Structure and urovirulence characteristics of the fecal Escherichia coli population among healthy women

The host specificity of pilus gene traA in Escherichia coli and its use in tracking human fecal pollution

A reliable and accurate fecal source tracking (FST) approach is important in water quality management and preventing foodborne and waterborne diseases. In this study, a genetic marker of Escherichia coli (E. coli) was identified and utilized to differentiate between human and animal sources of fecal contamination. Nucleotide polymorphisms of 14 genes coding for cellular surface proteins, mainly fimbriae, were analyzed using the 22 draft genomes of E. coli strains from human and three domestic animal sources in Japan. A signature sequence, traAh, within the pilin gene traA, was found to be highly associated with E. coli of human origin. Subsequently, an end-point polymerase chain reaction (PCR) assay, namely PCR-Htra, was developed, specifically targeting traAh. The high association between traAh and E. coli of human origin was validated through the PCR-Htra amplification. This encompassed 1045 E. coli strains isolated from surface water, human feces or sewages, and feces from 12 animal species, including domestic and wild animals in the states of Missouri and Virginia in the United States of America (USA). The data suggested that the sensitivity and specificity of PCR-Htra assay were 49.0 % and 99.5 % respectively in distinguishing human-origin E. coli from nonhuman-source ones. Furthermore, the result of our in silico analysis of GenBank® data suggests that traAh may have a global distribution as the sequence was found in human-origin E. coli isolated from at least 14 countries around the world. Thus, the PCR-Htra may provide a new FST tool for rapid and accurate detection of human-origin E. coli, serving as a means to identify human fecal contamination in water.

Under-Appreciated Phylogroup Diversity of Escherichia coli within and between Animals at the Urban-Wildland Interface

Wild animals have been implicated as reservoirs and even "melting pots" of pathogenic and antimicrobial-resistant bacteria of concern to human health. Though Escherichia coli is common among vertebrate guts and plays a role in the propagation of such genetic information, few studies have explored its diversity beyond humans nor the ecological factors that influence its diversity and distribution in wild animals. We characterized an average of 20 E. coli isolates per scat sample (n = 84) from a community of 14 wild and 3 domestic species. The phylogeny of E. coli comprises 8 phylogroups that are differentially associated with pathogenicity and antibiotic resistance, and we uncovered all of them in one small biological preserve surrounded by intense human activity. Challenging previous assumptions that a single isolate is representative of within-host phylogroup diversity, 57% of individual animals sampled carried multiple phylogroups simultaneously. Host species' phylogroup richness saturated at different levels across species and encapsulated vast within-sample and within-species variation, indicating that distribution patterns are influenced both by isolation source and laboratory sampling depth. Using ecological methods that ensure statistical relevance, we identify trends in phylogroup prevalence associated with host and environmental factors. The vast genetic diversity and broad distribution of E. coli in wildlife populations has implications for biodiversity conservation, agriculture, and public health, as well as for gauging unknown risks at the urban-wildland interface. We propose critical directions for future studies of the "wild side" of E. coli that will expand our understanding of its ecology and evolution beyond the human environment. IMPORTANCE To our knowledge, neither the phylogroup diversity of E. coli within individual wild animals nor that within an interacting multispecies community have previously been assessed. In doing so, we uncovered the globally known phylogroup diversity from an animal community on a preserve imbedded in a human-dominated landscape. We revealed that the phylogroup composition in domestic animals differed greatly from that in their wild counterparts, implying potential human impacts on the domestic animal gut. Significantly, many wild individuals hosted multiple phylogroups simultaneously, indicating the potential for strain-mixing and zoonotic spillback, especially as human encroachment into wildlands increases in the Anthropocene. We reason that due to extensive anthropogenic environmental contamination, wildlife is increasingly exposed to our waste, including E. coli and antibiotics. The gaps in the ecological and evolutionary understanding of E. coli thus necessitate a significant uptick in research to better understand human impacts on wildlife and the risk for zoonotic pathogen emergence.

Relationship between Escherichia coli virulence factors, notably kpsMTII, and symptoms of clinical metritis and endometritis in dairy cows

Although Escherichia coli is a commensal bacterium of the bovine vaginal microbiota, it is an important pathogenic bacterium that causes diseases of the reproductive tract and sub-fertility. Recent studies have focused on virulence factors (VFs) of intrauterine E. coli; however, actual endometrial VFs have not been clearly identified. The purpose of this study was to identify the VFs of E. coli associated with clinical metritis and endometritis. Thirty-two strains of E. coli and four mixed Trueperella pyogenes (TP) strains were detected in the uterus of 19 Holstein dairy cows with obvious clinical signs (between 8 and 66 days postpartum). The presence of six E. coli VFs (fimH, fyuA, kpsMTII, hra1, csgA, and astA) was examined by PCR, and clinical signs and reproductive performance (mixed TP, the percentage of polymorphonuclear neutrophils [PMN%], days to uterine involution, etc.) were evaluated. Four VFs (fimH, hra1, csgA, and astA) were detected in all E. coli strains, whereas fyuA and kpsMTII were detected in 94% and 50% of strains, respectively. Cows with E. coli strains harboring kpsMTII exhibited significantly severe clinical scores (vaginal discharge score, PMN%, uterine involution), suggesting that kpsMTII is a key VF for progression of clinical metritis and endometritis. In the present study, we clearly identified six VFs associated with clinical metritis and endometritis. In addition, E. coli strains with kpsMTII probably play a crucial role in the progression of clinical metritis and endometritis.

Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources

Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum β-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin; resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3')-Ia, bla_CTX-M-15, bla_TEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.

Bacterial "Virulence" Traits and Host Demographics Predict Escherichia coli Colonization Behaviors Within Households

Background

Although intestinal colonization precedes most extraintestinal Escherichia coli infections, colonization-promoting factors are incompletely understood. We compared within-household E. coli colonization patterns with host and bacterial traits.

Methods

Twenty-two veterans with a clinical E. coli isolate and their 46 human and animal household members underwent longitudinal fecal sampling. Distinct E. coli strains were characterized for phylogenetic background, virulence genes, antibiotic resistance, and colonization behaviors. Host and bacterial traits were assessed statistically as predictors of colonization behaviors.

Results

Among the 139 unique-by-household fecal E. coli strains, univariable predictors of colonization behavior included (i) host demographics, (ii) matching the index clinical isolate, and (iii) bacterial characteristics (2 phylogroups, 5 clonal lineages, 18 virulence genes, and molecular extraintestinal pathogenic E. coli status). Multivariable predictors of colonization behavior included veteran host, spouse host, matching the index clinical isolate, phylogroup F, ST73, hlyD (alpha hemolysin), hlyF (variant hemolysin), H7 fliC (flagellar variant), vat (vacuolating toxin), and iha (adhesin-siderophore).

Conclusions

Host demographics, multiple bacterial “virulence” traits, and matching the index clinical isolate predicted E. coli fecal colonization behaviors. Thus, certain bacterial characteristics may promote both colonization and pathogenicity. Future interventions directed toward such traits might prevent E. coli infections both directly and by disrupting antecedent colonization.

