Escherichia coli and urinary tract infections: the role of poultry-meat

Tracking Fecal Bacterial Dispersion from Municipal Wastewater to Peri-Urban Farms during Monsoon Rains in Hue City, Vietnam

Disease outbreaks attributed to monsoon flood-induced pathogen exposure are frequently reported, especially in developing cities with poor sanitation. Contamination levels have been monitored in past studies, yet the sources, routes, and extents of contamination are not always clear. We evaluated pollution from municipal wastewater (MWW) discharge and investigated fecal contamination by Escherichia coli (E. coli) in three agricultural fields on the outskirts of Hue City, Vietnam. After E. coli concentration was determined in irrigation water (IRW), MWW, soil, vegetables (VEG), and manure, its dispersion from MWW was tracked using multilocus sequence typing (MLST) and phylogenetic analyses during the wet and dry seasons. IRW was severely contaminated; 94% of the samples were positive with E. coli exceeding the stipulated standards, while VEG contamination was very low in both seasons. The confirmed total number of isolates was comparable between the seasons; however, results from MLST and phylogenetic clustering revealed more links between the sites and samples to MWW during the wet season. The wet season had four mixed clusters of E. coli isolates from multiple locations and samples linked to MWW, while only one mixed cluster also linking MWW to IRW was observed during the dry season. The most prevalent sequence type (ST) complex 10 and two others (40 and 155) have been associated with disease outbreaks, while other STs have links to major pathotypes. Irrigation canals are significant routes for E. coli dispersion through direct links to the urban drainage-infested river. This study clarified the genotype of E. coli in Hue city, and the numerous links between the samples and sites revealed MWW discharge as the source of E. coli contamination that was enhanced by flooding.

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, the disease with the highest economic loss for the broiler industry. However, studies focusing on the prevalence and population structure of APEC in the broiler production pyramid are scarce. Here, we used genotyping and serotyping data to elucidate the APEC population structure and its changes in different broiler production stages along with whole-genome sequencing (WGS) in a subset of APEC isolates to determine transmission patterns amongst dominant APEC sequence types (STs) and characterize them in detail. Comparison of genotypes encountered in both APEC and avian fecal E. coli (AFEC) provided further insights. Overall, APEC-related mortality, as the proportion of the total sampled mortality in the broiler production, was high (35%), while phylogroup C and serogroup O78 were predominant amongst APEC isolates. We found a low (34.0%) and high (53.3%) incidence of colibacillosis in chicks and end-cycle broilers, respectively, which may be related to a shift in APEC genotypes, suggesting a trend from commensalism to pathogenicity across different broiler production stages. Despite considerable APEC genotypic diversity, there was substantial genotype overlap (40.9%, overall) over the production stages and convergence of STs to the four clusters. Within these clusters, WGS data provided evidence of clonal transmission events and revealed an enriched virulence and resistance APEC repertoire. More specifically, sequenced APEC were assigned to defined pathotypes based on their virulence gene content while the majority (86%) was genotypically multi-drug resistant. Interestingly, WGS-based phylogeny showed that a subset of APEC, which are cephalosporin-resistant, may originate directly from cephalosporin-resistant AFEC. Finally, exploration of the APEC plasmidome indicated that the small fraction of the APEC virulome carried by IncF plasmids is pivotal for the manifestation of the APEC pathotype; thus, plasmid exchange can promote pathogenicity in strains that are at the edge of the commensal and pathogenic states.

The Pheno- and Genotypic Characterization of Porcine Escherichia coli Isolates

Escherichia (E.) coli is the main causative pathogen of neonatal and post-weaning diarrhea and edema disease in swine production. There is a significant health concern due to an increasing number of human infections associated with food and/or environmental-borne pathogenic and multidrug-resistant E. coli worldwide. Monitoring the presence of pathogenic and antimicrobial-resistant E. coli isolates is essential for sustainable disease management in livestock and human medicine. A total of 102 E. coli isolates of diseased pigs were characterized by antimicrobial and biocide susceptibility testing. Antimicrobial resistance genes, including mobile colistin resistance genes, were analyzed by PCR and DNA sequencing. The quinolone resistance-determining regions of gyrA and parC in ciprofloxacin-resistant isolates were analyzed. Clonal relatedness was investigated by two-locus sequence typing (CH clonotyping). Phylotyping was performed by the Clermont multiplex PCR method. Virulence determinants were analyzed by customized DNA-based microarray technology developed in this study for fast and economic molecular multiplex typing. Thirty-five isolates were selected for whole-genome sequence-based analysis. Most isolates were resistant to ampicillin and tetracycline. Twenty-one isolates displayed an ESBL phenotype and one isolate an AmpC β-lactamase-producing phenotype. Three isolates had elevated colistin minimal inhibitory concentrations and carried the mcr-1 gene. Thirty-seven isolates displayed a multi-drug resistance phenotype. The most predominant β-lactamase gene classes were bla_TEM-1 (56%) and bla_CTX-M-1 (13.71%). Mutations in QRDR were observed in 14 ciprofloxacin-resistant isolates. CH clonotyping divided all isolates into 51 CH clonotypes. The majority of isolates belonged to phylogroup A. Sixty-four isolates could be assigned to defined pathotypes wherefrom UPEC was predominant. WGS revealed that the most predominant sequence type was ST100, followed by ST10. ST131 was detected twice in our analysis. This study highlights the importance of monitoring antimicrobial resistance and virulence properties of porcine E. coli isolates. This can be achieved by applying reliable, fast, economic and easy to perform technologies such as DNA-based microarray typing. The presence of high-risk pathogenic multi-drug resistant zoonotic clones, as well as those that are resistant to critically important antibiotics for humans, can pose a risk to public health. Improved protocols may be developed in swine farms for preventing infections, as well as the maintenance and distribution of the causative isolates.

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.

Proteus mirabilis from community-acquired urinary tract infections (UTI-CA) shares genetic similarity and virulence factors with isolates from chicken, beef and pork meat

Proteus mirabilis is an opportunistic pathogen associated with a variety of infections in humans, especially those in the urinary tract. The isolation of this pathogen in foods of animal origin such as meat is poorly documented and should not be neglected, in view of the zoonotic risk that this can pose to human health. Thus, the objective of this study was to evaluate the prevalence, virulence profile, and similarity between P. mirabilis strains isolated from chicken, beef, and pork meat and those causing community-acquired urinary tract infections (UTI-CA), in order to better understand the role of this bacterium as a zoonotic pathogen. P. mirabilis was isolated from the three types of meat and was found to be more prevalent in chicken. All isolates exhibited several genotypic and phenotypic virulence characteristics, such as adhesion capacity in HEp-2 cell culture, biofilm formation, cytotoxicity in Vero cells and genes that express fimbriae (mrpA, pmfA, ucaA, atfA), hemolysin (hpmA), proteases (zapA and ptA) and siderophore receptor (ireA). UTI-CA strains showed a higher prevalence of ucaA and ireA genes, whereas those from the chicken meat had a higher prevalence of the atfA gene compared with the isolates from the beef and pork meat. It was observed that chicken meat and UTI-CA strains mainly formed very strong biofilms, whereas strains isolated from beef and pork formed more weak and moderate biofilms. Several strains from meat showed close genetic similarity to those from UTI-CA and had the same virulence profiles. Thus, meats may be an important source of the dissemination of P. mirabilis responsible for causing UTIs in the community.

