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

Multidrug resistance and virulence profile of the commensal Proteus mirabilis isolated from a native Iraqi frozen chicken carcass

This study aimed to determine the prevalence of Proteus mirabilis in frozen chicken carcass from local slaughterhouse. It assesses the activities of nine antimicrobial agents and the presence of antimicrobial resistance genes and virulence genes. Thirty samples were collected from five local Iraqi companies. and then the antibiotic-resistance genes and virulence factor-related genes were detected via polymerase chain reaction (PCR). The results revealed that Nine P. mirabilis isolates were recovered, and the majority of the isolates were resistant to both nalidixic acid and azithromycin at a ratio of (100 %), followed by trimethoprim-sulfamethoxazole (sul1) (88.8 %), whereas the isolates were susceptible to imipenem and meropenem, and both ceftazidime and cefotaxime were efficient at a ratio of (88.8 %). All the isolates (100 %) were resistant to at least three classes of antibiotics and were classified as multidrug resistant. The PCR results indicated that the most common resistance genes were DNA Gyrase Subunit A Gene (gyrA) (100 %), Dihydropteroate Synthase Gene (sul1) (88.8 %), and Florenicol Resistance Gene (floR) (88.8 %), followed by Aminoglycoside N-Acetyltransferase Gene (acc (6')-lb) (44.4 %) and Macrolide Phosphotransferase Gene (mphA) (33.3 %). In addition, the virulence genes Zinc Metalloprotease A Gene (zapA), Uridine Monophosphate Synthase Gene (uraC), Histone-Modifying Protein A Gene (hpmA), Flagellin A Gene (flaA), Anti-Sigma Factor RsbA Gene (rsbA), and Multidrug Resistance Protein A Gene (mrpA) were found in the same proportion (100 %) of all P. mirabilis isolates. Our study emphasized that Proteus mirabilis has a high frequency of antibiotic resistance as a multidrug resistance pattern and furthermore demonstrated a high level of virulence factor gene detection, which might be a threat to food safety and human health. The phylogenetic tree analysis of the P. mirabilis isolates from chicken meat revealed high similarity to the database strain.

Occurrence and characteristics of extended-spectrum ß-lactamase-producing Escherichia coli in Swiss and imported retail chicken meat

OBJECTIVE

The occurrence of extended-spectrum ß-lactamase (ESBL) producing Enterobacterales in food is of concern because of the possibility of transmission of ESBL-producers and/or blaESBL genes to humans. This study aimed to investigate the presence of ESBL-producing Enterobacterales in Swiss and imported retail chicken meat.

METHODS

A total of 200 samples of different types of Swiss and imported chicken meat obtained at retail level in Switzerland were screened for ESBL-producing Enterobacterales using a selective culture medium. All non-intrinsically resistant isolates were characterised by antimicrobial susceptibility testing (AST), multilocus sequence typing (MLST), and whole genome sequencing (WGS).

RESULTS

Eighteen meat samples (9%) yielded a total of 19 ESBL-producing Escherichia coli (ESBL-EC). The proportion of samples containing ESBL-EC was higher in imported meat (14/55; 25%) than in Swiss meat (4/145; 3%). Co-resistance to ciprofloxacin was highly prevalent (18/19, 95%). E. coli sequence types (STs) included ST602, ST744, ST1844, and extraintestinal pathogenic (ExPEC) E. coli ST38. The blaESBL genes comprised blaCTX-M-1 (n=7), blaCTX-M-2 (n=1), blaCTX-M-8 (n=1), blaCTX-M-55 (n=1), blaSHV-12 (n=8), and blaTEM-52B (n=1). They were chromosomally (n=2) encoded or carried on plasmids belonging to IncB/O/K/Z (n=1), IncFII (n=1), IncI1-I(Alpha) (n=9), IncX1 (n=1), and IncX3 (n=5). Many of the plasmids were identical to those detected globally in ESBL-producers associated with broilers.

CONCLUSIONS

The contamination with ESBL-EC in retail chicken meat in Switzerland is moderate; nevertheless, domestic and imported chicken meat is a potential vehicle for MDR ESBL-EC and for genes conferring resistance to clinically important antimicrobials including 3rd-generation cephalosporins and fluoroquinolones.

Emergence of multidrug resistant Escherichia coli coharboring fosA3 and ESBL genes from retail ducks along slaughter line

The excessive and indiscriminate use of antimicrobial agents in poultry production has increased antimicrobial resistance in E. coli, posing a significant threat to public health. This study investigated the prevalence of multidrug-resistant (MDR) E. coli co-harboring fosA3 and extended-spectrum β-lactamases (ESBLs) genes in large-scale retail duck slaughterhouses in Sichuan Province, China. The antimicrobial susceptibility to 9 categories and 16 types of antimicrobial agents was assessed by using the broth microdilution method. Phylogenetic grouping and pulsed-field gel electrophoresis (PFGE) were used to investigate the phylogenetic groups and genetic characteristics of the isolates. Moreover, whole-genome sequencing (WGS) was performed on 35 representative E. coli isolates. Among 1, 059 samples collected, 895 E. coli were isolated by MacConkey (MAC) agar and eosin methylene blue (EMB) agar and PCR identification, and 150 strains of MDR E. coli co-carrying fosA3 and ESBL genes were finally screened for further analysis. The results indicated that 141 isolates were resistant to fosfomycin and exhibited high resistance to β-lactam antibiotics. All isolates demonstrated MDR patterns, with 148 isolates resistant to six or more classes of antimicrobial agents. The majority (70/150, 46.67 %) belonged to phylogenetic group B1. Based on an 85 % similarity threshold, all isolates were categorized into 40 distinct PFGE types. Genomic analysis revealed 27 different serotypes and 19 sequence types (STs), with O8 (14.29 %, 5/35) and ST155 (22.86 %, 8/35) being the most common. The IncFIB (AP001918) was the most prevalent plasmid replicon type, identified in 74.29 % (26/35) of the isolates. In addition, 49 acquired antimicrobial resistance genes (ARGs) associated with resistance to 11 types of antimicrobial agents were identified and chromosomal mutation of p.S83L in gyrA gene (88.57 %, 31/35) was the most common. Furthermore, 110 virulence factors (VFs) were identified, with those related to iron uptake and storage, adhesion, secretion and endotoxin production being the most prevalent. This study underscored the importance of rational use of antimicrobial agents in poultry farming and provided critical insights into the distribution of ARGs and VFs among retail duck-derived MDR E. coli.

Antibiotic resistance genes in Escherichia coli - literature review

Antimicrobial resistance threatens humans and animals worldwide and is recognized as one of the leading global public health issues. Escherichia coli (E. coli) has an unquestionable role in carrying and transmitting antibiotic resistance genes (ARGs), which in many cases are encoded on plasmids or phage, thus creating the potential for horizontal gene transfer. In this literature review, the authors summarize the major antibiotic resistance genes occurring in E. coli bacteria, through the major antibiotic classes. The aim was not only listing the resistance genes against the clinically relevant antibiotics, used in the treatment of E. coli infections, but also to cover the entire resistance gene carriage in E. coli, providing a more complete picture. We started with the long-standing antibiotic groups (beta-lactams, aminoglycosides, tetracyclines, sulfonamides and diaminopyrimidines), then moved toward the newer groups (phenicols, peptides, fluoroquinolones, nitrofurans and nitroimidazoles), and in every group we summarized the resistance genes grouped by the mechanism of their action (enzymatic inactivation, antibiotic efflux, reduced permeability, etc.). We observed that the frequency of antibiotic resistance mechanisms changes in the different groups.

Shifts in surface microbiota after cleaning and disinfection in broiler processing plants: incomplete biofilm eradication revealed by robotic high-throughput screening

Broiler processing environments are a source of spoilage bacteria and potential pathogens. The aim of this study was to investigate the impact of cleaning and disinfection (C&D) on bacterial load and diversity in two broiler processing plants and to determine the efficacy of industry-standard disinfectants (DIs). C&D significantly reduced average bacterial loads on surfaces from 3.7 to 1.8 log CFU/cm2 in Plant A and from 7.0 to 3.8 log CFU/cm2 in Plant B (P < 0.001). Metataxonomics revealed that Acinetobacter and an unknown Enterobacteriaceae genus dominated before C&D in Plants A and B, respectively, while Pseudomonas was predominant after C&D in both plants. Bacterial diversity only declined significantly after C&D in Plant B. Bacterial loads also declined across hygienic zones along the broiler processing line in Plant A. During slaughter, Staphylococcus, Lactobacillus, and Anoxybacillus dominated, and bacterial loads were significantly higher compared with post-slaughter zones, which were dominated by Pseudomonas. Culture-dependent analyses confirmed the presence of Pseudomonas spp. and also bacteria affecting food safety, including Listeria monocytogenes, Escherichia coli, Yersinia enterocolitica, Acinetobacter baumannii, and Pseudomonas aeruginosa. A selection of these was tested against DIs using robotic high-throughput screening. At the recommended user concentrations, DIs effectively inhibited planktonic bacteria and significantly reduced mono-species biofilms. However, none of the DIs completely eradicated all biofilms at these concentrations, with survival rates ranging from 7% to 53%, depending on the DI. In conclusion, C&D effectively reduces the bacterial burden and reshapes the bacterial microbiota with incomplete biofilm eradication by commercial DIs.IMPORTANCEBroiler meat continues to be involved in bacterial disease outbreaks. The surface microbiota in broiler processing environments can be a source of contaminating bacteria. Our study highlights the importance of effective C&D routines since potential pathogens and spoilage bacteria are found in these environments. Furthermore, the study provides evidence of biofilms surviving high concentrations of industry-standard DIs. This emphasizes the importance of additional measures to facilitate biofilm removal, such as mechanical cleaning, but also suggests that there is a need for DIs with stronger biofilm eradication capabilities. Ultimately, it is important to understand and continuously improve the state of hygiene in broiler processing plants to mitigate the risk of foodborne disease outbreaks.

