Strains Of Phylogenetic Group B2 Research Articles

The distinct transcriptome of virulence-associated phylogenetic group B2 Escherichia coli.

Escherichia coli strains of phylogenetic group B2 are often associated with urinary tract infections (UTIs) and several other diseases. Recent genomic and transcriptomic analyses have not suggested or identified specific genes required for virulence, but have instead suggested multiple virulence strategies and complex host-pathogen interactions. Previous analyses have not compared core gene expression between phylogenetic groups or between pathogens and nonpathogens within phylogenetic groups. We compared the core gene expression of 35 strains from three phylogenetic groups that included both pathogens and nonpathogens after growth in a medium that allowed comparable growth of both types of strains. K-means clustering suggested a B2 cluster with 17 group B2 strains and two group A strains; an AD cluster with six group A strains, five group D strains and one B2 strain; and four outliers which included the highly studied model uropathogenic E. coli strains UTI89 and CFT073. Half of the core genes were differentially expressed between B2 and AD cluster strains, including transcripts of genes for all aspects of macromolecular synthesis-replication, transcription, translation, and peptidoglycan synthesis-energy metabolism, and environmental-sensing transcriptional regulators. Notably, core gene expression between nonpathogenic and uropathogenic transcriptomes within phylogenetic groups did not differ. If differences between pathogens and nonpathogens exist, then the differences do not require transcriptional reprogramming. In summary, B2 cluster strains have a distinct transcription pattern that involves hundreds of genes. We propose that this transcription pattern is one factor that contributes to virulence. IMPORTANCE Escherichia coli is a diverse species and an opportunistic pathogen that is associated with various diseases, such as urinary tract infections. When examined, phylogenetic group B2 strains are more often associated with these diseases, but the specific properties that contribute to their virulence are not known. From a comparative transcriptomic analysis, we found that group B2 strains grown in a nutrient-rich medium had a distinct transcription pattern, which is the first evidence that core gene expression differs between phylogenetic groups. Understanding the consequences of group B2 transcription pattern will provide important information on basic E. coli biology, the basis for E. coli virulence, and possibly for developing therapies for a majority of urinary tract infections and other group B2-associated diseases.

Geographic distribution of the major clone of extended-spectrum beta-lactamase-producing Escherichia coli infection in a pediatric community in southern Taiwan

BackgroundThe geographic distribution of the major clone of sequence type 131 (ST131) in extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) infections is not known. We analyzed the clinical features, resistance mechanisms, and geographic distribution of ESBL-producing E. coli clones in 120 children. MethodsWe studied the 120 ESBL-producing E. coli strains from children younger than 18 years. A VITEK 2 automated system was used to determine bacterial identification and ESBL production. Sequence type was determined by multi-locus sequence typing (MLST). The genetic relationship of the ESBL-producing strains was studied using pulsed-field gel electrophoresis (PFGE). Phylogenetic group and blaCTX-M group was performed using polymerase chain reaction (PCR). Multiplex PCR for detecting the common group 9 variant, CTX-M-14, and group 1 variant, CTX-M-15, was also performed. The addresses of the 120 children were collected, and plotted on the Taiwan map. ResultsThe groups in the center of Kaohsiung City lived mainly in urban areas with a population density of over 10,000 people per square kilometer, and the majority of the Kaohsiung groups on the outskirts of the city center lived in suburban areas with a population density of under 6000 people per square kilometer. There was no statistically significant difference between the city center and outskirt groups in terms of clinical presentation, laboratory, and imaging data. However, more ST131 clones, major pulsotype groups, and phylogenetic group B2 strains were found in the center of Kaohsiung than on the outskirts. ConclusionESBL-producing E. coli clones may be more challenging to treat clinically. Most infections were community-acquired, and there appeared to be major pulsotype clones, mainly in urban areas. This reinforces the necessity of environmental surveillance and sanitary procedures for ESBL-producing E. coli.

