stx genotype and molecular epidemiological analyses of Shiga toxin-producing Escherichia coli O157:H7/H- in human and cattle isolates

Unraveling the Resistome, Virulome, and Pathogenicity of Escherichia Coli O157:H7 From Cattle Feces

Antimicrobial-resistant Escherichia coli, especially those belonging to the serotype O157, are increasingly linked to foodborne diseases with significant fatality rates worldwide. The food and medical industries have focused on E. coli O157:H7 due to its ability to produce toxins coupled with its low infectious dose. The aim of this study was to assess the virulome, resistome, and pathogenicity of E. coli O157:H7 using whole genome sequencing. Three previously isolated E. coli O157:H7 strains from cattle feces were subjected to whole genome sequencing. The genome sizes of all three E. coli O157:H7 strains were 5,117,276 bp, 5,039,443 bp, and 5,034,351 bp. The C + G contents were 50.22%, 50.53%, and 50.54%, while the number of contigs was 110, 43, and 42, respectively, for E. coli O157:H7 strains J32, J57, and J69. Several virulence determinants (hemorrhagic E. coli pilus (HCP), eaeA, hemolysin, etc.) were found in the genomes of these isolates. In addition, antibiotic resistance genes conferring resistance to aminoglycosides, tetracyclines, macrolides, fluoroquinolones, penams, carbapenems, cephalosporins, cephamycin, rifamycin, phenicols, monobactams, and nitroimidazole were found in the genomes. Interestingly, the genomes of these isolates also harbored determinants encoding resistance to disinfectants and antiseptics, indicating their concern in the food production and medical sectors. This highlights the public health concerns of these isolates, indicating the need for constant surveillance.

Molecular epidemiology of virulent E. coli among rural small scale dairy herds and shops: Efficacy of selected marine algal extracts and disinfectants

Virulent pathotypes of E. coli seriously affect the livestock regarding the misuse of antibiotics. All 180 samples collected from cow's environment and dairy shops in Qena, Egypt were serologically and molecularly positive for coliforms. Enteropathogenic E. coli (EPEC), Shiga toxin-producing E. coli (STEC), Enteroinvasive E. coli (EIEC) and Enterotoxigenic E. coli (ETEC) pathotypes were isolated from water and milk-related samples. STEC serogroups O26, O55, O111, O113, O145 were also recovered. The non-O157 STEC serotypes were recovered from human diarrheagenic patients contacting cattle or consuming contaminated water/milk products. Bla_CTX-M and bla_TEM genes were detected in 25.5% and 100%, respectively. Disinfectants and algal extracts, identified by GC-MS, were evaluated in vitro for antibacterial activities. TH4+® disinfectant and methanol extract of Turbinaria decurrens reduced E. coli at 13 log10 at 1.5% and 3 mg/ml concentrations, respectively. Ag-NPs/T. decurrens showed 8-9 log10 reduction at concentration of 1.6 × 10⁵ NPs/ml. Examined water sources, milk and milk products were potential reservoirs for virulent antibiotic-resistant E.coli which may impose animal and public health threats.Abbreviations: APEC: Avian pathogenic E. coli; bla_CTX-M: β-lactamase inhibitors-Cefotaximase gene; bla_TEM: β-lactamase inhibitors-Temoneira gene; CFU: Colony-forming unit; DAEC: Diffusely adherent E. coli; DEC: Diarrheagenic Escherichia coli; DEMSO: Dimethyl sulfoxide; eaeA: Intimin or E. coli attaching gene; EAEC: Enteroaggregative E. coli; EHEC: Enterohemorrhagic E. coli; EIEC: Enteroinvasive E. coli; EOSQC: Egyptian Organization for Standardization and Quality Control; EPEC: Enteropathogenic E. coli; ETEC: Enterotoxigenic E. coli; ExPEC: Extra-intestinal pathogenic E. coli; GC-MS: Gas chromatography-mass spectrometry technique; hly: Hemolysin gene; STEC: Shiga like producing E. coli; stx1: Shiga-toxin 1 gene; ESBLs: Extended-spectrum beta-lactamases.

