Phylogenetic distribution of traits associated with plant colonization in Escherichia coli

Seasonality of Coliform Bacteria Detection Rates in New Jersey Domestic Wells

It is important that indicators of fecal pollution are reliable. Coliform bacteria are a commonly used indicator of fecal pollution. As other investigators have reported elsewhere, we observed a seasonal pattern of coliform bacteria detections in domestic wells in New Jersey. Examination of a statewide database of 10 years of water quality data from 93,447 samples, from 78,207 wells, generated during real estate transactions, revealed that coliform bacteria were detected in a higher proportion of wells during warm weather months. Further examination of the seasonal pattern of other data, including well water pH, precipitation, ground and surface water temperatures, surface water coliform bacteria concentrations, and vegetation, resulted in the hypothesis that these bacteria may be derived from nonfecal (or environmentally adapted) as well as fecal sources. We provide evidence that the coliform seasonality may be the result of seasonal changes in groundwater extraction volumes (and to a lesser extent precipitation), and temperature-driven changes in the concentration of surface or near-surface coliform sources. Nonfecal coliform sources may not indicate the presence of fecal wastes and hence the potential presence of pathogens, or do so in an inconsistent fashion. Additional research is needed to identify the sources of the coliforms detected in groundwater.

Live imaging of root-bacteria interactions in a microfluidics setup

Plant roots play a dominant role in shaping the rhizosphere, the environment in which interaction with diverse microorganisms occurs. Tracking the dynamics of root-microbe interactions at high spatial resolution is currently limited because of methodological intricacy. Here, we describe a microfluidics-based approach enabling direct imaging of root-bacteria interactions in real time. The microfluidic device, which we termed tracking root interactions system (TRIS), consists of nine independent chambers that can be monitored in parallel. The principal assay reported here monitors behavior of fluorescently labeled Bacillus subtilis as it colonizes the root of Arabidopsis thaliana within the TRIS device. Our results show a distinct chemotactic behavior of B. subtilis toward a particular root segment, which we identify as the root elongation zone, followed by rapid colonization of that same segment over the first 6 h of root-bacteria interaction. Using dual inoculation experiments, we further show active exclusion of Escherichia coli cells from the root surface after B. subtilis colonization, suggesting a possible protection mechanism against root pathogens. Furthermore, we assembled a double-channel TRIS device that allows simultaneous tracking of two root systems in one chamber and performed real-time monitoring of bacterial preference between WT and mutant root genotypes. Thus, the TRIS microfluidics device provides unique insights into the microscale microbial ecology of the complex root microenvironment and is, therefore, likely to enhance the current rate of discoveries in this momentous field of research.

Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae

Multidrug resistant and hypervirulent clones of Klebsiella pneumoniae are emerging pathogens. To understand the association between genotypic and phenotypic diversity in this process, we combined genomic, phylogenomic and phenotypic analysis of a diverse set of K. pneumoniae and closely related species. These species were able to use an unusually large panel of metabolic substrates for growth, many of which were shared between all strains. We analysed the substrates used by only a fraction of the strains, identified some of their genetic basis, and found that many could not be explained by the phylogeny of the strains. Puzzlingly, few traits were associated with the ecological origin of the strains. One noticeable exception was the ability to use D-arabinose, which was much more frequent in hypervirulent strains. The broad carbon and nitrogen core metabolism of K. pneumoniae might contribute to its ability to thrive in diverse environments. Accordingly, even the hypervirulent and multidrug resistant clones have the metabolic signature of ubiquitous bacteria. The apparent few metabolic differences between hypervirulent, multi-resistant and environmental strains may favour the emergence of dual-risk strains that combine resistance and hypervirulence.

