Molecular comparison of extraintestinal Escherichia coli isolates of the same electrophoretic lineages from humans and domestic animals

Characterization of the pathogenicity of extraintestinal pathogenic Escherichia coli isolates from pneumonia-infected lung samples of dogs and cats in South Korea

This study aimed to investigate the pathogenicity of extraintestinal pathogenic Escherichia coli (ExPEC) isolated from dog and cat lung samples in South Korea. A total of 101 E. coli isolates were analyzed for virulence factors, phylogroups, and O-serogroups, and their correlation with bacterial pneumonia-induced mortality was elucidated. P fimbriae structural subunit (papA), hemolysin D (hlyD), and cytotoxic necrotizing factor 1 (cnf1) were highly prevalent in both species, indicating correlation with bacterial pneumonia. Phylogroups B1 and B2 were the most prevalent phylogroups (36.6% and 32.7%, respectively) and associated with high bacterial pneumonia-induced mortality rates. Isolates from both species belonging to phylogroup B2 showed high frequency of papA, hlyD, and cnf1. O-serogrouping revealed 21 and 15 serogroups in dogs and cats, respectively. In dogs, O88 was the most prevalent serogroup (n = 8), and the frequency of virulence factors was high for O4 and O6. In cats, O4 was the most prevalent serogroup (n = 6), and the frequency of virulence factors was high for O4 and O6. O4 and O6 serogroups were mainly grouped under phylogroup B2 and associated with high bacterial pneumonia-induced mortality. This study characterized the pathogenicity of ExPEC and described the probability of ExPEC pneumonia-induced mortality.

Phylogenomic analysis of a highly virulent Escherichia coli ST83 lineage with potential animal-human transmission

The presence of specific virulence features conditions severe forms of urinary tract disease, but the frequency and distribution of these highly virulent extraintestinal pathogenic Escherichia coli strains in animals and humans is unclear. We used whole genome sequencing, comparative genomics, histological and clinical data to characterize the genetic basis for pathogenesis and origin of E. coli Ec_151217, a strain (B2, ST83, O83:H5:K5) that caused an extremely aggressive upper urinary tract infection (UTI) in a cat. We show that Ec_151217 and 52% of other highly related ST83 genomes (O6 and O83) identified from different animal species and human infections carry two copies of the hemolysin A operon, though this duplication is infrequent (~1%) among closed ExPEC genomes from multiple sources. Our data enlarges the list of E. coli genetic backgrounds carrying hlyA operon duplication which is potentially involved in severity of UTI, and demonstrates that it seems to occur infrequently amongst ExPEC. Its identification in E. coli lineages (diverse ST83 serotypes) of potential animal-human transmission is of concern and anticipates the need to screen larger collections.

Role of Plasmids in the Ecology and Evolution of "High-Risk" Extraintestinal Pathogenic Escherichia coli Clones

Bacterial plasmids have been linked to virulence in Escherichia coli and Salmonella since their initial discovery. Though the plasmid repertoire of these bacterial species is extremely diverse, virulence-associated attributes tend to be limited to a small subset of plasmid types. This is particularly true for extraintestinal pathogenic E. coli, or ExPEC, where a handful of plasmids have been recognized to confer virulence- and fitness-associated traits. The purpose of this review is to highlight the biological and genomic attributes of ExPEC virulence-associated plasmids, with an emphasis on high-risk dominant ExPEC clones. Two specific plasmid types are highlighted to illustrate the independently evolved commonalities of these clones relative to plasmid content. Furthermore, the dissemination of these plasmids within and between bacterial species is examined. These examples demonstrate the evolution of high-risk clones toward common goals, and they show that rare transfer events can shape the ecological landscape of dominant clones within a pathotype.

Poultry-origin extraintestinal Escherichia coli strains carrying the traits associated with urinary tract infection, sepsis, meningitis and avian colibacillosis in India

AIM

In-depth 'One Health' risk assessment of extraintestinal pathogenic Escherichia coli (ExPEC) strains carrying the traits of urinary tract infection, sepsis, meningitis and avian colibacillosis in poultry of India.

METHODS AND RESULTS

A total of 230 E. coli isolates were recovered from chicken samples representing the different sources (faeces vs caeca), stages (poultry farms vs retails butcher shop) or environments (rural vs urban) of poultry in India. Among all poultry-origin E. coli isolates, 49 (21·1%) strains were identified as ExPEC possessing multiple virulence determinants regardless of their association with any specific phylogenetic lineages. Of particular, potentially virulent ExPEC pathotypes, that is, uropathogenic E.coli (UPEC, 20·4%), avian pathogenic E. coli (APEC, 34·6%), septicaemia-associated E. coli (SEPEC, 47·0%) and neonatal meningitis-causing E.39 coli (NMEC, 2·0%) were also detected among all ExPEC strains.

CONCLUSIONS

Our study is the first to assess ExPEC strains circulating in the different settings of poultry in India and significantly demonstrates their potential ability to cause multiple extraintestinal infections both in humans and animals.

SIGNIFICANCE AND IMPACT OF THE STUDY

The data of our study are in favour of the possibility that poultry-origin putative virulent ExPEC pathotypes consequently constitute a threat risk to 'One Health' or for food safety and a great concern for poultry production of India.

Genomic analysis of phylogenetic group B2 extraintestinal pathogenic E. coli causing infections in dogs in Australia

This study investigated the prevalence of extraintestinal pathogenic E. coli (ExPEC)-associated sequence types (STs) from phylogenetic group B2 among 449 fluoroquinolone-susceptible dog clinical isolates from Australia. Isolates underwent PCR-based phylotyping and random amplified polymorphic DNA analysis to determine clonal relatedness. Of the 317 so-identified group B2 isolates, 77 underwent whole genome sequencing (WGS), whereas the remainder underwent PCR-based screening for ST complexes (STc) STc12, STc73, STc372, and ST131. The predominant ST was ST372 according to both WGS (31 % of 77) and ST-specific PCR (22 % of 240), followed by (per WGS) ST73 (17 %), ST12 (7 %), and ST80 (7 %). A WGS-based phylogenetic comparison of ST73 isolates from dogs, cats, and humans showed considerable overall phylogenetic diversity. Although most clusters were species-specific, some contained closely related human and animal (dog > cat) isolates. For dogs in Australia these findings both confirm ST372 as the predominant E. coli clonal lineage causing extraintestinal infections and clarify the importance of human-associated group B2 lineage ST73 as a cause of UTI, with some strains possibly being capable of bi-directional (i.e., dog-human and human-dog) transmission.

