and the selective pressure imposed by these compounds may affect the treatment of human diseases (Thiele-Bruhn, 2003; Segura et al., 2009). In addition, the prophylactic use of antibiotics in fish farms has led to a rise in the number of resistant bacteria (Cabello, 2006). However, the use of antibiotics by humans is not the only selective pressure for antibiotic resistance in natural microbial communities: compounds and conditions that occur in these communities may provide additional selection pressures. In fact, most antimicrobial agents are produced by strains of fungi and bacteria that occur naturally in all environments, including soil (Martin and Liras, 1989). Bacteria may also acquire resistance determinants without direct exposure to an antimicrobial through horizontally mobile elements including conjugative plasmids, integrons, and transposons (Middleton and Ambrose, 2005). These mobile elements can simply transfer antimicrobial resistance genes from one bacterium to another (Coque et al., 2008). Antimicrobial agents exert a selective pressure not only on pathogenic, but also on commensal bacteria of the intestinal tract of humans and animals (van den Bogaard and Stobberingh, 2000). In a broader view, increasing evidence suggests that components such as integrons and their gene cassettes played significant roles in genome evolution and fluidity within the bacterial kingdom (Duriez et al., 2001; Davies and Davies, 2010). In E. coli, the phylogenetic group A strains (Mammeri et al., 2009) and some group D strains (Deschamps et al., 2009) are especially permissive to the development of resistance to thirdgeneration cephalosporins. Conversely, phylogenetic group B2 strains are less resistant than the remaining strains (Picard and Goullet, 1989; Johnson et al., 1991, 1994), regardless of the molecular mechanism implicated in the acquisition of resistance, and have a lower prevalence of integrons in commensal E. coli strains www.frontiersin.org The genetic and evolutionary frontier of antimicrobial-resistant bacterial from both human (Skurnik et al., 2005) and animal hosts (Skurnik et al., 2006). This could reveal the relative decrease of phylogenetic group B2 strains in domesticated animals in which antimicrobials are used considerably (Tenaillon et al., 2010). The class of beta-lactam antibiotics is among the most important groups of antimicrobial agents in human and veterinary medicine. Besides the first widely used antimicrobial substance penicillin, other members of this family have gained a similar importance over the last decades, namely the first- to fourthgeneration cephalosporins and the beta-lactamase-inhibitors. All beta-lactams interfere with the final stage of peptidoglycan synthesis through acting on penicillin-binding proteins, thereby preventing the bacterial cell wall from forming. The most common resistance mechanism of Enterobacteriaceae spp. against betalactams is the inactivation of the antibiotic by breaking up the nitrogen-carbonyl bond in the beta-lactam ring (Walsh, 2003). The emergence and wide dissemination of ESBLs among clinical E. coli isolates in hospitals, has caused a major concern in several countries, being frequently implicated in human infections. These infections have a great impact on public health due to an increased incidence of treatment failure and severity of disease. ESBLs mainly include TEM, SHV, and CTX-M enzymes. Among them, the highest number of variants described in the last years corresponds to the CTX-M family (Naas et al., 2007). The presence of CTX-M enzymes render E. coli resistant to a variety of beta-lactams, and are transferred via plasmids that can also include resistance genes to several unrelated classes of antimicrobial agents (Canton et al., 2012). Carbapenems such as imipenem or meropenem possess the most consistent activity against ESBL-producing Enterobacteriaceae strains. Both antibiotics are considered the agents of choice in the treatment of infections due to ESBL-producing organisms (Nordmann et al., 2011) However, Enterobacteriaceae-producing carbapenemases have rapidly emerged and disseminated worldwide, including in the wild (Fischer et al., 2013). The carbapenemases, such as the New Delhi metallo-beta-lactamase 1 (NDM-1) hydrolyze all β-lactam antibiotics, including carbapenems, and their high potential for rapid, wide dissemination constitutes a major clinical and public health threat (Nordmann et al., 2009; Nordmann et al., 2011). The increase in the occurrence of nosocomial infections caused by enterococci in particular E. faecium, is at least partly due to the wide variety of intrinsic and acquired resistances to glycopeptides and aminoglycosides, among others, posing a challenge to therapeutic options. Moreover, infections caused by other Enterococcus species (E. faecalis, E. durans, E. mundtii, E. avium, E. raffinosus, E. gallinarum, and E. casseliflavus) occasionally