Comparison of Antimicrobial-Resistant Escherichia coli Isolates from Urban Raccoons and Domestic Dogs

Wildlife can be exposed to antimicrobial-resistant bacteria (ARB) via multiple pathways. Spatial overlap with domestic animals is a prominent exposure pathway. However, most studies of wildlife-domestic animal interfaces have focused on livestock and little is known about the wildlife-companion animal interface. Here, we investigated the prevalence and phylogenetic relatedness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli from raccoons (Procyon lotor) and domestic dogs (Canis lupus familiaris) in the metropolitan area of Chicago, IL, USA. To assess the potential importance of spatial overlap with dogs, we explored whether raccoons sampled at public parks (i.e., parks where people and dogs could enter) differed in prevalence and phylogenetic relatedness of ESC-R E. coli to raccoons sampled at private parks (i.e., parks where people and dogs could not enter). Raccoons had a significantly higher prevalence of ESC-R E. coli (56.9%) than dogs (16.5%). However, the richness of ESC-R E. coli did not vary by host species. Further, core single-nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that isolates did not cluster by host species, and in some cases displayed a high degree of similarity (i.e., differed by less than 20 core SNPs). Spatial overlap analyses revealed that ESC-R E. coli were more likely to be isolated from raccoons at public parks than raccoons at private parks, but only for parks located in suburban areas of Chicago, not urban areas. That said, ESC-R E. coli isolated from raccoons did not genetically cluster by park of origin. Our findings suggest that domestic dogs and urban/suburban raccoons can have a diverse range of ARB, some of which display a high degree of genetic relatedness (i.e., differ by less than 20 core SNPs). Given the differences in prevalence, domestic dogs are unlikely to be an important source of exposure for mesocarnivores in urbanized areas. IMPORTANCE Antimicrobial-resistant bacteria (ARB) have been detected in numerous wildlife species across the globe, which may have important implications for human and animal health. Wildlife can be exposed to ARB via numerous pathways, including via spatial overlap with domestic animals. However, the interface with domestic animals has mostly been explored for livestock and little is known about the interface between wild animals and companion animals. Our work suggests that urban and suburban wildlife can have similar ARB to local domestic dogs, but local dogs are unlikely to be a direct source of exposure for urban-adapted wildlife. This finding is important because it underscores the need to incorporate wildlife into antimicrobial resistance surveillance efforts, and to investigate whether certain urban wildlife species could act as additional epidemiological pathways of exposure for companion animals, and indirectly for humans.

mcr-Positive Escherichia coli ST131-H22 from Poultry in Brazil

Escherichia coli sequence type (ST) 131 is of concern because it can acquire antimicrobial resistance and cause extraintestinal infections. E. coli ST131-H22 sublineage appears capable of being transmitted to humans through poultry. We report on multidrug-resistant ST131-H22 poultry isolates in Brazil closely related to international human and poultry isolates.

Waterborne Urinary Tract Infections: Have We Overlooked an Important Source of Exposure?

The presence of intestinal pathogenic Escherichia coli in drinking water is well recognized as a risk for diarrhea. The role of drinking water in extraintestinal infections caused by E. coli-such as urinary tract infections (UTIs)-remains poorly understood. Urinary tract infections are a leading cause of outpatient infections globally, with a lifetime incidence of 50-60% in adult women. We reviewed the scientific literature on the occurrence of uropathogenic E. coli (UPEC) in water supplies to determine whether the waterborne route may be an important, overlooked, source of UPEC. A limited number of studies have assessed whether UPEC isolates are present in drinking water supplies, but no studies have measured whether their presence in water may increase UPEC colonization or the risk of UTIs in humans. Given the prevalence of drinking water supplies contaminated with E. coli across the globe, efforts should be made to characterize UTI-related risks associated with drinking water, as well as other pathways of exposure.

Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins

Antimicrobial-resistant Escherichia coli, particularly those resistant to critically important antimicrobials, are increasingly reported in wildlife. The dissemination of antimicrobial-resistant bacteria to wildlife indicates the far-reaching impact of selective pressures imposed by humans on bacteria through misuse of antimicrobials. The grey-headed flying fox (GHFF; Pteropus poliocephalus), a fruit bat endemic to eastern Australia, commonly inhabits urban environments and encounters human microbial pollution. To determine if GHFF have acquired human-associated bacteria, faecal samples from wild GHFF (n=287) and captive GHFF undergoing rehabilitation following illness or injury (n=31) were cultured to detect beta-lactam-resistant E. coli. Antimicrobial susceptibility testing, PCR and whole genome sequencing were used to determine phenotypic and genotypic antimicrobial resistance profiles, strain type and virulence factor profiles. Overall, 3.8 % of GHFF carried amoxicillin-resistant E. coli (wild 3.5 % and captive 6.5 %), with 38.5 % of the 13 GHFF E. coli isolates exhibiting multidrug resistance. Carbapenem (blaNDM-5) and fluoroquinolone resistance were detected in one E. coli isolate, and two isolates were resistant to third-generation cephalosporins (blaCTX-M-27 and ampC). Resistance to tetracycline and trimethoprim plus sulfamethoxazole were detected in 69.2% and 30.8 % of isolates respectively. Class 1 integrons, a genetic determinant of resistance, were detected in 38.5 % of isolates. Nine of the GHFF isolates (69.2 %) harboured extraintestinal virulence factors. Phylogenetic analysis placed the 13 GHFF isolates in lineages associated with humans and/or domestic animals. Three isolates were human-associated extraintestinal pathogenic E. coli (ST10 O89:H9, ST73 and ST394) and seven isolates belonged to lineages associated with extraintestinal disease in both humans and domestic animals (ST88, ST117, ST131, ST155 complex, ST398 and ST1850). This study provides evidence of anthropogenic multidrug-resistant and pathogenic E. coli transmission to wildlife, further demonstrating the necessity for incorporating wildlife surveillance within the One Health approach to managing antimicrobial resistance.

The changing microbiome of poultry meat; from farm to fridge

Chickens play host to a diverse community of microorganisms which constitute the microflora of the live bird. Factors such as diet, genetics and immune system activity affect this complex population within the bird, while external influences including weather and exposure to other animals alter the development of the microbiome. Bacteria from these settings including Campylobacter and Salmonella play an important role in the quality and safety of end-products from these birds. Further steps, including washing and chilling, within the production cycle aim to control the proliferation of these microbes as well as those which cause product spoilage. These steps impose specific selective pressures upon the microflora of the meat product. Within the next decade, it is forecast that poultry meat, particularly chicken will become the most consumed meat globally. However, as poultry meat is a frequently cited reservoir of zoonotic disease, understanding the development of its microflora is key to controlling the proliferation of important spoilage and pathogenic bacterial groups present on the bird. Whilst several excellent reviews exist detailing the microbiome of poultry during primary production, others focus on fate of important poultry pathogens such as Campylobacter and Salmonella spp. At farm and retail level, and yet others describe the evolution of spoilage microbes during spoilage. This review seeks to provide the poultry industry and research scientists unfamiliar with food technology process with a holistic overview of the key changes to the microflora of broiler chickens at each stage of the production and retail cycle.

Detection of Bacterial Metabolic Volatile Indole Using a Graphene-Based Field-Effect Transistor Biosensor

The existence of bacteria is a great threat to food safety. Volatile compounds secreted by bacteria during their metabolic process can be dissected to evaluate bacterial contamination. Indole, as a major volatile molecule released by Escherichia coli (E. coli), was chosen to examine the presence of E. coli in this research. In this work, a graphene field-effect transistor (G-FET) was employed to detect the volatile molecule-indole based on a π-π stacking interaction between the indole and the graphene. The exposure of G-FET devices to the indole provokes a change in electrical signal, which is ascribed to the adsorption of the indole molecule onto the graphene surface via π-π stacking. The adsorption of the indole causes a charge rearrangement of the graphene-indole complex, which leads to changes in the electrical signal of G-FET biosensors with a different indole concentration. Currently, the indole biosensor can detect indole from 10 ppb to 250 ppb and reach a limit of detection of 10 ppb for indole solution detection. We believe that our detection strategy for detecting bacterial metabolic gas molecules will pave a way to developing an effective platform for bacteria detection in food safety monitoring.