Genomic analysis of fluoroquinolone-susceptible phylogenetic group B2 extraintestinal pathogenic Escherichia coli causing infections in cats

Extraintestinal pathogenic Escherichia coli (ExPEC) can cause urinary tract and other types of infection in cats, but the relationship of cat ExPEC to human ExPEC remains equivocal. This study investigated the prevalence of ExPEC-associated sequence types (STs) from phylogenetic group B2 among fluoroquinolone-susceptible cat clinical isolates. For this, 323 fluoroquinolone-susceptible cat clinical E. coli isolates from Australia underwent PCR-based phylotyping and random amplified polymorphic DNA analysis to determine clonal relatedness. Of the 274 group B2 isolates, 53 underwent whole genome sequencing (WGS), whereas 221 underwent PCR-based screening for (group B2) sequence type complexes (STc) STc12, STc73, ST131, and STc372. Group B2 was the dominant phylogenetic group (274/323, 85 %), whereas within group B2 ST73 dominated, according to both WGS (43 % of 53; followed by ST127, ST12, and ST372 [4/53, 8 % each]) and ST-specific PCR (20 % of 221). In WGS-based comparisons of cat and reference human ST73 isolates, cat isolates had a relatively conserved virulence gene profile but were phylogenetically diverse. Although in the phylogram most cat and human ST73 isolates occupied host species-specific clusters within serotype-specific clades (O2:H1, O6:H1, O25:H1, O50/O2:H1), cat and human isolates were intermingled within two serotype-specific clades: O120:H31 (3 cat and 2 human isolates) and O22:H1 (3 cat and 5 human isolates). These findings confirm the importance of human-associated group B2 lineages as a cause of urinary tract infections in cats. The close genetic relationship of some cat and human ST73 strains suggests bi-directional transmission may be possible.

An Overview of Two-Component Signal Transduction Systems Implicated in Extra-Intestinal Pathogenic E. coli Infections

Extra-intestinal pathogenic E. coli (ExPEC) infections are common in mammals and birds. The predominant ExPEC types are avian pathogenic E. coli (APEC), neonatal meningitis causing E. coli/meningitis associated E. coli (NMEC/MAEC), and uropathogenic E. coli (UPEC). Many reviews have described current knowledge on ExPEC infection strategies and virulence factors, especially for UPEC. However, surprisingly little has been reported on the regulatory modules that have been identified as critical in ExPEC pathogenesis. Two-component systems (TCSs) comprise the predominant method by which bacteria respond to changing environments and play significant roles in modulating bacterial fitness in diverse niches. Recent studies have highlighted the potential of manipulating signal transduction systems as a means to chemically re-wire bacterial pathogens, thereby reducing selective pressure and avoiding the emergence of antibiotic resistance. This review begins by providing a brief introduction to characterized infection strategies and common virulence factors among APEC, NMEC, and UPEC and continues with a comprehensive overview of two-component signal transduction networks that have been shown to influence ExPEC pathogenesis.

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.

Reservoirs of Extraintestinal Pathogenic Escherichia coli

Several potential reservoirs for the Escherichia coli strains that cause most human extraintestinal infections (extraintestinal pathogenic E. coli; ExPEC) have been identified, including the human intestinal tract and various non-human reservoirs, such as companion animals, food animals, retail meat products, sewage, and other environmental sources. Understanding ExPEC reservoirs, chains of transmission, transmission dynamics, and epidemiologic associations will assist greatly in finding ways to reduce the ExPEC-associated disease burden. The need to clarify the ecological behavior of ExPEC is all the more urgent because environmental reservoirs may contribute to acquisition of antimicrobial resistance determinants and selection for and amplification of resistant ExPEC. In this chapter, we review the evidence for different ExPEC reservoirs, with particular attention to food and food animals, and discuss the public health implications of these reservoirs for ExPEC dissemination and transmission.

Dog Bite Transmission of Antibiotic-Resistant Bacteria to a Human

The prevalence of multidrug-resistant bacteria in the community is increasing, and companion animals serve as a potential reservoir for such bacteria. This report describes a case of a companion dog that was treated with multiple courses of antibiotics for a chronic illness and transmitted multidrug-resistant bacteria to a human through a bite.

Multilocus Sequence Typing and Virulence Profiles in Uropathogenic Escherichia coli Isolated from Cats in the United States

The population structure, virulence, and antimicrobial resistance of uropathogenic E. coli (UPEC) from cats are rarely characterized. The aim of this study was to compare and characterize the UPEC isolated from cats in four geographic regions of USA in terms of their multilocus sequence typing (MLST), virulence profiles, clinical signs, antimicrobial resistance and phylogenetic grouping. The results showed that a total of 74 E. coli isolates were typed to 40 sequence types with 10 being novel. The most frequent phylogenetic group was B2 (n = 57). The most frequent sequence types were ST73 (n = 12) and ST83 (n = 6), ST73 was represented by four multidrug resistant (MDR) and eight non-multidrug resistant (SDR) isolates, and ST83 were significantly more likely to exhibit no drug resistant (NDR) isolates carrying the highest number of virulence genes. Additionally, MDR isolates were more diverse, and followed by SDR and NDR isolates in regards to the distribution of the STs. afa/draBC was the most prevalent among the 29 virulence-associated genes. Linking virulence profile and antimicrobial resistance, the majority of virulence-associated genes tested were more prevalent in NDR isolates, and followed by SDR and MDR isolates. Twenty (50%) MLST types in this study have previously been associated with human isolates, suggesting that these STs are potentially zoonotic. Our data enhanced the understanding of E. coli population structure and virulence association from cats. The diverse and various combinations of virulence-associated genes implied that the infection control may be challenging.