occur and warrant attention (Murray, 1990; Prakash et al., 2005). Enterococci are expert in acquiring and transferring elements that confer resistance to antimicrobials and they are also known to be intrinsically resistant to numerous antimicrobials. As a result, therapeutic alternatives for treatment of enterococcal infections are increasingly limited (Murray, 1990). Evolution of enterococci toward resistance to multiple antimicrobials is also a major cause of concern. The acquisition of vancomycin resistance by enterococci has seriously affected the treatment and infection control of these February 2014 | Volume 5 | Article 23 | 5 Radhouani et al. The genetic and evolutionary frontier of antimicrobial-resistant bacterial An important difficulty in evaluating the causal relationship between antimicrobial use and resistance is the confounding influence of geography: the co-localization of resistant bacterial species with antimicrobial use does not essentially involve causation and could represent the presence of environmental conditions and factors that have independently contributed to the incidence of resistance (Singer et al., 2006). The collection of all antimicrobial resistance genes and their precursors in pathogenic and non-pathogenic bacteria and also in antimicrobial producing-organisms is referred as the antimicrobial resistome, a concept that has been advanced to serve as a framework for understanding the ecology of resistance on a global scale (Wright, 2010). Usually, wildlife is not exposed to clinical antimicrobial agents but can acquire antimicrobial-resistant bacteria through contact with humans, animals and the environment, where water polluted with feces appears to be the most significant vector of contamination. The incidence of commensal and pathogenic bacteria in fecal contaminations can be expected to be a connection between the environment and settings with regular or even constant antimicrobial pressure (aquaculture, livestock farming, human, and veterinary clinical settings), resulting in a constant release of antimicrobial-resistant human and animal bacteria into the environment through wastewater or manure (Martinez, 2009). Additionally, the detection of antimicrobialresistant bacteria in aquatic environments affected by human and animal wastewater and soil provides evidence for this hypothesis (Kummerer and Henninger, 2003). In this context the common use of antimicrobials in aquaculture is also of utmost importance due to possible direct influences on wild animals (Smith, 2008). As intestinal bacteria like E. coli and enterococci can be easily disseminated in different ecosystems through water, they are intensively used as indicator species for fecal pollution (Guenther et al., 2011). In this sense, it is essential to interpret the evolutionary and ecological forces that influence in the population structure of the commensal strains to fully understand the antimicrobial resistance and virulence of pathogenic strains. Certainly, the selective pressures in the habitats of commensal strains may coincidentally promote the emergence of antimicrobial resistance and virulence factors, rendering commensal strains reservoirs of virulent and resistant strains (Tenaillon et al., 2010). Despite the commensal character of E. coli and enterococci, they are commonly involved in animal and human infections that implicate the use of antimicrobials, which increases public health preoccupations to the list of implications that arise from the spread of ESBL-E. coli and VRE into wildlife. Furthermore, the increasing frequency of community-acquired ESBL-E. coli and VRE infections and the occurrence in livestock farming has been observed recently, suggesting a successful transmission as well as persistence of ESBL-E. coli and VRE strains outside hospital settings. An additional parallel global phenomenon is the spread of ESBL-E. coli and VRE into the environment beyond human and domesticated animal populations, and this appears to be directly induced by antimicrobial practice (Guenther et al., 2011). This might be a significant cause of the community-onset of ESBL-E. coli and VRE infections but can result (i) in an involvement of wildlife in ESBL-E. coli and VRE spread and transmission into fragile environmental niches, (ii) in subsequent colonization of wild animal populations which can turn into an infectious source or even a reservoir of ESBL-E. coli and VRE, (iii) in new putative infection cycles between wildlife, domesticated animals and humans, and (iv) in difficulties of wildlife medical treatment (Guenther et al., 2011). Monitoring the prevalence of resistance in indicator bacteria such as fecal E. coli and enterococci in different populations (animals, patients and healthy humans) makes it possible to compare the prevalence of resistance and to detect transfer of resistant bacteria or resistance genes from animals to humans