Correlation of Escherichia coli Strains Isolated from Wild Bird Feces and Human Urinary Tract Infections from Phylogenetic Point of View

Background: Escherichia coliis a typical occupant of the enteric system of vertebrates. Some E. coli strains are related to urinary tract infections (UTIs) in human. E. coli strains are divided namely to the four phylogenetic groups, A, B1, B2, and D. Some investigations have indicated the relationship between phylogenetic characteristics and pathogenicity of E. coli. Thus, determining the phylogeny of unknown E. coli strains may be useful in predicting the pathogenesis. Objectives: In the present study, we aimed to compare the distribution of E. coli phylogroups in human UTIs and wild bird feces as a possible source of infection for human in a cross-sectional survey. Methods: A total of 264 E. coli isolates were obtained from human UTIs and feces of wild birds around and phylogenetic determination was carried out using the Clermont Triplex-PCR technique. Results: Our results showed that phylogenetic group B2 strains were the most prevalent in UTI cases (47.2%) followed by group D (30.2%). Group B1 contained 32.5% of the isolates in feces of wild birds, followed by group A (27.5%). There was a significant difference in E. coli phylogeny between hosts so that groups B2 and D were more prevalent in human UTIs and groups B1 and A in wild birds. Also, when comparing the phylogroups within a host, group B1 showed a higher rate in wild birds than in human UTIs. Conclusions: Although the majority of isolates from wild birds belonged to nonpathogenic phylogenetic groups B1 and A, further research seems to necessary to assess the exact relation of wild birds as pathogen sources for human by genotyping E. coli strains via high throughput genotyping assays.

Escherichia coli strains of phylogenetic group B2 and D and bacteriocin production are associated with advanced colorectal neoplasia.

BackgroundColorectal cancer (CRC) is the 3rd most common cancer worldwide and the Czech Republic has the 6th highest incidence of CRC worldwide. Large intestinal microbiota play in its etiopathogenesis important role. Bacteriocins are proteins, produced by bacteria from the Enterobacteriaceae family. The aim of our prospective study was to assess the colonization of large intestinal mucosa by Escherichia coli strains and to investigate their bacteriocin production.MethodsA total of 30 consecutive patients with colorectal adenoma, CRA (17 men, 13 women, aged 39–79, mean age 63 ± 9), 30 patients with CRC (23 men, 7 women, aged 38–86, mean age 67 ± 11) and 20 healthy controls (9 men, 11 women, age 23–84, mean age 55 ± 15) were enrolled into prospective study. Mucosal biopsies were taken in the caecum, transverse colon and rectum during pancolonoscopy. Microbiological culture, isolation and identification of bacteria followed. Bacteriocin production was assessed by growth inhibition of indicator strains E. coli K12-Row, E. coli C6 (phi), and Shigella sonnei 17. Identification of bacteriocin-encoding determinants and E. coli phylogroups was performed using PCR methods.ResultsA total of 622 strains were isolated and further investigated. A significantly higher frequency of simultaneous production of colicins and microcins was revealed in the group of patients with CRC, when compared to patients with CRA, p = 0.031. A significantly higher frequency of E. coli phylogroup D was found in patients with CRC, when compared to controls, p = 0.044. A significantly higher prevalence of bacteriocinogeny was confirmed in patients with advanced adenoma when compared to patients with non-advanced adenoma, p = 0.010. Increasing bacteriocinogeny was associated with an increasing stage of CRC (assessed according to TNM classification). Either E. coli phylogroup B2 or E. coli phylogroup D were isolated in biopsies of patients with right-sided CRC. A statistically higher incidence of E. coli phylogroup B2 was found in patients with right-sided CRC when compared to patients with left-sided CRC, p = 0.028.ConclusionsLarge intestinal mucosa of patients with more advanced colorectal neoplasia is colonized with more virulent strains of E. coli and higher production of bacteriocins is observed in these patients when compared to those with less advanced colorectal neoplasia.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-014-0733-7) contains supplementary material, which is available to authorized users.