Commonality of adherent-invasive Escherichia coli isolated from patients with extraintestinal infections, healthy individuals and the environment

Adherent-invasive Escherichia coli (AIEC) has been implicated as a microbiological factor in inflammatory bowel disease (IBD) pathogenesis. These strains are defined by their ability to adhere to and invade intestinal epithelial cells, and to survive and replicate in macrophages. We postulated that AIEC strains may commonly inhabit the gut of healthy individuals (HI), cause extraintestinal infections, and be found in sewage treatment plants (STP) and surface waters (SW). A total of 808 E. coli strains isolated from HI; patients with community-acquired urinary tract infection (CA-UTI), septicaemia and urosepsis; STP; and SW, showing a diffuse adhesion pattern to Caco-2 cells were included in this study. Typing of the strains using a combination of RAPD-PCR and PhPlate fingerprinting grouped them into 48 common clones (CCs). Representatives of each CC were tested for the ability to invade Caco-2 cells, survive and replicate in macrophages, and for the presence of six virulence genes commonly found among AIEC strains. Twenty CCs were deemed AIEC based on their ability to survive and replicate in macrophages, while encoding htrA, dsbA and clbA genes. These CCs primarily originated from HI and CA-UTI patients but were also detected in secondary locations including STP and SW. Strains lacking intramacrophagic survival and replication abilities were regarded as diffusely adhering E. coli (DAEC). Certain clones of AIEC are common in the gut of HI whilst promoting CA-UTI. The survival and persistence of AIEC in STP and SW may have serious public health ramifications for individuals predisposed to IBD.

Core-Shell Beads as Microreactors for Phylogrouping of E. coli Strains

Multiplex polymerase chain reaction (PCR) is an effective tool for simultaneous detection of target genes. Nevertheless, their use has been restricted due to the intrinsic interference between primer pairs. Performing several single PCRs in an array format instead of a multiplex PCR is a simple way to overcome this obstacle. However, there are still major technical challenges in designing a new generation of single PCR microreactors with a small sample volume, rapid thermal cycling, and no evaporation during amplification. We report a simple and robust core-shell bead array for a series of single amplifications. Four core-shell beads with a polymer coating and PCR mixture were synthesized using liquid marble formation and subsequent photo polymerization. Each bead can detect one target gene. We constructed a customised system for thermal cycling of these core-shell beads. Phylogrouping of the E. coli strains was carried out based on the fluorescent signal of the core-shell beads. This platform can be a promising alternative for multiplex nucleic acid analyses due to its simplicity and high throughput. The platform reported here also reduces the cycling time and avoids evaporation as well as contamination of the sample during the amplification process.

Characterization of native Escherichia coli populations from bovine vagina of healthy heifers and cows with postpartum uterine disease

Even though Escherichia coli are common bacteria of the bovine vaginal microbiota, they represent an important pathogen that causes diseases in the reproductive tract and subfertility. However, the actual endometrial virulence profile of E. coli is poorly understood. The present study aims to characterize the phylogenetic structure and virulence potential of native vaginal populations of E. coli from healthy heifers (H), and cows with postpartum uterine diseases (PUD), such as metritis/endometritis (MT) or repeat breeder cows (RB). To this end, the virulence repertoire of 97 E. coli isolates was genotypically and phenotypically assessed. Most of them were assigned to phylogenetic group A (74%), followed by B1 (17%) and D (9%); RB strains were significantly (p < 0.05) more represented by B1. Seven of the 15 evaluated virulence genes (VFG) were detected and the most prevalent were fimH (87%), agn43 (41%) and csgA (35%); while traT (27%), fyuA (11%), hlyA (5%) and kpsMT II (5%) were observed in a lower proportion. Particularly, fyuA was significantly higher (p < 0.05) in MT cows whereas csgA showed the same behavior in PUD animals (p < 0.05). When comparing H and PUD strains, these last ones were associated to positive expression of biofilm, fimbriae curli/cellulose and motility; yet RB strains did not show motility. Vaginal B1 E. coli populations, that possess VFG (fyuA and csgA) as well as the expression of motility, curli fimbriae/cellulose and biofilm, may represent risk factors for endometrial disorders; specifically, those that also, have kpsMT II may have a pathogenic potential for causing the RB syndrome. Future research focusing on the detection of these strains in the vaginal microbiota of cows with postpartum uterine diseases should be done since the control of their presence in vagina could reduce the risk that they access the uterus during the postpartum period.

A snapshot of diversity: Intraclonal variation of Escherichia coli clones as commensals and pathogens

Whole-genome sequencing has enabled detailed studies on bacterial evolution during infection, but there is limited knowledge on intraclonal variation. In this study, we sought to provide a snapshot of the intraclonal diversity of Escherichia coli as both commensal in the faecal environment and pathogen during urinary tract infection, respectively. This was performed by whole-genome sequencing and analyses of single nucleotide polymorphisms (SNPs) and gene-content variation in ten isolates belonging to the same clone and isolated from rectal swabs or urine samples. We identified only one clone in eight of the nine urines sampled (89 %). In both the commensal and pathogenic state, the within-host diversity was limited with intraclonal SNP diversity of 0-2 non-synonymous SNPs for each clone. The genetic diversity showed variation in gene content in a range of 2-15 genes in total for all clones, including genes positioned on plasmids, and in the K- and O-antigen cluster. The observed SNP- and gene variation shows that sampling of one colony would be enough for surveillance, outbreak investigations and clonal evolution. However, for studies of adaptation during or between colonization and infection, this variation is relevant to consider.

Escherichia coli Clonobiome: Assessing the Strain Diversity in Feces and Urine by Deep Amplicon Sequencing

While microbiome studies have focused on diversity at the species level or higher, bacterial species in microbiomes are represented by different, often multiple, strains. These strains could be clonally and phenotypically very different, making assessment of strain content vital to a full understanding of microbiome function. This is especially important with respect to antibiotic-resistant strains, the clonal spread of which may be dependent on competition between them and susceptible strains from the same species. The pandemic, multidrug-resistant, and highly pathogenic Escherichia coli subclone ST131-H30 (H30) is of special interest, as it has already been found persisting in the gut and bladder in healthy people. In order to rapidly assess E. coli clonal diversity, we developed a novel method based on deep sequencing of two loci used for sequence typing, along with an algorithm for analysis of the resulting data. Using this method, we assessed fecal and urinary samples from healthy women carrying H30 and were able to uncover considerable diversity, including strains with frequencies at <1% of the E. coli population. We also found that, even in the absence of antibiotic use, H30 could completely dominate the gut and, especially, urine of healthy carriers. Our study offers a novel tool for assessing a species' clonal diversity (clonobiome) within the microbiome, which could be useful in studying the population structure and dynamics of multidrug-resistant and/or highly pathogenic strains in their natural environments.IMPORTANCE Bacterial species in the microbiome are often represented by multiple genetically and phenotypically different strains, making insight into subspecies diversity critical to a full understanding of the microbiome, especially with respect to opportunistic pathogens. However, methods allowing efficient high-throughput clonal typing are not currently available. This study combines a conventional E. coli typing method with deep amplicon sequencing to allow analysis of many samples concurrently. While our method was developed for E. coli, it may be adapted for other species, allowing microbiome researchers to assess clonal strain diversity in natural samples. Since assessment of subspecies diversity is particularly important for understanding the spread of antibiotic resistance, we applied our method to the study of a pandemic multidrug-resistant E. coli clone. The results we present suggest that this clone could be highly competitive in healthy carriers and that the mechanisms of colonization by such clones need to be studied.

Virulence-associated genes and drug susceptibility patterns of uropathogenic Escherichia coli isolated from patients with urinary tract infection

Background: Different Escherichia coli phylogenetic groups, such as A, B1, B2, and D, have four functional groups – adhesins, microcins, toxins, and capsules – which can cause urinary tract infections (UTIs). A phylogenetic group with a high virulence content becomes a worldwide health concern. Resistance to antimicrobial agents increasingly complicates the management of E. coli extraintestinal infections, as a major source of illness, death, and increased health care costs. The aim of this study was to determine the virulence content and the antimicrobial susceptibility pattern of different uropathogenic E. coli (UPEC) phylogenetic groups in Ahvaz, Iran.