and vice versa (Martel et al., 2001). Just recently, there has been increasing interest in resistant bacteria and resistance genes isolated from wild animals (Allen et al., 2011). The degree of colonization varies a lot between different animal species (Gordon and Cowling, 2003). Therefore, ESBL-E. coli and VRE prevalence is clearly influenced by sampling schemes, by geographic regions, by host spectrum of these bacteria and by the degree of synanthropic behavior shown by host species (Allen et al., 2010). It is important also to take in consideration the limitations that occur interpreting these results. For instance, ESBL-E. coli prevalence in different Portuguese geographical areas ranged from 0.5% in birds of the remote Azores islands in the Atlantic Ocean (Silva et al., 2011a) to 32% for birds of the Portugal’s Northern Portuguese coast (Simões et al., 2010). A lower prevalence of ESBL-E. coli was also observed (0.8%) in glaucous-winged gulls of Kamchatka peninsula in Russia (Hernandez et al., 2010). These findings suggest that wild animals living in urban areas are more susceptible to carry ESBL-E. coli than those living in remote areas. Due to their diversity in ecological niches and their ease in picking up human and environmental bacteria, wild birds might act as mirrors of human activities. Within the heterogeneous class of birds, two groups seem to be in the focus of ESBL-E. coli and VRE carriage in wildlife: birds of prey (Costa et al., 2006; Pinto et al., 2010; Radhouani et al., 2010a,b; Silva et al., 2011a) and waterfowl/water related species (Poeta et al., 2008; Bonnedahl et al., 2009; Dolejska et al., 2009; Guenther et al., 2010a; Hernandez et al., 2010; Literak et al., 2010a; Radhouani et al., 2010c; Simões Frontiers in Microbiology | Antimicrobials, Resistance and Chemotherapy February 2014 | Volume 5 | Article 23 | 6 organisms. Different types of glycopeptide resistance and their biochemical mechanisms have been described in enterococci: acquired type (vanA, vanB, vanD, vanE, vanG, and vanL); and low-level intrinsic type (vanC, associated with the E. gallinarum, E. casseliflavus, and E. flavescens species). VanA-type resistance, which was the first to be elucidated and which is the most common, is characterized by high levels of resistance to glycopeptides, vancomycin, and teicoplanin and is mediated by transposon Tn1546 or closely related elements that are chromosomally or plasmid located (Arthur et al., 1996). The development of newer antimicrobial drugs, such as linezolid and daptomycin with activity against many VRE strains (Lee et al., 2007). has improved this situation; however resistance to these agents has already been described (Miller et al., 2013; Patel et al., 2013). WILDLIFE AS RESERVOIRS OF ANTIBIOTIC RESISTANCE Radhouani et al. et al., 2010; Garmyn et al., 2011). However, recent studies in Passeriformes have also described a significant incidence of VRE (Silva et al., 2011a, 2012; Oravcova et al., 2013a,b). Although wild birds, such as birds of prey, have only rare contact with antimicrobial agents, in disagreement with the existence of direct selective pressure, they can be contaminated or colonized by resistant bacteria. Water contact and acquisition via food seem to be major aspects of transmission of resistant bacteria of human or veterinary origin to wild animals (Cole et al., 2005). In the other hand, wild birds such as seagulls are often opportunistic marine feeders along the shoreline or offshore, but also eat the food sources provided by humans, especially garbage. Migrating birds that travel long distance seem to act as transporters, or as reservoirs, of resistant bacteria and may consequently have a significant epidemiological role in the dissemination of resistance, as well as being mirrors of the spectrum of pathogenic microorganisms present in humans (Radhouani et al., 2010c; Silva et al., 2011a). Reports on marine fish showed the presence of ESBLE. coli (Sousa et al., 2011) and VRE (Barros et al., 2012) in gilthead seabream, indicating a dissemination of ESBL-E. coli and VRE into the Atlantic ocean. Moreover, it has previously been demonstrated that seagulls shared strains with isolates cultured from wastewater treatment plants and landfills (Nelson et al., 2008). This highlights the possibility of bacterial exchange between human sewage and birds. Another important host of these bacteria appears to be in wild rodents. Although these animals have previous been in the focus of research on ESBL in wildlife in different continents (Gilliver et al., 1999; Kozak et al., 2009; Guenther et al., 2010b; Literak et al., 2010b; Allen et al., 2011), they have only been detected in urban rats (Guenther et al., 2010a; Ho et al., 2011). On the other hand, VRE have been earlier described in wild rodents (Mallon et al., 2002). This synantropic species can easily pickup human waste and frequently interacts with