Extraintestinal isolates ofEscherichia coli: identification and prospects for vaccine development

Extraintestinal pathogenic Escherichia coli (ExPEC) cause a wide variety of infections that are responsible for significant morbidity, mortality and costs to our healthcare system. Thereby, the development of an efficacious ExPEC vaccine will minimize disease and may be cost-effective in selected patient groups. Surface polysaccharides, such as capsule, have been traditional targets for vaccine development. Considering that significant antigenic heterogeneity exists among surface polysaccharides present in various ExPEC strains, their use as vaccine candidates will be challenging. Therefore, alternative vaccine candidates/approaches are being identified and evaluated and are discussed in this review. The authors envision that an efficacious ExPEC vaccine will consist of either a polyvalent subunit vaccine or a genetically engineered killed whole-cell vaccine.

Prevalence of antimicrobial resistance in relation to virulence genes and phylogenetic origins among urogenital Escherichia coli isolates from dogs and cats in Japan

OBJECTIVE

To assess the status of antimicrobial resistance (AMR), identify extraintestinal virulence factors (VFs) and phylogenetic origins, and analyze relationships among these traits in extraintestinal pathogenic Escherichia coli (ExPEC) isolates from companion animals.

SAMPLE

104 E coli isolates obtained from urine or genital swab samples collected between 2003 and 2010 from 85 dogs and 19 cats with urogenital infections in Japan.

PROCEDURES

Antimicrobial susceptibility of isolates was determined by use of the agar dilution method; a multiplex PCR assay was used for VF gene detection and phylogenetic group assessment. Genetic diversity was evaluated via randomly amplified polymorphic DNA analysis.

RESULTS

Of the 104 isolates, 45 (43.3%) were resistant to > 2 antimicrobials. Phylogenetically, 64 (61.5%), 22 (21.2%), 13 (12.5%), and 5 (4.8%) isolates belonged to groups B2, D, B1, and A, respectively. Compared with other groups, group B2 isolates were less resistant to all tested antimicrobials and carried the pap, hly, and cnf genes with higher frequency and the aer gene with lower frequency. The aer gene was directly associated and the pap, sfa, hly, and cnf genes were inversely associated with AMR. Randomly amplified polymorphic DNA analysis revealed 3 major clusters, comprised mainly of group B1, B2, and D isolates; 2 subclusters of group B2 isolates had different VF and AMR status. CONCLUSIONS AND CLINICAL RELEVANCE; Prevalences of multidrug resistance and human-like phylogenetic origins among ExPEC isolates from companion animals in Japan were high. It is suggested that VFs, phylogenetic origins, and genetic diversity are significantly associated with AMR in ExPEC.

Animal and human pathogenic Escherichia coli strains share common genetic backgrounds

Escherichia coli is a versatile species encompassing both commensals of the digestive tracts of many vertebrates, including humans, and pathogenic strains causing various intra- and extraintestinal infections. Despite extensive gene flow between strains, the E. coli species has a globally clonal population structure, consisting of distinct phylogenetic groups. Little is known about the relationships between phylogenetic groups and host specificity. We therefore used multilocus sequence typing (MLST) to investigate phylogenetic relationships and evaluated the virulence gene content of 35 E. coli strains representative of the diverse diseases encountered in domestic animals. We compared these strains with a panel of 101 human pathogenic and 98 non-human and human commensal strains representative of the phylogenetic and pathovar diversity of this species. A global factorial analysis of correspondence indicated that extraintestinal infections were caused mostly by phylogenetic group B2 strains, whereas intraintestinal infections were caused mostly by phylogenetic group A/B1/E strains, with strains responsible from extraintestinal or intraintestinal infections having specific virulence factors. It was not possible to distinguish between strains of human and animal origin. A detailed phylogenetic analysis of the MLST data showed that numerous pathogenic animal and human strains are very closely related, and had a number of virulence genes in common. However, a set of specific adhesins was identified in animal non-B2 group strains of all pathotypes. In conclusion, human and animal pathogenic strains share common genetic backgrounds, but non-B2 strains of different origins seem to have different sets of adhesins that could be involved in host specificity.

Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

Background

Extraintestinal pathogenic Escherichia coli (ExPEC) strains represent a huge public health burden. Knowledge of their clonal diversity and of the association of clones with genomic content and clinical features is a prerequisite to recognize strains with a high invasive potential. In order to provide an unbiased view of the diversity of E. coli strains responsible for bacteremia, we studied 161 consecutive isolates from patients with positive blood culture obtained during one year in two French university hospitals. We collected precise clinical information, multilocus sequence typing (MLST) data and virulence gene content for all isolates. A subset representative of the clonal diversity was subjected to comparative genomic hybridization (CGH) using 2,324 amplicons from the flexible gene pool of E. coli.

Results

Recombination-insensitive phylogenetic analysis of MLST data in combination with the ECOR collection revealed that bacteremic E. coli isolates were highly diverse and distributed into five major lineages, corresponding to the classical E. coli phylogroups (A+B1, B2, D and E) and group F, which comprises strains previously assigned to D. Compared to other strains of phylogenetic group B2, strains belonging to MLST-derived clonal complexes (CCs) CC1 and CC4 were associated (P < 0.05) with a urinary origin. In contrast, no CC appeared associated with severe sepsis or unfavorable outcome of the bacteremia. CGH analysis revealed genomic characteristics of the distinct CCs and identified genomic regions associated with CC1 and/or CC4.

Conclusion

Our results demonstrate that human bacteremia strains distribute over the entire span of E. coli phylogenetic diversity and that CCs represent important phylogenetic units for pathogenesis and comparative genomics.

