The genetic structure of enteric bacteria from Australian mammals

Bacteria richness and antibiotic-resistance in bats from a protected area in the Atlantic Forest of Southeastern Brazil

Bats play key ecological roles, also hosting many zoonotic pathogens. Neotropical bat microbiota is still poorly known. We speculate that their dietary habits strongly influence their microbiota richness and antibiotic-resistance patterns, which represent growing and serious public health and environmental issue. Here we describe the aerobic microbiota richness of bats from an Atlantic Forest remnant in Southeastern Brazil, and the antibiotic-resistance patterns of bacteria of clinical importance. Oral and rectal cavities of 113 bats from Carlos Botelho State Park were swabbed. Samples were plated on 5% sheep blood and MacConkey agar and identified by the MALDI-TOF technique. Antibiotic susceptibility tests were performed using Kirby-Bauer’s antibiotic disc diffusion technique.We identified 596 isolates at the genus level and tentatively to the species level. Proteobacteria was the most abundant phylum in all the dietary guilds, representing 87% of the total identified samples. The most common bacteria within bat individuals were Escherichia coli, Klebsiella oxytoca and Serratia marcescens, and within bat species were Serratia marcescens, Pseudomonas sp. and Staphylococcus sp. Frugivores presented the most diverse microbiota. In general, the antibiogram results indicated a low occurrence of resistance on eigth potentially pathogenic bacteria species. The resistance to antibiotics found on our samples was related mostly to the intrinsic resistance of the tested species.The low occurrence of resistant bacteria in our samples could be related to the well preserved environment where bats were caught. Once the major causes of resistance-acquiring are related to anthropic activites, the controlled access of tourists on certain regions of the Park seems to be effectively protecting the environment.

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.

Diversity and evolutionary patterns of bacterial gut associates of corbiculate bees

The animal gut is a habitat for diverse communities of microorganisms (microbiota). Honeybees and bumblebees have recently been shown to harbour a distinct and species poor microbiota, which may confer protection against parasites. Here, we investigate diversity, host specificity and transmission mode of two of the most common, yet poorly known, gut bacteria of honeybees and bumblebees: Snodgrassella alvi (Betaproteobacteria) and Gilliamella apicola (Gammaproteobacteria). We analysed 16S rRNA gene sequences of these bacteria from diverse bee host species across most of the honeybee and bumblebee phylogenetic diversity from North America, Europe and Asia. These focal bacteria were present in 92% of bumblebee species and all honeybee species but were found to be absent in the two related corbiculate bee tribes, the stingless bees (Meliponini) and orchid bees (Euglossini). Both Snodgrassella alvi and Gilliamella apicola phylogenies show significant topological congruence with the phylogeny of their bee hosts, albeit with a considerable degree of putative host switches. Furthermore, we found that phylogenetic distances between Gilliamella apicola samples correlated with the geographical distance between sampling locations. This tentatively suggests that the environmental transmission rate, as set by geographical distance, affects the distribution of G. apicola infections. We show experimentally that both bacterial taxa can be vertically transmitted from the mother colony to daughter queens, and social contact with nest mates after emergence from the pupa greatly facilitates this transmission. Therefore, sociality may play an important role in vertical transmission and opens up the potential for co-evolution or at least a close association of gut bacteria with their hosts.

Escherichia coli in the Environment: Implications for Water Quality and Human Health

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.

Effect of diet and gut dynamics on the establishment and persistence of Escherichia coli

Escherichia coli population dynamics and diversity in rats fed diets differing in their crude fibre content were assessed. Female Wistar rats (n = 40) were fed diets containing 1, 4, 18 or 26 % crude fibre. Animals were housed in pairs, and one animal was inoculated with a phylogroup B1 strain of E. coli, the other with a phylogroup B2 strain. Natural strain transmission was allowed to occur between the animals in each cage. As expected, the diets had a significant effect on gut dynamics. Mean gut retention times were shorter in animals fed the 18 and 26 % crude fibre diets compared with animals on the low-fibre diets. The effect of diet on gastrointestinal dynamics in turn affected E. coli population dynamics and clonal composition. Animals fed the low-fibre diets had higher cell densities than animals fed the high-fibre diets. E. coli populations dominated by phylogroup B2 strains exhibited lower cell densities in animals fed the high-fibre diets compared with cell densities in animals fed the low-fibre diets. Overall, E. coli cell densities declined as gut transit times decreased. Results from this experiment support the results garnered from prospective studies examining the distribution of E. coli from hosts with differing diets, gut morphology and dynamics.