human feces in the sewage system in urban environments and can therefore easily acquire multiresistant bacteria. Remarkably, wild boars have also been described as hosts of these bacteria in Europe, which might expose their omnivorous feeding behavior (Poeta et al., 2007b, 2009; Literak et al., 2010b). Recent studies revealed the presence of ESBL-producing E. coli (Gonçalves et al., 2012a,b) and VRE isolates (Gonçalves et al., 2011) in Iberian wolf and/or Iberian lynx. The incidence of ESBL-E. coli (Radhouani et al., 2012a) and VRE (Radhouani et al., 2011a) in red foxes may be due their diet as these wild animals usually hunt wild rabbits, small rodents and birds. It is important to point out that some studies reported the presence of antimicrobial-resistant isolates in wild rabbits (Figueiredo et al., 2009; Silva et al., 2010) and wild rodents (Kozak et al., 2009; Guenther et al., 2010b). Foxes are on top of the food chain, perhaps accumulating multiresistant bacteria from their prey (Grobbel et al., 2012). All these evidences may contribute in the acquisition and spread of antimicrobial-resistant bacteria even in the absence of direct antimicrobial pressure. These wild animals act as reservoirs of resistance genes and they could spread resistant bacteria throughout the wild environment. These researchers address the issue of antimicrobial-resistant microorganism proliferation in the environment and the related potential human health and environmental impact. www.frontiersin.org The genetic and evolutionary frontier of antimicrobial-resistant bacterial The level of resistant bacteria detected in wild animals seems to relate well with the degree of association with human activity (Skurnik et al., 2006). In fact, human density, natural preservation state, livestock or the reserve of an area may be significant criteria for the proliferation of antimicrobial-resistant bacteria (Allen et al., 2010). Nevertheless, several studies report the occurrence of multidrug-resistant bacteria in remote places or preservation areas therefore underlining the complexity of the spread of antimicrobial resistance in wild animals. These discoveries propose, on one hand, an influence of migratory behavior of wild birds into remote areas, or on the other hand the omnipresence of human influence in various ecological niches of the planet via human feces (Guenther et al., 2011). Different reports showed that areas with high livestock and human density and an assumable frequent interaction of wildlife with human influenced habitats of any kind (livestock farms, landfills, sewage systems, or wastewater treatment facilities) result in a higher risk for wildlife to acquire antimicrobial-resistant bacteria (Allen et al., 2010). CONCLUSION The strength of trillions upon trillions of microorganisms, combined with the ancient force of evolution by constant, insistent variation, will inevitably overpower the drugs. Their spectrum is selected to involve pathogenic bacteria and antimicrobials constantly select naturally resistant bacteria (American Academy of Microbiology, 2009). As bacteria quickly evolve to acquire resistance to the available antimicrobials, it is a constant race for scientists to develop effective strategies to combat infection and to reveal new therapeutic targets (Davies and Davies, 2010). Moreover, antimicrobial resistance evolving and spreading among bacterial pathogens is a public health problem of increasing magnitude. Since the beginning of the antimicrobial era, the selective pressure caused by the use of antimicrobials in clinical, veterinary, husbandry, and agricultural practices is considered the major factor responsible for the occurrence and spread of antimicrobial-resistant bacteria. The evolution of antimicrobial resistance in bacteria is related to the evolution of antimicrobial production. Though, resistance has also been discovered in the absence of antimicrobial exposure, as in bacteria from wildlife, raising an interest about the mechanisms of emergence and persistence of resistant strains under similar conditions, and the implications for resistance control strategies (Pallecchi et al., 2008). Monitoring antimicrobial resistance in wildlife from remote areas could also be a useful tool to evaluate the impact of anthropic pressure (Thaller et al., 2010). Singer et al. (2006) support that in ecological studies of antimicrobial resistance, there has possibly been too much focus on resistant organisms and not enough on resistance genes. Due to the capability of bacteria to transfer resistance genes, even among distantly related bacteria, analyses of antimicrobial resistance emergence, dissemination and persistence might be better conducted at the gene level (Singer et al., 2006). Until now, genomics-based investigation into E. coli and enterococci has focused on the identification of genes directly implicated in virulence. However, the fundamental