Isolation of extraintestinal pathogenic Escherichia coli from diarrheic dogs and their antimicrobial resistance profile

From January to December 2006, 92 Escherichia coli isolates from 25 diarrheic dogs were analyzed by screening for the presence of adhesin-encoding genes (pap, sfa, afa), hemolysin and aerobactin genes. Virulence gene frequencies detected in those isolates were: 12% pap, 1% sfa, 10% hemolysin and 6.5% aerobactin. Ten isolates were characterized as extraintestinal pathogenic E. coli (ExPEC) strains; all showed a multidrug resistance phenotype that may represent a reason for concern due the risk of dissemination of antimicrobial resistant genes to the microbiota of human beings.

Extraintestinal pathogenic Escherichia coli-induced acute necrotizing pneumonia in cats

Extraintestinal pathogenic Escherichia coli (ExPEC) are pathogens involved in several disease conditions, ranging from urinary tract infection to meningitis in humans and animals. They comprise epidemiologically and phylogenetically distinct strains, affecting most species and involving any organ or anatomical site. Here, we report fatal cases of necrotizing pneumonia in cats. Over a 1-week period, 13 cats from an animal shelter in Stamford, Connecticut were presented for necropsy. All had a clinical history of acute respiratory disease. The gross and microscopic findings for all the cats were consistent. Escherichia coli was uniformly isolated from the lungs of all the tested cats. All the isolates were haemolytic, genetically related as determined by enterobacterial repetitive intergenic consensus PCR, and harboured genes encoding for cytotoxic necrotizing factor-1 and fimbriae and adhesions that are characteristic of ExPEC, implying a point source clonal outbreak. As cats are common household pets, this report raises concerns regarding zoonotic potential (in either direction) for these ExPEC strains.

Virulence genotypes and phylogenetic background of Escherichia coli serogroup O6 isolates from humans, dogs, and cats

Molecular evidence is limited for the hypothesis that humans, dogs, and cats can become colonized and infected with similar virulent Escherichia coli strains. To further assess this possibility, archived E. coli O6 isolates (n = 130) from humans (n = 55), dogs (n = 59), and cats (n = 16), representing the three main H (flagellar) types within serogroup O6 (H1, H7, and H31), were analyzed, along with selected reference strains. Isolates underwent PCR-based phylotyping, multilocus sequence typing, PCR-based detection of 55 virulence-associated genes, and XbaI pulsed-field gel electrophoresis (PFGE) profiling. Three major sequence types (STs), which corresponded closely with H types, accounted for 99% of the 130 O6 isolates. Each ST included human, dog, and cat isolates; two included reference pyelonephritis isolates CFT073 (O6:K2:H1) and 536 (O6:K15:H31). Virulence genotypes overlapped considerably among host species, despite statistically significant differences between human and pet isolates. Several human and dog isolates from ST127 (O6:H31) exhibited identical virulence genotypes and highly similar PFGE profiles, consistent with cross-species exchange of specific E. coli clones. In conclusion, the close similarity in the genomic backbone and virulence genotype between certain human- and animal-source E. coli isolates within serogroup O6 supports the hypothesis of zoonotic potential.

Extraintestinal pathogenic Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPEC) possesses virulence traits that allow it to invade, colonize, and induce disease in bodily sites outside of the gastrointestinal tract. Human diseases caused by ExPEC include urinary tract infections, neonatal meningitis, sepsis, pneumonia, surgical site infections, as well as infections in other extraintestinal locations. ExPEC-induced diseases represent a large burden in terms of medical costs and productivity losses. In addition to human illnesses, ExPEC strains also cause extraintestinal infections in domestic animals and pets. A commonality of virulence factors has been demonstrated between human and animal ExPEC, suggesting that the organisms are zoonotic pathogens. ExPEC strains have been isolated from food products, in particular from raw meats and poultry, indicating that these organisms potentially represent a new class of foodborne pathogens. This review discusses various aspects of ExPEC, including its presence in food products, in animals used for food or as companion pets; the diseases ExPEC can cause; and the virulence factors and virulence mechanisms that cause disease.

Extraintestinal pathogenic Escherichia coli strains of avian and human origin: link between phylogenetic relationships and common virulence patterns

Extraintestinal pathogenic Escherichia coli (ExPEC) strains of human and avian origin show similarities that suggest that the avian strains potentially have zoonotic properties. However, the phylogenetic relationships between avian and human ExPEC strains are poorly documented, so this possibility is difficult to assess. We used PCR-based phylotyping and multilocus sequence typing (MLST) to determine the phylogenetic relationships between 39 avian pathogenic E. coli (APEC) strains of serogroups O1, O2, O18, and O78 and 51 human ExPEC strains. We also compared the virulence genotype and pathogenicity for chickens of APEC strains and human ExPEC strains. Twenty-eight of the 30 APEC strains of serogroups O1, O2, and O18 were classified by MLST into the same subcluster (B2-1) of phylogenetic group B2, whereas the 9 APEC strains of serogroup O78 were in phylogenetic groups D (3 strains) and B1 (6 strains). Human ExPEC strains were closely related to APEC strains in each of these three subclusters. The 28 avian and 25 human strains belonging to phylogenetic subcluster B2-1 all expressed the K1 antigen and presented no significant differences concerning the presence of other virulence factors. Moreover, human strains of this phylogenetic subcluster were highly virulent for chicks, so no host specificity was identified. Thus, APEC strains of serotypes O1:K1, O2:K1, and O18:K1 belong to the same highly pathogenic clonal group as human E. coli strains of the same serotypes isolated from cases of neonatal meningitis, urinary tract infections, and septicemia. These APEC strains constitute a potential zoonotic risk.

