2 Serotyping of Escherichia coli

Epidemiology of Enterotoxigenic Escherichia coli among Children and Adults Seeking Care at Hospitals in Two Geographically Distinct Rural Areas in Bangladesh

Enterotoxigenic Escherichia coli (ETEC) infections undeniably continue to have substantial morbidity and mortality in younger children; however, limited data are available on the disease burden of older children and adults and on ETEC epidemiology by geographical location at the subnational level. Facility-based surveillance over the years was established to identify patients with ETEC diarrhea in two geographically distinct areas in rural Bangladesh, Chhatak in the north and Mathbaria in the southern coastal area. ETEC was highly prevalent in both areas, while the proportions, toxin types and colonization factors varied by location, season and age groups. Children < 5 years old and adults between 20 and 60 years old were at the highest risk of ETEC diarrhea which required urgent care. This study underscores the importance of capturing subnational and seasonal variations in ETEC epidemiology. ETEC vaccine developers and public health stakeholders may need to target adults between 20 and 60 years of age in addition to young children as new vaccines currently under development become licensed and introduction begins.

Characterization of uropathogenic E. coli from various geographical locations in India

Objectives

Uropathogenic Escherichia coli (UPEC) is the most common causative agent of urinary tract infection, accounting for more than 80% of cases worldwide. This study presents data on prevalent serotypes, resistance profiles, and colonization-aiding virulence characteristics of UPEC from different geographical regions in India.

Methods

UPEC were serotyped through microtiter plate agglutination. Standard techniques were used to detect various virulence characteristics, i.e., biofilm formation (tissue culture plate method), siderophore production (screened on Chrome Azurol S agar and categorized with Csaky's and Arnow's methods), colicin release (agar overlay technique), gelatin hydrolysis (on gelatinase agar), and cell surface hydrophobicity (salt aggregation method). Antibiotic resistance profiles (against 20 antimicrobial agents) and extended-spectrum beta-lactamase (ESBL) were evaluated according to Clinical and Laboratory Standards Institute guidelines.

Results

UPEC strains exhibited very high drug resistance rates to most of the commonly used antimicrobial agents; the highest resistance rates were observed for ampicillin (63.4%), nalidixic acid (63.4%), and cefotaxime (62.1%). High rates of multi-drug resistance (63.36%), ESBL-production (34.1%), and carbapenem-resistance (25.0%) were detected in UPEC strains from all geographical regions of India. Hydrophobicity (61.2%), biofilm production (62.5%), and siderophore production (67.7%) were the most common virulence characteristics of UPEC isolates. Co-expression of virulence characteristics was common (69.8%) in UPEC strains.

Conclusion

UPEC strains with very high antimicrobial-resistance are in circulation in India, and have diverse serotypes and virulence characteristics.

Genetic Diversity and Antimicrobial Resistance of Extraintestinal E. coli Populations Pre- and Post-Antimicrobial Therapy on Broilers Affected by Colisepticemia

The aim of the present study was to investigate the genetic diversity and antimicrobial resistance (AMR) of E. coli during enrofloxacin therapy in broilers affected by colisepticemia. Three unrelated farms with ongoing colibacillosis outbreaks were sampled at day 1 before treatment and at days 5, 10 and 24 post-treatment. A total of 179 E. coli isolates were collected from extraintestinal organs and submitted to serotyping, PFGE and the minimum inhibitory concentration (MIC) against enrofloxacin. PFGE clusters shifted from 3-6 at D1 to 10-16 at D5, D10 and D24, suggesting an increased population diversity after the treatment. The majority of strains belonged to NT or O78 and to ST117 or ST23. PFGE results were confirmed with SNP calling: no persistent isolates were identified. An increase in resistance to fluoroquinolones in E. coli isolates was observed along the treatment. Resistome analyses revealed qnrB19 and qnrS1 genes along with mutations in the gyrA, parC and parE genes. Interestingly, despite a fluoroquinolone selective pressure, qnr-carrying plasmids did not persist. On the contrary, two conjugative AMR plasmid clusters (AB233 and AA474) harboring AMR genes other than qnr were persistent since they were identified in both D1 and D10 genomes in two farms. Further studies should be performed in order to confirm plasmid persistence not associated (in vivo) to antimicrobial selective pressure.

Detection and analysis of Shiga toxin producing and enteropathogenic Escherichia coli in cattle from Tierra del Fuego, Argentina

Shiga toxin producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are pathovars that affect mainly infants' health. Cattle are the main reservoir of STEC. Uremic hemolytic syndrome and diarrheas can be found at high rates in Tierra del Fuego (TDF). This study aimed to establish the prevalence of STEC and EPEC in cattle at slaughterhouses in TDF and to analyze the isolated strains. Out of 194 samples from two slaughterhouses, STEC prevalence was 15%, and EPEC prevalence was 5%. Twenty-seven STEC strains and one EPEC were isolated. The most prevalent STEC serotypes were O185:H19 (7), O185:H7 (6), and O178:H19 (5). There were no STEC eae + strains (AE-STEC) or serogroup O157 detected in this study. The prevalent genotype was stx2c (10/27) followed by stx1a/stx2hb (4/27). Fourteen percent of the strains presented at least one stx non-typeable subtype (4/27). Shiga toxin production was detected in 25/27 STEC strains. The prevalent module for the Locus of Adhesion and Autoaggregation (LAA) island was module III (7/27). EPEC strain was categorized as atypical and with the ability to cause A/E lesion. The ehxA gene was present in 16/28 strains, 12 of which were capable of producing hemolysis. No hybrid strains were detected in this work. Antimicrobial susceptibility tests showed that all strains were resistant to ampicillin and 20/28 were resistant to aminoglycosides. No statistical differences could be seen in the detection of STEC or EPEC either by slaughterhouse location or by production system (extensive grass or feedlot). The rate of STEC detection was lower than the one reported for the rest of Argentina. STEC/EPEC relation was 3 to 1. This is the first study on cattle from TDF as reservoir for strains that are potentially pathogenic to humans.

Molecular analysis of enteropathogenic Escherichia coli (EPEC) isolates from healthy food-producing animals and humans with diarrhoea

Enteropathogenic Escherichia coli (EPEC) is a pathogen associated with acute diarrhoea in humans. To determine whether EPEC isolated from healthy food-producing animals possesses the same virulence gene repertoire as EPEC isolated from human with diarrhoea, we compared six typical EPEC (tEPEC) and 20 atypical EPEC (aEPEC) from humans with diarrhoea and 42 aEPEC from healthy animals (swine, sheep and buffaloes), using pulsed-field gel electrophoresis (PFGE), virulence markers, serotyping and subtyping of eae and tir genes. We found that human and animal isolates shared virulence genes, including nleB, nleE and nleF, which were associated with human diarrhoea. Serogroups and serotypes identified in isolates of food-producing animals such as O26:H11, O128:H2, O76:H7, O103, O108, O111 and O145, have previously been implicated in human disease. The subtypes eae and tir were also shared between human and animal isolates, being eae-γ1 and eae-β1 the most prevalent in both groups, while the most common tir subtypes were α and β. Despite PFGE analysis demonstrating that EPEC strains are heterogeneous and there was no prevalent clone identified, EPEC isolated from humans and food-producing animals shared some characteristics, such as virulence genes associated with human diarrhoea, indicating that food-producing animals could play a role as reservoirs for those genes.