physiology and response mechanisms to environmental conditions of E. coli February 2014 | Volume 5 | Article 23 | 7 Radhouani et al. and enterococci remained relatively poorly understood. This is a serious oversight because during infection the microbial fitness is an important reason in the success of any microbial pathogen. Further genome-wide reports aiming to define genes that are important during infection and colonization or exposure to antimicrobials will deliver significant data on relevant aspects of E. coli and enterococcal biology. This knowledge can consequently be useful for the development of novel treatment approaches to combat microbial infections. The genetic and evolutionary frontier of antimicrobial-resistant bacterial Adams, J. (2004). Microbial evolution in laboratory environments. Res. Microbiol. 155, 311–318. doi: 10.1016/j.resmic.2004.01.013 Allen, H. K., Donato, J., Wang, H. H., Cloud-Hansen, K. A., Davies, J., and Handelsman, J. (2010). Call of the wild: antibiotic resistance genes in natural environments. Nat. Rev. Microbiol. 8, 251–259. doi: 10.1038/nrmicro2312 Allen, S. E., Boerlin, P., Janecko, N., Lumsden, J. S., Barker, I. K., Pearl, D. L., et al. (2011). Antimicrobial resistance in generic Escherichia coli isolates from wild small mammals living in swine farm, residential, landfill, and natural environments in southern Ontario, Canada. Appl. Environ. Microbiol. 77, 882–888. doi: 10.1128/AEM.01111-10 American Academy of Microbiology. (2009). Antibiotic Resistance: An Ecological Perspective on an Old Problem. Washington, DC: American Academy of Microbiology. Anderson, J. F., Parrish, T. D., Akhtar, M., Zurek, L., and Hirt, H. (2008). Antibiotic resistance of enterococci in American bison (Bison bison) from a nature preserve compared to that of enterococci in pastured cattle. Appl. Environ. Microbiol. 74, 1726–1730. doi: 10.1128/AEM.02164-07 Arias, C. A., and Murray, B. E. (2012). The rise of the Enterococcus: beyond vancomycin resistance. Nat. Rev. Microbiol. 10, 266–278. doi: 10.1038/nrmicro2761 Arthur, M., Reynolds, P., and Courvalin, P. (1996). Glycopeptide resistance in enterococci. Trends Microbiol. 4, 401–407. doi: 10.1016/0966-842X(96)10063-9 Baldy-Chudzik, K., Mackiewicz, P., and Stosik, M. (2008). Phylogenetic background, virulence gene profiles, and genomic diversity in commensal Escherichia coli isolated from ten mammal species living in one zoo. Vet. Microbiol. 131, 173–184. doi: 10.1016/j.vetmic.2008.02.019 Barrick, J. E., Yu, D. S., Yoon, S. H., Jeong, H., Oh, T. K., Schneider, D., et al. (2009). Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243–1247. doi: 10.1038/nature08480 Barros, J., Andrade, M., Radhouani, H., Lopez, M., Igrejas, G., Poeta, P., et al. (2012). Detection of vanA-containing Enterococcus species in faecal microbiota of gilthead seabream (Sparus aurata). Microbes Environ. 27, 509–511. doi: 10.1264/jsme2.ME11346 Barros, J., Igrejas, G., Andrade, M., Radhouani, H., Lopez, M., Torres, C., et al. (2011). Gilthead seabream (Sparus aurata) carrying antibiotic resistant enterococci. A potential bioindicator of marine contamination? Mar. Pollut. Bull. 62, 1245–1248. doi: 10.1016/j.marpolbul.2011.03.021 Bingen, E., Picard, B., Brahimi, N., Mathy, S., Desjardins, P., Elion, J., et al. (1998). Phylogenetic analysis of Escherichia coli strains causing neonatal meningitis suggests horizontal gene transfer from a predominant pool of highly virulent B2 group strains. J. Infect. Dis. 177, 642–650. doi: 10.1086/514217 Bonnedahl, J., Drobni, M., Gauthier-Clerc, M., Hernandez, J., Granholm, S., Kayser, Y., et al. (2009). Dissemination of Escherichia coli with CTX-M type ESBL between humans and yellow-legged gulls in the south of France. PLoS ONE 4:e5958. doi: 10.1371/journal.pone.0005958 Botti, V., Navillod, F. V., Domenis, L., Orusa, R., Pepe, E., Robetto, S., et al. (2013). Salmonella spp. and antibiotic-resistant strains in wild mammals and birds in north-western Italy from 2002 to 2010. Vet. Ital. 49, 195–202. Cabello, F. C. (2006). Heavy use of prophylactic antibiotics in aquaculture: a growing problem for human and animal health and for the environment. Environ. Microbiol. 8, 1137–1144. doi: 10.1111/j.1462-2920.2006.01054.x Canton, R., Akova, M., Carmeli, Y., Giske, C. G., Glupczynski, Y., Gniadkowski, M., et al. (2012). Rapid evolution and spread of carbapenemases among Enterobacteriaceae in Europe. Clin. Microbiol. Infect. 18, 413–431. doi: 10.1111/j.1469-0691.2012.03821.x Carlos, C., Pires, M. M., Stoppe, N. C., Hachich, E. M., Sato, M. I., Gomes, T. A., et al. (2010). Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination. BMC Microbiol. 10:161. doi: 10.1186/1471-2180-10-161 Chao, L., and Levin, ...
Purchase answer to see full attachment
User generated content is uploaded by users for the purposes of learning and should be used following Studypool's honor code & terms of service.