A rapid detection of Avian Pathogenic Escherichia coli (APEC) strains based on minimal number of virulence markers identified by whole genome sequencing

BACKGROUND

Colibacillosis is an important epidemiological and economic issue in poultry farming and breeding. A common problem with avian pathogenic Escherichia coli strains (APEC) that cause this disease is a lack of an uniform identification system, resulting from a variety of serotypes, phylogenetic groups, sequence types and combinations of virulence factors. There are no clearly defined features that can be associated with pathogenicity. Therefore, without precise identification of pathogenic strains and differentiation from commensal strains, there is no possibility of appropriate selection of targeted therapy. The widespread use of whole genome sequencing (WGS) in recent years creates new possibilities in diagnostics. Therefore, the purpose of this study was to select features defining the APEC pathotype, based on next generation sequencing (NGS), and design a diagnostic test based on selected factors.

RESULTS

A PCR diagnostic test is proposed. Three predictors of virulence were chosen according to in silico analysis: two virulence genes: iroC and hlyF, as well as one molecular marker of O78 serotype (wzx-O-antigen flippase of the O78 serotype). A choice of markers was supported by a chicken embryo model.

CONCLUSIONS

Whole genome sequencing of E. coli genomes allowed for the development of a rapid diagnostic method identifying pathogenic strains for poultry: APEC. The developed test can support field observations connected with the strain isolation source and clinical symptoms of the disease.

Modeling the growth and dynamics of uropathogenic Escherichia coli in sugarcane juice for shelf life predictions

In this study, we assessed the effects of temperature and dilution on uropathogenic Escherichia coli (UPEC) growth in sugarcane juice and modeled the kinetics for shelf life simulation. Diluted and undiluted sugarcane juice samples inoculated with a four-strain UPEC cocktail were stored at 4, 10, 15, 20, 30, and 40 °C to evaluate their growth during storage. Changes in UPEC growth were fitted using three primary models (Baranyi, Huang, and reparameterized Gompertz models), and two secondary models (Huang square-root and Ratkowsky square-root models) were selected to evaluate the effect of temperature on specific growth rates. The best-fitted models (reparameterized Gompertz and Huang square-root models) were validated by an additional experiment under isothermal storage (35 °C). Combining differential forms of the Baranyi model, the prediction performances of these models were further validated under storage at dynamic temperature profiles (15 to 37 °C in 4-h cycles). Results revealed that UPEC growth was observed in diluted and undiluted juice samples at storage temperatures of 15 to 40 °C. No growth of UPEC was found in either type of juice at storage temperatures below 10 °C. The estimated minimum growth temperatures (Tmin) of UPEC in sugarcane juice and diluted juice were 10.7 and 11.2 °C, respectively. Validation results showed that the model perfectly estimated UPEC growth under isothermal conditions in both types of sugarcane juice (proportion of prediction error (pPE) = 1.00). Predictions of dynamic conditions in sugarcane juice (pPE = 0.73) and diluted juice (pPE = 0.91) were acceptable, at pPE > 0.7. Using the model, shelf life charts were derived based on the time to reach a certain microbial concentration. In conclusion, these results together with shelf life charts provide valuable information for the food industry to enhance sugarcane juice safety.

Longitudinal analysis of avian pathogenic Escherichia coli (APEC) serogroups and pathotypes from avian colibacillosis in Georgia: A continued investigation - year 2 analysis

Avian pathogenic Escherichia coli (APEC) is a significant cause of worldwide morbidity, mortality, and production loss in the poultry industry. Here, we characterized 115 E. coli isolates from avian-diagnosed colibacillosis cases from Georgia, USA in 2022 as part of a year two follow on surveillance using both current and a newly developed serogrouping tool (Klao9-SeroPCR). The isolates examined were classified into 18 serogroups with the majority classifying as O78, O25, O86, O2, O8, and O1 with 32 isolates classified as untypable serogroups. In this study, the Klao9-seroPCR was able to identify serogroups of 72/115 isolates (62.6 %) using the multiplex PCR assay. This diagnostic PCR assay proved to be a potential technique for the rapid identification of the most common APEC serogroups dominating in Georgia poultry. Genotyping based on detection of selected virulence genes (VAGs) found that 22.6 % of isolates did not harbor any of the targeted genes. This analysis also confirmed that the CoIV plasmid-associated genes (iroN, ompT, hlyF, iss, and aerJ,) are still frequently found among APEC isolates (54-65 %) with a slightly lower prevalence compared to the previous year's study. Phylogenetic analysis showed that the isolates belong to phylogenetic groups G (43 %), group B2 (13 %), group F (6 %), and group A (5 %). Of interest, 30 % were identified as an unknown or cryptic phylogenetic group. This study highlights that there is a shift in the APEC causing disease in birds in the state of Georgia with virulence commonly associated with the presence of the CoIV plasmid in disease strains. Of interest, the new serogrouping panel that is designed to target more common serogroups seen in Georgia has proven to be a rapid screening/ diagnostic tool for implementation in our workflow. This study highlights a need to continue to monitor the APEC serogroups in the field to apply appropriate preventive plans against colibacillosis.

The pathogenicity traits of avian pathogenic Escherichia coli O25-ST131 associated with avian colibacillosis in Georgia poultry and their genotypic and phenotypic overlap with other extraintestinal pathogenic E. coli

AIMS

To characterize Escherichia coli O25 ST131 (O25-ST131) isolated from Georgia poultry-a "global high-risk" clonal strain.

METHODS AND RESULTS

Using multiplex PCR to detect target genes in 98 isolates of avian pathogenic E. coli (APEC) O25 recovered from avians diagnosed with colibacillosis (n = 87) and healthy chicks (n = 11) in Georgia, USA. Eighty-eight isolates were classified as sequence type ST131 clade b and 56% (n = 49) belong to the phylogenetic group B2. Overall, 17% were identified as uropathogenic E. coli (UPEC)-like and 94% of the isolates formed strong to moderate biofilms. The extended-spectrum β-lactamases encoding genes, blaCTX M-15 (24%), carbapenemases encoding genes, and blaOXA48 (16%) were also detected. The isolates harbored FIB (88%), FIC (28%), A/C (14%), and FIIA (6%) plasmid replicons. Interestingly, 78% of the isolates were found to be resistant to chicken serum and 92% showed capabilities for growth in human urine. The isolates showed phenotypic resistance to several antibiotics including chloramphenicol (63%), ciprofloxacin (57%), trimethoprim-sulfamethoxazole (28%), streptomycin (17%), and cefoxitin and meropenem (14%) using the national antimicrobial resistance monitoring system panel.

CONCLUSIONS

Overall, our study provides evidence of the virulence of these global "high-risk" clones in Georgia poultry with some isolates showing genotypic overlap between APEC and UPEC. Also, this clone harbored several virulence genes, antimicrobial-resistant genes, and plasmids. Interestingly, the majority of APEC O25-ST131 isolates can survive and grow in both chicken serum and human urine and warrant further investigation of their potential pathogenicity for both chickens and humans.

Genetic diversity and antibiotic resistance patterns of Escherichia coli isolates causing septicemia: A phylogenetic typing and PFGE analysis

INTRODUCTION

This study aims to analyze clinical isolates of E. coli causing septicemia across various phylogroups utilizing the PFGE method.

MATERIALS AND METHODS

A total of 100 clinical isolates were collected. The presence of CTX-M, TEM, SHV, KPC, MBL and OXA-48 genes was detected by PCR. Additionally, phylotyping, serotyping, and virulence-typing assay were done by PCR and PFGE methods to investigate the genetic diversity of the isolates.