Methods: Phylogenetic groups, virulence-associated genes (VAGs), and antimicrobial susceptibility tests were detected by molecular and phenotypic methods in a total of 232 clinically well-characterized E. coli strains, isolated from two collections of patients with hospital-acquired (HA) and community-acquired (CA) UTIs.

Results: Our results revealed that among 232 UPEC strains, the most frequent phylogenetic group was phylogroup D (58%) with the greatest content in virulence factors, including kpsM (23%), neuA (76.3%, capsule), cnf (29.6%, toxin), and Pap (54.8%, adhesin). Phylogroups D and, to a lesser extent, B2 were the most drug-resistant phylogroups. In addition, phylogroup D was responsible for the majority of HA (64.7%) and CA (48.4%) infections.

Conclusion: Among UPEC strains causing UTIs, different phylogroups, through different VAGs, could cause severe infection. Knowledge about the distribution of the four functional groups and VAGs belonging to these phylogroups would significantly help to confine and prevent the development of lethal infection caused by these strains.

Genetic relatedness of the Escherichia coli fecal population and strains causing urinary tract infection in the same host

It is common knowledge that fecal microbiota is a primary source of Escherichia coli causing urinary tract infections (UTIs) via the fecal-perineal-urethral route. But, it is still unknown whether E. coli UTI is mainly caused by dominant fecal E. coli isolates (prevalence hypothesis) or the isolates that possess more virulence factors (special pathogenicity hypothesis). In the present study, the urine E. coli isolates of 30 women with UTI were compared with the fecal E. coli isolates of the same patients and healthy control individuals according to the phylogenetic group, virulence genotype, and antibiotic susceptibility pattern. The genetic relatedness of the isolates was specified and compared by pulsed-field gel electrophoresis (PFGE). PFGE analysis showed that most patients (73.3%) had distinct urine isolates which were not similar to any of their fecal isolates. Based on the phylogenetic analysis, most of the urine and fecal isolates of healthy women were assigned to phylogenetic group B2, followed by D. The distribution of phylogenetic groups was significantly different between the urine and the fecal isolates of patients (p < 0.05). The prevalence of fimH and ompT among urine isolates was significantly more than that among fecal isolates. The level of multidrug resistance was higher among urine isolates. Although more in-depth researches are required, the present study could be supported by pathogenicity hypothesis. Furthermore, concerning the antibiotic resistance pattern among uropathogenic E. coli should be highly considered.

Escherichia coli colonizing healthy children in Tunisia: High prevalence of extra-intestinal pathovar and occurrence of non-extended-spectrum-β-lactamase-producing ST131 clone

This study was performed to investigate the distribution of antimicrobial resistance genes and extra-intestinal virulence determinants in a collection of 98 Escherichia coli strains isolated from rectal swabs of healthy children. Forty-six isolated strains were resistant to at least one of the tested antibiotics (usually active against enterobacteria). They were mainly resistant to ampicillin and ticarcillin (42.97%), tetracyclin (26.5%), and trimethoprim/sulfamethoxazole (18.4%). No resistance to the third generation of cephalosporins, carbapenems, aminoglycosides and colistin was found. Resistance to penicillins was encoded by bla_TEM-1 (n=34) and bla_SHV-1 genes (n=4). Tetracyclin resistance was encoded by tetB (n=12), tetA (n= 5), and tetC (n=1) genes. Amongst resistant quinolones isolated (n=5), chromosomal mutations in gyrA and parC genes were detected in four isolates and qnrS1 gene in two strains. Nine plasmid replicon types were detected; IncFIB (n=36) and IncI1 (n=7) were the most frequent ones. Isolates frequently belonged to phylogenetic groups A (51.1%) and D (27.5%). Extra-intestinal pathovar (n=38) occurred mainly in B2 phylogroup (P=0.0002). Amongst them, two isolates (non-extended-spectrum-β-lactamase (ESBL)-producers) belonged to the pandemic clone ST131. A significant distribution of virulence determinants and pathogenicity island marker was observed within strains belonging to B2 and D phylogroups. Interestingly, our results showed that ExPEC strains, including ST131 pandemic clone, are present within fecal isolates in healthy children. These findings highlight the importance of intestinal microbiota as a reservoir for virulent and resistant strains. Thus, reinforcing hand hygiene and antibiotic rational use is imperative to avoid the diffusion of these pathogens in the community.

Comparative ecology of Escherichia coli in endangered Australian sea lion (Neophoca cinerea) pups

The dissemination of human-associated bacteria into the marine environment has the potential to expose wildlife populations to atypical microbes that can alter the composition of the gut microbiome or act as pathogens. The objective of the study was to determine whether endangered Australian sea lion (Neophoca cinerea) pups from two South Australian colonies, Seal Bay, Kangaroo Island and Dangerous Reef, Spencer Gulf, have been colonised by human-associated Escherichia coli. Faecal samples (n = 111) were collected to isolate E. coli, and molecular screening was applied to assign E. coli isolates (n = 94) to phylotypes and detect class 1 integrons; mobile genetic elements that confer resistance to antimicrobial agents. E. coli phylotype distribution and frequency differed significantly between colonies with phylotypes B2 and D being the most abundant at Seal Bay, Kangaroo Island (55% and 7%) and Dangerous Reef, Spencer Gulf (36% and 49%), respectively. This study reports the first case of antimicrobial resistant E. coli in free-ranging Australian sea lions through the identification of class 1 integrons from an individual pup at Seal Bay. A significant relationship between phylotype and total white cell count (WCC) was identified, with significantly higher WCC seen in pups with human-associated phylotypes at Dangerous Reef. The difference in phylotype distribution and presence of human-associated E. coli suggests that proximity to human populations can influence sea lion gut microbiota. The identification of antimicrobial resistance in a free-ranging pinniped population provides crucial information concerning anthropogenic influences in the marine environment.

Within-host evolution versus immigration as a determinant of Escherichia coli diversity in the human gastrointestinal tract

When a human host harbors two or more strains of Escherichia coli, the second strain is more likely to be a member of the same phylogroup rather than a different phylogroup. This outcome may be the consequence of a within host evolution event or an independent immigration/establishment event. To determine the relative importance of these two events in determining E. coli diversity in a host, a collection of multiple E. coli isolates recovered from each of 67 patients undergoing colonoscopies was used. Whole genome sequence data were available for one example of every REP-fingerprint type identified in a patient. Sequence type (ST) and single-nucleotide polymorphism (SNP) analyses revealed that 83% of strains observed in the host population were a consequence of immigration/establishment events. Restricting the analysis to hosts harboring two or more strains belonging to the same phylogroup revealed that in about half of these cases, the presence of a second strain belonging to the same phylogroup was the consequence of an independent immigration/establishment event. Thus, the results of this study show that despite hosts being exposed to a diversity of E. coli via their food, factors related to the host also determine what E. coli strains succeed in establishing.

Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates

Escherichia coli is an important microorganism in the gastrointestinal tract of warm-blooded animals. Commensal populations of E. coli consist of stable genetic isolates, which means that each individual has only one phylogenetic group (phylogroup). We evaluated the frequency of human commensal E. coli phylogroups from 116 people and observed that the majority of isolates belonged to group A. We also evaluated the frequency of phylogroups in wastewater samples and found a strong positive correlation between the phylogroup distribution in wastewater and human hosts. In order to find out if some factors, such as geographical location, and climate could influence the worldwide phylogroup distribution, we performed a meta-analysis of 39 different studies and 24 countries, including different climates, living areas, and feeding habits. Unexpectedly, our results showed no substructuring patterns of phylogroups; indicating there was no correlation between phylogroup distribution and geographic location, climate, living area, feeding habits, or date of collection.