Escherichia coli populations in Great Lakes waterfowl exhibit spatial stability and temporal shifting

Populations of Escherichia coli from juvenile and adult ring-billed gulls, juvenile common terns, and adult Canada geese were sampled over 6 years at five locations on Lake Superior (Duluth, MN, and Wisconsin) and Lake Michigan (Wisconsin, Illinois, and Indiana) to determine the extent of spatial and temporal variability in E. coli strains. Strain identity was determined using horizontal fluorophore-enhanced repetitive element palindromic DNA fingerprinting. Multivariate statistics were used to determine if spatial or temporal changes in E. coli populations occurred in waterfowl species. Pairwise multivariate analyses of variance revealed that E. coli populations of adult gulls from three regions of Lake Michigan and the Wisconsin shore of Lake Superior were similar to one another but different from an E. coli population of gulls from the Duluth region of Lake Superior. Juvenile and adult gulls from the Duluth area harbored different E. coli populations. The E. coli strains from juvenile gulls, however, were similar to those found in juvenile terns obtained from the same island rookery. Temporal changes in E. coli populations from several waterfowl species were also demonstrated for this site. Although portions of source tracking databases might be successfully used in other geographic regions, it is clear that juvenile birds should not be the sole source of E. coli strains used for source tracking databases, and multiple-year libraries should be constructed in order to identify the potential sources of E. coli in the environment.

Isolation and characterization of intestinal Escherichia coli clones from wild boars in Germany

Our understanding of the composition of Escherichia coli populations in wild boars is very limited. In order to obtain insight into the E. coli microflora of wild boars, we studied E. coli isolates from the jejunums, ileums, and colons of 21 wild boars hunted in five geographic locations in Germany. Ten isolates per section were subjected to clonal determination using pulsed-field gel electrophoresis. One representative isolate per clone was further investigated for virulence traits, phylogenetic affiliation, and antimicrobial susceptibility. Macrorestriction analysis of 620 isolates revealed a range of clone diversity among the sections and animals, with up to 9 and 16 different clones per section and animal, respectively. Most of the clones for a given animal were shared between two adjacent intestinal sections. The overall highest clonal diversity was observed within the colon. While the astA gene was present in a large number of clones, other virulence genes and hemolytic ability were detected only sporadically. Clones of all four ECOR groups dominated the intestinal sections. Phylogenetic analysis and the occurrence of virulence genes correlated with the isolation frequencies for clones. All E. coli clones from wild boars were susceptible to all antimicrobial agents tested. In conclusion, though several parameters (including an animal-specific and highly diverse E. coli clone composition, the simultaneous occurrence of single clones in two adjacent intestinal sections of a given animal, and a higher E. coli diversity in the large intestine than in the small intestine) of E. coli populations of wild boars were similar to those of previously described E. coli populations of conventionally reared domestic pigs, our data also indicate possible differences, as seen for the E. coli diversity in the large intestine, the occurrence of certain virulence genes and phylogenetic groups, and antimicrobial susceptibilities.

Molecular subtyping of mastitis-associated Klebsiella pneumoniae isolates shows high levels of diversity within and between dairy herds