Prevalence and Characterization of Quinolone-Resistance Determinants in Escherichia coli Isolated from Food-Producing Animals and Animal-Derived Food in the Philippines

Antimicrobial resistance to quinolones, which constitutes a threat to public health, has been increasing worldwide. In this study, we investigated the prevalence of quinolone-resistant determinants in Escherichia coli not susceptible to quinolones and isolated from food-producing animals and food derived from them, in the Philippines. A total of 791 E. coli strains were isolated in 56.4% of 601 beef, chicken, pork, egg, and milk samples, as well as environmental, cloacal, and rectal swab-collected samples from supermarkets, open markets, abattoirs, and poultry, swine, and buffalo farms. Using the disc diffusion method, it was determined that 78.6% and 55.4% of the isolates were resistant to at least one antimicrobial and multiple drugs, respectively. In 141 isolates not susceptible to quinolones, 115 (81.6%) harbored quinolone-resistant determinants and had mutations predominantly in the quinolone-resistance determining regions (QRDRs) of gyrA and parC. Plasmid-mediated, quinolone resistance (PMQR) and Qnr family (qnrA1, qnrB4, and qnrS1) genes were detected in all isolates. Forty-eight sequence types were identified in isolates harboring mutations in QRDR and/or PMQR genes by multilocus sequence typing analysis. Moreover, 26 isolates harboring mutations in QRDR and/or PMQR genes belonged mostly to phylogroup B1 and Enteroaggregative E. coli. In conclusion, a high prevalence of E. coli was found in food-producing animals and products derived from them, which could potentially spread high-risk clones harboring quinolone-resistance determinants.

Population structure and uropathogenic potential of extended-spectrum cephalosporin-resistant Escherichia coli from retail chicken meat

Background

Food-producing animals and their products are considered a source for human acquisition of antimicrobial resistant (AMR) bacteria, and poultry are suggested to be a reservoir for Escherichia coli resistant to extended-spectrum cephalosporins (ESC), a group of antimicrobials used to treat community-onset urinary tract infections in humans. However, the zoonotic potential of ESC-resistant E. coli from poultry and their role as extraintestinal pathogens, including uropathogens, have been debated. The aim of this study was to characterize ESC-resistant E. coli isolated from domestically produced retail chicken meat regarding their population genetic structure, the presence of virulence-associated geno- and phenotypes as well as their carriage of antimicrobial resistance genes, in order to evaluate their uropathogenic potential.

Results

A collection of 141 ESC-resistant E. coli isolates from retail chicken in the Norwegian monitoring program for antimicrobial resistance in bacteria from food, feed and animals (NORM-VET) in 2012, 2014 and 2016 (n = 141) were whole genome sequenced and analyzed. The 141 isolates, all containing the beta-lactamase encoding gene bla_CMY-2, were genetically diverse, grouping into 19 different sequence types (STs), and temporal variations in the distribution of STs were observed. Generally, a limited number of virulence-associated genes were identified in the isolates. Eighteen isolates were selected for further analysis of uropathogen-associated virulence traits including expression of type 1 fimbriae, motility, ability to form biofilm, serum resistance, adhesion- and invasion of eukaryotic cells and colicin production. These isolates demonstrated a high diversity in virulence-associated phenotypes suggesting that the uropathogenicity of ESC-resistant E. coli from chicken meat is correspondingly highly variable. For some isolates, there was a discrepancy between the presence of virulence-associated genes and corresponding expected phenotype, suggesting that mutations or regulatory mechanisms could influence their pathogenic potential.

Conclusion

Our results indicate that the ESC-resistant E. coli from chicken meat have a low uropathogenic potential to humans, which is important knowledge for improvement of future risk assessments of AMR in the food chains.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02160-y.

Antimicrobial Resistance Profile and ExPEC Virulence Potential in Commensal Escherichia coli of Multiple Sources

We recently described the genetic antimicrobial resistance and virulence profile of a collection of 279 commensal E. coli of food-producing animal (FPA), pet, wildlife and human origin. Phenotypic antimicrobial resistance (AMR) and the role of commensal E. coli as reservoir of extra-intestinal pathogenic Escherichia coli (ExPEC) virulence-associated genes (VAGs) or as potential ExPEC pathogens were evaluated. The most common phenotypic resistance was to tetracycline (76/279, 27.24%), sulfamethoxazole/trimethoprim (73/279, 26.16%), streptomycin and sulfisoxazole (71/279, 25.45% both) among the overall collection. Poultry and rabbit were the sources mostly associated to AMR, with a significant resistance rate (p > 0.01) to quinolones, streptomycin, sulphonamides, tetracycline and, only for poultry, to ampicillin and chloramphenicol. Finally, rabbit was the source mostly associated to colistin resistance. Different pandemic (ST69/69*, ST95, ST131) and emerging (ST10/ST10*, ST23, ST58, ST117, ST405, ST648) ExPEC sequence types (STs) were identified among the collection, especially in poultry source. Both ST groups carried high number of ExPEC VAGs (pandemic ExPEC STs, mean = 8.92; emerging ExPEC STs, mean = 6.43) and showed phenotypic resistance to different antimicrobials (pandemic ExPEC STs, mean = 2.23; emerging ExPEC STs, mean = 2.43), suggesting their role as potential ExPEC pathogens. Variable phenotypic resistance and ExPEC VAG distribution was also observed in uncommon ExPEC lineages, suggesting commensal flora as a potential reservoir of virulence (mean = 3.80) and antimicrobial resistance (mean = 1.69) determinants.

Virulence Properties of mcr-1-Positive Escherichia coli Isolated from Retail Poultry Meat

The great plasticity and diversity of the Escherichia coli genome, together with the ubiquitous occurrence, make E. coli a bacterium of world-wide concern. Of particular interest are pathogenic strains and strains harboring antimicrobial resistance genes. Overlapping virulence-associated traits between avian-source E. coli and human extraintestinal pathogenic E. coli (ExPEC) suggest zoonotic potential and safety threat of poultry food products. We analyzed whole-genome sequencing (WGS) data of 46 mcr-1-positive E. coli strains isolated from retail raw meat purchased in the Czech Republic. The investigated strains were characterized by their phylogroup-B1 (43%), A (30%), D (11%), E (7%), F (4%), B2 (2%), C (2%), MLST type, and serotype. A total of 30 multilocus sequence types (STs), of which ST744 was the most common (11%), were identified, with O8 and O89 as the most prevalent serogroups. Using the VirulenceFinder tool, 3 to 26 virulence genes were detected in the examined strains and a total of 7 (15%) strains met the pathogenic criteria for ExPEC. Four strains were defined as UPEC (9%) and 18 (39%) E. coli strains could be classified as APEC. The WGS methods and available on-line tools for their evaluation enable a comprehensive approach to the diagnosis of virulent properties of E. coli strains and represent a suitable and comfortable platform for their detection. Our results show that poultry meat may serve as an important reservoir of strains carrying both virulence and antibiotic resistance genes for animal and human populations.

Nanoemulsions of Satureja montana Essential Oil: Antimicrobial and Antibiofilm Activity against Avian Escherichia coli Strains

Satureja montana essential oil (SEO) presents a wide range of biological activities due to its high content of active phytochemicals. In order to improve the essential oil’s (EO) properties, oil in water nanoemulsions (NEs) composed of SEO and Tween-80 were prepared, characterized, and their antimicrobial and antibiofilm properties assayed against Escherichia coli strains isolated from healthy chicken. Since surfactant and oil composition can strongly influence NE features and their application field, a ternary phase diagram was constructed and evaluated to select a suitable surfactant/oil/water ratio. Minimal inhibitory concentration and minimal bactericidal concentration of NEs, evaluated by the microdilution method, showed that the SEO NE formulation exhibited higher inhibitory effects against planktonic E. coli than SEO alone. The quantification of biofilm production in the presence of NEs, assessed by crystal violet staining and scanning electron microscopy, evidenced that sub-MIC concentrations of SEO NEs enable an efficient reduction of biofilm production by the strong producer strains. The optimized nanoemulsion formulation could ensure food safety quality, and counteract the antibiotic resistance of poultry associated E. coli, if applied/aerosolized in poultry farms.

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38-39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa - suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.