The Escherichia coli argW-dsdCXA genetic island is highly variable, and E. coli K1 strains commonly possess two copies of dsdCXA

The genome sequences of Escherichia coli pathotypes reveal extensive genetic variability in the argW-dsdCXA island. Interestingly, the archetype E. coli K1 neonatal meningitis strain, strain RS218, has two copies of the dsdCXA genes for d-serine utilization at the argW and leuX islands. Because the human brain contains d-serine, an epidemiological study emphasizing K1 isolates surveyed the dsdCXA copy number and function. Forty of 41 (97.5%) independent E. coli K1 isolates could utilize d-serine. Southern blot hybridization revealed physical variability within the argW-dsdC region, even among 22 E. coli O18:K1:H7 isolates. In addition, 30 of 41 K1 strains, including 21 of 22 O18:K1:H7 isolates, had two dsdCXA loci. Mutational analysis indicated that each of the dsdA genes is functional in a rifampin-resistant mutant of RS218, mutant E44. The high percentage of K1 strains that can use d-serine is in striking contrast to our previous observation that only 4 of 74 (5%) isolates in the diarrheagenic E. coli (DEC) collection have this activity. The genome sequence of diarrheagenic E. coli isolates indicates that the csrRAKB genes for sucrose utilization are often substituted for dsdC and a portion of dsdX present at the argW-dsdCXA island of extraintestinal isolates. Among DEC isolates there is a reciprocal pattern of sucrose fermentation versus d-serine utilization. The ability to use d-serine is a trait strongly selected for among E. coli K1 strains, which have the ability to infect a wide range of extraintestinal sites. Conversely, diarrheagenic E. coli pathotypes appear to have substituted sucrose for d-serine as a potential nutrient.

Sharing of virulent Escherichia coli clones among household members of a woman with acute cystitis

BACKGROUND

Within-household transmission of extraintestinal pathogenic Escherichia coli (ExPEC) may contribute to the pathogenesis of urinary tract infection (UTI), but this is poorly understood.

METHODS

A woman with acute UTI, 4 human household members who cohabited with her, and the family's pet dog underwent prospective longitudinal surveillance for colonizing E. coli for 7-9 weeks after the woman's UTI episode. Unique clones were resolved by random amplified polymorphic DNA and pulsed-field gel electrophoresis analysis. Virulence genes, phylogenetic group, and O types were defined by PCR. Comparisons with reference strains were made using random amplified polymorphic DNA profiling.

RESULTS

Serial fecal and urine samples from the 6 household members yielded 7 unique E. coli clones (4 of which were ExPEC and 3 of which were non-ExPEC). For 3 clones, extensive among-host sharing was evident in patterns suggesting host-to-host transmission. The mother's UTI clone, which represented E. coli O1:K1:H7, was the clone that was most extensively shared (in 5 hosts, including the dog) and most frequently recovered (in 45% of samples and at all 3 time points). The other 3 ExPEC clones corresponded with E. coli O6:K2:H1, O1:K1:H7, and O2:F10,F48.

CONCLUSIONS

E. coli clones, including ExPEC, can be extensively shared among human and animal household members in the absence of sexual contact and in patterns suggesting host-to-host transmission.

Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis

The evolutionary origins of extraintestinal pathogenic Escherichia coli (ExPEC) remain uncertain despite these organisms' relevance to human disease. A valid understanding of ExPEC phylogeny is needed as a framework against which the observed distribution of virulence factors and clinical associations can be analyzed. Accordingly, phylogenetic relationships were defined by multi-locus sequence analysis among 44 representatives of selected ExPEC clonal groups and the E. coli Reference (ECOR) collection. Recombination, which significantly obscured the phylogenetic signal for several strains, was dealt with by excluding strains or specific sequences. Conflicting overall phylogenies, and internal phylogenies for virulence-associated phylogenetic group B2, were inferred depending on the specific dataset (i.e., how extensively purged of recombination), outgroup (Salmonella enterica and/or Escherichia fergusonii), and analysis method (neighbor joining, maximum parsimony, maximum likelihood, or Bayesian likelihood). Nonetheless, the major E. coli phylogenetic groups A, B1, and B2 were consistently well resolved, as was a major sub-component of group D and an ECOR 37-O157:H7 clade. Moreover, nine important ExPEC clonal groups within groups B2 and D, characterized by serotypes O6:K2:H1, O18:K1:H7, O6:H31, and O4:K+:H+ (from group B2), and O1:K1:H-, O7:K1:H-, O157:K+:H (non-7), O15:K52:H1, and O11/17/77:K52:H18 ("clonal group A") (from group D), were consistently well resolved, regardless of clinical background (cystitis, pyelonephritis, neonatal meningitis, sepsis, or fecal), host group, geographical origin, and virulence profile. Among the group B2-derived clonal groups the O6:K2:H1 clade appeared basal. Within group D, "clonal group A" and the O15:K52:H1 clonal group were consistently placed with ECOR 47 and ECOR 44, respectively, as nearest neighbors. These findings clarify phylogenetic relationships among key ExPEC clonal groups but also emphasize that recombination appears to obscure the oldest evolutionary relationships, despite extensive targeted sequencing and use of a wide range of analysis techniques.

The IrgA homologue adhesin Iha is an Escherichia coli virulence factor in murine urinary tract infection

The role of the Escherichia coli iron-regulated gene homologue adhesin (Iha) in the pathogenesis of urinary tract infections (UTIs) is unknown. We performed a series of complementary analyses to confirm or refute the hypothesis that Iha is a virulence factor in uropathogenic E. coli. Fecal E. coli isolates exhibited significantly lower prevalences of iha (range, 14 to 22%) than did clinical isolates from cases of pediatric cystitis or pyelonephritis, adult pyelonephritis or urosepsis, or bacteremia (range, 38 to 74%). Recombinant Iha from E. coli pyelonephritis isolate CFT073 conferred upon nonadherent E. coli ORN172 the ability to adhere to cultured T-24 human uroepithelial cells. In a well-established mouse model of ascending UTI, CFT073 and its derivative UPEC76 (a pap [P fimbriae] mutant version of strain CFT073) each significantly outcompeted their respective iha deletion mutants in CBA/J mice 48 h after bladder challenge (P < 0.03 for urine, both kidneys, and bladders of both constructs, except for bladders of mice challenged with UPEC76 and its deletion mutant, where P = 0.11). These data suggest that Iha(CFT073) is a virulence factor and might be a target for anti-UTI interventions.