Prevalence and Phylogenetic Characterization of Escherichia coli and Hygiene Indicator Bacteria Isolated from Leafy Green Produce, Beef, and Pork Obtained from Farmers' Markets in Pennsylvania

The popularity of farmers' markets in the United States has led to over 8,400 farmers' markets being in operation in 2015. As farmers' markets have increased in size and complexity in the kinds of foods sold at these venues, so have the potential food safety risks. Since 2008, seven major foodborne illness outbreaks and two recalls associated with food products from farmers' markets have occurred, causing 80 known reported illnesses and one death. Various researchers also have observed vendors performing high-risk food safety retail behaviors, and others have identified microbiological hazards in foods sold at farmers' markets. In this study, the presence of hygiene indicators (coliforms, fecal coliforms, Listeria spp., and Escherichia coli ) was assessed in select samples of leafy green produce and meat obtained from farmers' markets in Pennsylvania. E. coli isolates were further characterized by phylogenetic profile and virulence potential. E. coli was present in 40% (20 of 50) and 18% (9 of 50) of beef and pork samples, respectively, and in 28% (15 of 54), 29% (15 of 52), and 17% (8 of 46) of kale, lettuce, and spinach samples, respectively. Listeria spp. was found in 8% (4 of 50) of beef samples, 2% (1 of 54) of kale samples, 4% (2 of 52) of lettuce samples, and 7% (3 of 46) of spinach samples. Among the 10 Listeria spp. isolates, 3 were identified as L. monocytogenes . E. coli isolated from meat samples mainly clustered into phylogroup B1 (66%; 19 of 29), whereas produce isolates clustered into phylogroups B2 (36%; 14 of 39) and B1 (33%; 13 of 39). These E. coli isolates possessed the fimH, iroN, hlyD, and eae genes associated with extraintestinal pathogenic E. coli and Shiga toxin-producing E. coli . The high prevalence but low levels of E. coli and Listeria spp. found on both produce and meat products obtained from farmers' markets in this study strongly indicate that farmers' market vendors would benefit greatly from food safety training and increased public health oversight.

Expression of Curli by Escherichia coli O157:H7 Strains Isolated from Patients during Outbreaks Is Different from Similar Strains Isolated from Leafy Green Production Environments

We previously reported that the strains of Escherichia coli O157:H7 (EcO157) that survived longer in austere soil environment lacked expression of curli, a fitness trait linked with intestinal colonization. In addition, the proportion of curli-positive variants of EcO157 decreased with repeated soil exposure. Here we evaluated 84 and 176 clinical strains from outbreaks and sporadic infections in the US, plus 211 animal fecal and environmental strains for curli expression. These shiga-toxigenic strains were from 328 different genotypes, as characterized by multi-locus variable-number tandem-repeat analysis (MLVA). More than half of the fecal strains (human and animal) and a significant proportion of environmental isolates (82%) were found to lack curli expression. EcO157 strains from several outbreaks linked with the consumption of contaminated apple juice, produce, hamburgers, steak, and beef were also found to lack curli expression. Phylogenetic analysis of fecal strains indicates curli expression is distributed throughout the population. However, a significant proportion of animal fecal isolates (84%) gave no curli expression compared to human fecal isolates (58%). In addition, analysis of environmental isolates indicated nearly exclusive clustering of curli expression to a single branch of the minimal spanning tree. This indicates that curli expression depends primarily upon the type of environmental exposure and the isolation source, although genotypic differences also contribute to clonal variation in curli. Furthermore, curli-deficient phenotype appears to be a selective trait for survival of EcO157 in agricultural environments.

Prediction of bacterial associations with plants using a supervised machine-learning approach

Recent scenarios of fresh produce contamination by human enteric pathogens have resulted in severe food-borne outbreaks, and a new paradigm has emerged stating that some human-associated bacteria can use plants as secondary hosts. As a consequence, there has been growing concern in the scientific community about these interactions that have not yet been elucidated. Since this is a relatively new area, there is a lack of strategies to address the problem of food-borne illnesses due to the ingestion of fruits and vegetables. In the present study, we performed specific genome annotations to train a supervised machine-learning model that allows for the identification of plant-associated bacteria with a precision of ∼93%. The application of our method to approximately 9500 genomes predicted several unknown interactions between well-known human pathogens and plants, and it also confirmed several cases for which evidence has been reported. We observed that factors involved in adhesion, the deconstruction of the plant cell wall and detoxifying activities were highlighted as the most predictive features. The application of our strategy to sequenced strains that are involved in food poisoning can be used as a primary screening tool to determine the possible causes of contaminations.