Mo1141 Association of Right-Sided Colorectal Cancer and Ulcerative Colitis With Escherichia coli Strains of Phylogenetic Group B2, Which Harbour Genotoxic “PKS” Island

Mo1141 Association of Right-Sided Colorectal Cancer and Ulcerative Colitis With Escherichia coli Strains of Phylogenetic Group B2, Which Harbour Genotoxic “PKS” Island

Escherichia coli strains with the capacity for long-term persistence in the bowel microbiota carry the potentially genotoxic pks island

The pks genomic island found in Escherichia coli strains of phylogenetic group B2 encodes colibactin, a polyketide-peptide genotoxin that causes DNA double-strand breaks. We investigated the relationship between carriage of the pks island and the capacity of E. coli strains to persist in the gut microbiota of 130 Swedish infants, who were followed from birth to 18 months of age. Long-term colonizers were significantly more likely to have the pks island than either intermediate-term colonizers or transient strains, which suggests that the pks island contributes to the pronounced gut-colonizing capacity of group B2 strains. Long-term persistence in the colon of pks island-containing E. coli strains may be associated with the induction of genomic mutations in the host intestine.

Acute Escherichia coli Prostatitis in Previously Health Young Men: Bacterial Virulence Factors, Antimicrobial Resistance, and Clinical Outcomes

To investigate clinical outcomes, bacterial virulence factors, and antimicrobial resistance in E. coli from young men presenting with acute bacterial prostatitis. Initial E. coli isolates from previously healthy young men with no factors compromising urinary tract anatomy or function were tested for virulence-associated genes by polymerase chain reaction (PCR) assays, phylogenetic grouping by triplex polymerase PCR, and antibiotic resistance. All 18 patients responded to treatment, including 2 who required long-term therapy. E. coli were allocated to phylogenetic groups B2 (13 strains) and D (5 strains). Prostatitis isolates belonged to clones mainly represented by extraintestinal pathogenic E. coli (ExPEC) and preferentially uropathogenic E. coli and displayed marked accumulation of virulence genes (hly, cdt1, clb, pap, sfa/foc, fyuA, iroN, kpsMT(II), and traT) characteristic of highly virulent ExPEC. All phylogenetic group B2 strains coded for at least 1 toxin with carcinogenic potential (Colibactin, cytolethal distending toxins, or cytotoxic necrotizing factor). In contrast to their accumulation of virulence-associated traits, prostatitis strains were sensitive to standard antibiotics. The phylogenetic background and accumulation of an exceptional repertoire of extraintestinal pathogenic virulence-associated genes indicate that these E. coli strains belong to a highly virulent subset of uropathogenic variants. In contrast, antibiotic resistance was minimal in these E. coli strains from previously healthy, young outpatients.

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.

Prevalence and phylogenetic history of the TcpC virulence determinant in Escherichia coli

Extraintestinal pathogenic Escherichia coli (ExPECs) possess an armament of virulence factors to colonize and infect the host, such as adhesins, toxins, capsules and iron-uptake systems. Recently, we could identify a novel virulence factor of ExPECs that interferes with the innate immune response of the host by interrupting the NF-κB signaling pathway. This protein named TcpC shows considerable homology to motifs of the Tir domain of Toll-like receptors. Here we demonstrate that the tcpC gene is widely distributed among clinical ExPEC isolates with almost half of the E. coli strains from patients suffering pyelonephritis shown to be tcpC positive as compared to only 8% in commensal isolates. However, this gene is only present in phylogenetic group B2 strains. Interestingly, the tcpC gene is strongly associated with presence of the high-pathogenicity island (HPI). The phylogenetic history of the tcpC gene, in the E. coli reference collection (ECOR) and other well-defined E. coli strains, compared to the phylogenetic histories of the HPI and the strains, showed that the tcpC gene (i) is scattered among various B2 subgroups with specific O-types, (ii) has a phylogeny incongruent with the strain phylogeny, but (iii) congruent with the HPI phylogenetic history. This, together with the strong conservation of the tcpC gene, indicates a very recent introduction of this virulence factor into E. coli by horizontal gene transfer which occurred “en bloc” with the HPI at one major hot spot of recombination in the E. coli genome. The present data provide evidence for a strong impact of homologous recombination events in the spread of the TcpC virulence trait among E. coli.