Isolation, characterization and antibiotic resistance of Proteus mirabilis from Belgian broiler carcasses at retail and human stool

Proteus mirabilis is an important pathogen involved in human urinary tract infections, and also more isolated from stools of patients with diarrheal disease than from healthy patients. The role of food, especially poultry products as source for human infection and multi-resistant strains remains unclear. As a resident in broilers' intestines, P. mirabilis can contaminate broiler carcasses due to slaughter practices, and be a risk for human infection. The present study evaluated the performance of five isolation media, and subsequently examined the presence of P. mirabilis on broiler carcasses at retail. Additionally, isolates were characterized by the Dienes' test, repetitive element PCR fingerprinting and pulsed-field gel electrophoresis, and their antibiotic resistance profile determined. Using a combined isolation protocol on blood agar, xylose lysine deoxycholate agar and violet red bile glucose agar, P. mirabilis was isolated from 29 out of 80 broiler carcasses (36.25%) with a mean contamination level of 2.25 ± 0.50 log₁₀ CFU/g. A high strain heterogeneity was present in isolates from broilers and human stool. The same strains were not shared, but the antibiotic resistance profiling was similar. A role of poultry products as source for human infection should be taken into account.

Distinguishing Pathovars from Nonpathovars: Escherichia coli

Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.

Escherichia coli as Commensal and Pathogenic Bacteria Among Food-Producing Animals: Health Implications of Extended Spectrum β-lactamase (ESBL) Production

Simple Summary

This revision is about the problem of Escherichia coli as a commensal and pathogenic bacterium among food-producing animals and health implications. Escherichia coli may play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tract; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. The majority of E. coli strains are commensals inhabiting the intestinal tract of humans and warm-blooded animals and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. All over the word, antibiotic resistance is commonly detected among commensal bacteria from food-producing animals, raising important questions on the potential impact of antibiotic use in animals and the possible transmission of these resistant bacteria to humans through the food chain. The use, in food-producing animals, of antibiotics that are critically important in human medicine has been implicated in the emergence of new forms of resistant bacteria, including new strains of multidrug-resistant foodborne bacteria, such as extended spectrum β-lactamase (ESBL)-producing E. coli.

Abstract

Escherichia coli are facultative, anaerobic Gram-negative rods with many facets. Within resistant bacterial populations, they play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tracts; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. Thus, the prevalence of antimicrobial resistance in these commensal bacteria (or others, such as enterococci) can be a good indicator for the selective pressure caused by the use of antimicrobial agents, providing an early warning of the emergence of antimicrobial resistance in pathogens. As many as 90% of E. coli strains are commensals inhabiting the intestinal tracts of humans and warm-blooded animals. As a commensal, it lives in a mutually beneficial association with its hosts and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. In humans, it is the prominent cause of enteritis, community- and hospital-acquired urinary tract infection (UTI), septicemia, postsurgical peritonitis, and other clinical infections, such as neonatal meningitis, while, in farm animals, it is more prominently associated with diarrhea. On a global scale, E. coli can be considered the most important human pathogen, causing severe infection along with other major bacterial foodborne agents, such as Salmonella spp. and Campylobacter. Thus, the importance of resistance in E. coli, typically considered a benign commensal, should not be underestimated.

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

AIM

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

METHODS AND RESULTS

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

CONCLUSIONS

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

SIGNIFICANCE AND IMPACT OF THE STUDY

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

A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review

Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamases-producing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them.

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.

The occurrence of Salmonella, extended-spectrum β-lactamase producing Escherichia coli and carbapenem resistant non-fermenting Gram-negative bacteria in a backyard poultry flock environment

Increase in the number of small-scale backyard poultry flocks in the USA has substantially increased human-to-live poultry contact, leading to increased public health risks of the transmission of multi-drug resistant (MDR) zoonotic and food-borne bacteria. The objective of this study was to detect the occurrence of Salmonella and MDR Gram-negative bacteria (GNB) in the backyard poultry flock environment. A total of 34 backyard poultry flocks in Washington State (WA) were sampled. From each flock, one composite coop sample and three drag swabs from nest floor, waterer-feeder, and a random site with visible faecal smearing, respectively, were collected. The samples were processed for isolation of Salmonella and other fermenting and non-fermenting GNB under ceftiofur selection. Each isolate was identified to species level using MALDI-TOFF and tested for resistance against 16 antibiotics belonging to eight antibiotic classes. Salmonella serovar 1,4,[5],12:i:- was isolated from one (3%) out of 34 flocks. Additionally, a total of 133 ceftiofur resistant (Cef^R ) GNB including Escherichia coli (53), Acinetobacter spp. (45), Pseudomonas spp. (22), Achromobacter spp. (8), Bordetella trematum (1), Hafnia alvei (1), Ochrobactrum intermedium (1), Raoultella ornithinolytica (1), and Stenotrophomonas maltophilia (1) were isolated. Of these, 110 (82%) isolates displayed MDR. Each flock was found positive for the presence of one or more Cef^R GNB. Several MDR E. coli (n = 15) were identified as extended-spectrum β-lactamase (ESBL) positive. Carbapenem resistance was detected in non-fermenting GNB including Acinetobacter spp. (n = 20), Pseudomonas spp. (n = 11) and Stenotrophomonas maltophila (n = 1). ESBL positive E. coli and carbapenem resistant non-fermenting GNB are widespread in the backyard poultry flock environment in WA State. These GNB are known to cause opportunistic infections, especially in immunocompromised hosts. Better understanding of the ecology and epidemiology of these GNB in the backyard poultry flock settings is needed to identify potential risks of transmission to people in proximity.

Antibacterial Activity of Bacteriocinogenic Commensal Escherichia coli against Zoonotic Strains Resistant and Sensitive to Antibiotics

Antibiotic resistance concerns various areas with high consumption of antibiotics, including husbandry. Resistant strains are transmitted to humans from livestock and agricultural products via the food chain and may pose a health risk. The commensal microbiota protects against the invasion of environmental strains by secretion of bacteriocins, among other mechanisms. The present study aims to characterize the bactericidal potential of bacteriocinogenic Escherichia coli from healthy humans against multidrug-resistant and antibiotic-sensitive strains from pigs and cattle. Bacteriocin production was tested by the double-layer plate method, and bacteriocin genes were identified by the PCR method. At least one bacteriocinogenic E. coli was detected in the fecal samples of 55% of tested individuals, adults and children. Among all isolates (n = 210), 37.1% were bacteriocinogenic and contained genes of colicin (Col) Ib, ColE1, microcin (Mcc) H47, ColIa, ColM, MccV, ColK, ColB, and single ColE2 and ColE7. Twenty-five E. coli carrying various sets of bacteriocin genes were further characterized and tested for their activity against zoonotic strains (n = 60). Strains with ColE7 (88%), ColE1-ColIa-ColK-MccH47 (85%), MccH47-MccV (85%), ColE1-ColIa-ColM (82%), ColE1 (75%), ColM (67%), and ColK (65%) were most active against zoonotic strains. Statistically significant differences in activity toward antibiotic-resistant strains were shown by commensal E. coli carrying MccV, ColK-MccV, and ColIb-ColK. The study demonstrates that bacteriocinogenic commensal E. coli exerts antagonistic activity against zoonotic strains and may constitute a defense line against multidrug-resistant strains.

Escherichia coli strains of chicken and human origin: Characterization of antibiotic and heavy-metal resistance profiles, phylogenetic grouping, and presence of virulence genetic markers

Multiple antibiotic-resistant extra-intestinal pathogenic Escherichia coli (ExPEC) strains represent a serious health care problem both for poultry and humans. Recently isolates with combined resistance to both antibiotics and heavy metals have been increased worldwide, with growing concern for possible co-selection of antimicrobial resistant genes. In the present study we characterized, at a phenotypic and genetic level, 80 E. coli isolates: forty independent isolates were collected from manure samples of healthy chickens and 40 from independent human extra-intestinal infections (ExPEC strains). The results obtained indicated that i) compared to chicken, human isolates presented a broader spectrum of antibiotic resistance and virulence potentials; ii) although at a lower extent, ExPEC-associated virulence genes were also present in chicken isolates, suggesting they may be potentially pathogens; iii) that arsenic (As) and zinc (Zn) tolerance genetic determinants were significantly more prevalent among chicken and human isolates respectively, while those responsible for tolerance to cadmium (Cd), silver (Ag) and copper (Cu) were equally distributed among the two groups of strains; iv) a very strong correlation was found between chicken gentamicin (GM) resistance and cadmium (Cd) tolerance. Elucidating the role of heavy metals in the selection and spread of highly pathogenic E. coli strains (co-selection) is of primary importance to lower the potential risk of infections in poultry and humans. The control of bacterial zoonotic agents, that commonly occur in livestock and that may be transmitted, directly or via the food chain, to human populations, could be of relevant interest.

Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic

Background

Avian pathogenic Escherichia coli (APEC) can cause various extraintestinal infections in poultry, resulting in massive economic losses in poultry industry. In addition, some avian E. coli strains may have zoonotic potential, making poultry a possible source of infection for humans. Due to its extreme genetic diversity, this pathotype remains poorly defined. This study aimed to investigate the diversity of colibacillosis-associated E. coli isolates from Central European countries with a focus on the Czech Republic.

Results

Of 95 clinical isolates subjected to preliminary characterization, 32 were selected for whole-genome sequencing. A multi resistant phenotype was detected in a majority of the sequenced strains with the predominant resistance to β-lactams and quinolones being associated with TEM-type beta-lactamase genes and chromosomal gyrA mutations respectively. The phylogenetic analysis confirmed a great diversity of isolates, that were derived from nearly all phylogenetic groups, with predominace of B2, B1 and C phylogroups. Clusters of closely related isolates within ST23 (phylogroup C) and ST429 (phylogroup B2) indicated a possible local spread of these clones. Besides, the ST429 cluster carried bla_{CMY-2, − 59} genes for AmpC beta-lactamase and isolates of both clusters were generally well-equipped with virulence-associated genes, with considerable differences in distribution of certain virulence-associated genes between phylogenetically distant lineages. Other important and potentially zoonotic APEC STs were detected, incl. ST117, ST354 and ST95, showing several molecular features typical for human ExPEC.

Conclusions

The results support the concept of local spread of virulent APEC clones, as well as of zoonotic potential of specific poultry-associated lineages, and highlight the need to investigate the possible source of these pathogenic strains.

Whole genome sequence comparison of avian pathogenic Escherichia coli from acute and chronic salpingitis of egg laying hens

BACKGROUND

Infection in the oviduct (salpingitis) is the most common bacterial infection in egg laying hens and is mainly caused by Escherichia coli. The disease is responsible for decreased animal welfare, considerable economic loss as well as a risk of horizontal and vertical transmission of pathogenic E. coli. The outcome of salpingitis may be either acute or chronic. It has not yet been clarified whether the pathological manifestation is a result of the characteristics of the E. coli or whether the manifestation is associated with host factors such as host immunity.

RESULTS

From the core- and accessory genome analysis and comparison of 62 E. coli no genetic markers were found to be associated to either acute or chronic infection. Twenty of the 62 genomes harboured at least one antimicrobial resistance gene with resistance against sulfonamides being the most common. The increased serum survival and iron chelating genes iss and iroN were highly prevalent in genomes from both acute and chronic salpingitis.

CONCLUSION

Our analysis revealed that no genetic markers could differentiate the E. coli isolated from acute versus chronic salpingitis in egg laying hens. The difference in pathological outcome may be related to other factors such as immunological status, genetics and health of the host. These data indicate that salpingitis is another manifestation of colibacillosis.

Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages

Escherichia coli is a ubiquitous commensal and pathogen that has also been recognized as a multi-sectoral indicator of antimicrobial resistance (AMR). Given that latter focus, such as on resistances to extended-spectrum cephalosporins (ESC) and carbapenems, the reported population structure of E. coli is generally biased toward resistant isolates, with sequence type (ST)131 being widely reported in humans, and ST410 and ST648 being reported in animals. In this study, we characterized 618 non-duplicate E. coli isolates collected throughout France independently of their resistance phenotype. The B2 phylogroup was over-represented (79.6%) and positively associated with the presence of numerous virulence factors (VFs), including those defining the extra-intestinal pathogenic E. coli isolates (presence of ≥2 VFs: papA, sfaS, focG, afaD, iutA, and kpsMTII) and those more specifically related to uropathogenic E. coli (cnf1, hlyD). The major STs associated with clinical isolates from dogs were by far the dog-associated ST372 (20.7%) and ST73 (20.1%), a lineage that had commonly been considered until now as human-associated. Resistance to ESC was found in 33 isolates (5.3%), along with one carbapenemase-producing isolate, and was mostly restricted to non-B2 isolates. In conclusion, the presence of virulent E. coli lineages may be the issue, rather than the presence of ESC-resistant isolates, and the risk of transmission of such virulent isolates to humans needs to be further studied.

Whole-Genome Sequencing-Based Characteristics in Extended-Spectrum Beta-Lactamase-Producing Escherichia coli Isolated from Retail Meats in Korea

The spread of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) has posed a critical health risk to both humans and animals, because resistance to beta-lactam antibiotics makes treatment for commonly infectious diseases more complicated. In this study, we report the prevalence and genetic characteristics of ESBL-ECs isolated from retail meat samples in Korea. A total of 1205 E. coli strains were isolated from 3234 raw meat samples, purchased from nationwide retail stores between 2015 and 2018. Antimicrobial susceptibility testing was performed for all isolates by a broth microdilution method, and the ESBL phenotype was determined according to the Clinical and Laboratory Standards Institute (CLSI) confirmatory method. All ESBL-EC isolates (n = 29) were subjected to whole-genome sequencing (WGS). The antimicrobial resistance genes, plasmid incompatibility types, E. coli phylogroups, and phylogenetic relations were investigated based on the WGS data. The prevalence of ESBL-ECs in chicken was significantly higher than that in other meat samples. The results in this study demonstrate that clonally diverse ESBL-ECs with a multidrug resistance phenotype were distributed nationwide, although their prevalence from retail meat was 0.9%. The dissemination of ESBL-ECs from retail meat poses a potential risk to consumers and food-handlers, suggesting that the continuous surveillance of ESBL-ECs in retail meat should be conducted at the national level.

Extraintestinal Foodborne Pathogens

In general, foodborne diseases present themselves with gastrointestinal symptoms caused by bacterial, viral, and parasitic pathogens well established to be foodborne. These pathogens are also associated with extraintestinal clinical manifestations. Recent studies have suggested that Escherichia coli and Klebsiella pneumoniae, which both cause common extraintestinal infections such as urinary tract and bloodstream infections, may also be foodborne. The resolution and separation of these organisms into pathotypes versus commensals by modern genotyping methods have led to the identification of key lineages of these organisms causing outbreaks of extraintestinal infections. These epidemiologic observations suggested common- or point-source exposures, such as contaminated food. Here, we describe the spectrum of extraintestinal illnesses caused by recognized enteric pathogens and then review studies that demonstrate the potential role of extraintestinal pathogenic E. coli (ExPEC) and K. pneumoniae as foodborne pathogens. The impact of global food production and distribution systems on the possible foodborne spread of these pathogens is discussed.

Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli

Blood stream invasion by Escherichia coli is the commonest cause of bacteremia in the UK and elsewhere with an attributable mortality of about 15-20 %; antibiotic resistance to multiple agents is common in this microbe and is associated with worse outcomes. Genes conferring antimicrobial resistance, and their frequent location on horizontally transferred genetic elements is well-recognised, but the origin of these determinants, and their ability to be maintained and spread within clinically-relevant bacterial populations is unclear. Here, we set out to examine the distribution of antimicrobial resistance genes in chromosomes and plasmids of 16 bloodstream isolates of E. coli from patients within Scotland, and how these genes are maintained and spread. Using a combination of short and long-read whole genome sequencing methods, we were able to assemble complete sequences of 44 plasmids, with 16 Inc group F and 20 col plasmids; antibiotic resistance genes located almost exclusively within the F group. bla _CTX-M15 genes had re-arranged in some strains into the chromosome alone (five strains), while others contained plasmid copies alone (two strains). Integrons containing multiple antibiotic genes were widespread in plasmids, notably many with a dfrA7 gene encoding resistance to trimethoprim, thus linking trimethoprim resistance to the other antibiotic resistance genes within the plasmids. This will allow even narrow spectrum antibiotics such as trimethoprim to act as a selective agent for plasmids containing antibiotic resistance genes mediating much broader resistance, including blaC_TX-M15. To our knowledge, this is the first analysis to provide complete sequence data of chromosomes and plasmids in a collection of pathogenic human bloodstream isolates of E. coli. Our findings reveal the interplay between plasmids and integrative and conjugative elements in the maintenance and spread of antibiotic resistance genes within pathogenic E. coli.