Pathogenic Escherichia coli producing Extended-Spectrum β-Lactamases isolated from surface water and wastewater

To assess public health risks from environmental exposure to Extended-Spectrum β-Lactamases (ESBL)-producing bacteria, it is necessary to have insight in the proportion of relative harmless commensal variants and potentially pathogenic ones (which may directly cause disease). In the current study, 170 ESBL-producing E. coli from Dutch wastewater (n = 82) and surface water (n = 88) were characterized with respect to ESBL-genotype, phylogenetic group, resistance phenotype and virulence markers associated with enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), extraintesinal E. coli (ExPEC), and Shiga toxin-producing E. coli (STEC). Overall, 17.1% of all ESBL-producing E. coli were suspected pathogenic variants. Suspected ExPECs constituted 8.8% of all ESBL-producing variants and 8.3% were potential gastrointestinal pathogens (4.1% EAEC, 1.8% EPEC, 1.2% EIEC, 1.2% ETEC, no STEC). Suspected pathogens were significantly associated with ESBL-genotype CTX-M-15 (X² = 14.7, P < 0.001) and phylogenetic group B2 (X² = 23.5, P < 0.001). Finally, 84% of the pathogenic ESBL-producing E. coli isolates were resistant to three or more different classes of antibiotics. In conclusion, this study demonstrates that the aquatic environment is a potential reservoir of E. coli variants that combine ESBL-genes, a high level of multi-drug resistance and virulence factors, and therewith pose a health risk to humans upon exposure.

Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates

To gain insights into the adaptation of the Escherichia coli species to different environments, we monitored protein abundances using quantitative proteomics and measurements of enzymatic activities of central metabolism in a set of five representative strains grown in four contrasted culture media including human urine. Two hundred and thirty seven proteins representative of the genome-scale metabolic network were identified and classified into pathway categories. We found that nutrient resources shape the general orientation of metabolism through coordinated changes in the average abundances of proteins and in enzymatic activities that all belong to the same pathway category. For example, each culture medium induces a specific oxidative response whatever the strain. On the contrary, differences between strains concern isolated proteins and enzymes within pathway categories in single environments. Our study confirms the predominance of genotype by environment interactions at the proteomic and enzyme activity levels. The buffering of genetic variation when considering life-history traits suggests a multiplicity of evolutionary strategies. For instance, the uropathogenic isolate CFT073 shows a deregulation of iron demand and increased oxidative stress response.

Comparative accessory gene fingerprinting of surface water Escherichia coli reveals genetically diverse naturalized population

AIMS

To utilize comparative accessory gene fingerprinting to discriminate between naturalized and faecal Escherichia coli, with particular emphasis on strains from phylogroup B1.

METHODS AND RESULTS

Fourteen accessory genes that were potentially ecotype-specific were selected on the basis of comparative genomic DNA sequence analysis between faecal and environmental strains and also using a literature-based strategy. PCR assays were designed for each gene, and used to screen 107 faecal strains from various hosts and 106 environmental strains from surface water and sediment. While none of the 14 accessory genes were ecotype-specific, six of the genes were ecotype-enriched. Specifically, toxin-antitoxin system genes were more abundant among faecal strains, whereas genes involved in iron acquisition, complement resistance/surface exclusion, and biofilm formation were more abundant among environmental strains. These six genes were used to form composite fingerprints which revealed the presence of several ecotype-specific and -enriched fingerprints. Notably, some of the environmental strain-specific or -enriched fingerprints consisted of strains putatively belonging to clade ET-1, which has been previously recognized as a naturalized subpopulation.

CONCLUSIONS

Unlike single genes which did not reliably distinguish between faecal and naturalized phylogroup B1 E. coli strains, composite fingerprints of ecotype-enriched accessory genes may offer a novel method for distinguishing between these two populations.