Molecular typification of Escherichia coli from community-acquired urinary tract infections in Mexico

One hundred and five uropathogenic Escherichia coli (UPEC) strains from patients with community-acquired urinary tract infection were characterized according to their phylogenetic groups, virulence factors, serogroups, antibiotics resistance, and genotype. The pathogenic phylogenetic groups (B2, D, and F) were found in 71.4% of the tested strains. Among them, the main uropathogenic serogroups were O8, O25, and O75, in which 97.1% of the strains had a multidrug-resistant profile. Moreover, 16 virulence genes were analyzed using a combination of PCR assays, with the fimH, irp-2, iutA, aer, iucC, PAI, sat, iroN, usp, and cnf1 genes being mainly found in pathogenic phylogroups. The E. coli O25b-ST131 clone was identified in 32% of the strains assigned to the pathogenic phylogroup B2. Our findings demonstrate that virulence genes encoding adhesin components, iron acquisition systems, toxins, and pathogenicity-associated islands were highly prevalent among the pathogenic phylogroup of UPEC strains.

Virulence Factors and Antimicrobial Resistance Profile of Escherichia Coli Isolated from Laying Hens in Italy

Simple Summary

Colibacillosis is a disease of great importance in the poultry industry, but many of its features and characteristics still need to be identified. This survey on avian Escherichia coli investigated the correlation between the presence of specific virulence genes, antimicrobial resistance features and serogroups. The results highlighted that half of the tested strains were avian pathogenic Escherichia coli (APEC). Moreover, a high prevalence of two specific serogroups was detected, namely, O2 and O88. Finally, antimicrobial resistance was lower than in other studies. Further investigations of APEC strains’ antimicrobial resistance features would support farmers, veterinarians and local authorities in planning actions for a better control of colibacillosis in poultry production.

Abstract

Colibacillosis is the most common bacterial disease in the poultry industry. The isolation of Escherichia coli (E. coli) strains with multiple resistance to various classes of antimicrobials has been increasing in recent years. In this study, antimicrobial resistance features, serotyping and the presence of avian pathogenic Escherichia coli (APEC) virulence genes were investigated on a total of 71 E. coli strains isolated during outbreaks of colibacillosis in laying hens. The correlation between these features was evaluated. The most frequently isolated serogroups were O2 and O88. Resistance was often detected with nalidixic acid (49%) and ampicillin (38%), while all strains were sensitive to ceftiofur and florfenicol. Overall, 25% of the isolates showed resistance to at least three or more antimicrobial classes (multidrug-resistant strains), and 56% of the isolates were defined as APEC strains (due to the presence of at least five virulence genes). Correlation between the different parameters (virulence genes, serogroup and antimicrobial resistance) did not reveal relevant associations. The comparison of the obtained results with those of similar studies highlighted the importance of continuous monitoring in order to have a better understanding of colibacillosis. An evaluation of the national epidemiological situation would allow, especially with regard to antimicrobial resistance, to focus on the right measures in order to prioritize the available resources for effective disease control.

Carbapenemase-Producing Extraintestinal Pathogenic Escherichia coli From Argentina: Clonal Diversity and Predominance of Hyperepidemic Clones CC10 and CC131

Extraintestinal pathogenic Escherichia coli (ExPEC) causes infections outside the intestine. Particular ExPEC clones, such as clonal complex (CC)/sequence type (ST)131, have been known to sequentially accumulate antimicrobial resistance that starts with chromosomal mutations against fluoroquinolones, followed with the acquisition of bla_CTX–M–15 and, more recently, carbapenemases. Here we aimed to investigate the distribution of global epidemic clones of carbapenemase-producing ExPEC from Argentina in representative clinical isolates recovered between July 2008 and March 2017. Carbapenemase-producing ExPEC (n = 160) were referred to the Argentinean reference laboratory. Of these, 71 were selected for genome sequencing. Phenotypic and microbiological studies confirmed the presence of carbapenemases confirmed as KPC-2 (n = 52), NDM-1 (n = 16), IMP-8 (n = 2), and VIM-1 (n = 1) producers. The isolates had been recovered mainly from urine, blood, and abdominal fluids among others, and some were from screening samples. After analyzing the virulence gene content, 76% of the isolates were considered ExPEC, although non-ExPEC isolates were also obtained from extraintestinal sites. Pan-genome phylogeny and clonal analysis showed great clonal diversity, although the first phylogroup in abundance was phylogroup A, harboring CC10 isolates, followed by phylogroup B2 with CC/ST131, mostly H30Rx, the subclone co-producing CTX-M-15. Phylogroups D, B1, C, F, and E were also detected with fewer strains. CC10 and CC/ST131 were found throughout the country. In addition, CC10 nucleated most metalloenzymes, such as NDM-1. Other relevant international clones were identified, such as CC/ST38, CC155, CC14/ST1193, and CC23. Two isolates co-produced KPC-2 and OXA-163 or OXA-439, a point mutation variant of OXA-163, and three isolates co-produced MCR-1 among other resistance genes. To conclude, in this work, we described the molecular epidemiology of carbapenemase-producing ExPEC in Argentina. Further studies are necessary to determine the plasmid families disseminating carbapenemases in ExPEC in this region.

Classification of Parabacteroides distasonis and other Bacteroidetes using O- antigen virulence gene: RfbA-Typing and hypothesis for pathogenic vs. probiotic strain differentiation

Parabacteroides distasonis (Pdis) is the type species for the new Parabacteroides genus, and a gut commensal of the Bacteroidetes phylum. Emerging reports (primarily based on reference strain/ATCC-8503) concerningly propose that long-known opportunistic pathogen Pdis is a probiotic. We posit there is an urgent need to characterize the pathogenicity of Pdis strain-strain variability. Unfortunately, no methods/insights exist to classify Bacteroidetes for this purpose. Herein, we developed a virulence gene-based classification system for Pdis and Bacteroidetes to facilitate pathogenic-vs-probiotic characterization. We used DNA in silico methods to develop a system based on the virulence (lipopolysaccharide/bacterial wall) 'rfbA O-antigen-synthesis gene'. We then performed phylogenetic analysis of rfbA from fourteen Pdis complete genomes (21 genes), other Parabacteroides, Bacteroidetes, and Enterobacteriaceae; and proposed a PCR-based Restriction-Fragment Length Polymorphism method. Cluster analysis revealed that Pdis can be classified into four lineages (based on gene gaps/insertions) which we designated rfbA-Types I, II, III, and IV. In context, we found 14 additional rfbA-types (I-XVIII) interspersed with numerous Bacteroidetes and pathogenic Enterobacteriaceae forming three major "rfbA-superclusters." For laboratory rfbA-Typing implementation, we developed a PCR-primer strategy to amplify Pdis rfbA genes (100%-specificity) to conduct MboII-RFLP and sub-classify Pdis. In-silico primers for other Bacteroidetes are proposed/discussed. Comparative analysis of lipopolysaccharide/lipid-A gene lpxK confirmed rfbA as highly discriminant. In conclusion, rfbA-Typing classifies Bacteroidetes/Pdis into unique clusters/superclusters given rfbA copy/sequence variability. Analysis revealed that most pathogenic Pdis strains are single-copy rfbA-Type I . The relevance of the rfbA strain variability in disease might depend on their hypothetical modulatory interactions with other O-antigens/lipopolysaccharides and TLR4 lipopolysaccharide-receptors in human/animal cells.