The risk of urinary tract infection in vegetarians and non-vegetarians: a prospective study

Urinary tract infection (UTI) is caused principally by ascending Escherichia coli infection via an intestine-stool-urethra route. Recent studies found that the strains of E. coli causing UTIs, called extra-intestinal pathogenic E. coli (ExPEC), were distinct from the intestinal pathogenic strains and normal commensal strains. Further analysis found the meat including poultry and pork is the major reservoir for ExPECs. Vegetarians avoid meat and should theoretically have less exposure to ExPEC. However, no study thus far has examined whether vegetarian diets reduce the risk of UTI. Our aim was to examine the association between vegetarian diet and UTI risk in a Taiwanese Buddhist population. We prospectively followed 9724 Buddhists free of UTI from 2005 to 2014. During the 10-year follow-up, 661 incident UTI cases were confirmed. Diet was assessed through a food frequency questionnaire. Cox regression was used to evaluate the prospective association between a vegetarian diet on risk of UTI while adjusting for age, sex, educational level, alcohol-drinking, smoking, hypertension, diabetes mellitus, hyperlipidemia, and disease conditions predisposing to UTIs. Overall, vegetarian diet was associated with 16% lower hazards (hazard ratio [HR]: 0.84, 95% confidence interval [CI]: 0.71-0.99). In subgroup analysis, the protective association between vegetarian diet and UTI is observed mainly in the female (HR: 0.82, 95% CI: 0.69-0.99), never smokers (HR: 0.80, 95% CI: 0.67-0.95), and for uncomplicated UTI (HR: 0.81, 95% CI: 0.68-0.98).

Identification of ireA, 0007, 0008, and 2235 as TonB-dependent receptors in the avian pathogenic Escherichia coli strain DE205B

Avian pathogenic Escherichia coli (APEC), a pathotype of extraintestinal pathogenic E. coli, causes one of the most serious infectious diseases of poultry and shares some common virulence genes with neonatal meningitis-associated E. coli. TonB-dependent receptors (TBDRs) are ubiquitous outer membrane β-barrel proteins; they play an important role in the recognition of siderophores during iron uptake. Here, in the APEC strain DE205B, we investigated the role of four putative TBDRs-ireA, 0007, 0008, and 2235-in iron uptake. Glutathione-S-transferase pulldown assays indicated that the proteins encoded by these genes directly interact with TonB. Moreover, the expression levels of all four genes were significantly upregulated under iron-depleted conditions compared with iron-rich conditions. The expression levels of several iron uptake-related genes were significantly increased in the ireA, 0007, 0008, and 2235 deletion strains, with the upregulation being the most prominent in the ireA deletion mutant. Furthermore, iron uptake by the ireA deletion strain was significantly increased compared to that by the wild-type strain. Moreover, a tonB mutant strain was constructed to study the effect of tonB deletion on the TBDRs. We found that regardless of the presence of tonB, the expression levels of the genes encoding the four TBDRs were regulated by fur. In conclusion, our findings indicated that ireA, 0007, 0008, and 2235 indeed encode TBDRs, with ireA having the most important role in iron uptake. These results should help future studies explore the mechanisms underlying the TonB-dependent iron uptake pathway.

Genomic Characterization of Antibiotic Resistant Escherichia coli Isolated From Domestic Chickens in Pakistan

Poultry husbandry is important for the economic health of Pakistan, but the Pakistani poultry industry is negatively impacted by infections from Escherichia coli. We performed Illumina whole genome sequencing on 92 E. coli isolates obtained from the livers of deceased chickens originating in five Pakistani geographical regions. Our analysis indicates that the isolates are predominantly from the B1 and A clade and harbor a diverse number of antibiotic resistance and virulence genes, with no linkage between phylogeny and antibiotic resistance gene presence but some association between phylogeny and virulence gene and SNP presence for the B1 and E phylogroups. The colistin resistance gene mcr-1 and the quinolone resistance gene qnrS1 were both found in 13/92 isolates. Alarmingly, 82/92 of the E. coli strains characterized in this study are multidrug resistant with 100% (92/92) resistance to lincomycin, 81.5% (75/92) to streptomycin, 79.3% (73/92) to ampicillin and 66.3% (61/92) to ciprofloxacin. These results provide a high-resolution analysis of poultry-associated E. coli isolates in an area with a high endemic burden of antibiotic resistance. Surveillance of antibiotic resistance in poultry associated E. coli isolates is an important pillar of the One Health concept to integrate analysis of potential pathogens in human, animal, and environmental niches.

A self-contained and fully integrated fluidic cassette system for multiplex nucleic acid detection of bacteriuria

The gold standard for diagnosing infectious diseases is culture-based identification of bacterial pathogens, which is time-consuming and labour-intensive. Current advances in molecular diagnostics and microfluidic technologies have made the rapid detection of bacteria or viruses in clinical specimens possible. However, the need for rapid, sensitive and multiplex detection of pathogens in a "sample-in and answer-out" manner has not been fully satisfied. In this study, a self-contained and fully integrated fluidic cassette and its supporting analyser were constructed for multiplex detection of bacteria to accelerate the diagnosis of urinary tract infections (UTIs). The fully integrated cassette contains all the necessary components and reagents for bacterial analysis. All of the bacterial analysis processes, including bacterial lysis, magnetic silica bead-based DNA extraction, DNA elution and multiplex loop-mediated amplification (LAMP), are automatically conducted in the cassette. This cassette was successfully applied for the detection of four major pathogenic bacteria in UTIs, i.e., Escherichia coli, Proteus mirabilis, Salmonella typhimurium and Staphylococcus aureus. The first three were successfully detected with a limit of detection (LoD) of 1 colony-forming unit (CFU) μL^-1 and the last was with a LoD of 10 CFU μL^-1 in urine samples, demonstrating that the cassette has similar sensitivity compared to that of the manual protocol, which is lower than that required by UTIs. The turnaround time for this cassette-based sample-to-answer system was approximately 100 minutes, and the detection is sensitive, fully automated, and accurate, demonstrating the potential to be a useful diagnostic tool for UTIs.

Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids

The interplay between food production animals, humans and the environment with respect to the transmission of drug-resistant pathogens is widely debated and poorly understood. Pandemic uropathogenic Escherichia coli ST131-H30Rx, with conserved fluoroquinolone and cephalosporin resistance, are not frequently identified in animals. However, the phylogenetic precursor lineage ST131-H22 in animals and associated meat products is being reported with increasing frequency. Here we characterized two highly related ST131-H22 strains, one from a healthy pig and the other from a human infection (in 2007 and 2009, respectively). We used both long and short genome sequencing and compared them to ST131-H22 genome sequences available in public repositories. Even within the context of H22 strains, the two strains in question were highly related, separated by only 20 core SNPs. Furthermore, they were closely related to a faecal strain isolated in 2010 from a geographically distinct, healthy human in New South Wales, Australia. The porcine and hospital strains carried highly similar HI2-ST3 multidrug resistant plasmids with differences in the hospital strain arising due to IS-mediated insertions and rearrangements. Near identical ColV plasmids were also present in both strains, further supporting their shared evolutionary history. This work highlights the importance of adopting a One Health approach to genomic surveillance to gain insights into pathogen evolution and spread.