Despite advances in controlling mastitis (inflammation of the mammary gland), udder infections caused by Klebsiella pneumoniae continue to affect dairy cattle. Mastitis caused by K. pneumoniae responds poorly to antibiotic treatment, and as a consequence, infections tend to be severe and long lasting. We sought to determine whether a nonrandom distribution of specific genotypes of K. pneumoniae was associated with mastitis from 6 dairy herds located in 4 different states. A total of 635 isolates were obtained and fingerprinted by repetitive DNA sequence PCR. Significant genetic diversity was observed in 4 of the 6 dairy herds analyzed, and a total of 49 genotypic variants were identified. Within a herd, Simpson's diversity indices were 91.0, 94.1, 91.7, 88.6, 53.3, and 64.3% for dairies A, B, C, D, E, and F, respectively. The association between matrices of genetic similarity and matrices of temporal distance was negative in all the dairies analyzed. Four dairies had a high incidence of K. pneumoniae mastitis during the winter. The majority of genotypes were unique to herds of origin, and only 5 genotypes were detected in more than 2 dairies. Genotype 1 (arbitrary designation) occurred most frequently across dairies and was found in 25.2% of all mastitis cases and among 22.8% of reinfected and culled cows in dairy A. Specific genotypes also tended to be associated with a specific bedding type and dairy location. Analysis of molecular variance showed that 18% of the genetic diversity was due to variation among herds within states, and 82% of the genetic diversity was accounted for by variation of genotypes within herds. The data support the idea that mastitis is caused by a diverse group of K. pneumoniae genotypes and thus has major implications for the diagnosis, prevention, and treatment of udder infections in dairy cows.

Composition of intestinal Enterobacteriaceae populations of healthy domestic pigs

In this study, the Enterobacteriaceae microbiota, including their diversity as well as the distribution of haemolytic and virulence gene-harbouring Escherichia coli of 56-day-old healthy piglets, was characterized. Both the composition and the diversity of Enterobacteriaceae populations varied considerably between individual pigs and intestinal sections. E. coli, Enterobacter cloacae, Citrobacter freundii and Klebsiella pneumoniae dominated the Enterobacteriaceae microbiota. However, mucosa-associated Enterobacteriaceae were scarce or in some cases undetectable. The majority of E. coli clones from the jejunum were also found in the colon, with up to 10 different E. coli clones in one intestinal section. Other Enterobacteriaceae species were represented by only one clone localized to one intestinal section. While several piglets did not harbour virulence gene-positive or haemolytic E. coli, such strains dominated intestinal sections of other animals. This study reveals that the diversity of intestinal Enterobacteriaceae is clearly individual. In general, Enterobacteriaceae do not appear to be a consistent fraction of the microbiota of the jejunum. High numbers of adherent bacteria do not appear to be essential for successful intestinal colonization, and E. coli clones do not necessarily colonize distinct intestinal sections based on the particular phylogenetic affiliation. Furthermore, dominance of haemolytic or virulence gene-positive E. coli does not correlate with disease. Finally, probiotic Enterococcus faecium feed supplementation does not affect the Enterobacteriaceae microbiota.

Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification

The purpose of this study was to examine host distribution patterns among fecal bacteria in the order Bacteroidales, with the goal of using endemic sequences as markers for fecal source identification in aquatic environments. We analyzed Bacteroidales 16S rRNA gene sequences from the feces of eight hosts: human, bovine, pig, horse, dog, cat, gull, and elk. Recovered sequences did not match database sequences, indicating high levels of uncultivated diversity. The analysis revealed both endemic and cosmopolitan distributions among the eight hosts. Ruminant, pig, and horse sequences tended to form host- or host group-specific clusters in a phylogenetic tree, while human, dog, cat, and gull sequences clustered together almost exclusively. Many of the human, dog, cat, and gull sequences fell within a large branch containing cultivated species from the genus Bacteroides. Most of the cultivated Bacteroides species had very close matches with multiple hosts and thus may not be useful targets for fecal source identification. A large branch containing cultivated members of the genus Prevotella included cloned sequences that were not closely related to cultivated Prevotella species. Most ruminant sequences formed clusters separate from the branches containing Bacteroides and Prevotella species. Host-specific sequences were identified for pigs and horses and were used to design PCR primers to identify pig and horse sources of fecal pollution in water. The primers successfully amplified fecal DNAs from their target hosts and did not amplify fecal DNAs from other species. Fecal bacteria endemic to the host species may result from evolution in different types of digestive systems.

Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes

Escherichia coli has long been used as an indicator organism for water quality assessment. Recently there has been an accumulation of evidence that suggests some strains of this organism are able to proliferate in the environment, a characteristic that would detract from its utility as an indicator of faecal pollution. Phenotypic and genotypic characterization of E. coli isolated from blooms in two Australian lakes, separated by a distance of approximately 200 km, identified that the blooms were dominated by three E. coli strains. A major phenotypic similarity among the three bloom strains was the presence of a group 1 capsule. Genetic characterization of a conserved region of the cps gene cluster, which encodes group 1 capsules, identified a high degree of genetic variation within the bloom isolates. This differs from previously described encapsulated E. coli strains which are highly conserved at the cps locus. The phenotypic or genotypic profiles of the bloom strains were not identified in 435 E. coli strains isolated from vertebrates. The occurrence of these encapsulated strains suggests that some E. coli have evolved a free-living lifestyle and do not require a host in order to proliferate. The presence of the same three strains in bloom events in different geographical regions of a temperate climate, and at different times, indicates that free-living E. coli strains are able to persist in these water reservoirs. This study provides further evidence of circumstances where caution is required in using E. coli as an indicator organism for water quality.

The Influence of Ecological Factors on the Distribution and the Genetic Structure of Escherichia coli

This review focuses on recent data concerning the ecological factors that determine the distribution of Escherichia coli and the genetic structures of naturally occurring E. coli populations. It summarizes some of the older literature concerning the dynamics of E. coli populations within a host and poses some questions that arise from our more recently acquired understanding of the factors affecting the genetic structures of E. coli populations. Multilocus enzyme electrophoresis (MLEE) studies indicate that E. coli, relative to other members of the family Enterobacteriaceae, exhibits a moderate degree of genetic diversity. The existence of subspecific structure in E. coli has for the most part been determined by largely neutral in its effects on the fitness of a strain. The consequences for E. coli of the transition between its primary and secondary habitats are of considerable practical significance for water quality assessment and disease transmission. E. coli causes a significant fraction of human bacterial disease and is responsible for two main types of disease in humans and domestic animals: diarrheal disease and extraintestinal infections. The observed distribution of strains from the different E. coli genetic groups indicates that they have different life history tactics and ecological niches. A and B1 strains appear to be generalists, as they can be recovered from any vertebrate group. Group B2 and D strains appear to be more specialized, as they are largely restricted to endothermic vertebrates.

Diversity analysis of commensal porcine Escherichia coli - associations between genotypes and habitat in the porcine gastrointestinal tract

Diversity studies of enteric Escherichia coli have relied almost entirely on faecal isolations on the assumption that they are representative of flora found throughout the gastrointestinal tract. The authors have addressed this belief by analysing isolates obtained from the duodenum, ileum, colon and faeces of pigs. E. coli isolates were obtained from eight pigs and characterized using multi-locus enzyme electrophoresis and PCR-based screening for a range of factors thought to be associated with intestinal and extra-intestinal disease. There are four main genetic groups of commensal E. coli (A, B1, B2, D). Group A strains represented 76 % of the isolates from the duodenum, ileum and colon compared to 58 % of the strains isolated from faeces. A nested molecular analysis of variance based on the allozyme and virulence factor screening results showed that differences among individual pigs accounted for 6 % of the observed genetic diversity, whilst 27 % of the genetic variation could be explained by clonal composition differences among gut regions. Finally, the absence of virulence genes in these commensals indicates that they may be suitable as a probiotic consortium, particularly if they also display increased adherence to enterocytes and antagonistic activity against pathogenic strains of E. coli.

Coliform dynamics and the implications for source tracking

In many parts of the world, coliform counts in recreational waters are unacceptably high. In an attempt to rectify this problem, programmes are under way to develop methods that will allow the sources of the faecal contamination thought to be responsible for these elevated counts to be identified. The success of these efforts depends on the validity of several assumptions that underlie many of the proposed methods. One of the critical assumptions is that the clonal composition of the coliform species being monitored in a water body reflects the clonal composition of the species in the host populations responsible for the faecal inputs into that water body. To determine the extent to which among-strain variation in a coliform species might invalidate this assumption, a series of simple mathematical models was proposed and analysed. The first series of models assumed that all cells of species were identical. The question posed was - is the density of a coliform species in a body of water linearly related to the rate at which cells of the species enter the water body via faecal production? The results of these models suggest that, over a wide range of conditions, cell densities in the water body are linearly related to the rate at which cells enter the water body as a result of faecal contamination. This outcome occurs whether or not cells are capable of division in the external environment. When the rate of cell division depends on the concentration of available nutrients then, when nutrient input rates are 'high' and rates of faecal contamination are 'low', this linear relationship does not hold. The second series of models assumed that the coliform species consists of different strains and that these strains differ in their performance in the external environment. The results of these multistrain models show that the relative abundance of strains in the external environment is unlikely to reflect their relative abundance in the faecal inputs to the environment. Consequently, statements such as - domestic animals are responsible for 30% and wildlife for 70% of the faecal inputs to a water body - may well be meaningless.