Whole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls

The faecal flora is a common reservoir for urinary tract infection (UTI), and Escherichia coli (E. coli) is frequently found in this reservoir without causing extraintestinal infection. We investigated these E. coli reservoirs by whole-genome sequencing a large collection of E. coli from healthy controls (faecal), who had never previously had UTI, and from UTI patients (faecal and urinary) sampled from the same geographical area. We compared MLST types, phylogenetic relationship, accessory genome content and FimH type between patient and control faecal isolates as well as between UTI and faecal-only isolates, respectively. Comparison of the accessory genome of UTI isolates to faecal isolates revealed 35 gene families which were significantly more prevalent in the UTI isolates compared to the faecal isolates, although none of these were unique to one of the two groups. Of these 35, 22 belonged to a genomic island and three putatively belonged to a type VI secretion system (T6SS). MLST types and SNP phylogeny indicated no clustering of the UTI or faecal E. coli from patients distinct from the control faecal isolates, although there was an overrepresentation of UTI isolates belonging to clonal lineages CC73 and CC12. One combination of mutations in FimH, N70S/S78N, was significantly associated to UTI, while phylogenetic analysis of FimH and fimH identified no signs of distinct adaptation of UTI isolates compared to faecal-only isolates not causing UTI. In summary, the results showed that (i) healthy women who had never previously had UTI carried faecal E. coli which were overall closely related to UTI and faecal isolates from UTI patients; (ii) UTI isolates do not cluster separately from faecal-only isolates based on SNP analysis; and (iii) 22 gene families of a genomic island, putative T6SS proteins as well as specific metabolism and virulence associated proteins were significantly more common in UTI isolates compared to faecal-only isolates and (iv) evolution of fimH for these isolates was not linked to the clinical source of the isolates, apart from the mutation combination N70S/S78N, which was correlated to UTI isolates of phylogroup B2. Combined, these findings illustrate that faecal and UTI isolates, as well as faecal-only and faecal-UTI isolates, are closely related and can only be distinguished, if at all, by their accessory genome.

The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters

Escherichia coli strains belonging to serogroups O1 and O2 are frequently associated with human infections, especially extra-intestinal infections such as bloodstream infections or urinary tract infections. These strains can be associated with a large array of flagellar antigens. Because of their frequency and clinical importance, a reliable detection of E. coli O1 and O2 strains and also the frequently associated K1 capsule is important for diagnosis and source attribution of E. coli infections in humans and animals. By sequencing the O-antigen clusters of various O1 and O2 strains we showed that the serogroups O1 and O2 are encoded by different sets of O-antigen encoding genes and identified potentially new O-groups. We developed qPCR-assays to detect the various O1 and O2 variants and the K1-encoding gene. These qPCR assays proved to be 100% sensitive and 100% specific and could be valuable tools for the investigations of zoonotic and food-borne infection of humans with O1 and O2 extra-intestinal (ExPEC) or Shiga toxin-producing E. coli (STEC) strains.

Population Phylogenomics of Extraintestinal Pathogenic Escherichia coli

The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.

Metabolic Requirements of Escherichia coli in Intracellular Bacterial Communities during Urinary Tract Infection Pathogenesis

Uropathogenic Escherichia coli (UPEC) is the primary etiological agent of over 85% of community-acquired urinary tract infections (UTIs). Mouse models of infection have shown that UPEC can invade bladder epithelial cells in a type 1 pilus-dependent mechanism, avoid a TLR4-mediated exocytic process, and escape into the host cell cytoplasm. The internalized UPEC can clonally replicate into biofilm-like intracellular bacterial communities (IBCs) of thousands of bacteria while avoiding many host clearance mechanisms. Importantly, IBCs have been documented in urine from women and children suffering acute UTI. To understand this protected bacterial niche, we elucidated the transcriptional profile of bacteria within IBCs using microarrays. We delineated the upregulation within the IBC of genes involved in iron acquisition, metabolism, and transport. Interestingly, lacZ was highly upregulated, suggesting that bacteria were sensing and/or utilizing a galactoside for metabolism in the IBC. A ΔlacZ strain displayed significantly smaller IBCs than the wild-type strain and was attenuated during competitive infection with a wild-type strain. Similarly, a galK mutant resulted in smaller IBCs and attenuated infection. Further, analysis of the highly upregulated gene yeaR revealed that this gene contributes to oxidative stress resistance and type 1 pilus production. These results suggest that bacteria within the IBC are under oxidative stress and, consistent with previous reports, utilize nonglucose carbon metabolites. Better understanding of the bacterial mechanisms used for IBC development and establishment of infection may give insights into development of novel anti-virulence strategies.

Urinary tract infections (UTIs) are one of the most common bacterial infections, impacting mostly women. Every year, millions of UTIs occur in the U.S. with most being caused by uropathogenic E. coli (UPEC). During a UTI, UPEC invade bladder cells and form an intracellular bacterial community (IBC) that allows for the bacteria to replicate protected from the host immune response. In this study, we investigated genes that are expressed by UPEC within the IBC and determined how they contribute to the formation of this specialized community. Our findings suggest that galactose is important for UPEC growth in the IBC. Additionally, we found that a gene involved in oxidative stress is also important in the regulation of a key factor needed for UPEC invasion of bladder cells. These results may open the door for the development of treatments to diminish UTI frequency and/or severity.

Relationship between Escherichia coli virulence factors and postpartum metritis in dairy cows

The objectives of this study were to report the prevalence of Escherichia coli and Trueperella pyogenes in the uterus of postpartum dairy cows before the onset of postpartum metritis (PPM) and to quantify their association with subsequent occurrence of PPM, to quantify the association between the presence of genes encoding E. coli virulence factors (VF) and PPM, and to determine the accuracy of using early postpartum uterine bacteriology results (bacteria and VF) to identify cows at risk of PPM. A prospective cohort study was conducted on 3 commercial dairy farms. Uterine swabs were collected from 371 Holstein dairy cows (3 commercial herds) at 1 to 7d in milk and submitted to the laboratory for identification of E. coli, T. pyogenes, and E. coli VF. A total of 40 VF were tested using the radioactive probe hybridization method. Postpartum metritis was defined as the presence of a fetid watery red-brown uterine discharge, associated with fever (rectal temperature >39.5°C), and systemic signs of illness (dullness, reduced appetite, and milk production). Surveillance of PPM was done by trained farmers blinded to laboratory results and cows were followed until 21d in milk. Statistical analyses were conducted using 2×2 tables and mixed logistical regression models. Prevalences of E. coli, T. pyogenes, and PPM were 42, 34, and 15%, respectively. A total of 32 VF were found in E. coli isolates. Most prevalent VF were extraintestinal pathogenic genes such as fimH (89%), hlyE (87%), and iss (70%). Cows positive for intrauterine E. coli were 3.2 times more likely to have subsequent PPM compared with bacteriologically negative cows. Cows with VF hra1 in their uterus were 2.7 times more likely to have PPM than cows positive for E. coli and negative for hra1 and 5.9 times more likely than bacteriologically negative cows. Cows with VF kpsMTII in their uterus were 3.2 times more likely to have PPM than cows positive for E. coli and negative for kpsMTII and 6.2 times more likely than bacteriologically negative cows. Using E. coli, hra1, and kpsMTII as predictors for subsequent PPM, positive predictive values were 23, 31, and 42%, respectively, whereas the negative predictive values were 91, 80, and 78%, respectively. Overall, these results showed that E. coli and some VF were associated with PPM.