RESULTS

The O1 serotype and the HlyA gene were the most prevalent serotype and virulence gene, respectively. Notably, 34% of the isolates harbored SHV, TEM, and CTX-M-1 β-lactamase genes. All isolates showed resistance to amoxicillin and tetracycline, but no resistance to fosfomycin was seen. The most and least common phylotypes, according to PFGE analysis, belonged to phylogroups B2 and B1, respectively.

CONCLUSION

The data offers valuable insights into the genetic diversity and antibiotic resistance patterns of E. coli isolates responsible for septicemia.

Microbiological Evaluation of Local and Imported Raw Beef Meat at Retail Sites in Oman with Emphasis on Spoilage and Pathogenic Psychrotrophic Bacteria

Determining the microbial quality and safety of meat is crucial because of its high potential to harbor pathogens. To address the critical knowledge gap and shed light on potential contamination risk in the meat supply chain, this study aimed to assess the underexplored microbial quality and safety of marketed beef meat in Oman. Thirty-three beef meat samples from six hypermarkets were analyzed for Aerobic Plate Count (APC), Psychrotrophic Bacteria Count (PBC), and coliform and Escherichia coli counts. Prevalences were 93% and 94% (means: 2.8 ± 1.1 and 2.6 ± 0.8 log CFU/g, respectively) for coliform, and 80% and 83% (means: 1.8 ± 1.4 and 1.7 ± 0.9 log CFU/g, respectively) for E. coli in imported and local samples, respectively. The mean counts of APC (6.3 ± 0.1 log CFU/g) and PBC (6.2 ± 0.2 log CFU/g) were statistically similar but different from those of coliform and E. coli. Bacterial identification using VITEK 2 compact revealed spoilage bacteria (Pseudomonas luteola, Pseudomonas fluorescens, and Shewanella putrefaciens) and pathogenic bacteria (Acinetobacter bumannii complex, Aerococcus viridans, Enterococcus faecalis, and Oligella ureolytica), which demonstrates a potential for both spoilage and pathogen-related risks. It is concluded that the APC counts of all samples exceeded acceptable standards set by the G.C.C. Standardization Organization (GSO), which was established to protect food safety and public health in Oman and other Gulf countries. This suggests an increased risk of spoilage and pathogen contamination. This study provides one of the earliest reports of microbial contamination levels in meat, serving as an eye-opener for policymakers and stakeholders. It highlights a need for stricter hygiene protocols and improved meat handling and processing practices to enhance meat safety and protect public health in Oman and the Gulf region.

Extended-spectrum ß-lactamase (ESBL)- and Carbapenemase-producing Enterobacterales Isolated from Fresh Herbs and Salads at Retail Level in Switzerland

Fresh produce is usually consumed raw or minimally processed, making it a potential vehicle for the transmission of antimicrobial-resistant (AMR) microorganisms to humans. The objective of the study was to assess the occurrence of extended-spectrum ß-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (ESBL-E and CPE), respectively, in 118 fresh herbs and 101 bagged salads collected at retail level in Switzerland and to characterize the isolates' phenotypic and genotypic properties using culture-based methods and whole genome sequencing (WGS). Of the fresh herbs, 6/118 contained ESBL-E and 7/118 yielded CPE. Of the salads, 13/101 contained ESBL-E and 1/101 CPE. Antimicrobial susceptibility testing (AST) identified 9/29 isolates as multidrug-resistant (MDR). ESBL-E were Escherichia coli (n = 6), Klebsiella pneumoniae (n = 4) Enterobacter chuandaensis (n = 1), and Kluyvera spp. (n = 1) carrying ß-lactamase (bla) genes belonging to the cefotaximase-München (blaCTX-M)-groups, Proteus spp. (n = 1) containing Hôpital-Universitaire-de-Genève-bla (blahugA), Raoultella ornithinolytica (n = 1) carrying sulfhydryl reagent variable bla (blaSHV), and Serratia fonticola (n = 7) carrying S. fonticula bla (blaFONA) genes. CPE were Enterobacter asburiae (n = 1) E. cloacae (n = 6) and E. vonholyi (n = 1) carrying imipenemase bla (blaIMI) genes. Several K. pneumoniae sequence types (STs) were identified (ST967, ST628, ST219, and ST1823), which have been linked to human disease and nosocomial outbreaks. They carried blaCTX-M-15 on plasmids detected globally in environmental and clinical samples. E. coli (ST10, ST48, ST609, ST2040, ST6215 and ST3580) and enterotoxigenic E. coli (ETEC) ST2040 carrying blaCTX-M-15 were found. E. cloacae (ST820 and ST1516) with blaIMI-1 have been found previously in clinical settings and community outbreaks. The occurrence and consumption of fresh produce containing MDR ESBL-E and CPE pose substantial public health risks and raise significant food safety concerns.

Determinants of Antibiotic Resistance and Virulence Factors in the Genome of Escherichia coli APEC 36 Strain Isolated from a Broiler Chicken with Generalized Colibacillosis

Objective: Multidrug-resistant, highly pathogenic Escherichia coli strains are the primary causative agents of intestinal and extraintestinal human diseases. The extensive utilization of antibiotics for farm animals has been identified as a contributing factor to the emergence and dissemination of E. coli strains that exhibit multidrug resistance and possess high pathogenic potential. Consequently, a significant research objective is to examine the genetic diversity of pathogenic E. coli strains and to identify those that may pose a threat to human health. Methods: In this study, we present the results of genome sequencing and analysis, as well as the physiological characterization of E. coli strain APEC 36, which was isolated from the liver of a broiler chicken with generalized colibacillosis. Results: We found that APEC 36 possess a number of mechanisms of antibiotic resistance, including antibiotic efflux, antibiotic inactivation, and antibiotic target alteration/replacement/protection. The most widely represented group among these mechanisms was that of antibiotic efflux. This finding is consistent with the strain's documented resistance to multiple antibiotics. APEC 36 has an extremely rare variant of the beta-lactamase CTX-M-169. Notwithstanding the multitude of systems for interfering with foreign DNA present in the strain, seven plasmids have been identified, three of which may possess novel replication origins. Additionally, qnrS1, which confers resistance to fluoroquinolones, was found to be encoded in the genome rather than in the plasmid. This suggests that the determinants of antibiotic resistance may be captured in the genome and stably transmitted from generation to generation. Conclusions: The APEC 36 strain has genes for toxins, adhesins, protectins, and an iron uptake system. The obtained set of genetic and physiological characteristics allowed us to assume that this strain has a high pathogenic potential for humans.

Escherichia coli ST117: exploring the zoonotic hypothesis

Extraintestinal pathogenic Escherichia coli (ExPEC) can lead to severe infections, with additional risks of increasing antimicrobial resistance rates. Genotypic similarities between ExPEC and avian pathogenic E. coli (APEC) support a possible role for a poultry meat reservoir in human disease. Some genomic studies have been done on the ST117 lineage which contaminates poultry meat, carries multidrug resistance, can be found in the human intestinal microbiota, and causes human extraintestinal disease. This study analyzed the genomes of 61 E. coli from Brazilian poultry outbreaks focusing on ST117, to further define its possible zoonotic characteristics by genotypic and phylogenomic analyses, along with 1,699 worldwide ST117 isolates originating from human, animal, and environment sources. A predominance of ST117 was detected in the Brazilian isolates (n = 20/61) frequently carrying resistance to critical antibiotics (>86%) linked to IncFII, IncI1, or IncX4 replicons. High similarities were found between IncX4 from Brazilian outbreaks and those from E. coli recovered from imported Brazilian poultry meat and human clinical cases. The ST117 phylogeny showed non-specificity according to host and continent and an AMR index score indicated the highest resistance in Asia and South America, with the latter statistically more resistant and overrepresented with resistance to extended-spectrum beta-lactamases (ESBL). Most ST117 human isolates were predicted to have a poultry origin (93%, 138/148). In conclusion, poultry is a likely source for zoonotic ExPEC strains, particularly the ST117 lineage which can also serve as a reservoir for resistance determinants against critical antibiotics encoded on highly transmissible plasmids.

IMPORTANCE

Certain extraintestinal pathogenic Escherichia coli (ExPEC) are particularly important as they affect humans and animals. Lineages, such as ST117, are predominant in poultry and frequent carriers of antibiotic resistance, presenting a risk to humans handling or ingesting poultry products. We analyzed ExPEC isolates causing outbreaks in Brazilian poultry, focusing on the ST117 as the most detected lineage. Genomic comparisons with international isolates from humans and animals were performed describing the potential zoonotic profile. The Brazilian ST117 isolates carried resistance determinants against critical antibiotics, mainly on plasmids, in some cases identical to those carried by international isolates. South American ST117 isolates from all sources generally exhibit more resistance, including to critical antibiotics, and worldwide, the vast majority of human isolates belonging to this lineage have a predicted poultry origin. As the world's largest poultry exporter, Brazil has an important role in developing strategies to prevent the dissemination of multidrug-resistant zoonotic ExPEC strains.