O-Serogroups and Pathovirotypes of Escherichia coli Isolated from Post-Weaning Piglets Showing Diarrhoea and/or Oedema in South Korea

This study aimed to determine the prevalence of several pathovirotypes and evaluate the association of haemolysis with the virotypes of pathogenic E. coli isolated from post-weaning piglets in South Korea from 2015 to 2019. We isolated 890 E. coli and tested for O-serogroups, virulence genes, haemolysis, and multilocus sequence typing. The predominant virotypes were STb:EAST1:AIDA-I, F18b:Stx2e:AIDA-I, F18:STa:STb:Stx2e, and eae:Paa in enterotoxigenic E. coli (ETEC), Shiga toxin-producing E. coli (STEC), ETEC/STEC, and enteropathogenic E. coli (EPEC), respectively. Regarding serogroups, O139, O149, O141, and O121 were mostly detected in F18:Stx2e:AIDA-I, F4:LT:STb:EAST1, F18:STa:STb, and F18:Stx2e:EAST1, respectively. There was a significant change in the frequency of the O141:F18ac:STa:STb (an increase from 1.6% to 10.1%) and O139:F18ab:Stx2e:AIDA-I (a decrease from 13.0% to 5.3%) virotypes in ETEC and STEC, respectively, from 2015 to 2019. The O141:F18ac:STa:STb virotype was mostly detected in the central area and was spreading to the southern area. The odds ratios between haemolysis and virotypes were 11.0, 6.25, and 8.57 in F18:STa:STb, F18:Stx2e:AIDA-I, and F4:LT:STb:EAST1, respectively. Our findings provide insights regarding the recent prevalence of pathogenic E. coli in South Korea and could be used for the development of vaccines for E. coli responsible for PWD and ED in post-weaning piglets.

Capsules and Extracellular Polysaccharides in Escherichia coli and Salmonella

Escherichia coli and Salmonella isolates produce a range of different polysaccharide structures that play important roles in their biology. E. coli isolates often possess capsular polysaccharides (K antigens), which form a surface structural layer. These possess a wide range of repeat-unit structures. In contrast, only one capsular polymer (Vi antigen) is found in Salmonella, and it is confined to typhoidal serovars. In both genera, capsules are vital virulence determinants and are associated with the avoidance of host immune defenses. Some isolates of these species also produce a largely secreted exopolysaccharide called colanic acid as part of their complex Rcs-regulated phenotypes, but the precise function of this polysaccharide in microbial cell biology is not fully understood. E. coli isolates produce two additional secreted polysaccharides, bacterial cellulose and poly-N-acetylglucosamine, which play important roles in biofilm formation. Cellulose is also produced by Salmonella isolates, but the genes for poly-N-acetylglucosamine synthesis appear to have been lost during its evolution toward enhanced virulence. Here, we discuss the structures, functions, relationships, and sophisticated assembly mechanisms for these important biopolymers.

Molecular Characteristics, Ecology, and Zoonotic Potential of Escherichia coli Strains That Cause Hemorrhagic Pneumonia in Animals

Hemorrhagic pneumonia (HP) is a rare but highly lethal disease, mainly of dogs and cats, caused by hemolytic Escherichia coli strains that contain cnf1 (encoding cytotoxic necrotizing factor 1). After encountering fatal HP in two dogs, we used contemporary molecular methods, including multilocus sequence typing and whole-genome sequencing, to compare the corresponding case isolates with published HP clinical isolates and newly obtained fecal E. coli isolates from 20 humans and animals in the index HP case household. We also compared the aggregated HP clinical isolates, which represented 13 discrete strains, by pulsotype with a large, private pulsotype library of diverse-source E. coli. The HP clinical isolates represented a narrow range of phylogenetic group B2 lineages (mainly sequence types 12 and 127), O types (mainly O4 and O6), and H types (mainly H5 and H31), but diverse fimH alleles (type-1 fimbriae adhesin). Their extensive, highly conserved virulence genotypes, which qualified as extraintestinal pathogenic E. coli (ExPEC), encoded diverse adhesins, toxins, iron uptake systems, and protectins. Household surveillance identified multiple HP-like fecal strains, plus abundant between-host strain sharing, including of the household's index HP strain. The pulsotype library search identified, for five HP clinical strains, same-pulsotype human and animal fecal and clinical (predominantly urine) isolates, from diverse locales and time periods. Thus, E. coli strains that cause HP derive from a narrow range of ExPEC lineages within phylogroup B2, contain multiple virulence genes other than cnf1, are shared extensively between hosts, and likely function in nature mainly as intestinal colonizers and uropathogens. IMPORTANCE This study clarifies the clonal background and extensive virulence genotypes of the E. coli strains that cause hemorrhagic pneumonia in domestic animals (mainly dogs and cats), shows that such strains circulate among animals and humans, identifies a substantial intestinal colonization component to their lifestyle, and extends their known clinical manifestations to include bacteremia and urinary tract infection. The findings place these strains better into context vis-à-vis current understandings of E. coli phylogeny, ecology, and pathogenesis; identify questions for future research; and may prove relevant for surveillance and prevention efforts.

Diversity of Potentially Pathogenic Escherichia coli O104 and O9 Serogroups Isolated before 2011 from Fecal Samples from Children from Different Geographic Regions

In 2011, an outbreak of hemorrhagic colitis and hemolytic uremic syndrome (HUS) was reported in Europe that was related to a hybrid STEAEC of Escherichia coli (E. coli) O104:H4 strain. The current study aimed to analyze strains of E. coli O104 and O9 isolated before 2011. The study included 47 strains isolated from children with and without diarrhea between 1986 and 2009 from different geographic regions, as well as seven reference strains. Serotyping was carried out on 188 anti-O and 53 anti-H sera. PCR was used to identify DEC genes and phylogenetic groups. Resistance profiles to antimicrobials were determined by diffusion in agar, while PFGE was used to analyze genomic similarity. Five serotypes of E. coli O104 and nine of O9 were identified, as well as an antigenic cross-reaction with one anti-E. coli O9 serum. E. coli O104 and O9 presented diarrheagenic E. coli (DEC) genes in different combinations and were located in commensal phylogenetic groups with different antimicrobial resistance. PFGE showed that O104:H4 and O9:(H4, NM) strains from SSI, Bangladesh and México belong to a diverse group located in the same subgroup. E. coli O104 and O9 were classified as commensal strains containing DEC genes. The groups were genetically diverse with pathogenic potential making continued epidemiologic surveillance important.

Development of a multiplex-PCR serotyping assay for characterizing Legionella pneumophila serogroups based on the diversity of LPS biosynthetic loci

Legionella pneumophila, which is the main cause of Legionnaires' disease, comprises at least 15 serogroups (SGs). We show here the diversity of LPS biosynthetic loci among serogroups and describe the development of a PCR serotyping assay for 15 SGs based on the sequences of LPS biosynthetic loci. Using this multiplex-PCR (M-PCR) system, serogroup(s) were detected using primers that specifically amplify the sequences of SG1, SG2, SG5, SG7, SG8, SG9, SG11, SG13, SG3/15, and SG6/12. When PCR products of the expected sizes were not detected, we used primers that identified SG4/10/14. The PCR serotyping system specifically amplified the sequences corresponding SGs of 238 L. pneumophila strains. This method will be very useful for conducting epidemiological studies and investigating outbreak of Legionnaires' disease.