Evolution of multi-resistance plasmids in Australian clinical isolates of Escherichia coli

Plasmids allow the movement of genetic material, including antimicrobial resistance genes, between bacterial species and genera. They frequently mediate resistance to multiple antimicrobials and can result in the acquisition by a pathogen of resistance to all or most clinically relevant antimicrobials. Unfortunately, there are still large gaps in our understanding of how new multi-resistance plasmids evolve. Five Australian clinical institutions collaborated in this study of multi-resistance plasmids in clinical isolates ofEscherichia coli. We characterized 72 resistance plasmids in terms of the antimicrobial resistance profile they conferred, their size and their incompatibility group. Restriction fragment length polymorphisms were used to determine the genetic relationships between the plasmids. Relationships between the host cells were determined using multi-locus enzyme electrophoresis. A lack of correlation between the evolutionary history of the host cells and their plasmids suggests that the horizontal transfer of resistance plasmids between strains ofE. coliis common. The resistance plasmids were very diverse, with a wide range of resistance profiles and a lack of discrete evolutionary lineages. Multi-resistance plasmids did not evolve via the co-integrative capture of smaller resistance plasmids; rather, the roles of recombination and the horizontal movement of mobile genetic elements appeared to be most important.

Genetic and ecological structure of Hafnia alvei in Australia

Multilocus enzyme electrophoresis of 161 Hafnia alvei isolates from 158 hosts and 3 water column samples collected in Australia revealed that this species consists of two genetically distinct groups. The two groups of H. alvei differed significantly in their genetic structure and host distribution. The taxonomic class of the host but not geographic locality explained a significant proportion of the observed genetic and biochemical variation among strains within each genetic group.

A molecular phylogeny of enteric bacteria and implications for a bacterial species concept

A molecular phylogeny for seven taxa of enteric bacteria (Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca, Klebsiella pneumoniae, and Serratia plymuthica) was made from multiple isolates per taxa taken from a collection of environmental enteric bacteria. Sequences from five housekeeping genes (gapA, groEL, gyrA, ompA, and pgi) and the 16S rRNA gene were used to infer individual gene trees and were concatenated to infer a composite molecular phylogeny for the species. The isolates from each taxa formed tight species clusters in the individual gene trees, suggesting the existence of 'genotypic' clusters that correspond to traditional species designations. These sequence data and the resulting gene trees and consensus tree provide the first data set with which to assess the utility of the recently proposed core genome hypothesis (CGH). The CGH provides a genetically based approach to applying the biological species concept to bacteria.

The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects

Escherichia coliwas isolated from more than 2300 non-domesticated vertebrate hosts living in Australia.E. coliwas most prevalent in mammals, less prevalent in birds and uncommon in fish, frogs and reptiles. Mammals were unlikely to harbourE. coliif they lived in regions with a desert climate and less likely to haveE. coliif they lived in the tropics than if they lived in semi-arid or temperate regions. In mammals, the likelihood of isolatingE. colifrom an individual depended on the diet of the host andE. coliwas less prevalent in carnivores than in herbivores or omnivores. In both birds and mammals, the probability of isolatingE. coliincreased with the body mass of the host. Hosts living in close proximity to human habitation were more likely to harbourE. colithan hosts living away from people. The relative abundance ofE. coligroups A, B1, B2 and D strains in mammals depended on climate, host diet and body mass. Group A strains were uncommon, but were isolated from both ectothermic and endothermic vertebrates. Group B1 strains could also be isolated from any vertebrate group, but were predominant in ectothermic vertebrates, birds and carnivorous mammals. Group B2 strains were unlikely to be isolated from ectotherms and were most abundant in omnivorous and herbivorous mammals. Group D strains were rare in ectotherms and uncommon in endotherms, but were equally abundant in birds and mammals. The results of this study suggest that, at the species level, the ecological niche ofE. coliis mammals with hindgut modifications to enable microbial fermentation, or in the absence of a modified hindgut,E. colican only establish a population in ‘large-bodied’ hosts. The non-random distribution ofE. coligenotypes among the different host groups indicates that strains of the fourE. coligroups may differ in their ecological niches and life-history characteristics.