Temporal influence of different antibiotics onto the inhibition of Escherichia coli bacterium grown in different media

Escherichia coli (E. coli) is a Gram-negative bacterium commonly found in the lower intestine of warm-blooded organisms, including humans. Although the majority of the strains are considerably harmless, some serotypes are pathogenic, frequently causing diarrhea and other illnesses outside the intestinal tract. The standard antidote against bacteria is the use of antibiotics. Depending on their type, the antibiotics have various mechanisms of action on bacteria. Moreover, in case of in-vitro cultivation of bacteria, the used growth media plays a crucial role, since it influences bacterial inhibition as well. In the present study, we emphasize the importance of cultivability in bacterial inhibition under the treatment with five different antibiotics belonging to different classes. Consequently, E. coli was cultivated in three different growth media: trypcase soy broth (TSB), Mueller Hinton (MH), and minimal salts (M9) enriched with glucose, respectively. MALDI-TOF MS (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) analyses, that were used for fast characterization of changes that occur in ribosomal protein profiles, revealed differentiation and similarities between investigated cases, while flow cytometry (FCM) tests better explained the given changes that occurred in the analyzed samples after 3, 24 and 48 h of experimental campaign.

Antibacterial Activity of Terpenes and Terpenoids Present in Essential Oils

Background: The antimicrobial activity of essential oils has been reported in hundreds of studies, however, the great majority of these studies attribute the activity to the most prevalent compounds without analyzing them independently. Therefore, the aim was to investigate the antibacterial activity of 33 free terpenes commonly found in essential oils and evaluate the cellular ultrastructure to verify possible damage to the cellular membrane. Methods: Screening was performed to select substances with possible antimicrobial activity, then the minimal inhibitory concentrations, bactericidal activity and 24-h time-kill curve studies were evaluated by standard protocols. In addition, the ultrastructure of control and death bacteria were evaluated by scanning electron microscopy. Results: Only 16 of the 33 compounds had antimicrobial activity at the initial screening. Eugenol exhibited rapid bactericidal action against Salmonella enterica serovar Typhimurium (2 h). Terpineol showed excellent bactericidal activity against S. aureus strains. Carveol, citronellol and geraniol presented a rapid bactericidal effect against E. coli. Conclusions: The higher antimicrobial activity was related to the presence of hydroxyl groups (phenolic and alcohol compounds), whereas hydrocarbons resulted in less activity. The first group, such as carvacrol, l-carveol, eugenol, trans-geraniol, and thymol, showed higher activity when compared to sulfanilamide. Images obtained by scanning electron microscopy indicate that the mechanism causing the cell death of the evaluated bacteria is based on the loss of cellular membrane integrity of function. The present study brings detailed knowledge about the antimicrobial activity of the individual compounds present in essential oils, that can provide a greater understanding for the future researches.

Genotypic and phenotypic profiles of virulence factors and antimicrobial resistance of Proteus mirabilis isolated from chicken carcasses: potential zoonotic risk

Proteus mirabilis is an opportunistic pathogen often associated with a variety of human infections acquired both in the community and in hospitals. In this context, the present work aimed to evaluate the genotypic and phenotypic characteristics of the virulence factors and antimicrobial resistance determinants of 32 P. mirabilis strains isolated from chicken carcasses in a poultry slaughterhouse in the north of the state of Paraná, Brazil, in order to assess a potential zoonotic risk. The isolates presented a variety of virulence genes that contribute to the development of infection in humans. The mrpA, pmfA, atfA (fimbriae), ireA (siderophores receptor), zapA, ptA (Proteases), and hpmA (hemolysin) genes were found in 32 (100%) isolates and ucaA (fimbriae) in 16 (50%). All isolates showed aggregative adherence in HEp-2 cells and formed biofilms. Of all strains, 27 (84.38%) showed cytotoxic effects in Vero cells. Antimicrobial susceptibility was tested using 20 antimicrobials, in which 25 (78.13%) strains were considered multidrug-resistant. The presence of blaESBL and blaampC genes conferring resistance to β-lactams and qnr to quinolones were also detected in the isolates after presumption in the phenotypic test, in which 7 (21.88%) isolates contained the CTX-M-2 group, 11 (34.38%) contained CIT group and 19 (59.38%) contained qnrD. Therefore, chicken carcasses contaminated with P. mirabilis may pose a health risk to the consumer, as these isolates have a variety of virulence and antimicrobial resistance characteristics that can be found in P. mirabilis strains isolated from human infections.

Dissemination of Escherichia coli carrying plasmid-mediated quinolone resistance (PMQR) genes from swine farms to surroundings

Different samples were collected from three swine farms in China to investigate the spread of antibiotic-resistant Escherichia coli. A total of 130 E. coli isolates were obtained from feces, air, river water, silt, and soil samples and characterized. The susceptibility of the E. coli isolates to 19 antibiotics was tested. The results revealed that the resistance rates of the E. coli isolates against 9 antibiotics were high. The minimum inhibitory concentration (MIC) values of ciprofloxacin, ofloxacin, and nalidixic acid were mainly in the ranges of 2-64, 8-64, and 8-64 μg/ml. The plasmid-mediated quinolone resistance (PMQR) genes qnr, aac(6')-Ib-cr, qepA, and oqxAB were detected by polymerase chain reaction (PCR), and the similarity of E. coli from different samples was identified by pulsed-field gel electrophoresis (PFGE). The detection rates of the qnrA, qnrB, qnrS, aac(6')-Ib-cr, qepA, and oqxAB genes in the E. coli isolates from three swine farms were in the range of 10.87-23.08%, 13.04-20.51%, 40.00-43.48%, 30.43-38.46%, 6.52-12.82%, and 7.69-17.39%, respectively. The PFGE result showed that 49% (49/100) of isolates originating from air, river water, soil, and silt samples had ≥85% similarity to fecal-obtained isolates, and 40.82% (20/49) of them shared the same PMQR genes with fecal-obtained isolates. This indicated that E. coli carrying PMQR genes and originating from feces in swine farms could spread to the external environment, which could be a potential threat to the public environment and human health.

Virulent Escherichia coli strains among Egyptian patients with acute diarrhoea versus urinary tract infection, and their antibiotic susceptibility

BACKGROUND AND STUDY AIMS

Diarrhoea and urinary tract infection (UTI) are common clinical problems. Meanwhile, Escherichia coli (E. coli), is the commonest bacterial pathogen reported in both of them. This study aimed to evaluate the pathogenic E. coli (PEC) in stool of acute diarrhoea and urine of UTI regarding their virulence genes and their influence on the susceptibility to routinely prescribed antibiotics.

PATIENTS AND METHODS

Twenty two stool and another 22 urine samples of patients with acute diarrhoea and UTI respectively were collected from patients admitted at Kasr Al-Ainy Hospital, Faculty of Medicine, Cairo University, Egypt. E. coli isolation, identification of their phyla; chuA, yjaA, and TspE4.C2, and further identification of 10 virulent genes; fimH, papC, papG//, papG///, papEF, afa, sfa, CNF1, iroN & hlyA was performed. Antibiotic susceptibility was studied against quinolones, gentamicin (GM), and trimethoprim-sulphamethoxazole (TMP-SMX).

RESULTS

The studied virulence genes were comparably detected in both pathogenic samples. In diarrheogenic E. coli (DEC); phylum A was significantly related to both ciprofloxacin (CIP) and TMP-SMX resistance, and both of the virulence genes fimH and iroN were significantly related to all the studied antibiotics resistance, while afa was significantly related to nalidixic acid (NA) resistance. In uropathogenic E. coli (UEC); phylum D was significantly related to CIP and levofloxacin resistance, and both of the virulence genes fimH and iroN were significantly related to most of the studied antibiotics resistance.

CONCLUSION

The isolated PEC was evidently and broadly resistant to the studied antibiotics, with limited influence of their phyla and virulence genes (fimH and iroN).

Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: recent reports

Extraintestinal pathogenic E. coli (ExPEC) are facultative pathogens that are part of the normal human intestinal flora. The ExPEC group includes uropathogenic E. coli (UPEC), neonatal meningitis E. coli (NMEC), sepsis-associated E. coli (SEPEC), and avian pathogenic E. coli (APEC). Virulence factors (VF) related to the pathogenicity of ExPEC are numerous and have a wide range of activities, from those related to bacteria colonization to those related to virulence, including adhesins, toxins, iron acquisition factors, lipopolysaccharides, polysaccharide capsules, and invasins, which are usually encoded on pathogenicity islands (PAIs), plasmids and other mobile genetic elements. Mechanisms underlying the dynamics of ExPEC transmission and the selection of virulent clones are still poorly understood and require further research. The time shift between colonization of ExPEC and the development of infection remains problematic in the context of establishing the relation between consumption of contaminated food and the appearance of first disease symptoms. What appears to be most difficult is to prove that ExPEC strains cause disease symptoms and to examine the mechanism of transition from the asymptomatic colonization of the intestines to the spreading of the bacteria outside the digestive system. A significant problem for researchers who are trying to ascribe ExPEC transmission to food, people or the environment is to draw the distinction between colonization of ExPEC and infection. Food safety is an important challenge for public health both at the production stage and in the course of its processing and distribution. Examination of the genetic similarity of ExPEC strains will allow to determine their origin from different sources. Many levels of genotyping have been proposed in which the typing of strains, plasmids and genes is compared in order to obtain a more complete picture of this complex problem. The aim of our study was to characterize E. coli strains isolated from humans, animals and food for the presence of bacterial genes encoding virulence factors such as toxins, and iron acquisition systems (siderophores) in the context of an increasing spread of ExPEC infections.

Restructuring of Lipid Membranes by an Arginine-Capped Peptide Bolaamphiphile

We study the self-assembly of arginine-capped bolaamphiphile peptide RA₃R (A: alanine, R: arginine) together with its binding to model membranes and its cytotoxicity and antimicrobial activity. Anionic 2-oleoyl-1-palmitoyl- sn-glycero-3-phospho-rac-(1-glycerol) sodium salt/2-oleoyl-1-palmitoyl- sn-glycero-3-phosphoethanolamine (POPG/POPE) vesicles and zwitterionic 1,2-dioleoyl- sn-glycero-3-phosphocholine/2-oleoyl-1-palmitoyl- sn-glycero-3-phosphocholine (POPC/DOPC) vesicles are used as model membranes to mimic bacterial and mammalian cell membranes, respectively. We show that RA₃R adopts a polyproline-II collagen-like conformation in water. Binding of RA₃R to POPG/POPE vesicles induces a strong correlation between the lipid bilayers, driven by RA₃R/POPG attractive electrostatic interaction together with a shift of the intramolecular POPE zwitterionic interaction toward an attractive electrostatic interaction with the RA₃R. Populations of RA₃R/POPG/POPE vesicles comprise different bilayer spacings, d_A and d_B, controlled by the conformation of the lipid chains corresponding to the L_β (gel-like) and L_α (liquid-crystal) phases, respectively. Cryo-TEM images reveal the presence of vesicles with no internal structure, compartmentalized thin-wall vesicles, or multilayer vesicles with uncorrelated layers and compartmentalization depending on the RA₃R/POPG/POPE composition. In contrast, the interaction of RA₃R with multilamellar POPC/DOPC vesicles leads to the decorrelation of the lipid bilayers. RA₃R was tolerated by skin fibroblast cells for a concentration up to 0.01 wt %, while 0.25 wt % RA₃R proved to be an efficient antibacterial agent against Gram-positive bacteria L. monocytogenes. Our results highlight the ability of RA₃R to distinguish between bacterial and mammalian cells and establish this peptide as a candidate to reduce the proliferation of L. monocytogenes bacteria.

Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26

Porcine faecal waste is a serious environmental pollutant. Carriage of antimicrobial-resistance genes (ARGs) and virulence-associated genes (VAGs), and the zoonotic potential of commensal Escherichia coli from swine are largely unknown. Furthermore, little is known about the role of commensal E. coli as contributors to the mobilization of ARGs between food animals and the environment. Here, we report whole-genome sequence analysis of 103 class 1 integron-positive E. coli from the faeces of healthy pigs from two commercial production facilities in New South Wales, Australia. Most strains belonged to phylogroups A and B1, and carried VAGs linked with extraintestinal infection in humans. The 103 strains belonged to 37 multilocus sequence types and clonal complex 10 featured prominently. Seventeen ARGs were detected and 97 % (100/103) of strains carried three or more ARGs. Heavy-metal-resistance genes merA, cusA and terA were also common. IS26 was observed in 98 % (101/103) of strains and was often physically associated with structurally diverse class 1 integrons that carried unique genetic features, which may be tracked. This study provides, to our knowledge, the first detailed genomic analysis and point of reference for commensal E. coli of porcine origin in Australia, facilitating tracking of specific lineages and the mobile resistance genes they carry.

Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene

Avian pathogenic Escherichia coli (APEC) cause widespread economic losses in poultry production and are potential zoonotic pathogens. Genome sequences of 95 APEC from commercial poultry operations in four Australian states that carried the class 1 integrase gene intI1, a proxy for multiple drug resistance (MDR), were characterized. Sequence types ST117 (22/95), ST350 (10/95), ST429 and ST57 (each 9/95), ST95 (8/95) and ST973 (7/95) dominated, while 24 STs were represented by one or two strains. FII and FIB repA genes were the predominant (each 93/95, 98 %) plasmid incompatibility groups identified, but those of B/O/K/Z (25/95, 26 %) and I1 (24/95, 25 %) were also identified frequently. Virulence-associated genes (VAGs) carried by ColV and ColBM virulence plasmids, including those encoding protectins [iss (91/95, 96 %), ompT (91/95, 96 %) and traT (90/95, 95 %)], iron-acquisition systems [sitA (88/95, 93 %), etsA (87/95, 92 %), iroN (84/95, 89 %) and iucD/iutA (84/95, 89 %)] and the putative avian haemolysin hylF (91/95, 96 %), featured prominently. Notably, mobile resistance genes conferring resistance to fluoroquinolones, colistin, extended-spectrum β-lactams and carbapenems were not detected in the genomes of these 95 APEC but carriage of the sulphonamide resistance gene, sul1 (59/95, 63 %), the trimethoprim resistance gene cassettes dfrA5 (48/95, 50 %) and dfrA1 (25/95, 27 %), the tetracycline resistance determinant tet(A) (51/95, 55 %) and the ampicillin resistance genes bla_TEM-1A/B/C (48/95, 52 %) was common. IS26 (77/95, 81 %), an insertion element known to capture and mobilize a wide spectrum of antimicrobial resistance genes, was also frequently identified. These studies provide a baseline snapshot of drug-resistant APEC in Australia and their role in the carriage of ColV-like virulence plasmids.

Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95

APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.

Avian-pathogenic Escherichia coli (APEC) is a subgroup of extraintestinal pathogenic E. coli (ExPEC) presumed to be zoonotic and to represent an external reservoir for extraintestinal infections in humans, including uropathogenic E. coli (UPEC) causing urinary tract infections. Comparative genomics has previously been applied to investigate whether APEC and human ExPEC are distinct entities. Even so, whole-genome-based studies are limited, and large-scale comparisons focused on single sequence types (STs) are not available yet. In this study, comparative genomic analysis was performed on 323 APEC and human ExPEC genomes belonging to sequence type 95 (ST95) to investigate whether APEC and human ExPEC are distinct entities. Our study showed that APEC of ST95 did not constitute a unique ExPEC branch and was genetically diverse. A large genetic overlap between APEC and certain human ExPEC was observed, with APEC located on multiple branches together with closely related human ExPEC, including nearly identical APEC and human ExPEC. These results illustrate that certain ExPEC clones may indeed have the potential to cause infection in both poultry and humans. Previously described ExPEC-associated genes were found to be encoded on ColV plasmids. These virulence-associated plasmids seem to be crucial for ExPEC strains to cause avian colibacillosis and are strongly associated with strains of the mixed APEC/human ExPEC clusters. The phylogenetic analysis revealed two distinct branches consisting of exclusively closely related human ExPEC which did not carry the virulence-associated plasmids, emphasizing a lower avian virulence potential of human ExPEC in relation to an avian host.

IMPORTANCE APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.