Genotypic Features of Clinical and Bovine Escherichia coli O157 Strains Isolated in Countries with Different Associated-Disease Incidences

There is great geographical variation in the frequency of Escherichia coli O157 infections that correlates with important differences in the bovine reservoir of each country. Our group carried out a broad molecular characterization of human and bovine E. coli O157 strains circulating in Argentina using different methodologies. Our data allows us to conclude that in Argentina, a high homogeneity is observed in both cattle and human strains, with almost exclusive circulation of strains belonging to the hypervirulent clade 8 described by Manning. The aim of this review was to compare the genetic background of E. coli O157 strains isolated in countries that have conducted similar studies, to try to correlate specific O157 genotypes with the incidence and severity of E. coli O157 associated diseases. The characteristics of the strains that cause disease in humans reflect the predominant genotypes in cattle in each of the countries analyzed. The main features clearly linked to high incidence or severity of E. coli O157 infections are lineage-specific polymorphism assay-6 lineage I/II, clade 8 strains and probably, clade 6 strains, the stx_2a/stx_2c genotype, the presence of q933 and q21 simultaneously, and putative virulence factor EC_3286. In countries with an absence of these features in O157 strains, the overall incidence of O157 disease is low. Argentina, where these characteristics are detected in most strains, shows the highest incidence of hemolytic uremic syndrome (HUS) worldwide.

Occurrence of virulent and antibiotic-resistant Shiga toxin-producing Escherichia coli in some food products and human stool in Egypt

AIM

Shiga toxin-producing Escherichia coli (STEC) represent a severe public health issue worldwide, causing life-threatening diseases in the human gastrointestinal tract. This study aimed to determine the occurrence of virulent and antibiotic-resistant STEC in retail meat and milk products and human stool samples and to characterize the genes encoding for virulence and antibiotic resistance among the identified STEC isolates.

MATERIALS AND METHODS

A total of 260 food samples were randomly collected from retail markets in different localities of El Giza Governorate, Egypt. 50 stool specimens were obtained from children that had diarrhea at Embaba Fever Hospital. All collected samples were initially subjected to bacteriological examination and serotyping, and then subsequently, the isolates were exposed to polymerase chain reaction application and sequencing for the identification of the virulence-related genes. Finally, the virulent STEC isolates were tested for antibiotic susceptibility.

RESULTS

Serotyping of the 76 biochemically identified isolates showed that 18 were STEC with a predominance of non-O157 (16) while 2 O157:K-serotype was detected only in one food and one human isolate. Molecular identification of the virulence genes illustrated that the minced meat showed the highest prevalence of STEC (8%) as compared to the other food products. In the humans, the O157 was the only serotype that expresses the Shiga toxin-associated gene (eaeA). Antibiotic susceptibility test displayed that 13 of the 17 food and human isolates (76.47%) were resistant to cephalothin (KF30). 9 of the 13 cephalothin-resistant isolates harbor the β lactamase (blaTEM )-resistant gene. All isolates were sensitive to chloramphenicol, ciprofloxacin, amikacin, and gentamicin. DNA sequencing and phylogenetic analysis of the stx2-positive minced meat isolate revealed a high genetic relatedness with beef minced meat from the USA and Australia.

CONCLUSION

This study showed the predominance of non-O157 among the identified isolates. Minced meat showed the highest prevalence of STEC as compared to the other food products, and this work illustrates the necessity to consider the food products as a potential source of the non-O157 STEC serotypes. DNA sequencing and phylogenetic analysis revealed a high genetic relatedness with beef minced meat from the USA and Australia. This highlights the high probability of worldwide spread of such serotypes, signifying the importance of the one world concept.

Serotypes, virulence markers and cell invasion ability of Shiga toxin-producing Escherichia coli strains isolated from healthy dairy cattle

AIM

The occurrence of virulence markers, serotypes and invasive ability were investigated in Shiga toxin-producing Escherichia coli (STEC) isolated from faecal samples of healthy dairy cattle at Rio de Janeiro State, Brazil.