Potential Zoonotic Pathovars of Diarrheagenic Escherichia coli Detected in Lambs for Human Consumption from Tierra del Fuego, Argentina

Diarrheagenic Escherichia coli (DEC) pathovars impact childhood health. The southern region of Argentina shows the highest incidence of hemolytic uremic syndrome (HUS) in children of the country. The big island of Tierra del Fuego (TDF) in Argentina registered an incidence of five cases/100,000 inhabitants of HUS in 2019. This work aimed to establish the prevalence of STEC, EPEC, and EAEC in lambs slaughtered in abattoirs from TDF as well as to characterize the phenotypes and the genotypes of the isolated pathogens. The prevalence was 26.6% for stx+, 5.7% for eae+, and 0.27% for aagR+/aaiC+. Twelve STEC isolates were obtained and belonged to the following serotypes: O70:HNT, O81:H21, O81:HNT, O102:H6, O128ab:H2, O174:H8, and O174:HNT. Their genotypic profiles were stx_1c (2), stx_1c/ehxA (3), stx_2b/ehxA (1), stx_1c/stx_2b (2), and stx_1c/stx₂/ehxA (4). Six EPEC isolates were obtained and corresponded to five serotypes: O2:H40, O32:H8, O56:H6, O108:H21, and O177:H25. All the EPEC isolates were bfpA- and two were ehxA+. By XbaI-PFGE of 17 isolates, two clusters were identified. By antimicrobial susceptibility tests, 8/12 STEC and 5/6 EPEC were resistant to at least one antibiotic. This work provides new data to understand the ecology of DEC in TDF and confirms that ovine are an important carrier of these pathogens in the region.

First isolation of atypical enteropathogenic Escherichia coli from geese (Anser anser domestica) and first description of atypical EPEC from turkeys and pigeons in Hungary

Background

Escherichia coli is a bacterial species widely distributed among mammals and avian species, and also a member of the normal intestinal microbiota. However, some E. coli strains of different pathotypes can cause disease in both humans and animals. Atypical enteropathogenic E. coli (aEPEC) can infect both animals and humans or influence the severity of other ongoing infections.

Results

In the present study, a total of 332 samples were collected from ducks, geese, turkeys, chickens, and pigeons from the Hungarian Veterinary Diagnostic Directorate, two slaughterhouses, two pigeon keepers and one backyard chicken farm. E. coli was isolated and verified from 319 samples. The isolates were screened by PCR for diarrheagenic E. coli pathotypes. Altogether seven atypical enteropathogenic E. coli (aEPEC) strains were identified: two from four-week-old dead turkeys, two from force-fed geese, and three from pigeons. No further pathotypes were identified in the collection. The atypical EPEC strains were classified phylogenetically to B1, B2, and F, and four out of the seven aEPEC isolates proved to be multidrug resistant. Serotypes of aEPEC strains were uniform collected from same farms and showed diversity between their origins with O76, O145, O109 serogroups.

Conclusions

This is the first report in the literature about aEPEC in goose (Anser anser domestica). Furthermore, this is the first isolation of aEPEC from turkeys and pigeons in Hungary. The uneven distribution of aEPEC in different age groups of poultry suggests that aEPEC disappears with growing up, but stress (e.g.: force-feeding) and concurrent diseases might promote its reappearance in the intestine.

Genetic diversity and pathogenic potential of Shiga toxin-producing Escherichia coli (STEC) derived from German flour

Shiga toxin-producing Escherichia coli (STEC) can cause severe human illness, which are frequently linked to the consumption of contaminated beef or dairy products. However, recent outbreaks associated with contaminated flour and undercooked dough in the United States and Canada, highlight the potential of plant based food as transmission routes for STEC. In Germany STEC has been isolated from flour, but no cases of illness have been linked to flour. In this study, we characterized 123 STEC strains isolated from flour and flour products collected between 2015 and 2019 across Germany. In addition to determination of serotype and Shiga toxin subtype, whole genome sequencing (WGS) was used for isolates collected in 2018 to determine phylogenetic relationships, sequence type (ST), and virulence-associated genes (VAGs). We found a high diversity of serotypes including those frequently associated with human illness and outbreaks, such as O157:H7 (stx2c/d, eae), O145:H28 (stx2a, eae), O146:H28 (stx2b), and O103:H2 (stx1a, eae). Serotypes O187:H28 (ST200, stx2g) and O154:H31 (ST1892, stx1d) were most prevalent, but are rarely linked to human cases. However, WGS analysis revealed that these strains, as well as, O156:H25 (ST300, stx1a) harbour high numbers of VAGs, including eae, nleB and est1a/sta1. Although STEC-contaminated flour products have yet not been epidemiologically linked to human clinical cases in Germany, this study revealed that flour can serve as a vector for STEC strains with a high pathogenic potential. Further investigation is needed to determine the sources of STEC contamination in flour and flour products particularly in regards to these rare serotypes.

Characterization of multidrug-resistant avian pathogenic Escherichia coli: an outbreak in canaries

The canary (Serinus canaria) is appreciated for its beautiful song, colors, and docile temperament and drives a lucrative business. However, diseases caused by avian pathogenic Escherichia coli (APEC) compromise the health of canaries, and the inadequate antimicrobial treatment can lead to the emergence of resistant strains. This study aimed to characterize 21 isolates of E. coli obtained from canaries infected with colibacillosis during an outbreak in northern Paraná State, Brazil. APEC and diarrheagenic E. coli (DEC) virulence genes were screened for by polymerase chain reaction (PCR). All isolates were positive for the hlyF, iss, and ompT genes, which are characteristic of APEC. The iroN gene was found in 95.2% of isolates, and none had the iutA gene. The ipaH gene, characteristic of enteroinvasive E. coli (EIEC), was found in 71.4% of isolates, all belonging to the phylogenetic group B1. High genetic similarity (>95%) was found using enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). The isolates belonged to serotypes O117:H4 (71.4%) and O1:H20 (23.8%). This is the first report of a clonal colibacillosis outbreak in canaries caused by APEC. All isolates were resistant to ampicillin, nalidixic acid, ciprofloxacin, enrofloxacin, norfloxacin, and tetracycline. The high rate of multidrug resistance in our study shows the importance of avoiding the inadequate antibiotic treatment. We suggest that further studies should be conducted to contribute to the understanding of colibacillosis in canaries since the health of animals is linked to human and environmental health, as defined by the concept of One Health.

In Vitro Antibacterial Activity of Manuka (Leptospermum scoparium J.R. et G. Forst) and winter Savory (Satureja montana L.) Essential Oils and Their Blends against Pathogenic E. coli Isolates from Pigs

Simple Summary

Neonatal diarrhoea (ND), post-weaning diarrhoea (PWD) and oedema disease (OD) are particularly important in terms of economic losses in pig farming worldwide. Aetiological agents of these diseases belong to Escherichia coli, in particular to a few serogroups of enterotoxigenic Escherichia coli (ETEC) and enteropathogenic Escherichia coli (EPEC). The necessity for a reduction in antibiotic use, related to the growing antibiotic resistance phenomenon, encourages research in the study of alternative antibacterial substances as antibacterial tools. Essential oils could represent a valid solution.