Genome-Based Molecular Diversity of Extended-Spectrum β-Lactamase-Producing Escherichia coli From Pigeons in China

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) strains present a significant menace to the well-being of both animals and humans. However, limited information is available regarding their profiles in pigeons. Using a combination of whole genome sequencing, drug susceptibility testing, and bioinformatics analysis, we examined the genomic features and epidemiology of 95 ESBL-EC strains (41 racing and 54 meat pigeons) that were isolated from 11 Chinese cities. These strains belonged to seven phylogenetic groups (A, B1, B2, C, D, E, and F). Moreover, these isolates have 51 serotypes, including several pathogenic ones (e.g., O51, O8, O4, O25, and O6). Notably, two high-risk clones, ST131 O25:H4, were found in racing pigeons and were responsible for the worldwide outbreaks of highly pathogenic and multidrug-resistant (MDR) E. coli infections. In addition, we found 41 multilocus sequence typing types, of which the dominant types were ST155, ST20, ST1011, and ST1196. In total, 91 isolates (95.79%) showed MDR, while eight isolates (8.42%) showed resistance to up to eight classes of antibiotics. Furthermore, we identified a series of ESBL genes in these isolates, including bla CTX-M, bla TEM, bla OXA, bla LAP, and bla CMY. Also, 50 other antibiotic resistance genes (ARGs) were accompanied by the carriage of 33 plasmid replicon types, facilitating the horizontal spread of ARGs. Interestingly, three mcr-1, four mcr-1.1, and one tet(X4) were found in isolates of meat pigeons, and it was possible to successfully transfer the plasmids containing tet(X4) and mcr-1.1 to E. coli C600. In summary, this work presents the complexity of MDR profiles, plasmid profiles, and multiple typing profiles of Chinese ESBL-EC isolates of pigeon origin for the first time. The thorough investigation of ESBL-EC in pigeons presented in this work suggests that racing and meat pigeons are significant ARGs reservoirs.

Unveiling the traits of antibiotic resistance and virulence in Escherichia coli obtained from poultry waste

Antibiotic resistance and virulence factors in avian pathogenic Escherichia coli (APEC) have become significant concerns, contributing to adverse environmental effects. The extensive use of antibiotics in poultry farming has resulted in the emergence of antibiotic-resistant APEC strains. This study prioritizes the molecular screening of APEC to uncover their antibiotic resistance and virulence attributes, with specific attention to their environmental impact. To address the imperative of understanding APEC pathogenesis, our study analyzed 50 poultry waste samples including 10 poultry litter, 15 fecal matter, 15 wastewater, and 10 anatomical waste samples. For the presence of virulence genes, 35 Escherichia coli isolates were subjected to molecular characterization. Amongst these, 27 were APEC strains demonstrating the presence of at least four virulence genes each. Notably, virulence genes such as fimH, ompA, ybjX, waaL, cvaC, hlyF, iss, ompT, and iroN were observed among all the E. coli isolates. Furthermore, eleven of the APEC strains exhibited resistance to tetracycline, ampicillin, sulphonamides, and fluoroquinolones.These findings highlight the role of APEC as a potential source of environmental pollution serving as a reservoir for virulence and resistance genes. Understanding the dynamics of antibiotic resistance and virulence in APEC is essential due to its potential threat to broiler chickens and the broader population through the food chain, intensifying concerns related to environmental pollution. Recognizing the ecological impact of APEC is essential for developing effective strategies to mitigate environmental pollution and safeguard the health of ecosystems and human populations.

Prevalence of specific serogroups, antibiotic resistance and virulence factors of avian pathogenic Escherichia coli (APEC) isolated from clinical cases: A systematic review and meta-analysis

Pathogenic strains of Escherichia coli infecting poultry, commonly called avian pathogenic E. coli (APEC) present significant risks, to the health of both poultry and the general public. This systematic review aimed to examine the prevalence of APEC serotypes, sequence types (ST), phylogenetic groups, virulence factors and antibiotic resistance patterns based on 189 research papers sourced from PubMed, Web of Science, and ProQuest. Then, data were extracted from the selected studies and analyzed to assess the global distribution and characteristics of APEC strains. The metaprop codes in the Meta and Metafor packages of R as implemented in RStudio were then used to conduct meta-analysis. Among APEC strains identified from these different research reports serogroup O78 had the highest overall prevalence (16 %), followed by serogroups O2 (10 %), and O117 (8 %). The most common ST profiles were ST117 (20 %), ST140 (15 %), ST95 (12 %), and ST131 (9 %). ST117 and ST140 are known reservoirs for pathogenic E. coli in humans. Moreover, phylogenetic assessment highlighted the prevalence of phylogroups A, A1, F, D, and B2 among APEC strains indicating diversity in phylogenetic origin within poultry populations. The presence of antimicrobial resistance was notable among APEC strains against antibiotics such as tetracyclines, penicillins, and cephalosporins. This resistance may be linked to use of antimicrobials in poultry production in certain regions presenting challenges for both animal health management and human infection control. Analysis of sequences linked to adherence or virulence indicated that genes encoding adhesins (csg, fimC), iron/metal uptake (sitB, sitC, iroD) and cytotoxicity (estB, hlyF), and serum resistance (traT, iss) were highly prevalent. These factors have been reported to contribute to APEC host colonization and virulence in poultry. In summary, this overview of the characteristics of APEC highlights the pressing importance of monitoring and implementing management approaches to reduce antimicrobial resistance considering that a phylogenetic diversity of E. coli strains causes infections in both poultry and humans and represents a risk to both animal and public health. Further, determining the major conserved aspects and predominant mechanisms of virulence of APEC is critical for improving diagnostics and developing preventative measures to reduce the burden of infection caused by pathogenic E. coli in poultry and lower risks associated with foodborne transmission of E. coli to humans through poultry and poultry products.

Phylogenetic diversity and virulence gene characteristics of Escherichia coli from pork and patients with urinary tract infections in Thailand

Extraintestinal pathogenic Escherichia coli (ExPEC), especially uropathogenic E. coli (UPEC) are responsible for urinary tract infections (UTIs), while diarrheagenic E. coli (DEC) cause foodborne illnesses. These pathogenic E. coli are a serious threat to human health and a public concern worldwide. However, the evidence on pork E. coli (PEC) harboring UPEC virulence-associated genes is currently limited. Therefore, this study aimed to determine the phylogroups, virulence genes, and their association between PEC and UPEC from UTI patients. In this study, 330 E. coli were obtained from archived stock culture isolated from pork (PEC; n = 165) and urine of patients with UTIs (UPEC; n = 165) during 2014-2022. Phylogroups, UPEC- and diarrheagenic E. coli (DEC) associated virulence genes were assessed using PCR assays. The results showed that phylogroups A (50.3%), and B1 (32.1%) were commonly found among PEC whereas phylogroups B2 (41.8%), and C (25.5%) were commonly detected in the UPEC. PEC and UPEC carried similar virulence-associated genes with different percentages. The most frequent UPEC virulence-associated gene among UPEC, and PEC strains was fimH, (93.3%, and 92.1%), followed by iucC (55.2%, and 12.7%), papC (21.8%, and 4.2%), afaC (22.4%, and 0%), hlyCA (17%, and 0.6%), cnf (16.4%, and 0.6%), and sfa/focDE (8.5%, and 4.8%). Additionally, 6 of 27 UPEC virulence-associated gene patterns were found in both PEC and UPEC strains regardless of phylogroups. Furthermore, the DEC virulence-associated genes were found in only 3 strains, one from PEC harboring eae, and two from UPEC carried fimH-bfpA or afaC-CVD432 indicating hybrid strains. Cluster analysis showed a relationship between PEC and UPEC strains and demonstrated that PEC harboring UPEC virulence-associated genes in pork may be associated with UPEC in humans. Food safety and hygiene practices during pork production chain are important procedures for minimizing cross-contamination of these strains that could be transmitted to the consumers.

Comparative genomics of quinolone-resistant Escherichia coli from broilers and humans in Norway

BACKGROUND

The usage of fluoroquinolones in Norwegian livestock production is very low, including in broiler production. Historically, quinolone-resistant Escherichia coli (QREC) isolated from Norwegian production animals rarely occur. However, with the introduction of a selective screening method for QREC in the Norwegian monitoring programme for antimicrobial resistance in the veterinary sector in 2014; 89.5% of broiler caecal samples and 70.7% of broiler meat samples were positive. This triggered the concern if there could be possible links between broiler and human reservoirs of QREC. We are addressing this by characterizing genomes of QREC from humans (healthy carriers and patients) and broiler isolates (meat and caecum).