Absence of Escherichia coli Phylogenetic Group B2 Strains in Humans and Domesticated Animals from Jeonnam Province, Republic of Korea

Multiplex PCR analyses of DNAs from genotypically unique Escherichia coli strains isolated from the feces of 138 humans and 376 domesticated animals from Jeonnam Province, South Korea, performed using primers specific for the chuA and yjaA genes and an unknown DNA fragment, TSPE4.C2, indicated that none of the strains belonged to E. coli phylogenetic group B2. In contrast, phylogenetic group B2 strains were detected in about 17% (8 of 48) of isolates from feces of 24 wild geese and in 3% (3 of 96) of isolates obtained from the Yeongsan River in Jeonnam Province, South Korea. The distribution of E. coli strains in phylogenetic groups A, B1, and D varied depending on the host examined, and there was no apparent seasonal variation in the distribution of strains in phylogenetic groups among the Yeongsan River isolates. The distribution of four virulence genes (eaeA, hlyA, stx(1), and stx(2)) in isolates was also examined by using multiplex PCR. Virulence genes were detected in about 5% (38 of 707) of the total group of unique strains examined, with 24, 13, 13, and 9 strains containing hlyA, eaeA, stx(2), and stx(1), respectively. The virulence genes were most frequently present in phylogenetic group B1 strains isolated from beef cattle. Taken together, results of these studies indicate that E. coli strains in phylogenetic group B2 were rarely found in humans and domesticated animals in Jeonnam Province, South Korea, and that the majority of strains containing virulence genes belonged to phylogenetic group B1 and were isolated from beef cattle. Results of this study also suggest that the relationship between the presence and types of virulence genes and phylogenetic groupings may differ among geographically distinct E. coli populations.

Phylogenetic group B2 Escherichia coli strains from the bowel microbiota of Pakistani infants carry few virulence genes and lack the capacity for long-term persistence

Escherichia coli strains of phylogenetic group B2 obtained from Western human hosts are enriched in virulence-associated genes and have a superior capacity to persist in the colonic microbiota. Here, E. coli strains from 22 infants born in Pakistan whose rectal flora was sampled regularly over the first 6 months of life were examined. B2 strains did not carry the virulence-associated genes sfaD/E, papC, neuB or hlyA more often than strains of other phylogenetic groups. B2 origin was not associated with persistence in the bowel microbiota. As compared with B2 strains from Swedish infants, Pakistani B2 strains carried significantly less often the virulence genes fimH (p 0.04), papC (p 0.02), papG class III (p 0.01), sfaD/E (p ≤0.0001), neuB (p ≤0.0001), and hlyA (p 0.005), and also the high-pathogenicity island (p ≤0.0001). A minority of Pakistani B2 strains belonged to recognized uropathogenic O-groups, which are common among ‘Western’ B2 strains. Thus, extra-intestinal pathogenicity may be the foremost characteristic of B2 strains colonizing Western populations.

Characterization of a β-Glucoside Operon (bgc) Prevalent in Septicemic and UropathogenicEscherichia coliStrains

Escherichia coli strains, in general, do not ferment cellobiose and aryl-beta-D-glucosidic sugars, although "cryptic" beta-d-glucoside systems have been characterized. Here we describe an additional cryptic operon (bgc) for the utilization of cellobiose and the aryl-beta-d-glucosides arbutin and salicin at low temperature. The bgc operon was identified by the characterization of beta-glucoside-positive mutants of an E. coli septicemia strain (i484) in which the well-studied bgl (aryl-beta-d-glucoside) operon was deleted. These bgc* mutants appeared after 5 days of incubation on salicin indicator plates at 28 degrees C. The bgc operon codes for proteins homologous to beta-glucoside/cellobiose-specific phosphoenolpyruvate-dependent phosphotransfer system permease subunits IIB (BgcE), IIC (BgcF), and IIA (BgcI); a porin (BgcH); and a phospho-beta-D-glucosidase (BgcA). Next to the bgc operon maps the divergent bgcR gene, which encodes a GntR-type transcriptional regulator. Expression of the bgc operon is dependent on the cyclic-AMP-dependent regulator protein CRP and positively controlled by BgcR. In the bgc* mutants, a single nucleotide exchange enhances the activity of the bgc promoter, rendering it BgcR independent. Typing of a representative collection of E. coli demonstrated the prevalence of bgc in strains of phylogenetic group B2, representing mainly extraintestinal pathogens, while it is rare among commensal E. coli strains. The bgc locus is also present in the closely related species Escherichia albertii. Further, bioinformatic analyses demonstrated that homologs of the bgc genes exist in the enterobacterial Klebsiella, Enterobacter, and Citrobacter spp. and also in gram-positive bacteria, indicative of horizontal gene transfer events.

Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

BackgroundExtraintestinal 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.ResultsRecombination-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.ConclusionOur 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.

Characteristics of human intestinal Escherichia coli with changing environments

To investigate if the characteristics of human intestinal Escherichia coli are changing with the environment of the host, we studied intestinal E. coli from subjects having recently migrated from a temperate to a tropical area. We determined the phylogenetic group, the prevalence of the antibiotic resistance, the presence of integrons and the strain diversity in faecal isolates from 25 subjects originally from metropolitan France and expatriated to French Guyana. These characteristics were compared with those of 25 previously studied Wayampi Amerindian natives of French Guyana and from 25 metropolitan French residents. The three groups of subjects were matched for age and sex, had not taken antibiotics for at least 1 month, nor had been hospitalized within the past year. In all, the characteristics of intestinal E. coli from Expatriates were intermediate between those found in residents from metropolitan France and those found in natives of French Guyana. Prevalence of carriage of resistant Gram-negative bacteria in Expatriates was intermediate between French residents and Wayampi as were the prevalence of integrons in E. coli (12.3% versus 16.3% and 7.8% respectively), and the intra-host diversity of E. coli (2.3 strains/subject versus 1.9 and 3.1, respectively); lastly, in Expatriates, the prevalence of carriage of phylogenetic group B2 strains was lower than in French residents (16% versus 56%, P = 0.005), while carriage of phylogenetic group A strains was lower than in Wayampi (56% versus 88%, P = 0.03). Our results suggest that the composition of the commensal intestinal flora of humans is not static but changes dynamically in response to new environmental conditions.

Both urinary and rectal Escherichia coli isolates are dominated by strains of phylogenetic group B2.

To compare the genetic structures of uropathogenic and commensal Escherichia coli populations, a total of 181 urinary and rectal E. coli isolates were classified into intraspecies phylogenetic groups by PCR amplifications of phylogenetic markers. The genetic variability of these isolates within phylogenetic groups was further assessed by enterobacterial repetitive intergenic consensus (ERIC) typing. The distributions of 10 known virulence factors were also examined. In contrast with most reports, phylogenetic group B2 not only accounted for the majority of urinary isolates from young women with urinary tract infections (69%) but also was the dominant group among the rectal isolates from healthy young women (48%). Such difference may be explained by geographic variation, difference in host population characteristics, or differences in sampling method, or a combination of the three. Strains with known virulence factors most frequently belonged to phylogenetic groups B2 and D. Additionally, group B2 and D rectal isolates were more heterogeneous than urinary isolates. Two subclusters existed within group B2 strains by ERIC typing. These subclusters were not evenly distributed between rectal and urine isolates and differed in virulence gene distribution.

Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations.

An intraspecies phylogenetic grouping of 168 human commensal Escherichia coli strains isolated from the stools of three geographically distinct human populations (France, Croatia, Mali) was generated by triplex PCR. The distributions of seven known extraintestinal virulence determinants (ibeA, pap, sfa/foc, afa, hly, cnf1, aer) were also determined by PCR. The data from the three populations were compiled, which showed that strains from phylogenetic groups A (40%) and B1 (34%) were the most common, followed by phylogenetic group D strains (15%). Strains of the phylogenetic group B2 were rare (11%). However, a significant specific distribution for strains of groups A, B1 and B2 within each population was observed, which may indicate the influence of (i) geographic/climatic conditions, (ii) dietary factors and/or the use of antibiotics or (iii) host genetic factors on the commensal flora. Virulence determinants were rarely detected, with only 25.6% of the strains harbouring at least one of the virulence genes tested. The strains with virulence factors most frequently belonged to phylogenetic group B2. The commensal strains of phylogenetic groups A, B1 and D had fewer virulence determinants than pathogenic strains of the corresponding groups when these data were compared with those for previous collections of virulent extraintestinal infection strains studied using the same approach. However, the virulence patterns of commensal and pathogenic B2 phylogenetic group strains were the same. The data thus suggest that strains of the A, B1 and D phylogenetic groups predominate in the gut flora and that these strains must acquire virulence factors to become pathogenic. In contrast, commensal phylogenetic group B2 strains are rare but appear to be potentially virulent.