Abstract

Neonatal diarrhoea (ND), post-weaning diarrhoea (PWD) and oedema disease (OD) are among the most important diseases affecting pig farming due to economic losses. Among the main aetiological agents, strains of Escherichia coli are identified as the major responsible pathogens involved. Several strategies have been put in place to prevent these infections and, today, research is increasingly studying alternative methods to antibiotics to reduce the antibiotic resistance phenomenon. Essential oils (EOs) are among the alternative tools that are being investigated. In this study, the in vitro effectiveness of winter savory and manuka essential oils and their mixtures in different proportions against strains of E. coli isolated from episodes of disease in pigs was evaluated. The EOs alone demonstrated slight antibacterial effectiveness, whereas the blends, by virtue of their synergistic action, showed remarkable activity, especially the 70%–30% winter savory–manuka blend, showing itself as a potential tool for prevention and therapy.

Avian Pathogenic Escherichia coli and Clostridium perfringens: Challenges in No Antibiotics Ever Broiler Production and Potential Solutions

United States is the largest producer and the second largest exporter of broiler meat in the world. In the US, broiler production is largely converting to antibiotic-free programs which has caused an increase in morbidity and mortality within broiler farms. Escherichia coli and Clostridium perfringens are two important pathogenic bacteria readily found in the broiler environment and result in annual billion-dollar losses from colibacillosis, gangrenous dermatitis, and necrotic enteritis. The broiler industry is in search of non-antibiotic alternatives including novel vaccines, prebiotics, probiotics, and housing management strategies to mitigate production losses due to these diseases. This review provides an overview of the broiler industry and antibiotic free production, current challenges, and emerging research on antibiotic alternatives to reduce pathogenic microbial presence and improve bird health.

High Frequency of Multidrug-Resistant (MDR) Atypical Enteropathogenic Escherichia coli (aEPEC) in Broilers in Hungary

Escherichia coli (EC) strains belong to several pathotypes capable of infecting both humans and animals. Some of them have zoonotic potential and can sporadically cause epidemic outbreaks. Our aim was to screen for the distribution of these pathotypes in broilers and their related products. Therefore, E. coli strains were isolated (n = 118) from poultry intestine (n = 57), carcass (n = 57), and wastewater (n = 4) samples from one slaughterhouse with own reared poultry source and the National Reference Laboratory (NRL) poultry E. coli collection (n = 170) from the year 2017 was also studied. All 288 E. coli strains were screened by PCR for pathotype-specific genes stx, eae, st-lt, aggR, ipaH, and for further EPEC-specific virulence genes (bfp, EAF, tir, perA, ler). Altogether 35 atypical enteropathogenic E. coli (aEPEC) strains from the slaughterhouse and 48 aEPEC strains from the NRL collection were found. Regarding the phylogenetic groups of aEPEC, all four main groups were represented but there was a shift toward the B2 group (25%) as compared with the non-EPEC isolates (3%). The aEPEC isolates belonged to serogroups O14, O108, and O45. Multidrug resistance (MDR) was abundant in aEPEC strains (80 out of 83 aEPEC) with a diverse resistance pattern (n = 56). Our results of this study indicate that the high frequency of aEPEC in broilers and on their carcass surface, with frequent MDR to several antibiotic groups, raises the possibility that these strains pose a zoonotic risk to humans.

Shiga Toxin-Producing Escherichia coli Contamination of Raw Beef and Beef-Based Ready-to-Eat Products at Retail Outlets in Pretoria, South Africa

ABSTRACT

A cross-sectional study was conducted to determine the prevalence of and factors associated with Shiga toxin-producing Escherichia coli (STEC) in raw beef and ready-to-eat (RTE) beef products sold in 31 retail outlets in Pretoria, South Africa, and nearby areas. A total of 463 beef and RTE samples were screened for four STEC virulence genes (stx1, stx2, eaeA, and hlyA) and seven O-serogroups (O113, O157, O26, O91, O145, O111, and O103) with a multiplex PCR assay. The total aerobic plate count (TAPC) per gram was also determined. A total of 38 STEC isolates were recovered and characterized by conventional PCR assay and serotyping. The overall prevalence of STEC in the beef and RTE samples tested was 16.4% (76 of 463 samples; 95% confidence interval, 13 to 20%). The prevalence of STEC differed significantly by product type (P < 0.0001), with the highest prevalence (35%) detected in boerewors (spicy sausage). The STEC prevalences in minced beef, brisket, RTE cold beef, and biltong were 18, 13, 9, and 5%, respectively. The most frequently detected stx gene was stx2 (13%), and STEC serogroups from recovered isolates were detected at the following prevalences: O2, 15%; O8, 12%; O13, 15%; O20, 8%; O24, 3%; O39, 3%; O41, 8%; O71, 3%; O76, 3%; O150, 12%; and O174, 3%. A high proportion (77%) of the samples had TAPCs that exceeded the South African microbiological standards for meat export (5.0 log CFU/g). The prevalence of O157 STEC (16%) and the diversity of non-O157 STEC serogroups found in five common beef-based products from retail outlets in South Africa suggest exposure of raw beef and beef products to multiple contamination sources during carcass processing and/or cutting and handling at retail outlets. These data provide direct estimates of the potential health risk to consumers from undercooked contaminated products and indicate the need to improve sanitary practices during slaughter and processing of beef and beef-based RTE products. A risk-based surveillance system for STEC may be needed.

HIGHLIGHTS

Molecular characterization of multidrug-resistant Shiga toxin-producing Escherichia coli harboring antimicrobial resistance genes obtained from a farmhouse

Shiga toxin-producing Escherichia coli (STEC) colonize the gastrointestinal tract of animals; however, STEC may also cause severe diarrheal diseases. Food-producing animals have been acting as reservoirs and disseminators of multidrug-resistant (MDR) bacteria and antimicrobial resistance genes (ARGs); however, there are few studies characterizing molecularly bacterial isolates from sheep. Therefore, this study aimed to characterize E. coli isolates obtained from feces of sheep in a Brazilian farmhouse. A total of 14 MDR E. coli isolates were obtained from 100 feces samples, six of which were classified as non-O157 STEC (stx1, stx2 and ehxA). MDR E. coli isolates presented different ARGs [bla_CTX-M-Gp9, bla_CMY, bla_SHV, qnrS, oqxB, aac(6')-Ib, tet(A), tet(B), tet(C), sul1, sul2, and cmlA] and plasmids (IncI1, IncF_repB, IncFIB, IncFIA, IncHI1, IncK, and ColE-like). In addition, mutations in the quinolone-resistance determining region of GyrA (Ser83Leu; Asp87Asn) and ParC (Glu84Asp) were detected. PFGE showed a high genetic diversity (30.9 to 83.9%) and thirteen STs were detected (ST25, ST48, ST155, ST162, ST642, ST1247, ST1518, ST1725, ST2107, ST2522, ST3270, ST5036, and ST7100). Subtyping of the fimH gene showed seven fimH-type (25, 32, 38, 41, 54, 61, and 366). The results found in the present study showed high genetic diversity among MDR ARGs-producing E. coli obtained from a farmhouse. This study reports for the first time, the presence of MDR STEC and non-STEC belonging to ST25, ST162, ST642, ST1247, ST1518, ST1725, ST2107, ST3270, ST5036, and ST7100 in sheep, and contributes to the surveillance studies associated with One Health concept.