SIGNIFICANCE AND IMPACT OF THE STUDY

Accessory gene fingerprinting may have important practical implications for improving the specificity of methods that are widely used for quantifying and identifying the sources of faecal contamination in surface water.

Molecular hazard identification of non-O157 Shiga toxin-producing Escherichia coli (STEC)

The complexity regarding Shiga toxin-producing Escherichia coli (STEC) in food safety enforcement as well as clinical care primarily relates to the current inability of an accurate risk assessment of individual strains due to the large variety in serotype and genetic content associated with (severe) disease. In order to classify the clinical and/or epidemic potential of a STEC isolate at an early stage it is crucial to identify virulence characteristics of putative pathogens from genomic information, which is referred to as 'predictive hazard identification'. This study aimed at identifying associations between virulence factors, phylogenetic groups, isolation sources and seropathotypes. Most non-O157 STEC in the Netherlands belong to phylogroup B1 and are characterized by the presence of ehxA, iha and stx2, but absence of eae. The large variability in the number of virulence factors present among serogroups and seropathotypes demonstrated that this was merely indicative for the virulence potential. While all the virulence gene associations have been worked out, it appeared that there is no specific pattern that would unambiguously enable hazard identification for an STEC strain. However, the strong correlations between virulence factors indicate that these arrays are not a random collection but are rather specific sets. Especially the presence of eae was strongly correlated to the presence of many of the other virulence genes, including all non-LEE encoded effectors. Different stx-subtypes were associated with different virulence profiles. The factors ehxA and ureC were significantly associated with HUS-associated strains (HAS) and not correlated to the presence of eae. This indicates their candidacy as important pathogenicity markers next to eae and stx2a.

Variation in siderophore biosynthetic gene distribution and production across environmental and faecal populations of Escherichia coli

Iron is essential for Escherichia coli growth and survival in the host and the external environment, but its availability is generally low due to the poor solubility of its ferric form in aqueous environments and the presence of iron-withholding proteins in the host. Most E. coli can increase access to iron by excreting siderophores such as enterobactin, which have a very strong affinity for Fe3+. A smaller proportion of isolates can generate up to 3 additional siderophores linked with pathogenesis; aerobactin, salmochelin, and yersiniabactin. However, non-pathogenic E. coli are also able to synthesise these virulence-associated siderophores. This raises questions about their role in the ecology of E. coli, beyond virulence, and whether specific siderophores might be linked with persistence in the external environment. Under the assumption that selection favours phenotypes that confer a fitness advantage, we compared siderophore production and gene distribution in E. coli isolated either from agricultural plants or the faeces of healthy mammals. This population-level comparison has revealed that under iron limiting growth conditions plant-associated isolates produced lower amounts of siderophores than faecal isolates. Additionally, multiplex PCR showed that environmental isolates were less likely to contain loci associated with aerobactin and yersiniabactin synthesis. Although aerobactin was linked with strong siderophore excretion, a significant difference in production was still observed between plant and faecal isolates when the analysis was restricted to strains only able to synthesise enterobactin. This finding suggests that the regulatory response to iron limitation may be an important trait associated with adaptation to the non-host environment. Our findings are consistent with the hypothesis that the ability to produce multiple siderophores facilitates E. coli gut colonisation and plays an important role in E. coli commensalism.

Type III secretion system and virulence markers highlight similarities and differences between human- and plant-associated pseudomonads related to Pseudomonas fluorescens and P. putida