RESULTS

The most frequent mechanism for quinolone resistance in both broiler and human E. coli isolates were mutations in the chromosomally located gyrA and parC genes, although plasmid mediated quinolone resistance (PMQR) was also identified. There was some relatedness of the isolates within human and broiler groups, but little between these two groups. Further, some overlap was seen for isolates with the same sequence type isolated from broiler and humans, but overall, the SNP distance was high.

CONCLUSION

Based on data from this study, QREC from broiler makes a limited contribution to the incidence of QREC in humans in Norway.

Molecular epidemiology, antibiotic resistance profile and frequency of integron 1 and 2 in adherent-invasive Escherichia coli isolates of colorectal cancer patients

This study explores the prevalence of adherent-invasive Escherichia coli (AIEC) in colorectal cancer (CRC) patients and investigates the potential of effective intracellular antibiotics as a therapeutic strategy for CRC patients with AIEC infections. Considering the pivotal role of integrons in bacterial antibiotic resistance, the frequency of class 1 and 2 integrons in AIEC isolated from CRC patients, in one of the referenced 3 gastroenterology clinics in Isfahan, Iran was examined. AIEC strains were isolated from the colorectal biopsies and their antimicrobial sensitivity was assessed using the disc diffusion method. Polymerase chain reaction (PCR) was employed to detect intl1 and intl2. The multilocus sequence typing (MLST) method was utilized to type 10 selected isolates. Of the 150 samples, 24 were identified as AIEC, with the highest number isolated from CRC2 (33.4%) and CRC1 (29.16%), and the least from the FH group (8.3%) and control group (12.5%). int1 in 79.2% and int2 in 45.8% of AIEC strains were found and 41.6% of strains had both integrons. AIEC isolates with int1 exhibited the highest sensitivity to trimethoprim-sulfamethoxazole (57.9%), while those with int2 showed the highest sensitivity to ciprofloxacin (63.6%). A significant association between resistance to rifampin and integron 2 presence in AIEC isolates was observed. Furthermore, a significant correlation between integron 1 presence, invasion, survival, and replication within macrophages in AIEC strains was identified. MLST analysis revealed ST131 from CC131 with integron 1 as the most common sequence type (ST). The emergence of such strains in CRC populations poses a serious public health threat. The distribution pattern of STs varied among studied groups, with pandemic STs highlighting the importance of examining and treating patients infected with these isolates. Comprehensive prospective clinical investigations are warranted to assess the prognostic value of detecting this pathovar in CRC and to evaluate therapeutic techniques targeting drug-resistant AIECs, such as phage therapy, bacteriocins, and anti-adhesion compounds, for CRC prevention and treatment.

Whole-genome sequencing of Escherichia coli from retail meat in China reveals the dissemination of clinically important antimicrobial resistance genes

Escherichia coli is one of the important reservoirs of antimicrobial resistance genes (ARG), which often causes food-borne diseases and clinical infections. Contamination with E. coli carrying clinically important antimicrobial resistance genes in retail meat products can be transmitted to humans through the food chain, posing a serious threat to public health. In this study, a total of 330 E. coli strains were isolated from 464 fresh meat samples from 17 food markets in China, two of which were identified as enterotoxigenic and enteropathogenic E. coli. Whole genome sequencing revealed the presence of 146 different sequence types (STs) including 20 new STs, and 315 different clones based on the phylogenetic analysis, indicating the high genetic diversity of E. coli from retail meat products. Antimicrobial resistance profiles showed that 82.42 % E. coli were multidrug-resistant strains. A total of 89 antimicrobial resistance genes were detected and 12 E. coli strains carried clinically important antimicrobial resistance genes blaNDM-1, blaNDM-5, mcr-1, mcr-10 and tet(X4), respectively. Nanopore sequencing revealed that these resistance genes are located on different plasmids with the ability of horizontal transfer, and their genetic structure and environment are closely related to plasmids isolated from humans. Importantly, we reported for the first time the presence of plasmid-mediated mcr-10 in E. coli from retail meat. This study revealed the high genetic diversity of food-borne E. coli in retail meat and emphasized their risk of spreading clinically important antimicrobial resistance genes.

Phenotypic and genotypic characterization of Escherichia coli isolated from the chicken liver in relation to slaughterhouse conditions

Avian pathogenic Escherichia coli (APEC) has been identified as a sub-group of extraintestinal pathogenic E. coli (ExPEC). Recent studies indicate APEC as a potential foodborne zoonotic pathogen and a source or reservoir of human extraintestinal infections. The slaughtering and processing of poultry in low-income countries such as Jordan occurs in two distinct ways: in informal facilities known as Natafat and in formal slaughterhouses. This study compared E. coli phenotypes and genotypes according to slaughtering conditions (formal slaughterhouses vs. informal slaughter facilities). Therefore, liver samples (n = 242) were collected from formal (n = 121) and informal slaughter facilities (n = 121). Results revealed a high prevalence (94.2%) of E. coli among all isolates, with 59 (17 formal and 42 informal) isolates considered avian pathogenic E. coli (APEC) based on the virulence-associated genes. The prevalence of resistance among isolates was relatively high, reaching up to 99% against penicillin and 97% against nalidixic acid. However, the prevalence of resistance was the lowest (1.3%) against both meropenem and imipenem. Based on the MIC test findings, colistin resistance was 46.9% (107/228). The mcr -1 gene prevalence was 51.4% (55/107), of which 17.1 % were from formal plants (6/36) and 68.1% from informal facilities (49/72). Interestingly, only one isolate (0.9%) expressed mcr-10. Escherichia coli O157:H7 and associated virulence genes were found more in informal (n = 15 genes) than in formal slaughterhouses (n = 8). Phylogroups B1, C, and A were the most frequent in 228 E. coli isolates, while G, B2, and clade were the least frequent. In conclusion, these findings highlight the importance of implementing biosecurity measures in slaughterhouses to reduce antibiotic-resistant E. coli spread. Furthermore, this study provides valuable insights into the effects of wet market (Natafat) slaughter conditions on increasing bacterial resistance and virulence.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021-2022

This report by the European Food Safety Authority and the European Centre for Disease prevention and Control, provides an overview of the main findings of the 2021-2022 harmonised Antimicrobial Resistance (AMR) monitoring in Salmonella spp., Campylobacter jejuni and C. coli from humans and food-producing animals (broilers, laying hens and fattening turkeys, fattening pigs and cattle under one year of age) and relevant meat thereof. For animals and meat thereof, AMR data on indicator commensal Escherichia coli, presumptive extended-spectrum beta-lactamases (ESBL)-/AmpC beta-lactamases (AmpC)-/carbapenemase (CP)-producing E. coli, and the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) are also analysed. Generally, resistance levels differed greatly between reporting countries and antimicrobials. Resistance to commonly used antimicrobials was frequently found in Salmonella and Campylobacter isolates from humans and animals. In humans, increasing trends in resistance to one of two critically antimicrobials (CIA) for treatment was observed in poultry-associated Salmonella serovars and Campylobacter, in at least half of the reporting countries. Combined resistance to CIA was however observed at low levels except in some Salmonella serovars and in C. coli from humans and animals in some countries. While CP-producing Salmonella isolates were not detected in animals in 2021-2022, nor in 2021 for human cases, in 2022 five human cases of CP-producing Salmonella were reported (four harbouring bla OXA-48 or bla OXA-48-like genes). The reporting of a number of CP-producing E. coli isolates (harbouring bla OXA-48, bla OXA-181, bla NDM-5 and bla VIM-1 genes) in fattening pigs, cattle under 1 year of age, poultry and meat thereof by a limited number of MSs (5) in 2021 and 2022, requires a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC-producers in E. coli) showed an encouraging progress in reducing AMR in food-producing animals in several EU MSs over the last 7 years.

Characteristics of antimicrobial resistance in Escherichia coli isolated from retail meat products in North Carolina

BACKGROUND

Escherichia coli is commonly used as an indicator for antimicrobial resistance (AMR) in food, animal, environment, and human surveillance systems. Our study aimed to characterize AMR in E. coli isolated from retail meat purchased from grocery stores in North Carolina, USA as part of the National Antimicrobial Resistance Monitoring System (NARMS).

MATERIALS AND METHODS

Retail chicken (breast, n = 96; giblets, n = 24), turkey (n = 96), and pork (n = 96) products were purchased monthly from different counties in North Carolina during 2022. Label claims on packages regarding antibiotic use were recorded at collection. E. coli was isolated from meat samples using culture-based methods and isolates were characterized for antimicrobial resistance using whole genome sequencing. Multi-locus sequence typing, phylogroups, and a single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenic tree was generated. Data were analyzed statistically to determine differences between antibiotic use claims and meat type.