Escherichia coli diversity in the lower intestinal tract of humans

Previous studies examining the clonal diversity of Escherichia coli populations within humans have been based on faecal isolates. In this study E. coli were isolated from biopsies taken from the terminal ileum, ascending, transverse and descending colon, and rectum of 69 individuals. Multiple isolates from each biopsy were characterized using Rep-PCR. An average of 3.5 genotypes were recovered per host, and in hosts with two or more strains, the phylogroup membership of the second most abundant strain was significantly more likely to be the same as the dominant strain. There was no indication of a non-random distribution of E. coli phylogroups among the regions of the lower intestine. In hosts with multiple genotypes, as defined by Repetitive extragenic palindromic-PCR, genotypes were non-randomly distributed among gut regions in over half the individuals. The phylogroup membership of an individual's numerically dominant strain explained some of the variation in the extent to which strains within an individual were heterogeneously distributed, with most heterogeneity observed when the numerically dominant strain belonged to phylogroups E or F, and the least when the dominant strain belonged to phylogroup B2. The results of this study support previous studies on pigs that demonstrated faecal sampling underestimates the genotype diversity present within a host.

Spatial Variation and Survival of Salmonella enterica Subspecies in a Population of Australian Sleepy Lizards (Tiliqua rugosa)

The life cycles of many enteric bacterial species require a transition between two very distinct environments. Their primary habitat is the gastrointestinal tract of the host, while their secondary habitat, during transmission from one host to another, consists of environments external to the host, such as soil, water, and sediments. Consequently, both host and environmental factors shape the genetic structure of enteric bacterial populations. This study examined the distribution of four Salmonella enterica subspecies in a population of sleepy lizards, Tiliqua rugosa, in a semiarid region of South Australia. The lizards living within the 1,920-m by 720-m study site were radio tracked, and their enteric bacteria were sampled at regular intervals throughout their active seasons in the years 2001, 2002, and 2006. Four of the six subspecies of S. enterica were present in this population and were nonrandomly distributed among the lizards. In particular, S. enterica subsp. diarizonae was restricted to lizards living in the most shaded parts of the study site with an overstorey of Casuarina trees. Experiments undertaken to investigate the survival of S. enterica cells under seminatural conditions revealed that cell survival decreased with increased exposure to elevated temperatures and UV light. Among the three S. enterica subspecies tested, S. enterica subsp. diarizonae consistently had an average expected life span that was shorter than that observed for the other two subspecies. There was no indication in the data that there was any competitive dominance hierarchy among the S. enterica subspecies within individual hosts. Thus, the nonrandom distribution of S. enterica subspecies in this population of lizards appears to be driven by their different survival characteristics in the external environment.

Quantitative analysis of commensal Escherichia coli populations reveals host-specific enterotypes at the intra-species level

The primary habitat of the Escherichia coli species is the gut of warm-blooded vertebrates. The E. coli species is structured into four main phylogenetic groups A, B1, B2, and D. We estimated the relative proportions of these phylogroups in the feces of 137 wild and domesticated animals with various diets living in the Ile de France (Paris) region by real-time PCR. We distinguished three main clusters characterized by a particular abundance of two or more phylogroups within the E. coli animal commensal populations, which we called “enterocolitypes” by analogy with the enterotypes defined in the human gut microbiota at the genus level. These enterocolitypes were characterized by a dominant (>50%) B2, B1, or A phylogroup and were associated with different host species, diets, and habitats: wild and herbivorous species (wild rabbits and deer), domesticated herbivorous species (domesticated rabbits, horses, sheep, and cows), and omnivorous species (boar, pigs, and chickens), respectively. By analyzing retrospectively the data obtained using the same approach from 98 healthy humans living in Ile de France (Smati et al. 2013, Appl. Environ. Microbiol. 79, 5005–5012), we identified a specific human enterocolitype characterized by the dominant and/or exclusive (>90%) presence of phylogroup B2. We then compared B2 strains isolated from animals and humans, and revealed that human and animal strains differ regarding O-type and B2 subgroup. Moreover, two genes, sfa/foc and clbQ, were associated with the exclusive character of strains, observed only in humans. In conclusion, a complex network of interactions exists at several levels (genus and intra-species) within the intestinal microbiota.

Virulence potential for extraintestinal infections among commensal Escherichia coli isolated from healthy humans--the Trojan horse within our gut

Previous investigations have indicated that the reservoir of extraintestinal pathogenic Escherichia coli (ExPEC) strains is the intestinal microbiota. Nevertheless, studies focused on the prevalence of potential ExPEC strains among the bowel microbiota in healthy human individuals practically do not exist and a strong bias towards pathogenic strains among the E. coli data set is obvious. To assess the prevalence of potential ExPEC strains among E. coli from the intestinal microbiota of healthy humans, we performed a search for data on the prevalence of virulence-associated genes and pathogenicity islands among fecal E. coli found in published studies, including studies comparing isolates from patients suffering from extraintestinal E. coli infections with E. coli from feces of healthy humans. An extensive literature search, including more than 500 published papers, revealed 24 papers with data on prevalences of ≥ 5 virulence-associated genes among 21 E. coli collections including ≥ 20 fecal/rectal strains obtained from healthy individuals and 4 papers with prevalences of pathogenicity islands among E. coli collections from healthy humans. The gathered data are presented in this minireview and clearly show that potential ExPEC strains are present among fecal isolates with a prevalence of around ≥ 10%.

Impact of UV and peracetic acid disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenic Escherichia coli in wastewater effluents

Wastewater discharges may increase the populations of pathogens, including Escherichia coli, and of antimicrobial-resistant strains in receiving waters. This study investigated the impact of UV and peracetic acid (PAA) disinfection on the prevalence of virulence and antimicrobial resistance genes in uropathogenic Escherichia coli (UPEC), the most abundant E. coli pathotype in municipal wastewaters. Laboratory disinfection experiments were conducted on wastewater treated by physicochemical, activated sludge, or biofiltration processes; 1,766 E. coli isolates were obtained for the evaluation. The target disinfection level was 200 CFU/100 ml, resulting in UV and PAA doses of 7 to 30 mJ/cm(2) and 0.9 to 2.0 mg/liter, respectively. The proportions of UPECs were reduced in all samples after disinfection, with an average reduction by UV of 55% (range, 22% to 80%) and by PAA of 52% (range, 11% to 100%). Analysis of urovirulence genes revealed that the decline in the UPEC populations was not associated with any particular virulence factor. A positive association was found between the occurrence of urovirulence and antimicrobial resistance genes (ARGs). However, the changes in the prevalence of ARGs in potential UPECs were different following disinfection, i.e., UV appears to have had no effect, while PAA significantly reduced the ARG levels. Thus, this study showed that both UV and PAA disinfections reduced the proportion of UPECs and that PAA disinfection also reduced the proportion of antimicrobial resistance gene-carrying UPEC pathotypes in municipal wastewaters.