Explanation & Answer

Attached.

Running head: LITERATURE REVIEW

1

Literature Review
Name
Institution

LITERATURE REVIEW

2
Literature Review

Escherichia coli dwell mostly in warm-blooded animals, and for humans in the duodenal
tract. It can exist in over 700 serotypes differentiated by their antigens ‘O’ and ‘H’ in their
flagella and bodies. Shiga toxin (Stx) especially Escherichia coli O157: H7 producing serotypes
are harmful because they cause infections through contaminated beverages and foods (Frenzen et
al., 2005). This bacterium has a significant economic burden in the United States estimated at
$405millions annually inclusive of premature deaths, lost productivity and medical care. The
estimate cost of illness caused by this bacterium through contaminated food is $344million
yearly. This can be prevented by maintaining high standards of hygiene, as well as tight
regulation from the government. For instance, the government through HACCP program in 2003
increased the yearly production expenses for beef producers by approximately $310million
through testing for these pathogens to regulate foodborne microorganisms (Frenzen et al., 2005).
E. coli is deposited in the environment via feces. Hence this bacterium is broadly applied
as a sign of fecal pollution of watercourses. This study is committed toward identification of
possible origins of fecal pollution affecting the beaches and watercourses, what is commonly
known as microbial source tracing (Ishii & Sadowsky, 2008). The ideal bacteria to prove fecal
pollution should; 1-be non-pathogenic; 2- inhabit in the duodenal ducts of warm-blooded
organisms, and 3- should be inept to reproduce in the environment. Presently E. coli have
antigens 173O, 103k, and 56H and keep on increasing. Possible origins of fecal pollution in
sediments, soil, and water, comprise of waterfowl, human sewage, farm animals, pets and
wildlife (Ishii & Sadowsky, 2008). This study claims that fecal pollution emanating from human
sources poses higher health h...


Anonymous
I was struggling with this subject, and this helped me a ton!

Studypool
4.7
Trustpilot
4.5
Sitejabber
4.4

Similar Content

Related Tags