Feline uropathogenic Escherichia coli from Great Britain and New Zealand have dissimilar virulence factor genotypes

We investigated the prevalence of 30 known virulence factor genes (VFGs) in uropathogenic E. coli (UPEC) from two geographically distinct feline populations, using a PCR-based approach. E. coli isolates were also subjected to macrorestriction analysis to assess their phylogenetic relationships. VFG profiles differed considerably according to the geographic origin of the isolates, enabling discriminant analysis to correctly predict population membership for 15/15 NZ isolates and 18/22 UK isolates. The prevalence of gene markers for P-fimbriae (PapA, PapC, PapEF, and PapG III), colicin V (CvaC), increased serum survival factor (Iss), complement resistance factor (TraT), pathogenicity-associated island (MalX), iron-regulated siderophore receptor (IreA) and haemolysin (HlyD) differed significantly between UK and NZ isolates. Significant phylogenetic differences between the two populations were also identified, but VFG profiles could not be predicted on the basis of phylogenetic relationships. Consequently, a geographically uneven distribution of certain virulence genes, independent of phylogeny, is the likely cause of VFG differences between populations. We cannot rule out that subtle differences in patient disease status may have contributed to the dissimilarity of VFG profiles.

Escherichia coli infections in newborn puppies--clinical and epidemiological investigations

Epidemiological analyses were performed in five breeding kennels with Escherichia coli infections in newborn pups using pulsed field gel electrophoresis (PFGE). Previous reports demonstrated the high discriminatory power of this method and its usefulness for detecting epidemiologically related isolates. A total of 113 E. coli strains were isolated from vagina, faeces, oral cavity, milk and organs from 19 adult dogs, and 57 diseased or dead pups from 12 litters. Restriction enzyme analyses were performed using XbaI and BlnI digests and the resulting 91 DNA patterns were aligned for comparison. The results showed that a total of 60% of E. coli strains from progeny were also found in vaginal samples of the mothers. Another bacterial source was the faeces found within the kennels. One instance of milk and oral cavity isolates of the mother was found to be identical with strains isolated from the pups. The results indicate that for repeated cases of E. coli infections in neonates, diagnostic procedures of vaginal and faecal swabs from dams result in isolation of the responsible bacteria with high probability and further suggest that preterm treatment could help to control bacterial diseases and losses in pups. In addition, the observation that two canine strains were found to be identical with an E. coli strain isolated from a human case of diarrhoea strongly supports the canine reservoir hypothesis.

Antimicrobial resistance of Escherichia coli strains isolated from urine of women with cystitis or pyelonephritis and feces of dogs and healthy humans

OBJECTIVE

To assess the prevalence and patterns of antimicrobial resistance among Escherichia coli strains isolated from the urine of women with cystitis or pyelonephritis and from fecal samples from dogs and healthy humans.

DESIGN

Cross-sectional survey.

SAMPLE POPULATION

Escherichia coli isolates from 82 women with cystitis, 170 women with pyelonephritis, 45 dogs, and 76 healthy human volunteers.

PROCEDURE

Susceptibility to 12 antimicrobial agents was determined by means of disk diffusion testing as specified by the NCCLS.

RESULTS

Overall, the 4 most common antimicrobial resistance patterns were resistance to ampicillin, sulfisoxazole, trimethoprim, and trimethoprim-sulfamethoxazole (n = 45 [12% of all isolates]); ampicillin alone (33 [9%]); ampicillin and sulfisoxazole (29 [8%]); and sulfisoxazole alone (14 [4%]). None of the isolates were resistant to ceftazidime, ciprofloxacin, nitrofurantoin, or piperacillin-tazobactam. Resistance was significantly more common and extensive among isolates from women with cystitis or pyelonephritis than among isolates from healthy humans or dogs. Resistance was least common among isolates from dogs. The only resistance phenotype that was more common among canine isolates than human isolates was resistance to sulfisoxazole alone.

CONCLUSIONS AND CLINICAL RELEVANCE

Results suggest that dogs are unlikely to be an important external reservoir of antimicrobial-resistant E. coli strains causing infections in humans. On the contrary the data suggest that dogs conceivably could acquire resistant E. coli strains from humans.

Molecular Epidemiology of Acute, Uncomplicated Urinary Tract Infections in Young Women

Molecular biological methods, a relatively new addition to the epidemiologist's tool chest, are now applied to the study of urinary tract infection (UTI). By combining sound epidemiologic methods and the ability to genetically stratify UTI-causing Escherichia coli, recent studies have added to our understanding of UTI. These advancements include the possible identification of outbreaks of community-acquired UTI, the contribution of person-to-person transmission of E. coli to the risk for UTI in young women, and changes in the community prevalence and distribution of UTI caused by drug-resistant organisms. The application of molecular methods to future UTI research studies may yield novel approaches to UTI prevention.

Epidemic and nonepidemic multidrug-resistant Enterococcus faecium

The epidemiology of vancomycin-resistant Entero- coccus faecium (VREF) in Europe is characterized by a large community reservoir. In contrast, nosocomial outbreaks and infections (without a community reservoir) characterize VREF in the United States. Previous studies demonstrated host-specific genogroups and a distinct genetic lineage of VREF associated with hospital outbreaks, characterized by the variant esp-gene and a specific allele-type of the purK housekeeping gene (purK1). We investigated the genetic relatedness of vanA VREF (n=108) and vancomycin-susceptible E. faecium (VSEF) (n=92) from different epidemiologic sources by genotyping, susceptibility testing for ampicillin, sequencing of purK1, and testing for presence of esp. Clusters of VSEF fit well into previously described VREF genogroups, and strong associations were found between VSEF and VREF isolates with resistance to ampicillin, presence of esp, and purK1. Genotypes characterized by presence of esp, purK1, and ampicillin resistance were most frequent among outbreak-associated isolates and almost absent among community surveillance isolates. Vancomycin-resistance was not specifically linked to genogroups. VREF and VSEF from different epidemiologic sources are genetically related; evidence exists for nosocomial selection of a subtype of E. faecium, which has acquired vancomycin-resistance through horizontal transfer.