Pseudomonas fluorescens is commonly considered a saprophytic rhizobacterium devoid of pathogenic potential. Nevertheless, the recurrent isolation of strains from clinical human cases could indicate the emergence of novel strains originating from the rhizosphere reservoir, which could be particularly resistant to the immune system and clinical treatment. The importance of type three secretion systems (T3SSs) in the related Pseudomonas aeruginosa nosocomial species and the occurrence of this secretion system in plant-associated P. fluorescens raise the question of whether clinical isolates may also harbor T3SSs. In this study, isolates associated with clinical infections and identified in hospitals as belonging to P. fluorescens were compared with fluorescent pseudomonads harboring T3SSs isolated from plants. Bacterial isolates were tested for (i) their genetic relationships based on their 16S rRNA phylogeny, (ii) the presence of T3SS genes by PCR, and (iii) their infectious potential on animals and plants under environmental or physiological temperature conditions. Two groups of bacteria were delineated among the clinical isolates. The first group encompassed thermotolerant (41°C) isolates from patients suffering from blood infections; these isolates were finally found to not belong to P. fluorescens but were closely related and harbored highly conserved T3SS genes belonging to the Ysc-T3SS family, like the T3SSs from P. aeruginosa. The second group encompassed isolates from patients suffering from cystic fibrosis; these isolates belonged to P. fluorescens and harbored T3SS genes belonging to the Hrp1-T3SS family found commonly in plant-associated P. fluorescens.

Microbiological survey of locally grown lettuce sold at farmers' markets in Vancouver, British Columbia

Increased consumer demand for fresh leafy produce has been paralleled by an increase in outbreaks and illness associated with these foods. Presently, data on the microbiological quality and safety of produce harvested in the Lower Mainland of British Columbia is lacking. Therefore, fresh green, red, and romaine lettuce samples (n = 68) were obtained from five regional farmers' markets in late summer of 2012 and subsequently analyzed to determine total numbers of aerobic bacteria, coliforms, and Escherichia coli. Additionally, enrichment procedures were used to detect low concentrations of E. coli. Obtained E. coli isolates were subjected to multiplex PCRs to determine phylogenetic groupings and the presence of virulence genes (eaeA, hlyA, stx1, and stx2). All E. coli were tested for resistance to 15 antibiotics using a disk diffusion assay. Lettuce samples yielded mean aerobic colony counts of 6.3 log CFU/g. Coliforms were detected in 72% of samples, with a median concentration of 1.9 log CFU/g. Of samples, 13% were found to harbor E. coli, with a median level of 0.7 log CFU/g. Antibiogram typing of all E. coli (n = 33) revealed that 97% possessed resistance to one or more antimicrobials, with resistance to amikacin (58%), trimethoprim (48%), and trimethoprim-sulfamethoxazole (45%) being the most common. Phylogroup typing showed that 79% of these isolates belonged to group B1, with the remaining assigned to groups A (9%) or D (12%); no virulence genes were detected. Considering that phylogroup indicators suggestive of fecal contamination (groups A and D E. coli) were recovered in lettuce samples presented at retail, further work is required to explore at what point along the food chain contamination occurs. Also, this study shows the presence of multidrug-resistant E. coli in fresh vegetables. Summed, these data provide important information on the microbiological quality of leafy vegetables grown in British Columbia through the detection and characterization of frequently used indicator organisms.

Biofilm formation by enteric pathogens and its role in plant colonization and persistence

The significant increase in foodborne outbreaks caused by contaminated fresh produce, such as alfalfa sprouts, lettuce, melons, tomatoes and spinach, during the last 30 years stimulated investigation of the mechanisms of persistence of human pathogens on plants. Emerging evidence suggests that Salmonella enterica and Escherichia coli, which cause the vast majority of fresh produce outbreaks, are able to adhere to and to form biofilms on plants leading to persistence and resistance to disinfection treatments, which subsequently can cause human infections and major outbreaks. In this review, we present the current knowledge about host, bacterial and environmental factors that affect the attachment to plant tissue and the process of biofilm formation by S. enterica and E. coli, and discuss how biofilm formation assists in persistence of pathogens on the plants. Mechanisms used by S. enterica and E. coli to adhere and persist on abiotic surfaces and mammalian cells are partially similar and also used by plant pathogens and symbionts. For example, amyloid curli fimbriae, part of the extracellular matrix of biofilms, frequently contribute to adherence and are upregulated upon adherence and colonization of plant material. Also the major exopolysaccharide of the biofilm matrix, cellulose, is an adherence factor not only of S. enterica and E. coli, but also of plant symbionts and pathogens. Plants, on the other hand, respond to colonization by enteric pathogens with a variety of defence mechanisms, some of which can effectively inhibit biofilm formation. Consequently, plant compounds might be investigated for promising novel antibiofilm strategies.