RESULTS

Of 312 retail meat samples, 138 (44.2%) were positive for E. coli, with turkey (78/138; 56.5%) demonstrating the highest prevalence. Prevalence was lower in chicken (41/138; 29.7%) and pork (19/138;13.8%). Quality sequence data was available from 84.8% (117/138) of the E. coli isolates, which included 72 (61.5%) from turkey, 27 (23.1%) from chicken breast, and 18 (15.4%) from pork. Genes associated with AMR were detected in 77.8% (91/117) of the isolates and 35.9% (42/117) were defined as multidrug resistant (MDR: being resistant to ≥3 distinct classes of antimicrobials). Commonly observed AMR genes included tetB (35%), tetA (24.8%), aph(3'')-lb (24.8%), and blaTEM-1 (20.5%), the majority of which originated from turkey isolates. Antibiotics use claims had no statistical effect on MDR E. coli isolates from the different meat types (X2 = 2.21, p = 0.33). MDR was observed in isolates from meat products with labels indicating "no claims" (n = 29; 69%), "no antibiotics ever" (n = 9; 21.4%), and "organic" (n = 4; 9.5%). Thirty-four different replicon types were observed. AMR genes were carried on plasmids in 17 E. coli isolates, of which 15 (88.2%) were from turkey and two (11.8%) from chicken. Known sequence types (STs) were described for 81 E. coli isolates, with ST117 (8.5%), ST297 (5.1%), and ST58 (3.4%) being the most prevalent across retail meat types. The most prevalent phylogroups were B1 (29.1%) and A (28.2%). Five clonal patterns were detected among isolates.

CONCLUSIONS

E. coli prevalence and the presence of AMR and MDR were highest in turkey retail meat. The lack of an association between MDR E. coli in retail meat and antibiotic use claim, including those with no indication of antimicrobial use, suggests that additional research is required to understand the origin of resistance. The presence of ST117, an emerging human pathogen, warrants further surveillance. The isolates were distinctly diverse suggesting an instability in population dynamics.

Virulome analysis of Escherichia coli ST117 from bovine sources identifies similarities and differences with strains isolated from other food animals

Escherichia coli ST117 is a pandemic extraintestinal pathogenic E. coli (ExPEC) causing significant morbidity globally. Poultry are a known reservoir of this pathogen, but the characteristics of ST117 strains from other animal sources have not been adequately investigated. Here we characterize the genomes of 36 ST117 strains recovered primarily from preweaned dairy calves, but also from older postweaned calves and lactating cows, in the context of other bovine-associated strains and strains from poultry, swine, and humans. Results of this study demonstrate that bovine-associated ST117 genomes encode virulence factors (VFs) known to be involved in extraintestinal infections, but also occasionally encode the Shiga toxin, a virulence factor (VF) involved in severe gastrointestinal infections and more frequently identified in E. coli from ruminants than other animals. Bovine-associated ST117 genomes were also more likely to encode afa-VIII (adhesins), pap (P-fimbriae), cdt (cytolethal distending toxin), and stx (Shiga toxins) than were poultry and swine-associated genomes. All of the ST117 genomes were grouped into seven virulence clusters, with bovine-associated genomes grouping into Clusters 1, 2, 4, 5, but not 3, 6, or 7. Major differences in the presence of virulence factors between clusters were observed as well. Antimicrobial resistance genes were detected in 112 of 122 (91%) bovine-associated genomes, with 103 of these being multidrug-resistant (MDR). Inclusion of genomes that differed from ST117 by one multi-locus sequence type (MLST) allele identified 31 STs, four of these among the bovine-associated genomes. These non-ST117 genomes clustered with the ST117 genomes suggesting that they may cause similar disease as ST117. Results of this study identify cattle as a reservoir of ST117 strains, some of which are highly similar to those isolated from other food animals and some of which have unique bovine-specific characteristics.

Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract

Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.

Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock

The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3')-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.

Complete genome sequence of an avian pathogenic Escherichia coli strain isolated from poultry

Avian pathogenic Escherichia coli found in the avian intestinal tract can cause systemic disease in birds and act as a foodborne zoonotic pathogen associated with human disease. Here, we report the complete genome sequence of E. coli strain H1998 isolated from a chicken with colisepticemia.

Strain belonging to an emerging, virulent sublineage of ST131 Escherichia coli isolated in fresh spinach, suggesting that ST131 may be transmissible through agricultural products

Food contamination with pathogenic Escherichia coli can cause severe disease. Here, we report the isolation of a multidrug resistant strain (A23EC) from fresh spinach. A23EC belongs to subclade C2 of ST131, a virulent clone of Extraintestinal Pathogenic E. coli (ExPEC). Most A23EC virulence factors are concentrated in three pathogenicity islands. These include PapGII, a fimbrial tip adhesin linked to increased virulence, and CsgA and CsgB, two adhesins known to facilitate spinach leaf colonization. A23EC also bears TnMB1860, a chromosomally-integrated transposon with the demonstrated potential to facilitate the evolution of carbapenem resistance among non-carbapenemase-producing enterobacterales. This transposon consists of two IS26-bound modular translocatable units (TUs). The first TU carries aac(6')-lb-cr, bla OXA-1, ΔcatB3, aac(3)-lle, and tmrB, and the second one harbors bla CXT-M-15. A23EC also bears a self-transmissible plasmid that can mediate conjugation at 20°C and that has a mosaic IncF [F(31,36):A(4,20):B1] and Col156 origin of replication. Comparing A23EC to 86 additional complete ST131 sequences, A23EC forms a monophyletic cluster with 17 other strains that share the following four genomic traits: (1) virotype E (papGII+); (2) presence of a PAI II536-like pathogenicity island with an additional cnf1 gene; (3) presence of chromosomal TnMB1860; and (4) frequent presence of an F(31,36):A(4,20):B1 plasmid. Sequences belonging to this cluster (which we named "C2b sublineage") are highly enriched in septicemia samples and their associated genetic markers align with recent reports of an emerging, virulent sublineage of the C2 subclade, suggesting significant pathogenic potential. This is the first report of a ST131 strain belonging to subclade C2 contaminating green leafy vegetables. The detection of this uropathogenic clone in fresh food is alarming. This work suggests that ST131 continues to evolve, gaining selective advantages and new routes of transmission. This highlights the pressing need for rigorous epidemiological surveillance of ExPEC in vegetables with One Health perspective.

Comparison of antibiotic-resistant Escherichia coli and extra-intestinal pathogenic E. coli from main river basins under different levels of the sewer system development

Antimicrobial-resistant Escherichia coli in the aquatic environments is considered a strong indicator of sewage or animal waste contamination and antibiotic pollution. Sewer construction and wastewater treatment plant (WWTP) infrastructure may serve as concentrated point sources of contamination of antibiotic-resistant bacteria and antibiotic resistance genes. In this study, we focused on the distribution of antimicrobial-resistant E. coli in two rivers with large drainage areas and different urbanisation levels. E. coli from Kaoping River with drainage mainly from livestock farming had higher resistance to antibiotics (e.g. penicillins, tetracyclines, phenicols, aminoglycosides, and sulpha drugs) and presented more positive detection of antibiotic-resistance genes (e.g. ampC, blaTEM, tetA, and cmlA1) than that from Tamsui River. In Kaoping River with a lower percentage of sewer construction nearby (0-30%) in contrast to a higher percentage of sewer construction (55-92%) in Tamsui River, antimicrobial-resistant E. coli distribution was related to livestock farming waste. In Tamsui River, antimicrobial resistant E. coli isolates were found more frequently in the downstream drainage area of WWTPs with secondary water treatment than that of WWTPs with tertiary water treatment. The Enterobacterial Repetitive Intergenic Consensus (ERIC) PCR showed that the fingerprinting group was significantly related to the sampling site (p < 0.01) and sampling date (p < 0.05). By utilising ERIC-PCR in conjunction with antibiotic susceptibility and antibiotic-resistance gene detection, the relationship among different strains of E. coli could be elucidated. Furthermore, we identified the presence of six extra-intestinal pathogenic E. coli isolates and antibiotic-resistant E. coli isolates near drinking water sources, posing a potential risk to public health through community transmission. In conclusion, this study identified environmental factors related to antibiotic-resistant bacteria and antibiotic-resistance gene contamination in rivers during urban development. The results facilitate the understanding of specific management of different waste streams across different urban areas. Periodic surveillance of the effects of WWTPs and livestock waste containing antibiotic-resistant bacteria and antibiotic-resistance genes on river contamination is necessary.