Genotypic and phenotypic characterization of Escherichia coli isolates from feces, hands, and soils in rural Bangladesh via the Colilert Quanti-Tray System

The increased awareness of the role of environmental matrices in enteric disease transmission has resulted in the need for rapid, field-based methods for fecal indicator bacteria and pathogen detection. Evidence of the specificity of β-glucuronidase-based assays for detection of Escherichia coli from environmental matrices relevant to enteric pathogen transmission in developing countries, such as hands, soils, and surfaces, is limited. In this study, we quantify the false-positive rate of a β-glucuronidase-based E. coli detection assay (Colilert) for two environmental reservoirs in Bangladeshi households (hands and soils) and three fecal composite sources (cattle, chicken, and humans). We investigate whether or not the isolation source of E. coli influences phenotypic and genotypic characteristics. Phenotypic characteristics include results of biochemical assays provided by the API-20E test; genotypic characteristics include the Clermont phylogroup and the presence of enteric and/or environmental indicator genes sfmH, rfaI, and fucK. Our findings demonstrate no statistically significant difference in the false-positive rate of Colilert for environmental compared to enteric samples. E. coli isolates from all source types are genetically diverse, representing six of the seven phylogroups, and there is no difference in relative frequency of phylogroups between enteric and environmental samples. We conclude that Colilert, and likely other β-glucuronidase-based assays, is appropriate for detection of E. coli on hands and in soils with low false-positive rates. Furthermore, E. coli isolated from hands and soils in Bangladeshi households are diverse and indistinguishable from cattle, chicken, and human fecal isolates, using traditional biochemical assays and phylogrouping.

Sex-dependent competitive dominance of phylogenetic group B2 Escherichia coli strains within human hosts

Escherichia coli can be divided into several distinct phylogenetic groups that differ in their capacity to cause disease. However, what drives the relative abundance of these different phylogenetic groups in the commensal intestinal community of humans is poorly understood. This study investigated how host age and sex influences E. coli community structure in humans. Faecal samples were collected from 205 outpatients in Australia. Different strains within each sample were identified using rep-PCR profiles and their phylogenetic group membership was determined by quadruplex PCR. Female individuals carrying a dominant B2 strain were found to possess fewer strains than those carrying dominant A or B1 strains. Additionally, strains from the same phylogenetic group were more likely to co-occur in females. By contrast, strain diversity and phylogenetic group associations did not differ significantly from random in males. Host age was found to have a significant effect on the phylogenetic group of the dominant strain. Together these findings indicate that the distribution of the different phylogenetic groups within the human intestinal tract may be mediated by a complex interaction between the host environment and the competitive interactions between strains.

Identification of virulence factors genes in Escherichia coli isolates from women with urinary tract infection in Mexico

E coli isolates (108) from Mexican women, clinically diagnosed with urinary tract infection, were screened to identify virulence genes, phylogenetic groups, and antibiotic resistance. Isolates were identified by MicroScan4 system; additionally, the minimum inhibitory concentration (MIC) was assessed. The phylogenetic groups and 16 virulence genes encoding adhesins, toxins, siderophores, lipopolysaccharide (LPS), and invasins were identified by PCR. Phylogenetic groups distribution was as follows: B1 9.3%, A 30.6%, B2 55.6%, and D 4.6%. Virulence genes prevalence was ecp 98.1%, fimH 86.1%, traT 77.8%, sfa/focDE 74.1%, papC 62%, iutA 48.1%, fyuA 44.4%, focG 2.8%, sfaS 1.9%, hlyA 7.4%, cnf-1 6.5%, cdt-B 0.9%, cvaC 2.8%, ibeA 2.8%, and rfc 0.9%. Regarding antimicrobial resistance it was above 50% to ampicillin/sulbactam, ampicillin, piperacillin, trimethoprim/sulfamethoxazole, ciprofloxacin, and levofloxacin. Uropathogenic E. coli clustered mainly in the pathogenic phylogenetic group B2. The isolates showed a high presence of siderophores and adhesion genes and a low presence of genes encoding toxins. The high frequency of papC gene suggests that these isolates have the ability to colonize the kidneys. High resistance to drugs considered as first choice treatment such as trimethoprim/sulfamethoxazole and fluoroquinolones was consistently observed.

Faecal Escherichia coli from patients with E. coli urinary tract infection and healthy controls who have never had a urinary tract infection

Urinary tract infections (UTIs) are primarily caused by Escherichia coli with the patient's own faecal flora acting as a reservoir for the infecting E. coli. Here we sought to characterize the E. coli faecal flora of UTI patients and healthy controls who had never had a UTI. Up to 20 E. coli colonies from each rectal swab were random amplified polymorphic DNA (RAPD) typed for clonality, dominance in the sample and correlation to the infecting UTI isolate in patients. Each distinct clone was phylotyped and tested for antimicrobial susceptibility. Eighty-seven per cent of the UTI patients carried the infecting strain in their faecal flora, and faecal clones causing UTI were more often dominant in the faecal flora. Patients had a larger diversity of E. coli in their gut flora by carrying more unique E. coli clones compared to controls, and patient faecal clones were more often associated with multidrug resistance compared to controls. We found a similar phylotype distribution of faecal clones from UTI patients and healthy controls, including a large proportion of B2 isolates in the control group. Faecal-UTI isolates from patients were more often associated with multidrug resistance compared to faecal-only clones, indicating a link between UTI virulence and antimicrobial resistance. Intake of any antibiotic less than 6 months prior to inclusion in the experiment occurred significantly more in patients with UTI than in controls. In contrast, presence of an intrauterine device was significantly more common in controls indicating a protective effect against UTI. In conclusion, healthy controls have a large proportion of potentially pathogenic E. coli phylotypes in their faecal flora without this causing infection.

Adhesion of human and animal Escherichia coli strains in association with their virulence-associated genes and phylogenetic origins

Intestinal colonization is influenced by the ability of the bacterium to inhabit a niche, which is based on the expression of colonization factors. Escherichia coli carries a broad range of virulence-associated genes (VAGs) which contribute to intestinal (inVAGs) and extraintestinal (exVAGs) infection. Moreover, initial evidence indicates that inVAGs and exVAGs support intestinal colonization. We developed new screening tools to genotypically and phenotypically characterize E. coli isolates originating in humans, domestic pigs, and 17 wild mammal and avian species. We analyzed 317 isolates for the occurrence of 44 VAGs using a novel multiplex PCR microbead assay (MPMA) and for adhesion to four epithelial cell lines using a new adhesion assay. We correlated data for the definition of new adhesion genes. inVAGs were identified only sporadically, particularly in roe deer (Capreolus capreolus) and the European hedgehog ( Erinaceus europaeus). The prevalence of exVAGs depended on isolation from a specific host. Human uropathogenic E. coli isolates carried exVAGs with the highest prevalence, followed by badger (Meles meles) and roe deer isolates. Adhesion was found to be very diverse. Adhesion was specific to cells, host, and tissue, though it was also unspecific. Occurrence of the following VAGs was associated with a higher rate of adhesion to one or more cell lines: afa-dra, daaD, tsh, vat, ibeA, fyuA, mat, sfa-foc, malX, pic, irp2, and papC. In summary, we established new screening methods which enabled us to characterize large numbers of E. coli isolates. We defined reservoirs for potential pathogenic E. coli. We also identified a very broad range of colonization strategies and defined potential new adhesion genes.

Functional genotypes are associated with commensal Escherichia coli strain abundance within-host individuals and populations

The selective pressures that determine genotype abundance and distribution frequently vary between ecological levels. Thus, it is often unclear whether the same functional genotypes will become abundant at different levels and how selection acting at these different scales is linked. In this study, we examined whether particular functional genotypes, defined by the presence or absence of 34 genes, of commensal Escherichia coli strains were associated with within-host abundance and/or host population abundance in a wild population of 54 adult mountain brushtail possums (Trichosurus cunninghami). Our results revealed that there was a positive correlation between a strain's relative abundance within individuals and the strain's abundance in the host population. We also found that strain abundance at both ecological levels was predicted by the same group of functional genes (agn43, focH, micH47, iroN, ygiL, ompT, kspmT2 and K1) that had associated patterns of occurrence. We propose that direct selection on the same functional genes at both levels may in part be responsible for the observed correlation between the ecological levels. However, a potential link between abundance within the host and excretion rate may also contribute.