Production of cytolethal distending toxins by pathogenic Escherichia coli strains isolated from human and animal sources: establishment of the existence of a new cdt variant (Type IV)

Three types of cytolethal distending toxin (CDT), namely, CDT-I, CDT-II, and CDT-III, have been described in Escherichia coli. Using primers designed for the detection of sequences common to the cdtB genes, we analyzed by PCR a set of 21 CDT-producing E. coli strains of intestinal and extraintestinal origins isolated from human and different animal species in several European countries and in the United States. On the basis of the existing differences in the cdtB genes, cdt-I-, cdt-II-, and cdt-III-specific primer pairs were designed and used for cdt typing. These new primers successfully differentiated all of the previously described cdt genes. Six strains proved to be cdt-I; eight strains proved to be cdt-III. However, none of the type I-, II-, and III-specific primers generated amplicons from six CDT(+) strains, suggesting the existence of a new cdt variant. Sequence analysis of the amplicons from two untypeable genes confirmed the existence of a new cdt variant that we called cdt-IV. Using the new specific primers, cdt-IV was detected in human, porcine, and poultry strains of intestinal and extraintestinal origins. To validate all sets of cdt specific primers, a group of 353 human E. coli strains isolated in Hungary was then investigated for the presence of cdt genes. This included 190 strains isolated from patients with urinary tract infections (UTI), 51 strains isolated from other (nonurinary) extraintestinal infections, and 112 intestinal strains isolated from healthy individuals. Of 190 UTI strains, 15 (7.9%) had cdt genes. Of 51 non-UTI extraintestinal strains 3 (5.9%) contained the cdt gene, and 1 (0.9%) of 112 healthy intestinal strains was PCR positive. Five strains proved to be cdt-I, and fourteen strains proved to be cdt-IV. The CDT-producing extraintestinal strains belonged to a wide variety of serogroups, including O2, O6, O75, and O170. In conclusion, we have developed a new PCR typing system for CDT able to detect a new CDT variant present in pathogenic E. coli strains obtained from animals and humans.

Identification of urovirulence traits in Escherichia coli by comparison of urinary and rectal E. coli isolates from dogs with urinary tract infection

Spontaneously occurring urinary tract infection (UTI) in dogs was exploited as an experiment of nature to gain insights into UTI pathogenesis in humans. Concurrent urinary and rectal Escherichia coli isolates from 37 dogs with UTI were compared with respect to phylogenetic background, O antigens, and extended virulence genotype. In 54% of the UTI episodes, the dog's urinary and rectal isolates represented the same strain. Urinary isolates differed dramatically from rectal-only isolates in that they derived predominantly from E. coli phylogenetic group B2, expressed typical (human) UTI-associated O antigens, and possessed many virulence-associated genes, most notably pap elements (P fimbriae), papG (adhesin) allele III, sfa/foc and sfaS (S fimbriae), hly (hemolysin), fyuA (yersiniabactin), iroN (siderophore), and ompT (outer membrane protease T). The 20 urinary isolates that corresponded with the host's predominant rectal strain were no less virulent according to the markers analyzed than were the 17 urinary isolates that differed from the host's predominant rectal strain. These findings suggest that UTI pathogenesis is similar in dogs and humans, provide added support for the special-pathogenicity over the prevalence hypothesis of UTI pathogenesis, and identify numerous specific virulence-associated factors as significant correlates of urovirulence.

Extended virulence genotype of pathogenic Escherichia coli isolates carrying the afa-8 operon: evidence of similarities between isolates from humans and animals with extraintestinal infections

The afimbrial AfaE-VIII adhesin is common among Escherichia coli isolates from calves with intestinal and/or extraintestinal infections and from humans with sepsis or pyelonephritis. The virulence genotypes of 77 Escherichia coli afa-8 isolates from farm animals and humans were compared to determine whether any trait of commonality exists between isolates of the different host species. Over half of the extraintestinal afa-8 isolates were associated with pap and f17Ac adhesin genes and contained virulence genes (pap, hly, and cnf1) which are characteristic of human extraintestinal pathogenic E. coli (ExPEC). PapG, which occurs as three known variants (variants I to III), is encoded by the corresponding three alleles of papG. Among the pap-positive strains, new papG variants (papGrs) that differed from the isolates with genes for the three adhesin classes predominated over isolates with papG allele III, which in turn were more prevalent than those with allele II. The data showed the substantial prevalence of the enteroaggregative E. coli heat-stable enterotoxin gene (east1) among afa-8 isolates. Most of the afa-8 isolates harbored the high-pathogenicity island (HPI) present in pathogenic Yersinia; however, two-thirds of the HPI-positive strains shared a truncated HPI integrase gene. The presence of ExPEC-associated virulence factors (VFs) in extraintestinal isolates that carry genes typical of enteric strains and that express O antigens associated with intestinal E. coli is consistent with transfer of VFs and O-antigen determinants between ExPEC and enteric strains. The similarities between animal and human ExPEC strains support the hypothesis of overlapping populations, with members of certain clones or clonal groups including animal and human strains. The presence of multiple-antibiotic-resistant bovine afa-8 strains among such clones may represent a potential public health risk.

Haemolytic Escherichia coli isolated from dogs with diarrhea have characteristics of both uropathogenic and necrotoxigenic strains

Twenty-four haemolytic Escherichia coli strains were isolated from dogs with diarrhea. The strains were serotyped and analysed by polymerase chain reaction (PCR) for genes encoding virulence factors associated with E. coli that cause diarrhea in animals. Adhesion antigen production was deduced from haemagglutination experiments. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) of heat extracts was also used as an indication for the production of adhesive structures. The majority of the strains was shown to produce this type of virulence factor. Adhesion and invasion tests of the strains and Caco-2 cells showed that all strains adhered and that two were invasive. The two invasive strains were positive in the intimin PCR and one of them also contained genes encoding CS31A. The PCR for heat stable toxin (ST) was positive in only four strains, as was the presence of F17 fimbrial genes. Surprisingly, 19 strains had intact P fimbrial operons, coding for an adhesin involved in urinary tract infection (UTI). The cytotoxic necrotising factor 1 (CNF1) gene, also mainly found in UTI was likewise detected in these 19 strains. Cytolethal distending toxin (Cdt) genes were found in five strains. The high number of strains positive for CNF1 and P fimbriae prompted us to test the strains in a multiplex PCR used to test E. coli isolated from UTI in various species for 30 virulence associated genes. The data showed that the majority of the diarrhea isolates have virulence factor profiles highly similar to UTI E. coli isolates from dogs. This raises the question whether these isolates are real intestinal pathogens or "innocent bystanders". However, since CNF1 producing necrotoxic E. coli (NTEC) strains isolated from humans, pigs and calves with diarrhea appear to be highly related to our strains, it might be that in dogs this type of isolate is capable of causing not only UTI, but also diarrhea. If this is the case and this type of isolate is "bifunctional", domestic animals likely constitute a reservoir of NTEC strains which can be also pathogenic for humans.