METHODS AND RESULTS

From 1562 stx-positive faecal samples, 105 STEC strains were isolated by immuno-magnetic separation (IMS) or plating onto MacConkey agar (MC) followed by colony hybridisation. Fifty (47·6%) strains belonged to nine serotypes (O8:H19, O22:H8, O22:H16, O74:H42, O113:H21, O141:H21, O157:H7, O171:H2 and ONT:H21). The prevalent serotypes were O157:H7 (12·4%), O113:H21 (6·7%) and O8:H19 (5·7%). Virulence genes were identified by polymerase chain reaction (PCR). E-hlyA (77·1%) was the more prevalent virulence marker, followed by espP (64·8%), saa (39%), eae (24·8%) and astA (21·9%). All O157:H7 strains carried the γ (gamma) variant of the locus of enterocyte effacement (LEE) genes and the stx2c gene, while the stx1/stx2 genotype prevailed among the eae-negative strains. None of the eae-positive STEC produced the localized adherence (LA) phenotype in HEp-2 or Caco-2 cells. However, intimate attachment (judged by the fluorescent actin staining test) was detected in some eae-positive strains, both in HEp-2 (23·1%) and in Caco-2 cells (11·5%). Most strains (87·5%) showed 'peripheral association' (PA) adherence phenotype to undifferentiated Caco-2 cells. Twenty-five (92·6%) of 27 strains invaded Caco-2 cells. The highest average value of invasion (9·6%) was observed among the eae-negative bovine strains from serotypes described in human disease.

CONCLUSION

Healthy dairy cattle is a reservoir of STEC carrying virulence genes and properties associated with human disease.

SIGNIFICANCE AND IMPACT OF THE STUDY

Although reports of human disease associated with STEC are scarce in Brazil, the colonization of the animal reservoir by potentially pathogenic strains offers a significant risk to our population.

Shiga toxin-producing escherichia coli infections in Norway, 1992-2012: characterization of isolates and identification of risk factors for haemolytic uremic syndrome

BACKGROUND

Shiga toxin-producing E. coli (STEC) infection is associated with haemolytic uremic syndrome (HUS). Therefore Norway has implemented strict guidelines for prevention and control of STEC infection. However, only a subgroup of STEC leads to HUS. Thus, identification of determinants differentiating high risk STEC (HUS STEC) from low risk STEC (non-HUS STEC) is needed to enable implementation of graded infectious disease response.

METHODS

A national study of 333 STEC infections in Norway, including one STEC from each patient or outbreak over two decades (1992-2012), was conducted. Serotype, virulence profile, and genotype of each STEC were determined by phenotypic or PCR based methods. The association between microbiological properties and demographic and clinical data was assessed by univariable analyses and multiple logistic regression models.

RESULTS

From 1992 through 2012, an increased number of STEC cases including more domestically acquired infections were notified in Norway. O157 was the most frequent serogroup (33.6 %), although a decrease of this serogroup was seen over the last decade. All 25 HUS patients yielded STEC with stx2, eae, and ehxA. In a multiple logistic regression model, age ≤5 years (OR = 16.7) and stx2a (OR = 30.1) were independently related to increased risk of HUS. eae and hospitalization could not be modelled since all HUS patients showed these traits. The combination of low age (≤5 years) and the presence of stx2a, and eae gave a positive predictive value (PPV) for HUS of 67.5 % and a negative predictive value (NPV) of 99.0 %. SF O157:[H7] and O145:H?, although associated with HUS in the univariable analyses, were not independent risk factors. stx1 (OR = 0.1) was the sole factor independently associated with a reduced risk of HUS (NPV: 79.7 %); stx2c was not so.

CONCLUSIONS

Our results indicate that virulence gene profile and patients' age are the major determinants of HUS development.

PCR-based detection and molecular characterization of shiga toxin-producing Escherichia coli strains in a routine microbiology laboratory over 16 years

Shiga toxin-producing Escherichia coli (STEC) is a heterogeneous group of bacteria causing disease ranging from asymptomatic carriage and mild infection to hemolytic uremic syndrome (HUS). Here, we describe patients with STEC infection and characterize the STEC strains detected in our laboratory by use of PCR for stx1, stx2, and eae from 1996 through 2011. Patient information was collected from referral forms and from the Norwegian Surveillance System for Communicable Diseases. STEC isolates were characterized with respect to serogroup or serotype, selected potential virulence genes, and multilocus variable-number tandem-repeat analysis (MLVA) genotype. STEC strains were isolated from 138 (1.09%) of 12,651 patients tested. STEC strains of serogroups O26, O103, O121, O145, and O157 were the most frequent. These serogroups, except non-sorbitol-fermenting O157, were also the most frequent among the 11 patients (all ≤5 years old) who developed HUS. Twenty-four STEC strains were classified as being HUS associated based on an epidemiological link to a HUS case, including an MLVA genotype identical to that of the STEC strain. The age of the patient (≤5 years) and the genes eae and stx2a were significantly associated with HUS-associated STEC (P < 0.05 for each parameter), while stx1 was associated with non-HUS-associated STEC (P < 0.05). All of the potential virulence genes analyzed, except ehxA, were significantly more frequent among HUS-associated than non-HUS-associated strains (P < 0.05 for each gene). However, these genes were also present in some non-HUS-associated STEC strains and could therefore not reliably differentiate between HUS-associated and non-HUS-associated STEC strains.