Targeted sampling protocol as prelude to bacterial source tracking with Enterococcus faecalis

Recent studies suggest that host origin databases for bacterial source tracking (BST) must contain a large number of isolates because bacterial subspecies change with geography and time. A new targeted sampling protocol was developed as a prelude to BST to minimize these changes. The research was conducted on the Sapelo River, a tidal river on the Georgia coast. A general sampling of the river showed fecal enterococcal numbers ranging from <10 (below the limit of detection) to 990 colony-forming units (CFU) per 100 mL. Locations with high enterococcal numbers were combined with local knowledge to determine targeted sampling sites. Fecal enterococcal numbers around one site ranged from <10 to 24,000 CFU per 100 mL. Bacterial source tracking was conducted to determine if a wastewater treatment facility at the site was responsible for this contamination. The fecal indicator bacterium was Enterococcus faecalis. Ribotyping, automated with a RiboPrinter (DuPont Qualicon, Wilmington, DE), was the BST method. Thirty-seven ribotypes were observed among 83 Ent. faecalis isolates obtained from the Sapelo River and the wastewater lagoon. Sixteen ribotypes were associated with either the river or the lagoon, and only five ribotypes (14%) were shared. Nevertheless, these five ribotypes represented 39 of the 83 Ent. faecalis isolates, almost a majority (47%). These results suggest that the fecal contamination in the river came from the wastewater treatment facility. As a prelude to BST, targeted sampling minimized subspecies changes with geography and time, and eliminated the need for a permanent host origin database by restricting BST to a small geographic area and requiring sampling to be completed in one day.

A phylogenetic approach to assessing the targets of microbial warfare

Bacteriocins are the most abundant and diverse defense systems in bacteria. As a result of the specific mechanisms of bacteriocin recognition and translocation into the target cell it is assumed that these toxins mediate intra-specific or population-level interactions. However, no published studies specifically address this question. We present here a survey of bacteriocin production in a collection of enteric bacteria isolated from wild mammals in Australia. A subset of the bacteriocin-producing strains was assayed for the ability to kill a broad range of enteric bacteria from the same bacterial collection. A novel method of estimating killing breadth was developed and used to compare the surveyed bacteriocins in terms of the phylogenetic range over which they kill. The most striking result is that although bacteriocin-producers kill members of their own species most frequently, some kill phylogenetically distant taxa more frequently than they kill closer relatives. This study calls into question the role these toxins play in natural populations. A significant number of bacteriocins are highly effective in killing inter-specific strains and thus bacteriocins may serve to mediate bacterial community interactions.

Genetic characterization of Escherichia coli populations from host sources of fecal pollution by using DNA fingerprinting

Escherichia coli isolates were obtained from common host sources of fecal pollution and characterized by using repetitive extragenic palindromic (REP) PCR fingerprinting. The genetic relationship of strains within each host group was assessed as was the relationship of strains among different host groups. Multiple isolates from a single host animal (gull, human, or dog) were found to be identical; however, in some of the animals, additional strains occurred at a lower frequency. REP PCR fingerprint patterns of isolates from sewage (n = 180), gulls (n = 133), and dairy cattle (n = 121) were diverse; within a host group, pairwise comparison similarity indices ranged from 98% to as low as 15%. A composite dendrogram of E. coli fingerprint patterns did not cluster the isolates into distinct host groups but rather produced numerous subclusters (approximately >80% similarity scores calculated with the cosine coefficient) that were nearly exclusive for a host group. Approximately 65% of the isolates analyzed were arranged into host-specific groups. Comparable results were obtained by using enterobacterial repetitive intergenic consensus PCR and pulsed-field gel electrophoresis (PFGE), where PFGE gave a higher differentiation of closely related strains than both PCR techniques. These results demonstrate that environmental studies with genetic comparisons to detect sources of E. coli contamination will require extensive isolation of strains to encompass E. coli strain diversity found in host sources of contamination. These findings will assist in the development of approaches to determine sources of fecal pollution, an effort important for protecting water resources and public health.