Extraintestinal pathogenic Escherichia coli: "the other bad E coli"

Extraintestinal pathogenic Escherichia coli (ExPEC), the specialized strains of E coli that cause most extraintestinal E coli infections, represent a major but little-appreciated health threat. Although the reasons for their evolution remain mysterious, by virtue of their numerous virulence traits ExPEC clearly possess a unique ability to cause disease outside the host intestinal tract. Broader appreciation of the existence and importance of ExPEC and better understandings of their distinctive virulence mechanisms, reservoirs, and transmission pathways may lead to effective preventive interventions against the morbid and costly infections ExPEC cause.

PCR for specific detection of H7 flagellar variant of fliC among extraintestinal pathogenic Escherichia coli

A newly developed PCR-based assay for the H7 variant of the Escherichia coli flagellin gene, fliC, was 100% sensitive and specific in comparison with serology and probe hybridization. It revealed broad conservation of the H7 fliC variant among phylogenetically diverse lineages of extraintestinal pathogenic E. coli (ExPEC) and superseded serotyping for certain isolates with ambiguous or non-H7 serotyping results. The H7 primers functioned well when incorporated into a multiplex PCR assay for diverse virulence-associated genes of ExPEC.

Ongoing horizontal and vertical transmission of virulence genes and papA alleles among Escherichia coli blood isolates from patients with diverse-source bacteremia

The phylogenetic distributions of multiple putative virulence factors (VFs) and papA (P fimbrial structural subunit) alleles among 182 Escherichia coli blood isolates from patients with diverse-source bacteremia were defined. Phylogenetic correspondence among these strains, the E. coli Reference (ECOR) collection, and other collections of extraintestinal pathogenic E. coli (ExPEC) was assessed. Although among the 182 bacteremia isolates phylogenetic group B2 predominated, exhibited the greatest concentration of individual VFs, and contained the largest number of familiar virulent clones, other phylogenetic groups exhibited greater concentrations of certain VFs than did group B2 and included several additional virulent clones. Certain of the newly detected VF genes, e.g., fyuA (yersiniabactin; 76%) and focG (F1C fimbriae; 25%), were as prevalent or more prevalent than their more familiar traditional counterparts, e.g., iut (aerobactin; 57%) and sfaS (S fimbriae; 14%), thus possibly offering additional useful targets for preventive interventions. Considerable diversity of VF profiles was observed at every level within the phylogenetic tree, including even within individual lineages. This suggested that many different pathways can lead to extraintestinal virulence in E. coli and that the evolution of ExPEC, which involves extensive horizontal transmission of VFs and continuous remodeling of pathogenicity-associated islands, is a highly active, ongoing process.

Novel molecular variants of allele I of the Escherichia coli P fimbrial adhesin gene papG

P fimbriae of extraintestinal pathogenic Escherichia coli mediate digalactoside-specific adherence via the tip adhesin molecule PapG, which occurs in three known variants (I to III), which are encoded by the corresponding three alleles of papG. In the present study, newly discovered variants of papG allele I and the respective wild-type source strains were characterized. One of the new papG allele I variants conferred a unique agglutination phenotype that combined the phenotypes associated with papG alleles I, II, and III. Comparative hydrophilicity analysis of predicted PapG peptides revealed regions that might explain the observed phenotypic similarities and differences between the PapG variants. The new papG allele I variants occurred either as the sole papG allele or together with both papG alleles II and III, rather than with only papG allele III, as in archetypal strains J96 and CP9. They also occurred in the absence of the usual F13 papA allele. One of the new papG allele I variants occurred in a serogroup O6 strain that, according to random amplified polymorphic DNA analysis, was phylogenetically distant from the "J96-like" clonal group of E. coli O4:H5, which includes all previously identified examples of papG allele I. Cluster analysis of nucleotide and predicted peptide sequences suggested that papG allele I represents the earliest evolutionary branch from a common papG ancestor. These results demonstrate unexpected diversity within papG allele I and, together with previous findings, suggest that the J96-like clonal group of E. coli O4:H5 may represent the original source of papG within the species.

Canine feces as a reservoir of extraintestinal pathogenic Escherichia coli

To test the canine reservoir hypothesis of extraintestinal pathogenic Escherichia coli (ExPEC), 63 environmental canine fecal deposits were evaluated for the presence of ExPEC by a combination of selective culturing, extended virulence genotyping, hemagglutination testing, O serotyping, and PCR-based phylotyping. Overall, 30% of canine fecal samples (56% of those that yielded viable E. coli) contained papG-positive E. coli, usually as the predominant E. coli strain and always possessing papG allele III (which encodes variant III of the P-fimbrial adhesin molecule PapG). Multiple other virulence-associated genes typical of human ExPEC were prevalent among the canine fecal isolates. According to serotyping, virulence genotyping, and random amplified polymorphic DNA analysis, over 50% of papG-positive fecal E. coli could be directly correlated with specific human clinical isolates from patients with cystitis, pyelonephritis, bacteremia, or meningitis, including archetypal human ExPEC strains 536, CP9, and RS218. Five canine fecal isolates and (clonally related) archetypal human pyelonephritis isolate 536 were found to share a novel allele of papA (which encodes the P-fimbrial structural subunit PapA). These data confirm that ExPEC representing known virulent clones are highly prevalent in canine feces, which consequently may provide a reservoir of ExPEC for acquisition by humans.