Meta-regression analysis of commensal and pathogenic Escherichia coli survival in soil and water

The extent to which pathogenic and commensal E. coli (respectively PEC and CEC) can survive, and which factors predominantly determine the rate of decline, are crucial issues from a public health point of view. The goal of this study was to provide a quantitative summary of the variability in E. coli survival in soil and water over a broad range of individual studies and to identify the most important sources of variability. To that end, a meta-regression analysis on available literature data was conducted. The considerable variation in reported decline rates indicated that the persistence of E. coli is not easily predictable. The meta-analysis demonstrated that for soil and water, the type of experiment (laboratory or field), the matrix subtype (type of water and soil), and temperature were the main factors included in the regression analysis. A higher average decline rate in soil of PEC compared with CEC was observed. The regression models explained at best 57% of the variation in decline rate in soil and 41% of the variation in decline rate in water. This indicates that additional factors, not included in the current meta-regression analysis, are of importance but rarely reported. More complete reporting of experimental conditions may allow future inference on the global effects of these variables on the decline rate of E. coli.

Enteric pathogen-plant interactions: molecular connections leading to colonization and growth and implications for food safety

Leafy green vegetables have been identified as a source of foodborne illnesses worldwide over the past decade. Human enteric pathogens, such as Escherichia coli O157:H7 and Salmonella, have been implicated in numerous food poisoning outbreaks associated with the consumption of fresh produce. An understanding of the mechanisms responsible for the establishment of pathogenic bacteria in or on vegetable plants is critical for understanding and ameliorating this problem as well as ensuring the safety of our food supply. While previous studies have described the growth and survival of enteric pathogens in the environment and also the risk factors associated with the contamination of vegetables, the molecular events involved in the colonization of fresh produce by enteric pathogens are just beginning to be elucidated. This review summarizes recent findings on the interactions of several bacterial pathogens with leafy green vegetables. Changes in gene expression linked to the bacterial attachment and colonization of plant structures are discussed in light of their relevance to plant-microbe interactions. We propose a mechanism for the establishment and association of enteric pathogens with plants and discuss potential strategies to address the problem of foodborne illness linked to the consumption of leafy green vegetables.

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major generalist lineages of C. jejuni do not show evidence of recombination with each other in nature, despite having a high degree of host niche overlap and recombining extensively with specialist lineages. However, transformation experiments show that the generalist lineages readily recombine with one another in vitro. This suggests ecological rather than essential barriers to recombination, caused by a cryptic niche structure within the hosts.

The influence of social structure, habitat, and host traits on the transmission of Escherichia coli in wild elephants

Social structure is proposed to influence the transmission of both directly and environmentally transmitted infectious agents. However in natural populations, many other factors also influence transmission, including variation in individual susceptibility and aspects of the environment that promote or inhibit exposure to infection. We used a population genetic approach to investigate the effects of social structure, environment, and host traits on the transmission of Escherichia coli infecting two populations of wild elephants: one in Amboseli National Park and another in Samburu National Reserve, Kenya. If E. coli transmission is strongly influenced by elephant social structure, E. coli infecting elephants from the same social group should be genetically more similar than E. coli sampled from members of different social groups. However, we found no support for this prediction. Instead, E. coli was panmictic across social groups, and transmission patterns were largely dominated by habitat and host traits. For instance, habitat overlap between elephant social groups predicted E. coli genetic similarity, but only in the relatively drier habitat of Samburu, and not in Amboseli, where the habitat contains large, permanent swamps. In terms of host traits, adult males were infected with more diverse haplotypes, and males were slightly more likely to harbor strains with higher pathogenic potential, as compared to adult females. In addition, elephants from similar birth cohorts were infected with genetically more similar E. coli than elephants more disparate in age. This age-structured transmission may be driven by temporal shifts in genetic structure of E. coli in the environment and the effects of age on bacterial colonization. Together, our results support the idea that, in elephants, social structure often will not exhibit strong effects on the transmission of generalist, fecal-oral transmitted bacteria. We discuss our results in the context of social, environmental, and host-related factors that influence transmission patterns.