Short communication: Molecular characterization and antimicrobial resistance of pathogenic Escherichia coli isolated from raw milk and Minas Frescal cheeses in Brazil

The aim of this study was to quantify, identify, evaluate antimicrobial resistance, and characterize the virulence factors of enteropathogenic (EPEC), Shiga-toxigenic (STEC), and enterohemorrhagic (EHEC) Escherichia coli in raw milk (RM) and legal (LMFC) and illegal (IMFC) Minas Frescal cheeses in southern and northeast Brazil. Illegal cheeses are those made without official inspection service or sanitary surveillance. We evaluated samples of RM produced in Paraná (southern) and Maranhão (northeast) States, LMFC produced using pasteurized milk in inspected industries, and IMFC potentially produced with raw milk. Mean total coliform counts were 8.4 × 10⁴ cfu/mL for RM, 1.4 × 10⁷ cfu/mL for LMFC, and 2.9 × 10⁷ cfu/mL for IMFC. Mean E. coli counts were 2.4 × 10³ cfu/mL for RM, 1.9 × 10² cfu/mL for LMFC, and 1.1 × 10⁵ cfu/mL for IMFC. Among the 205 E. coli isolates from RM, 9.75% were identified as EPEC, mainly (90%) in samples from Paraná. Of the total isolates from the cheese samples, 97.4% (n = 111) came from IMFC, of which 1.8 and 2.7% were identified as EPEC and STEC, respectively; no EHEC was detected. The phylogenetic group A (60%) and typical EPEC (68%) predominated, which confirms the possible human origin of pathogenic isolates in RM and IMFC. Of these, 50% were resistant to at least one antibiotic, and streptomycin was the antimicrobial with the highest number (8) of EPEC and STEC resistant isolates. This study reports the first isolation of serogroup O28ac in Brazilian milk. We found no predominance of a specific serogroup of EPEC or STEC in milk or cheese or clonal isolates in the same sample, indicating different origins of the contamination in these products, presumably mostly related to poor hygienic handling.

Characterization of beta-lactamase and biofilm producing Enterobacteriaceae isolated from organized and backyard farm ducks

This study was undertaken to detect the occurrence of beta-lactamase and biofilm producing Enterobacteriaceae in healthy ducks. A total 202 cloacal swabs were collected from ducks kept in organized (n = 92) and backyard (n = 110) farms in West Bengal (India). The ducks had no history of antibiotic intake. Among the 87 phenotypically beta-lactamase producing Escherichia coli, 19 (17·43%), 6 (5·05%) and 15 (13·76%) isolates possessed bla_TEM , bla_SHV and bla_CTX-M respectively. Whereas, 5 (38·46%) Salmonella isolates were found to harbour bla_CTX-M . In K. pneumoniae 10 (33·33%), 3 (13·33%), 4 (13·33%) isolates possessed bla_TEM , bla_SHV and bla_CTX-M respectively. The sequences of selected PCR products were found 98% cognate with bla_CTX-M-9, bla_SHV-12 and bla_TEM-1 . Beta-lactamase producing E. coli isolates belonged to 14 different serogroups such as O1, O2, O3, O5, O7, O8, O35, O83, O84, O88, O119, O128, O145 and O157. Moreover, 87 E. coli (79·82%), six Samonella (46·15%) and 13 K. pneumoniae (43·33%) isolates were detected as AmpC producers possessing bla_AmpC . Majority of E. coli (46·79%), Salmonella (46·15%) and K. pneumoniae (70%) isolates were detected as biofilm producers and possessed the associated genes (csgA, sdiA, rcsA, rpoS). Significantly higher occurrence of beta-lactamase and biofilm producing Enterobacteriaceae isolates was detected in backyard ducks than organized farms. SIGNIFICANCE AND IMPACT OF THE STUDY: Consumption of antibiotic through feed or during therapy is considered as potential reason for generation of antimicrobial resistant bacteria in birds. This study provides valuable evidence that exposure to contaminated environment may be an additional source for generation of antimicrobial resistant bacteria in backyard ducks. The backyard ducks are reared by marginal farmers in India who cannot offer antibiotics to them either through feed or during therapy due to high cost. The study also reveals a significant correlation between biofilm formation and possession of antimicrobial resistance genes in the bacterial isolates from the ducks.

Characterization of non-O157 Shiga toxin-producing Escherichia coli (STEC) obtained from feces of sheep in Brazil

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens and may induce severe diarrheagenic diseases in humans and other animals. Non-O157 STEC have been emerging as important pathogens causing outbreaks worldwide. Bacterial resistance to antimicrobials has become a global public health problem, which involves different ecological spheres, including animals. This study aimed to characterize the resistance to antimicrobials, plasmids and virulence, as well as the serotypes and phylogenetic groups in E. coli isolated from sheep in Brazil. A total of 57 isolates were obtained and showed different antimicrobial resistance profiles. Nineteen isolates presented acquired antimicrobial resistance genes (ARGs) (bla_CTX-M-Gp9, qnrB, qnrS, oqxB, oqxA, tetA, tetB, tetC, sul1 and sul2) and plasmid families (F, FIA, FIB, I1, K, HI1 and ColE-like). The stx1, stx2 and ehxA virulence genes were detected by PCR, being 50 isolates (87.7%) classified as STEC. A great diversity of serotypes was detected, being O176:HNM the most predominant. Phylogenetic group E was the most prevalent, followed by B1, A and B2. To the best of our knowledge, this is the first report in the world of bla_CTX-M-Gp9 (O75, O114, O100, O128ac and O176 serogroups), qnrB and oqxB genes in non-O157 STEC in healthy sheep. The results obtained in the present study call attention to the monitoring of antimicrobial-resistant non-O157 STEC harboring acquired ARGs worldwide and indicate a zoonotic risk due to the profile of virulence, resistance and serotype found.

Molecular serogrouping ofEscherichia coli

O-antigens present on the surface ofEscherichia coliprovide antigenic specificity for the strain and are the main components for O-serogroup designation. Serotyping using O-group-specific antisera for the identification ofE. coliO-serogroups has been traditionally the gold-standard for distinguishingE. colistrains. Knowledge of the O-group is important for determining pathogenic lineage, classifyingE. colifor epidemiological studies, for determining virulence, and for tracing outbreaks of diseases and sources of infection. However, serotyping has limitations, as the antisera generated against each specific O-group may cross-react, many strains are non-typeable, and others can autoagglutinate or be rough (lacking an O-antigen). Currently, the nucleotide sequences are available for most of the 187 designatedE. coliO-groups. Public health and other laboratories are considering whole genome sequencing to develop genotypic methods to determine O-groups. These procedures require instrumentation and analysis that may not be accessible and may be cost-prohibitive at this time. In this review, we have identified unique gene sequences within the O-antigen gene clusters and have targeted these genes for identification of O-groups using the polymerase chain reaction. This information can be used to distinguish O-groups by developing other platforms forE. colidiagnostics in the future.

Detection and Characterization of Enteropathogenic and Shiga Toxin-Producing Escherichia coli Strains in Rattus spp. from Buenos Aires

Enteropathogenic Escherichia coli (EPEC) and Shiga toxin-producing E. coli (STEC) are pathovars of E. coli that impact human health by causing childhood diseases. In this work, 118 synanthropic rodents of the genus Rattus from Buenos Aires, Argentina were evaluated as EPEC and STEC carriers. Rectal swab samples from captured animals were evaluated by conventional PCR to detect the presence of the eae, stx1, stx2, and rfbO157 genes. Twenty-one isolates were obtained (17 EPEC isolates from seven animals and four STEC isolates from the same animal). All EPEC isolates tested negative for the presence of the bfpA gene. One EPEC isolate carried the iha gene, and five EPEC isolates carried the toxB gene. STEC isolates exhibited two different virulence profiles: stx1a/stx2a/stx2c/stx2d/saa/ehxA/subA (3/4) and stx1a/stx2a/saa/ehxA/subA (1/4). EPEC isolate serotypes included O109:H46 (7), O71:H40 (4), O71:NM (2), O138:H40 (1), O108:H21 (1), O88:H25 (1), and O76:NM (1), and STEC isolates belonged to the O108:H11 (4) serotype. Antimicrobial susceptibility testing was carried out, and resistance to tetracycline was observed in one EPEC strain. Our results demonstrate that Rattus spp. may act as carriers of EPEC and STEC strains and may be involved in the epidemiology of diarrheal disease in infancy.