Real-time PCR for quantitative analysis of human commensal Escherichia coli populations reveals a high frequency of subdominant phylogroups

Escherichia coli is divided into four main phylogenetic groups, which each exhibit ecological specialization. To understand the population structure of E. coli in its primary habitat, we directly assessed the relative proportions of these phylogroups from the stools of 100 healthy human subjects using a new real-time PCR method, which allows a large number of samples to be studied. The detection threshold for our technique was 0.1% of the E. coli population, i.e., 10(5) CFU/g of feces; in other methods based on individual colony analysis, the threshold is 10%. One, two, three, or four phylogenetic groups were simultaneously found in 21%, 48%, 21%, and 8% of the subjects, respectively. Phylogroups present at a threshold of less than 10% of the population were found in 40% of the subjects, revealing high within-individual diversity. Phylogroups A and B2 were detected in 74% and 70% of the subjects, respectively; phylogroups B1 and D were detected in 36% and 32%, respectively. When phylogroup B2 was dominant, it tended not to cooccur with other phylogroups. In contrast, other phylogroups were present when phylogroup A was dominant. These data indicate a complex pattern of interactions between the members of a single species within the human gut and identify a reservoir of clones that are present at a low frequency. The presence of these minor clones could explain the fluctuation in the composition of the E. coli microbiota within single individuals that may be seen over time. They could also constitute reservoirs of virulent and/or resistant strains.

Genotypic and phenotypic characterization of Escherichia coli isolates from children with urinary tract infection and from healthy carriers

BACKGROUND

Urinary tract infections (UTI) are common in children and contribute significantly to morbidity and mortality. The major cause is Escherichia coli, carrying multiple virulence-associated factors (VFs). However, the specific traits that distinguish childhood uropathogenic E. coli from fecal commensals of healthy children are incompletely defined.

METHODS

We used a multiplex polymerase chain reaction-based reverse line blot assay, several additional polymerase chain reactions and phenotypic methods to compare distributions of virulence traits (22 VF genes, UTI-associated O types, phylogenetic groups, sequence type 131 and expression of selected VFs), between 212 E. coli isolates from children ≤ 5 years with UTI (109 cystitis and 103 pyelonephritis) and 115 fecal isolates from healthy children of similar age, collected during the same time period.

RESULTS

The studied traits were most prevalent among pyelonephritis, followed closely by cystitis isolates and were uncommon among fecal isolates. Eight VF genes differentiated pyelonephritis from cystitis isolates, but aggregate VF scores in these 2 UTI groups were similar. Most of the studied phenotypic characteristics showed a similar descending prevalence gradient from pyelonephritis, through cystitis, to fecal isolates. Coexpression of biofilm components, curli and cellulose, was strongly associated with pyelonephritis, phylogenetic group B2, individual VF genes and higher VF scores. Two-thirds (67%) of clinical isolates belonged to phylogenetic group B2 and, of these, 12% belonged to the sequence type 131 clonal group, compared with 14% and 1%, respectively, of fecal isolates.

CONCLUSIONS

These findings identify specific virulence factors, O types and a virulent clonal group (sequence type 131), as potential targets for UTI prevention strategies in children.

Phylogenetic group-associated differences in regulation of the common colonization factor Mat fimbria in Escherichia coli

Heterogeneity of cell population is a key component behind the evolutionary success of Escherichia coli. The heterogeneity supports species adaptation and mainly results from lateral gene transfer. Adaptation may also involve genomic alterations that affect regulation of conserved genes. Here we analysed regulation of the mat (or ecp) genes that encode a conserved fimbrial adhesin of E. coli. We found that the differential and temperature-sensitive expression control of the mat operon is dependent on mat promoter polymorphism and closely linked to phylogenetic grouping of E. coli. In the mat promoter lineage favouring fimbriae expression, the mat operon-encoded regulator MatA forms a positive feedback loop that overcomes the repression by H-NS and stabilizes the fimbrillin mRNA under low growth temperature, acidic pH or elevated levels of acetate. The study exemplifies phylogenetic group-associated expression of a highly common surface organelle in E. coli.

Biological and physicochemical wastewater treatment processes reduce the prevalence of virulent Escherichia coli

Effluents discharged from wastewater treatment plants are possible sources of pathogenic bacteria, including Escherichia coli, in the freshwater environment, and determining the possible selection of pathogens is important. This study evaluated the impact of activated sludge and physicochemical wastewater treatment processes on the prevalence of potentially virulent E. coli. A total of 719 E. coli isolates collected from four municipal plants in Québec before and after treatment were characterized by using a customized DNA microarray to determine the impact of treatment processes on the frequency of specific pathotypes and virulence genes. The percentages of potentially pathogenic E. coli isolates in the plant influents varied between 26 and 51%, and in the effluents, the percentages were 14 to 31%, for a reduction observed at all plants ranging between 14 and 45%. Pathotypes associated with extraintestinal pathogenic E. coli (ExPEC) were the most abundant at three of the four plants and represented 24% of all isolates, while intestinal pathogenic E. coli pathotypes (IPEC) represented 10% of the isolates. At the plant where ExPEC isolates were not the most abundant, a large number of isolates were classified as both ExPEC and IPEC; overall, 6% of the isolates were classified in both groups, with the majority being from the same plant. The reduction of the proportion of pathogenic E. coli could not be explained by the preferential loss of one virulence gene or one type of virulence factor; however, the quinolone resistance gene (qnrS) appears to enhance the loss of virulence genes, suggesting a mechanism involving the loss of pathogenicity islands.

Natural genome diversity of AI-2 quorum sensing in Escherichia coli: conserved signal production but labile signal reception

Quorum sensing (QS) regulates the onset of bacterial social responses in function to cell density having an important impact in virulence. Autoinducer-2 (AI-2) is a signal that has the peculiarity of mediating both intra- and interspecies bacterial QS. We analyzed the diversity of all components of AI-2 QS across 44 complete genomes of Escherichia coli and Shigella strains. We used phylogenetic tools to study its evolution and determined the phenotypes of single-deletion mutants to predict phenotypes of natural strains. Our analysis revealed many likely adaptive polymorphisms both in gene content and in nucleotide sequence. We show that all natural strains possess the signal emitter (the luxS gene), but many lack a functional signal receptor (complete lsr operon) and the ability to regulate extracellular signal concentrations. This result is in striking contrast with the canonical species-specific QS systems where one often finds orphan receptors, without a cognate synthase, but not orphan emitters. Our analysis indicates that selection actively maintains a balanced polymorphism for the presence/absence of a functional lsr operon suggesting diversifying selection on the regulation of signal accumulation and recognition. These results can be explained either by niche-specific adaptation or by selection for a coercive behavior where signal-blind emitters benefit from forcing other individuals in the population to haste in cooperative behaviors.

High metabolic potential may contribute to the success of ST131 uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) is the predominant cause of urinary tract infection in both hospital and community settings. The recent emergence of multidrug-resistant clones like the O25b:H4-ST131 lineage represents a significant threat to health, and numerous studies have explored the virulence potential of these organisms. Members of the ST131 clone have been described as having variable carriage of key virulence factors, and it has been suggested that additional unidentified factors contribute to virulence. Here we demonstrated that ST131 isolates have high metabolic potential and biochemical profiles that distinguish them from isolates of many other sequence types (STs). A collection of 300 UPEC isolates recovered in 2007 and 2009 in the Northwest region of England were subjected to metabolic profiling using the Vitek2 Advanced Expert System (AES). Of the 47 tests carried out, 30 gave a positive result with at least one of the 300 isolates examined. ST131 isolates demonstrated significant association with eight tests, including those for peptidase, decarboxylase, and alkalinization activity. Metabolic activity also correlated with antibiotic susceptibility profiles, with resistant organisms displaying the highest metabolic potential. This is the first comprehensive study of metabolic potential in the ST131 lineage, and we suggest that high metabolic potential may have contributed to the fitness of members of the ST131 clone, which are able to exploit the available nutrients in both the intestinal and urinary tract environments.