Assessments of total and viable Escherichia coli O157:H7 on field and laboratory grown lettuce

Leafy green produce has been associated with numerous outbreaks of foodborne illness caused by strains of Escherichia coli O157:H7. While the amounts of culturable E. coli O157:H7 rapidly decline after introduction onto lettuce in the field, it remains to be determined whether the reduction in cell numbers is due to losses in cell viability, cell injury and a subsequent inability to be detected by standard laboratory culturing methods, or a lack of adherence and hence rapid removal of the organism from the plants during application. To assess which of these options is most relevant for E. coli O157:H7 on leafy green produce, we developed and applied a propidium monoazide (PMA) real-time PCR assay to quantify viable (with PMA) and total (without PMA) E. coli O157:H7 cells on growth chamber and field-grown lettuce. E. coli O157:H7, suspended in 0.1% peptone, was inoculated onto 4-week-old lettuce plants at a level of approximately 10(6) CFU/plant. In the growth chamber at low relative humidity (30%), culturable amounts of the nontoxigenic E. coli O157:H7 strain ATCC 700728 and the virulent strain EC4045 declined 100 to 1000-fold in 24 h. Fewer E. coli O157:H7 cells survived when applied onto plants in droplets with a pipette compared with a fine spray inoculation. Total cells for both strains were equivalent to inoculum levels for 7 days after application, and viable cell quantities determined by PMA real-time PCR were approximately 10(4) greater than found by colony enumeration. Within 2 h after application onto plants in the field, the number of culturable E. coli ATCC 700728 was reduced by up to 1000-fold, whereas PCR-based assessments showed that total cell amounts were equivalent to inoculum levels. These findings show that shortly after inoculation onto plants, the majority of E. coli O157:H7 cells either die or are no longer culturable.

Evidence for coexistence of distinct Escherichia coli populations in various aquatic environments and their survival in estuary water

Escherichia coli, a commensal bacterium from the intestinal tracts of humans and vertebrate animals, has been used as one of two bacterial indicators of fecal contamination, along with intestinal enterococci, to monitor the microbiological quality of water. However, water environments are now recognized as a secondary habitat where some strains can survive. We investigated the survival of E. coli isolates collected from bodies of water in France exhibiting distinct profiles of contamination, defined according to the following criteria: vicinity of the point sources of contamination, land use, hydrology, and physicochemical characteristics of the receiving water. We selected 88 E. coli strains among a collection of 352 strains to carry out a microcosm experiment in filtered estuarine water for 14 days at 10°C. The relationship between the survival of E. coli strains and genotypic and phenotypic characteristics was analyzed. This work showed that distinct E. coli survival types, able to survive from between 7 and 14 days to less than 2 days, coexisted in the water. E. coli isolates that rapidly lost their culturability were more frequently isolated in water recently contaminated by fecal bacteria of human origin, and most were multiresistant to antibiotics and harbored several virulence factors. In contrast, persistent strains able to survive from 4 to 14 days were more often found in water with low levels of fecal bacteria, belonged mainly to the B1 phylogroup, often harbored only one virulence factor, kspE or ompT, and were able to grow at 7°C.

Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche

BACKGROUND

Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche.

RESULTS

Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles.

CONCLUSIONS

Our results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties.

From Exit to Entry: Long-term Survival and Transmission of Salmonella

Salmonella spp. are a leading cause of human infectious disease worldwide and pose a serious health concern. While we have an improving understanding of pathogenesis and the host-pathogen interactions underlying the infection process, comparatively little is known about the survival of pathogenic Salmonella outside their hosts. This review focuses on three areas: (1) in vitro evidence that Salmonella spp. can survive for long periods of time under harsh conditions; (2) observations and conclusions about Salmonella persistence obtained from human outbreaks; and (3) new information revealed by genomic- and population-based studies of Salmonella and related enteric pathogens. We highlight the mechanisms of Salmonella persistence and transmission as an essential part of their lifecycle and a prerequisite for their evolutionary success as human pathogens.