Geographical Genetic Structure of Xylella fastidiosa from Citrus in São Paulo State, Brazil

ABSTRACT A total of 360 Xylella fastidiosa strains were isolated from sweet orange (Citrus sinensis) cv. Pera plants growing in five geographic regions in the Brazilian state of São Paulo. The genetic variation of these strains was determined by 15 variable number tandem repeat (VNTR) and 58 random amplified polymorphic DNA (RAPD) markers. The mean values of genetic diversity (H) of X. fastidiosa strains within each geographic region determined by RAPD (H(RAPD)) were substantially lower than H(VNTR) values. H(RAPD) values ranged from 0.00 to 0.095, whereas the H(VNTR) values ranged from 0.024 to 0.285. A highly significant value of Nei's coefficient of gene differentiation (G(ST) = 0.355; P = 0.000) was detected among all five populations. Analysis of the molecular variance (AMOVA) also revealed significant genetic differentiation among regions or populations ( phi(STAT) = 0.810; P< 0.001). In addition, genetic differentiation among subpopulations (plants) within the regions (phi(STAT) = 0.699; P < 0.001) and within each plant (phi(STAT) = 368; P < 0.001) were statistically significant. These high values of genetic differentiation among X. fastidiosa strains from different regions suggest a genetic structure according to region of host origin. However, no apparent correlation between genetic distance and region of origin of populations were supported statistically by Mantel analysis (r = 0.27; P = 0.22).

The genetic structure of Escherichia coli populations in primary and secondary habitats

Escherichia coli were recovered from the members of two two-person households and their associated septic tanks. The E. coli were isolated using selective and non-selective isolation techniques, characterized using the method of multi-locus enzyme electrophoresis and screened for the presence of virulence factors associated with extra-intestinal disease by using PCR. The growth rate-temperature relationships of strains from the two habitats were also determined. Temporal variation explained 25% of the observed electrophoretic type (ET) diversity in the humans. Among-host variation accounted for 29% of the observed allelic diversity. In one household, ET diversity of the E. coli population in the septic tank was significantly lower than ET diversity in the humans providing the inputs to the septic tank. Molecular analysis of variance revealed that, on average, strains recovered from the septic tank of this household were genetically distinct from strains recovered from the humans providing the faecal inputs to the septic tank. Further, the growth rate-temperature response of strains differed between strains isolated from the septic tank and strains isolated from the humans. Septic tank isolates grew better at low temperatures than strains isolated from humans, but more slowly at high temperatures compared to the human isolates. By contrast, no real differences in ET diversity, allelic diversity, or the growth characteristics of strains could be detected between strains from the humans and strains from the septic tank of the other household. The results of this study suggest there are strains of E. coli that are better "adapted" to conditions found in the external environment compared to strains isolated from the gastrointestinal habitat. Further, the finding that the numerically dominant clones and clonal diversity in secondary habitats can differ substantially from those found in the source populations will confound efforts to identify the sources of faecal pollution in the environment.

The influence of host dynamics on the clonal composition of Escherichia coli populations

Species, be they plant or animal, vary in their capacity for population growth or decline. Populations of the same species may also differ in their capacity for population change. A series of mathematical models were developed with the aim of determining if host population dynamics could influence the clonal composition of the Escherichia coli community in that host population. The biological assumptions underlying the models are described in some detail. Analytical and numerical approaches were used to investigate the behaviour of these models. The results demonstrate that host dynamics can have a profound influence on the E. coli clonal composition of the host population. This outcome is largely independent of the nature of the assumptions underlying the models. The ways in which the predictions of these models may be tested empirically are discussed, as are the implications of these models for understanding the nature of host-bacterial pathogen dynamics.