Prevalence of genes encoding virulence factors among Escherichia coli with K1 antigen and non-K1 E. coli strains

Multiplex PCR was used to detect genes encoding selected virulence determinants associated with strains of Escherichia coli with K1 antigen (K1(+)) and non-K1 E. coli (K1(-)). The prevalence of the fimA, fimH, sfa/foc, ibeA, iutA and hlyF genes was studied for 134 (67 K1(+) and 67 K1(-)) E. coli strains isolated from pregnant women and neonates. The fimA gene was present in 83.6 % of E. coli K1(+) and in 86.6 % of E. coli K1(-) strains. The fimH gene was present in all tested E. coli K1(+) strains and in 97.0 % of non-K1 strains. E. coli K1(+) strains were significantly more likely to possess the following genes than E. coli K1(-) strains: sfa/foc (37.3 vs 16.4 %, P = 0.006), ibeA (35.8 vs 4.5 %, P<0.001), iutA (82.1 vs 35.8 %, P<0.001) and hlyF (28.4 vs 6.0 %, P<0.001). In conclusion, E. coli K1(+) seems to be more virulent than E. coli K1(-) strains in developing severe infections, thereby increasing possible sepsis or neonatal bacterial meningitis.

Effect of fructooligosaccharide metabolism on chicken colonization by an extra-intestinal pathogenic Escherichia coli strain

Extra-intestinal pathogenic Escherichia coli (ExPEC) strains cause many diseases in humans and animals. While remaining asymptomatic, they can colonize the intestine for subsequent extra-intestinal infection and dissemination in the environment. We have previously identified the fos locus, a gene cluster within a pathogenicity island of the avian ExPEC strain BEN2908, involved in the metabolism of short-chain fructooligosaccharides (scFOS). It is assumed that these sugars are metabolized by the probiotic bacteria of the microbiota present in the intestine, leading to a decrease in the pathogenic bacterial population. However, we have previously shown that scFOS metabolism helps BEN2908 to colonize the intestine, its reservoir. As the fos locus is located on a pathogenicity island, one aim of this study was to investigate a possible role of this locus in the virulence of the strain for chicken. We thus analysed fos gene expression in extracts of target organs of avian colibacillosis and performed a virulence assay in chickens. Moreover, in order to understand the involvement of the fos locus in intestinal colonization, we monitored the expression of fos genes and their implication in the growth ability of the strain in intestinal extracts of chicken. We also performed intestinal colonization assays in axenic and Specific Pathogen-Free (SPF) chickens. We demonstrated that the fos locus is not involved in the virulence of BEN2908 for chickens and is strongly involved in axenic chicken cecal colonization both in vitro and in vivo. However, even if the presence of a microbiota does not inhibit the growth advantage of BEN2908 in ceca in vitro, overall, growth of the strain is not favoured in the ceca of SPF chickens. These findings indicate that scFOS metabolism by an ExPEC strain can contribute to its fitness in ceca but this benefit is fully dependent on the bacteria present in the microbiota.

Population structure and uropathogenic virulence-associated genes of faecal Escherichia coli from healthy young and elderly adults

We investigated the population structures of faecal Escherichia coli in 30 healthy young adults (13 males and 17 females) aged between 20 and 45 years and 29 elderly adults (14 females and 15 males) aged between 65 and 77 years. In all, 1566 strains were typed with the PhPlate system and grouped into biochemical phenotypes (BPTs). Strains with shared BPTs were further typed using randomly amplified polymorphic DNA analysis. Forty-four per cent of the strains were shared between two or more age and gender groups. Elders had a significantly higher (P<0.001) number of BPTs (mean±standard error 3.3±0.27) than younger groups (1.82±0.27). Phylogenetic affiliation and virulence-associated genes (VAGs) of the strains showed that more than 80 % of the strains belonging to dominant types belonged to phylogroups B2 and D. Amongst dominant BPTs, phylogenetic group A was significantly associated with females (P<0.0001), and elders were more likely to carry group D (P<0.0124). Elderly males had a higher prevalence of VAGs than young males (P<0.0001) and young females (P<0.0005). We conclude that there is a lower prevalence of E. coli with uropathogenic properties in healthy young adults than in elders.

The interaction between a non-pathogenic and a pathogenic strain synergistically enhances extra-intestinal virulence in Escherichia coli

Finding two or more genotypes of a single species within an infected sample is a not infrequent event. In this work, three Escherichia coli strains of decreasing extra-intestinal virulence (pathogenic B2S and B1S strains, and the avirulent K-12 MG1655 strain) were tested in septicaemia and urinary tract infection (UTI) mouse models, either separately or in pairs. Survival was monitored and bacteria were counted in various organs. Serum interleukin (IL)-6, tumour necrosis factor alpha (TNFα) and IL-10 were measured. We show that a mix of high amounts of B1S or of MG1655 with low amounts of B2S killed more rapidly (B1S), or killed more mice (MG1655), than either high amounts of B1S, high amounts of MG1655 or low amounts of B2S separately in the mouse septicaemia model. This bacterial synergy persisted when high amounts of dead or abnormal-LPS K-12 cells were injected together with a low amount of B2S. In both septicaemia and UTI models, significantly more bacteria were recovered from the organs of mice injected with the MG1655/B2S mix than from those of mice injected with the inocula separately. Consistently, in the septicaemia model, more IL-6 was secreted before death by the mice that were injected with the mix of bacteria than by the mice that were injected with the inocula separately. The synergistically enhanced mortality in the case of co-infection in the septicaemia model persisted in RFcγ(-/-), Myd88(-/-) and IL-6(-/-) knockout mice. This synergistically increased virulence resulting from the interaction between an avirulent and a pathogenic strain of the same bacterial species raises questions about the role of avirulent bacteria in the development of some extra-intestinal infections.

Pathogenicity-associated islands in extraintestinal pathogenic Escherichia coli are fitness elements involved in intestinal colonization

The virulence of many human pathogens does not seem to be an evolutionarily selected trait, but an accidental by-product of the selection that operates in another ecological context. We investigated the possibility that virulence of the extraintestinal pathogenic Escherichia coli (ExPEC) strains, which frequently cause disease in the host in which they asymptomatically colonize the intestine, is the consequence of commensalism. Most of the ExPEC virulence factors are clustered on genomic islands called pathogenicity-associated islands (PAIs). We constructed and characterized several mutants of the ExPEC 536 strain with either (i) deletions of each single PAI or (ii) a complete deletion of all seven PAIs. In vitro phenotypic characterization of 536 mutants showed that the seven PAIs were dispensable for growth in the absence of external stress, as well as under a range of biologically relevant stressors, i.e., serum, bile, and oxidative, nitrosative, hyperosmotic, and acidic stress. However, challenge against the wild-type (WT) strain in a murine model shows that the deletion of all seven PAIs drastically reduces the fitness of 536 during persistent intestinal colonization. This defect seems to be linked to the hypermotility observed for mutants devoid of all seven PAIs. In addition, we show that PAIs diminish fitness of their carrier during growth in urine, suggesting that urinary tract infections are unlikely to provide selective pressure for the maintenance of ExPEC PAIs. Our results are in accordance with the coincidental-evolution hypothesis postulating that extraintestinal E. coli virulence is a by-product of commensalism.