Taxonomy Meets Public Health: The Case of Shiga Toxin-Producing Escherichia coli

To help assess the clinical and public health risks associated with different Shiga toxin-producing Escherichia coli (STEC) strains, an empirical classification scheme was used to classify STEC into five “seropathotypes” (seropathotype A [high risk] to seropathotypes D and E [minimal risk]). This definition is of considerable value in cases of human infection but is also problematic because not all STEC infections are fully characterized and coupled to reliable clinical information. Outbreaks with emerging hybrid strains continuously challenge our understanding of virulence potential and may result in incorrect classification of specific pathotypes; an example is the hybrid strain that caused the 2011 outbreak in Germany, STEC/EAggEC O104:H4, which may deserve an alternative seropathotype designation. The integration of mobile virulence factors in the stepwise and parallel evolution of pathogenic lineages of STEC collides with the requirements of a good taxonomy, which separates elements of each group into subgroups that are mutually exclusive, unambiguous, and, together, include all possibilities. The concept of (sero)-pathotypes is therefore challenged, and the need to identify factors of STEC that absolutely predict the potential to cause human disease is obvious. Because the definition of hemolytic-uremic syndrome (HUS) is distinct, a basic and primary definition of HUS-associated E. coli (HUSEC) for first-line public health action is proposed: stx2 in a background of an eae- or aggR -positive E. coli followed by a second-line subtyping of stx genes that refines the definition of HUSEC to include only stx2a and stx2d . All other STEC strains are considered “low-risk” STEC.

Lineage and genogroup-defining single nucleotide polymorphisms of Escherichia coli O157:H7

Escherichia coli O157:H7 is a zoonotic human pathogen for which cattle are an important reservoir host. Using both previously published and new sequencing data, a 48-locus single nucleotide polymorphism (SNP)-based typing panel was developed that redundantly identified 11 genogroups that span six of the eight lineages recently described for E. coli O157:H7 (J. L. Bono, T. P. Smith, J. E. Keen, G. P. Harhay, T. G. McDaneld, R. E. Mandrell, W. K. Jung, T. E. Besser, P. Gerner-Smidt, M. Bielaszewska, H. Karch, M. L. Clawson, Mol. Biol. Evol. 29:2047-2062, 2012) and additionally defined subgroups within four of those lineages. This assay was applied to 530 isolates from human and bovine sources. The SNP-based lineage groups were concordant with previously identified E. coli O157:H7 genotypes identified by other methods and were strongly associated with carriage of specific Stx genes. Two SNP lineages (Ia and Vb) were disproportionately represented among cattle isolates, and three others (IIa, Ib, and IIb) were disproportionately represented among human clinical isolates. This 48-plex SNP assay efficiently and economically identifies biologically relevant lineages within E. coli O157:H7.

Carriage of stx2a differentiates clinical and bovine-biased strains of Escherichia coli O157

Background

Shiga toxin (Stx) are cardinal virulence factors of enterohemorrhagic E. coli O157:H7 (EHEC O157). The gene content and genomic insertion sites of Stx-associated bacteriophages differentiate clinical genotypes of EHEC O157 (CG, typical of clinical isolates) from bovine-biased genotypes (BBG, rarely identified among clinical isolates). This project was designed to identify bacteriophage-mediated differences that may affect the virulence of CG and BBG.

Methods

Stx-associated bacteriophage differences were identified by whole genome optical scans and characterized among >400 EHEC O157 clinical and cattle isolates by PCR.