Virulence Genes and Antimicrobial Resistance in Escherichia coli from Cheese Made from Unpasteurized Milk in Brazil

Cow raw milk cheese is widely eaten in Brazil. These products may be contaminated with pathogenic bacteria. In this work, we investigated the presence of Escherichia coli in raw milk cheese from different States in Brazil. From 147 "Minas" cheese samples, 28 cheeses were positive for E. coli. Among 39 E. coli isolates of the cheeses, one was positive for eae and negative for bpfA and efa1/lifA using PCR, and so was classified as atypical Enteropathogenic E. coli (aEPEC). Two other isolates were positive for extraintestinal pathogenic E. coli (ExPEC) genes. The aEPEC isolate belongs to serogroup O127 and was classified in A phylogenetic group, and ExPEC isolates were found in O73:H12 (EC-2 strain) and O64474:H8 (EC-9 strain) serotype. This ExPEC belongs to A and C phylogenetic group, respectively. Most of E. coli strains belonged to Clermont phylogenetic groups A (28.2%), C, and E (23.1%). Six strains (15.4%) of E. coli were positive for group B1 and two (5.1%) for B2. E. coli isolates presented an aggregative (46.0%) and diffuse (12.6%) adherence pattern to HeLa cells, and the other isolates did not show adhesion (41.4%). Four E. coli isolates (10.3%) were shown to produce moderate biofilm. The antimicrobial resistance rate was tetracycline (25.6%), followed by ampicillin (17.9%), cefoxitin (7.7%), nalidixic acid (5.1%), and amoxicillin-clavulanic acid (2.6%). One strain was resistant to three antimicrobials (tetracycline, ampicillin, and nalidixic acid). The presence of these microorganisms, the O127 strain, and a new serogroup in Brazil is a potential risk for public health.

First Report of Human Gastroenteritis Caused by Escherichia coli O157:NM in Brazil

In September 2005, the Sanitary Surveillance Service of Rio de Janeiro (SSS/RJ), Brazil, investigated a case of gastroenteritis involving a 13-year-old teenager hospitalized because of bloody diarrhea and severe abdominal pain. Owing to the severity of the symptoms, an epidemiological investigation was conducted in two states of Brazil. Escherichia coli O157:NM was isolated from stools and from a tomato and cheese salad prepared at the school canteen where the teenager attended. This is the first report of a human case of gastroenteritis related to E. coli O157:NM infection in Brazil.

Photo-assisted inactivation of Escherichia coli bacteria by silver functionalized titanate nanotubes, Ag/H2Ti2O5·H2O

One-dimensional titanate nanotubes functionalized with silver nanoparticles exhibit unique properties for the effective inactivation of the Gram-negative E. coli in 45 min. under irradiation using a 65 W halogen lamp.

Characterization of Escherichia coli causing community acquired urinary tract infections in Mexico City

The O25-ST131 clone was identified within 169 uropathogenic Escherichia coli (UPEC) strains. The 44.8% of the 29 O25-ST131 clones detected were positive to least to one extended-spectrum β-lactamase gene. The phylogroup D was mainly found. The O25-ST131 clone appeared to be associated with community-acquired UTI in Mexico City.

Multidrug-resistant pathogenic Escherichia coli isolated from wild birds in a veterinary hospital

Wild birds are carriers of Escherichia coli. However, little is known about their role as reservoirs for extra-intestinal pathogenic E. coli (ExPEC). In this work we investigated E. coli strains carrying virulence genes related to human and animal ExPEC isolated from free-living wild birds treated in a veterinary hospital. Multidrug resistance was found in 47.4% of the strains, but none of them were extended-spectrum beta-lactamase producers. Not only the virulence genes, but also the serogroups (e.g. O1 and O2) detected in the isolates of E. coli have already been implicated in human and bird diseases. The sequence types detected were also found in wild, companion and food animals, environmental and human clinical isolates in different countries. Furthermore, from the 19 isolates, 17 (89.5%) showed a degree of pathogenicity on an in vivo infection model. The isolates showed high heterogeneity by pulsed-field gel electrophoresis indicating that E. coli from these birds are clonally diverse. Overall, the results showed that wild birds can be reservoirs and/or vectors of highly pathogenic and multidrug-resistant E. coli that have the potential to cause disease in humans and poultry.

Six Novel O Genotypes from Shiga Toxin-Producing Escherichia coli

Serotyping is one of the typing techniques used to classify strains within the same species. O-serogroup diversification shows a strong association with the genetic diversity of O-antigen biosynthesis genes. In a previous study, based on the O-antigen biosynthesis gene cluster (O-AGC) sequences of 184 known Escherichia coli O serogroups (from O1 to O187), we developed a comprehensive and practical molecular O serogrouping (O genotyping) platform using a polymerase chain reaction (PCR) method, named E. coli O-genotyping PCR. Although, the validation assay using the PCR system showed that most of the tested strains were successfully classified into one of the O genotypes, it was impossible to classify 6.1% (35/575) of the strains, suggesting the presence of novel O genotypes. In this study, we conducted sequence analysis of O-AGCs from O-genotype untypeable Shiga toxin-producing E. coli (STEC) strains and identified six novel O genotypes; OgN1, OgN8, OgN9, OgN10, OgN12 and OgN31, with unique wzx and/or wzy O-antigen processing gene sequences. Additionally, to identify these novel O-genotypes, we designed specific PCR primers. A screen of O genotypes using O-genotype untypeable strains showed 13 STEC strains were classified into five novel O genotypes. The O genotyping at the molecular level of the O-AGC would aid in the characterization of E. coli isolates and will assist future studies in STEC epidemiology and phylogeny.

Advances in Molecular Serotyping and Subtyping of Escherichia coli

Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.

Enteropathogenic Escherichia coli in Psittaciformes

A total of 103 Escherichia coli isolates from psittaciform birds were examined for the presence of genes coding for shigatoxin 1 (Stx1), shigatoxin 2 (Stx2) and for intimin (eae), using the polymerase chain reaction (PCR). Sixty-eight E. coli strains were isolated from necropsy cases and faecal samples, the other 35 were from 205 cloacal swabs from Psittaciformes with various conditions. All isolates were tested for enterohaemorrhagic E. coli-haemolysin (HlyEHEC), some also for Stx production, but there was no geno-typic or phenotypic evidence of Stx in any of them. Seven isolates, six from birds with diarrhoea, harboured the eae gene, three of them belonging to the O110:H6 serotype, one each to serotypes O153:H10, O131:H-, O63:H6 and Osp:H6. These seven eae-positive strains were negative for shigatoxin and HlyEHEC, and the hlyEHEC gene was not detectable by PCR. However, a PCR amplifying the enteropathogenic E. coli (EPEC)-specific bundle-forming pili structural gene bfpA detected four bfpA positive strains (three of serotype O110:H6, one O131:H-) among the seven eae positive strains, which classifies them as EPEC. Our findings suggest that shigatoxin-producing E. coli are uncommon, but that EPEC should be considered as potential pathogens in psittaciform birds, which may be a source of human EPEC infections.