A culture-based assessment of the microbiota of conventional and free-range chicken meat from Irish processing facilities

Chicken meat is the most popularly consumed meat worldwide, with free-range and ethically produced meat a growing market among consumers. However, poultry is frequently contaminated with spoilage microbes and zoonotic pathogens which impact the shelf-life and safety of the raw product, constituting a health risk to consumers. The free-range broiler microbiota is subject to various influences during rearing such as direct exposure to the external environment and wildlife which are not experienced during conventional rearing practices. Using culture-based microbiology approaches, this study aimed to determine whether there is a detectable difference in the microbiota from conventional and free-range broilers from selected Irish processing plants. This was done through analysis of the microbiological status of bone-in chicken thighs over the duration of the meat shelf-life. It was found that the shelf-life of these products was 10 days from arrival in the laboratory, with no statistically significant difference (P > 0.05) evident between free-range and conventionally raised chicken meat. A significant difference, however, was established in the presence of pathogenesis-associated genera in different meat processors. These results reinforce past findings which indicate that the processing environment and storage during shelf-life are key determinants of the microflora of chicken products reaching the consumer.

Antimicrobial Resistance and Clonal Lineages of Escherichia coli from Food-Producing Animals

Escherichia coli are one of the most important pathogenic bacteria readily found in the livestock and widely studied as an indicator that carries drug-resistant genes between humans, animals, and the environment. The use of antimicrobials in the food chain, particularly in food-producing animals, is recognized as a significant contributor to the development and spread of antimicrobial resistance (AMR) and resistance genes can be transferred from the farm through the food-chain. The objective of this review is to highlight the background of the antimicrobials use in food-producing animals, more specifically, to study clonal lineages and the resistance profiles observed in E. coli, as well as in extended spectrum beta-lactamases (ESBL) producing E. coli, in a set of food-production animals with greater relevance in food consumption, such as pigs, poultry, cattle, fish farming and rabbits. Regarding the prevalence of ESBL-producing E. coli among farm animals, high-to-moderate prevalence was observed, and the highest resistance rates to tetracycline and ampicillin was detected in different farms in all geographic regions. Worldwide pandemic clones and high-risk zoonotic E. coli clones have been identified in most food-producing animals, and some of these clones are already disseminated in different niches, such as the environment and humans. A better understanding of the epidemiology of E. coli and ESBL-producing E. coli in livestock is urgently needed. Animal production is one of the major causes of the antibiotic resistance problem worldwide and a One Health approach is needed.

Genomics, biofilm formation and infection of bladder epithelial cells in potentially uropathogenic Escherichia coli (UPEC) from animal sources and human urinary tract infections (UTIs) further support food-borne transmission

Escherichia coli is the main cause of urinary tract infections (UTI). While genomic comparison of specific clones recovered from animals, and human extraintestinal infections show high identity, studies demonstrating the uropathogenicity are lacking. In this study, comparative genomics combined with bladder-cell and biofilm formation assays, were performed for 31 E. coli of different origins: 7 from meat (poultry, beef, and pork); 2 from avian-farm environment; 12 from human uncomplicated UTI, uUTI; and 10 from human complicated UTI, cUTI. These isolates were selected based on their genetic uropathogenic (UPEC) status and phylogenetic background. In silico analysis revealed similar virulence-gene profiles, with flagella, type 1 and curli fimbriae, outer-membrane proteins (agn43, ompT, iha), and iron-uptake (iutA, entA, and fyuA) associated-traits as the most prevalent (>65%). In bladder-cell assays, moderate to strong values of association (83%, 60%, 77.8%) and invasion (0%, 70%, 55.5%) were exhibited by uUTI, cUTI, and animal-derived isolates, respectively. Of interest, uUTI isolates exhibited a significantly lower invasive capacity than cUTI isolates (p < 0.05). All isolates but one produced measurable biofilm. Notably, 1 turkey meat isolate O11:H6-F-ST457, and 2 cUTI isolates of the pandemic lineages O83:H42-F-ST1485-CC648 and O25b:H4-B2-ST131, showed strong association, invasion and biofilm formation. These isolates showed common carriage of type 1 fimbriae and csg operons, toxins (hlyF, tsh), iron uptake systems (iutA, entA, iroN), colicins, protectins (cvaC, iss, kpsM, traT), ompT, and malX. In summary, the similar in vitro behaviour found here for certain E. coli clones of animal origin would further reinforce the role of food-producing animals as a potential source of UPEC. Bladder-cell infection assays, combined with genomics, might be an alternative to in vivo virulence models to assess uropathogenicity.

Core genome multilocus sequence typing (cgMLST) confirms systemic spread of avian pathogenic Escherichia coli (APEC) in broilers with cellulitis

Broiler cellulitis has emerged as an important cause of economic losses for farmers and slaughter plants from carcass condemnation at processing. Avian pathogenic Escherichia coli (APEC) has been identified as the main causative agent. The aim was to characterize E. coli isolated from cellulitis and organs in broilers at slaughter by whole genome sequencing analysis to study if systemic spread could be confirmed. Isolates were collected post-mortem from 101 carcasses condemned due to dermatitis/cellulitis from five commercial farms and six flocks. Forty-six isolates were characterised to determine serotypes, sequence types and virulence-associated genes. Analysis by cgMLST was performed to study the genetic similarity between isolates from the same broiler, among birds from the same flock and between flocks. Escherichia coli was isolated from 90% of birds from subcutaneous samples. In 20 broilers, E. coli was isolated from organs in pure culture or mixed with sparse growth of other bacteria. In eight of these, there were post-mortem findings suggestive of systemic bacterial spread. The majority of the isolates from the same bird and flock belonged to the same serotype and sequence type and were genetically indistinguishable, but differed when compared between flocks. Common APEC virulence genes, i.e. chuA, fyuA, hlyF, iroN, irp2, iss, ompT, sitA, TerC, TraT, were present in > 87% of the isolates. We conclude that evidence of systemic spread of E. coli from cellulitis was present in some birds at time of slaughter but cannot be reliably detected at meat inspection.

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

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

Salmonella Heidelberg and Salmonella Minnesota in Brazilian broilers: Genomic characterization of third-generation cephalosporin and fluoroquinolone-resistant strains

Salmonella serovars Heidelberg and Minnesota encoding antimicrobial resistance to third-generation cephalosporins and fluoroquinolones are often detected in poultry/poultry meat. We analysed the genomes of 10 Salmonella Heidelberg (SH) and 4 Salmonella Minnesota (SM) from faecal isolates of Brazilian poultry. These featured virulent and multidrug-resistant characteristics, with AmpC beta-lactamase (bla_CMY-2 ) predominance (9/14), for all SM (4/4) and some SH (3/10) located on IncC plasmid replicons. IncC carrying bla_CTX-M-2 was only detected among SH (3/10). Mutation in the gyrA/parC genes was present in all SH, whereas SM harboured parC mutation plus qnrB19 on ColRNAI plasmids (3/4). In silico resistance overall corroborated with phenotypic results. Core genome phylogenies showed close clustering and high similarities between the Brazilian and poultry meat/food isolates from Europe, and to human isolates from European countries with documented import of Brazilian poultry meat. Conjugation assays with SM successfully transferred bla_CMY-2 , and qnrB19 to an Escherichia coli recipient. The findings reinforce the ongoing antimicrobial resistance acquisition of SH and Minnesota and the risks for disseminating resistant strains and/or mobile elements which may increasingly affect importing countries and the need for controlling AMR in major poultry-exporting countries like Brazil.

The Diversity of Escherichia coli Pathotypes and Vaccination Strategies against This Versatile Bacterial Pathogen

Escherichia coli (E. coli) is a gram-negative bacillus and resident of the normal intestinal microbiota. However, some E. coli strains can cause diseases in humans, other mammals and birds ranging from intestinal infections, for example, diarrhea and dysentery, to extraintestinal infections, such as urinary tract infections, respiratory tract infections, meningitis, and sepsis. In terms of morbidity and mortality, pathogenic E. coli has a great impact on public health, with an economic cost of several billion dollars annually worldwide. Antibiotics are not usually used as first-line treatment for diarrheal illness caused by E. coli and in the case of bloody diarrhea, antibiotics are avoided due to the increased risk of hemolytic uremic syndrome. On the other hand, extraintestinal infections are treated with various antibiotics depending on the site of infection and susceptibility testing. Several alarming papers concerning the rising antibiotic resistance rates in E. coli strains have been published. The silent pandemic of multidrug-resistant bacteria including pathogenic E. coli that have become more difficult to treat favored prophylactic approaches such as E. coli vaccines. This review provides an overview of the pathogenesis of different pathotypes of E. coli, the virulence factors involved and updates on the major aspects of vaccine development against different E. coli pathotypes.

Hospital-acquired and zoonotic bacteria from a veterinary hospital and their associated antimicrobial-susceptibility profiles: A systematic review

Background

Hospital-acquired infections (HAIs) are associated with increased mortality, morbidity, and an economic burden due to costs associated with extended hospital stays. Furthermore, most pathogens associated with HAIs in veterinary medicine are zoonotic. This study used published data to identify organisms associated with HAIs and zoonosis in veterinary medicine. Furthermore, the study also investigated the antimicrobial-susceptibility profile of these bacterial organisms.