Results

Optical restriction maps of BBG strains consistently differed from those of CG strains only in the chromosomal insertion sites of Stx2-associated bacteriophages. Multiplex PCRs (stx1, stx2a, and stx2c as well as Stx-associated bacteriophage - chromosomal insertion site junctions) revealed four CG and three BBG that accounted for >90% of isolates. All BBG contained stx2c and Stx2c-associated bacteriophage – sbcB junctions. All CG contained stx2a and Stx2a-associated bacteriophage junctions in wrbA or argW.

Conclusions

Presence or absence of stx2a (or another product encoded by the Stx2a-associated bacteriophage) is a parsimonious explanation for differential virulence of BBG and CG, as reflected in the distributions of these genotypes in humans and in the cattle reservoir.

Phylogeny of Shiga toxin-producing Escherichia coli O157 isolated from cattle and clinically ill humans

Cattle are a major reservoir for Shiga toxin-producing Escherichia coli O157 (STEC O157) and harbor multiple genetic subtypes that do not all associate with human disease. STEC O157 evolved from an E. coli O55:H7 progenitor; however, a lack of genome sequence has hindered investigations on the divergence of human- and/or cattle-associated subtypes. Our goals were to 1) identify nucleotide polymorphisms for STEC O157 genetic subtype detection, 2) determine the phylogeny of STEC O157 genetic subtypes using polymorphism-derived genotypes and a phage insertion typing system, and 3) compare polymorphism-derived genotypes identified in this study with pulsed field gel electrophoresis (PFGE), the current gold standard for evaluating STEC O157 diversity. Using 762 nucleotide polymorphisms that were originally identified through whole-genome sequencing of 189 STEC O157 human- and cattle-isolated strains, we genotyped a collection of 426 STEC O157 strains. Concatenated polymorphism alleles defined 175 genotypes that were tagged by a minimal set of 138 polymorphisms. Eight major lineages of STEC O157 were identified, of which cattle are a reservoir for seven. Two lineages regularly harbored by cattle accounted for the majority of human disease in this study, whereas another was rarely represented in humans and may have evolved toward reduced human virulence. Notably, cattle are not a known reservoir for E. coli O55:H7 or STEC O157:H⁻ (the first lineage to diverge within the STEC O157 serogroup), which both cause human disease. This result calls into question how cattle may have originally acquired STEC O157. The polymorphism-derived genotypes identified in this study did not surpass PFGE diversity assessed by BlnI and XbaI digestions in a subset of 93 strains. However, our results show that they are highly effective in assessing the evolutionary relatedness of epidemiologically unrelated STEC O157 genetic subtypes, including those associated with the cattle reservoir and human disease.

Identification of shiga toxin and intimin coding genes in Escherichia coli isolates from pigeons (Columba livia) in relation to phylotypes and antibiotic resistance patterns

Shiga toxin-producing Escherichia coli (STEC) strains are responsible for outbreaks of human intestinal diseases worldwide. Pigeons are distributed in public areas and are potential reservoirs for pathogenic bacteria. One hundred fifty-four fresh fecal samples were obtained from trapped pigeons in southeast of Iran and were cultured for isolation of E. coli. The isolates were examined to determine the prevalence of stx1, stx2, and eae genes, antimicrobial resistance, and their phylotypes. The confirmed E. coli isolates (138) belong to four phylogenetic groups: A (54.34%), B1 (34.05%), B2 (3.62%), and D (7.79%). Thirteen (9.42%) isolates were positive for one of the examined genes. Eight isolates (5.79%) were positive for eae, four (2.89%) for stx2, and one isolate (1.44%) for stx1 gene. Phylotyping assays showed that eight eae-positive isolates fall into three phylogroups; A (three isolates), B1 (three isolates), and D (two isolates), whereas four stx2-positive isolates belonged to the A (three isolates) and D (one isolate) groups. The stx1-positive isolate belonged to phylogroup A. One hundred six isolates (76.81%) showed resistance to at least one of the selected antibacterial agents. The maximum resistance rate was against oxytetracycline (73.91%), and the minimum was against flumequine (2.17%). Twenty different patterns of drug resistance were observed. According to the results, pigeons could be considered as carriers of STEC strains. However, E. coli isolates of pigeon feces increase the potential of these birds to act as a reservoir of multiple antibiotic resistant bacteria.