Host and geographical factors influence the thermal niche of enteric bacteria isolated from native Australian mammals

The thermal profiles of 118 bacterial strains, representing six species of the family Enterobacteriaceae, isolated from a variety of native Australian mammals were determined under in vitro conditions. Each of the bacterial species had a unique thermal profile and differed in their minimum or maximum temperature for growth and in their response to changing temperatures. The taxonomic classification of the host from which the bacterial strains were isolated explained a significant amount of the variation in thermal profile among strains of a species. Host effects were detected at all taxonomic levels: order, family, genus, and species. The locality (State or Territory) or climate zone from which the strain was collected explained a significant amount of the variation in the thermal profile of Citrobacter freundii, Enterobacter cloacae and Klebsiella pneumoniae strains. Genetically similar strains, as determined by allozyme profiles, had similar thermal profiles for the bacterial species Hafnia alvei and Escherichia coli. The results of this study indicate that there are potentially many aspects of host biology that may determine the thermal profile of these bacteria.

Clonal populations of thermotolerant Enterobacteriaceae in recreational water and their potential interference with fecal Escherichia coli counts

Bacterial strains were isolated from beach water samples using the original Environmental Protection Agency method for Escherichia coli enumeration and analyzed by pulsed-field gel electrophoresis (PFGE). Identical PFGE patterns were found for numerous isolates from 4 of the 9 days sampled, suggesting environmental replication. 16S rRNA gene sequencing, API 20E biochemical testing, and the absence of beta-glucuronidase activity revealed that these clonal isolates were Klebsiella, Citrobacter, and Enterobacter spp. In contrast, 82% of the nonclonal isolates from water samples were confirmed to be E. coli, and 16% were identified as other fecal coliforms. These nonclonal isolates produced a diverse range of PFGE patterns similar to those of isolates obtained directly from untreated sewage and gull droppings. beta-Glucuronidase activity was critical in distinguishing E. coli from other fecal coliforms, particularly for the clonal isolates. These findings demonstrate that E. coli is a better indicator of fecal pollution than fecal coliforms, which may replicate in the environment and falsely elevate indicator organism levels.

Variations in antibiotic resistance profile in Enterobacteriaceae isolated from wild Australian mammals

We carried out a retrospective analysis of 946 strains of Enterobacteriaceae isolated from wild Australian mammals between 1993 and 1997. The prevalence of resistance to fixed concentrations of 32 antimicrobial agents was determined, and the respective roles that taxonomic family of the host, state of origin and bacterial species play in defining prevalence and range of resistance were investigated. Our results demonstrated a low but widespread prevalence of antimicrobial resistance in wild isolates. Only amikacin, ciprofloxacin, meropenem and gentamicin inhibited growth in all 946 samples. There was extensive variation in the combination of antibiotics to which isolates were resistant, and multiple antibiotic resistance was common. Geographical location and host group significantly influenced the antibiotic resistance profile of an isolate, whereas bacterial species influenced both the resistance profile of an isolate and the number of antibiotics it was resistant to. The role of these factors in determining observed antibiotic resistance profiles suggests that any study measuring resistance in wild isolates should include the broadest possible range of bacterial species, host species and sampling locations. As such, this study provides an important new baseline for future measurements of antibiotic resistance in the Australian environment.

The distribution of enteric bacteria from Australian mammals: host and geographical effects

Bacteria of the family Enterobacteriaceae were isolated from 642 mammalian hosts, representing 16 families and 79 species, collected from throughout Australia. Escherichia coli was the most common of the 24 enteric species recovered and represented almost half of the isolates. Association analysis revealed that most other species of bacteria were less likely to be recovered from hosts in which E. coli was present. The composition of the enteric community of a host was found to be determined by both the taxonomic family to which the host belonged and the geographical area from which the host was collected. Hosts collected from the northern areas of Queensland and the Northern Territory had more diverse enteric communities than hosts collected from New South Wales or Western Australia. Hosts of the families Petauridae and Vespertilionidae had more diverse enteric communities than did members of the Macropodidae or Phalangeridae. The probability of occurrence of Citrobacter freundii, Enterobacter cloacae, Escherichia coli, Hafnia alvei, Klebsiella oxytoca and K. pneumoniae in a host was found to vary with respect to host family and/or host locality. The non-random distribution of these species demonstrates the presence of extensive population structure and may suggest the existence of adaptations specific to both the primary and secondary habitats of these enteric bacteria.