Genetic features of human and bovine Escherichia coli O157:H7 strains isolated in Argentina

Shiga toxin-producing Escherichia coli (STEC) are important food-borne pathogens associated with human diseases. In Argentina, O157:H7 is the dominant serotype in hemolytic uremic syndrome (HUS) cases. Previously, we have described the almost exclusive circulation of human E. coli O157 strains belonging to the hypervirulent clade 8 in Neuquén Province. The aim of the present study was to investigate, by a broad molecular characterization, if this particular distribution of E. coli O157 clades in Neuquén is similar to the situation in other regions of the country and if it may be originated in a similar profile in cattle, its main reservoir. Two-hundred and eighty O157 strains (54 bovine and 226 human) isolated between 2006 and 2008 in different regions of Argentina were studied. All strains harbored rfbO157, fliCH7, eae, and ehxA genes. The predominant genotype was stx2a/stx2c in human (76.1%) and bovine (55.5%) strains. All human isolates tested by Lineage-Specific Polymorphism Assay (LSPA-6), were lineage I/II; among bovine strains, 94.1% belonged to lineage I/II and 5.9% to lineage I. No LSPA-6 lineage II isolates were detected. Single nucleotide polymorphism (SNP) analysis has revealed the existence of nine clade phylogenetic groups. In our clinical strains collection, 87.6% belonged to the hypervirulent clade 8, and 12.4% were classified as clade 4/5. In bovine isolates, 59.3% strains were clade 8, 33.3% clade 4/5 and 7.4% clade 3. More than 80% of human strains showed the presence of 6 of the 7 virulence determinants described in the TW14359 O157 strain associated with the raw spinach outbreak in the U.S. in 2006. More than 80% of bovine strains showed the presence of 3 of these factors. The q933 allele, which has been related to high toxin production, was present in 98.2% of clinical strains and 75.9% of the bovine isolates. The molecular characterization of human STEC O157 strains allows us to conclude that the particular situation previously described for Neuquén Province, may actually be a characteristic of the whole country. These genetic features are quite similar to those observed in the bovine reservoir and may be derived from it. This data confirms that, unlike the rest of the world, in Argentina most of the STEC O157 strains present in cattle may cause human infections of varying severity and the marked virulence described for these strains may be related to the high incidence of HUS in our country.

Detection of Shiga Toxin-Producing Escherichia coli from Nonhuman Sources and Strain Typing

Shiga toxin-producing Escherichia coli (STEC) strains are commonly found in the intestine of ruminant species of wild and domestic animals. Excretion of STEC with animal feces results in a broad contamination of food and the environment. Humans get infected with STEC through ingestion of contaminated food, by contact with the environment, and from STEC-excreting animals and humans. STEC strains can behave as human pathogens, and some of them, called enterohemorrhagic E. coli (EHEC), may cause hemorrhagic colitis (HC) and hemolytic-uremic syndrome (HUS). Because of the diversity of STEC types, detection strategies for STEC and EHEC are based on the identification of Shiga toxins or the underlying genes. Cultural enrichment of STEC from test samples is needed for identification, and different protocols were developed for this purpose. Multiplex real-time PCR protocols (ISO/CEN TS13136 and USDA/FSIS MLG5B.01) have been developed to specifically identify EHEC by targeting the LEE (locus of enterocyte effacement)-encoded eae gene and genes for EHEC-associated O groups. The employment of more genetic markers (nle and CRISPR) is a future challenge for better identification of EHEC from any kinds of samples. The isolation of STEC or EHEC from a sample is required for confirmation, and different cultivation protocols and media for this purpose have been developed. Most STEC strains present in food, animals, and the environment are eae negative, but some of these strains can cause HC and HUS in humans as well. Phenotypic assays and molecular tools for typing EHEC and STEC strains are used to detect and characterize human pathogenic strains among members of the STEC group.

Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing

Escherichia coli strains are classified based on O-antigens that are components of the lipopolysaccharide (LPS) in the cell envelope. O-antigens are important virulence factors, targets of both the innate and adaptive immune system, and play a role in host-pathogen interactions. Because they are highly immunogenic and display antigenic specificity unique for each strain, O-antigens are the biomarkers for designating O-types. Immunologically, 185 O-serogroups and 11 OX-groups exist for classification. Conventional serotyping for O-typing entails agglutination reactions between the O-antigen and antisera generated against each O-group. The procedure is labor intensive, not always accurate, and exhibits equivocal results. In this report, we present the sequences of 71 O-antigen gene clusters (O-AGC) and a comparison of all 196 O- and OX-groups. Many of the designated O-types, applied for classification over several decades, exhibited similar nucleotide sequences of the O-AGCs and cross-reacted serologically. Some O-AGCs carried insertion sequences and others had only a few nucleotide differences between them. Thus, based on these findings, it is proposed that several of the E. coli O-groups may be merged. Knowledge of the O-AGC sequences facilitates the development of molecular diagnostic platforms that are rapid, accurate, and reliable that can replace conventional serotyping. Additionally, with the scientific knowledge presented, new frontiers in the discovery of biomarkers, understanding the roles of O-antigens in the innate and adaptive immune system and pathogenesis, the development of glycoconjugate vaccines, and other investigations, can be explored.

The molecular characterisation of Escherichia coli K1 isolated from neonatal nasogastric feeding tubes

BACKGROUND

The most common cause of Gram-negative bacterial neonatal meningitis is E. coli K1. It has a mortality rate of 10-15 %, and neurological sequelae in 30-50 % of cases. Infections can be attributable to nosocomial sources, however the pre-colonisation of enteral feeding tubes has not been considered as a specific risk factor.

METHODS

Thirty E. coli strains, which had been isolated in an earlier study, from the residual lumen liquid and biofilms of neonatal nasogastric feeding tubes were genotyped using pulsed-field gel electrophoresis, and 7-loci multilocus sequence typing. Potential pathogenicity and biofilm associated traits were determined using specific PCR probes, genome analysis, and in vitro tissue culture assays.

RESULTS

The E. coli strains clustered into five pulsotypes, which were genotyped as sequence types (ST) 95, 73, 127, 394 and 2076 (Achman scheme). The extra-intestinal pathogenic E. coli (ExPEC) phylogenetic group B2 ST95 serotype O1:K1:NM strains had been isolated over a 2 week period from 11 neonates who were on different feeding regimes. The E. coli K1 ST95 strains encoded for various virulence traits associated with neonatal meningitis and extracellular matrix formation. These strains attached and invaded intestinal, and both human and rat brain cell lines, and persisted for 48 h in U937 macrophages. E. coli STs 73, 394 and 2076 also persisted in macrophages and invaded Caco-2 and human brain cells, but only ST394 invaded rat brain cells. E. coli ST127 was notable as it did not invade any cell lines.

CONCLUSIONS

Routes by which E. coli K1 can be disseminated within a neonatal intensive care unit are uncertain, however the colonisation of neonatal enteral feeding tubes may be one reservoir source which could constitute a serious health risk to neonates following ingestion.