Methods

A systematic literature review was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. Search terms and five electronic databases were used to identify studies published over 20 years (2000-2020). The risk of bias was assessed using the "Strengthening the Reporting of Observational Studies in Epidemiology-Vet" (STROBE-Vet) checklist.

Results

Out of the identified 628 papers, 27 met the inclusion criteria for this study. Most studies (63%, 17/27) included were either from small animal or companion animal clinics/hospitals, while 5% (4/27) were from large animal clinics/hospitals inclusive of bovine and equine hospitals. Hospital-acquired bacteria were reported from environmental surfaces (33%, 9/27), animal clinical cases (29.6%, 8/27), and fomites such as cell phones, clippers, stethoscopes, and computers (14.8%, 4/27). Staphylococcus spp. was the most (63%; 17/27) reported organism, followed by Escherichia coli (19%; 5/27), Enterococcus spp. (15%, 4/27), Salmonella spp. (15%; 4/27), Acinetobacter baumannii (15%, 4/27), Clostridioides difficile (4%, 1/27), and Pseudomonas aeruginosa (4%; 1/27). Multidrug-resistant (MDR) organisms were reported in 71% (12/17) of studies linked to Methicillin-resistant Staphylococcus aureus (MRSA), Methicillin-resistant Staphylococcus pseudintermedius (MRSP), Enterococcus spp., Salmonella Typhimurium, A. baumannii, and E. coli. The mecA gene was identified in both MRSA and MRSP, the blaCMY-2 gene in E. coli and Salmonella spp., and the vanA gene in E. faecium isolate. Six studies reported organisms from animals with similar clonal lineage to those reported in human isolates.

Conclusion

Organisms associated with hospital-acquired infections and zoonosis have been reported from clinical cases, environmental surfaces, and items used during patient treatment and care. Staphylococcus species is the most reported organism in cases of HAIs and some isolates shared similar clonal lineage to those reported in humans. Some organisms associated with HAIs exhibit a high level of resistance and contain genes associated with antibiotic resistance.

Molecular detection and antimicrobial resistance profiles of Extended-Spectrum Beta-Lactamase (ESBL) producing Escherichia coli in broiler chicken farms in Malaysia

Antimicrobial resistance is one of the major public health threats globally. This challenge has been aggravated with the overuse and misuse of antibiotics in food animals and humans. The present study aimed to investigate the prevalence of Extended-Spectrum β-lactamase (ESBL) genes in Escherichia coli (E. coli) isolated from broiler chickens in Kelantan, Malaysia. A total of 320 cloacal swabs were collected from farms in different districts of Kelantan and were analyzed using routine bacteriology, antimicrobial susceptibility test, and molecular techniques for further identification and characterization of ESBL encoding genes. Based on PCR detection for the E. coli species-specific Pho gene, 30.3% (97/320) of isolates were confirmed as E. coli, and 84.5% (82/97) of the isolates were positive for at least one ESBL gene. Majority of the isolates, 62.9% (61/97) were harboring blaCTX-M followed by 45.4% (44/97) of blaTEM genes, while 16.5% (16/97) of the isolates were positive for both mcr-1 and ESBL genes. Overall, 93.8% (90/97) of the E. coli were resistant to three or more antimicrobials; indicating that the isolates were multi-drug resistance. 90.7% of multiple antibiotic resistance (MAR) index value greater than 0.2, would also suggest the isolates were from high-risk sources of contamination. The MLST result shows that the isolates are widely diverse. Our findings provide insight into the alarmingly high distribution of antimicrobial resistant bacteria, mainly ESBL producing E. coli in apparently healthy chickens indicating the role of food animals in the emergence and spread of antimicrobial resistance, and the potential public health threats it may pose.

Exposure to industrial hog and poultry operations and urinary tract infections in North Carolina, USA

An increasing share of urinary tract infections (UTIs) are caused by extraintestinal pathogenic Escherichia coli (ExPEC) lineages that have also been identified in poultry and hogs with high genetic similarity to human clinical isolates. We investigated industrial food animal production as a source of uropathogen transmission by examining relationships of hog and poultry density with emergency department (ED) visits for UTIs in North Carolina (NC). ED visits for UTI in 2016-2019 were identified by ICD-10 code from NC's ZIP code-level syndromic surveillance system and livestock counts were obtained from permit data and aerial imagery. We calculated separate hog and poultry spatial densities (animals/km2) by Census block with a 5 km buffer on the block perimeter and weighted by block population to estimate mean ZIP code densities. Associations between livestock density and UTI incidence were estimated using a reparameterized Besag-York-Mollié (BYM2) model with ZIP code population offsets to account for spatial autocorrelation. We excluded metropolitan and offshore ZIP codes and assessed effect measure modification by calendar year, ZIP code rurality, and patient sex, age, race/ethnicity, and health insurance status. In single-animal models, hog exposure was associated with increased UTI incidence (rate ratio [RR]: 1.21, 95 % CI: 1.07-1.37 in the highest hog-density tertile), but poultry exposure was associated with reduced UTI rates (RR: 0.86, 95 % CI: 0.81-0.91). However, the reference group for single-animal poultry models included ZIP codes with only hogs, which had some of the highest UTI rates; when compared with ZIP codes without any hogs or poultry, there was no association between poultry exposure and UTI incidence. Hog exposure was associated with increased UTI incidence in areas that also had medium to high poultry density, but not in areas with low poultry density, suggesting that intense hog production may contribute to increased UTI incidence in neighboring communities.

Antimicrobial resistance profile of Escherichia coli isolated from poultry litter

Antimicrobial resistance is a threat to animal and human health. As a commensal and zoonotic bacterium, Escherichia coli has the potential to be a pathogenic source of antimicrobial resistance. The purpose of this study aimed to investigate the antimicrobial resistance profile of E. coli isolated from litter collected from pens in a broiler chicken experiment. E. coli was isolated from litter samples (n = 68 isolates) of 16 pens housing broilers to d 53 of age. Resistance to 10 antimicrobials was observed by disc diffusion. The presence of 23 antimicrobial and heavy metal resistance genes, O serogroups, and avian pathogenic E. coli (APEC-like) minimal predictor genes were identified through PCR. E. coli isolates presented the greatest resistance to cephalothin (54.4%), tetracycline (27.9%), streptomycin (29.4%), ampicillin (20.6%), colistin (13.2%), sulphonamides (8.8%), and imipenem (1.5%). Multidrug resistance to at least 3 antimicrobials was observed in 22.1% of isolates. The identified O-types of the E. coli isolates were O15, O75, O78, and O91. There was a greater likelihood that the genes groEL, aph(3)IA, silP, sull, aadA, qacEdelta1, iroN, ompTp, and hlyF were present in isolates that exhibited ampicillin resistance (P ≤ 0.05). There was a greater likelihood that the groEL gene was present in isolates resistant to ampicillin, colistin, tetracycline, sulphonamides, or cephalothin (P ≤ 0.05). Further characterizing E. coli antimicrobial resistance is essential and aids in developing effective solutions, thereby furthering the One Health objective.

Complete genomic analysis of ST117 lineage extraintestinal pathogenic Escherichia coli (ExPEC) to reveal multiple genetic determinants to drive its global transmission: ST117 E. coli as an emerging multidrug-resistant foodborne ExPEC with zoonotic potential

Avian pathogenic Escherichia coli (APEC) is recognized as a primary source of foodborne extraintestinal pathogenic E. coli (ExPEC), which poses a significant risk of extraintestinal infections in humans. The potential of human infection with ST117 lineage APEC/ExPEC from poultry is particularly concerning. However, relatively few whole-genome studies have focused on ST117 as an emerging ExPEC lineage. In this study, the complete genomes of 11 avian ST117 isolates and the draft genomes of 20 ST117 isolates in China were sequenced to reveal the genomic islands and large plasmid composition of ST117 APEC. With reference to the extensive E. coli genomes available in public databases, large-scale comprehensive genomic analysis of the ST117 lineage APEC/ExPEC was performed to reveal the features of the ST117 pan-genome and population. The high variability of the accessory genome emphasized the diversity and dynamic traits of the ST117 pan-genome. ST117 isolates recovered from different hosts and geographic sources were randomly located on a phylogeny tree, suggesting that ST117 E. coli lacked host specificity. A time-scaled phylogeny tree showed that ST117 was a recent E. coli lineage with a relatively short evolutionary period. Further characterization of a wide diversity of ExPEC-related virulence genes, pathogenicity islands (PAIs), and resistance genes of the ST117 pan-genome provided insights into the virulence and resistance of ST117 APEC/ExPEC. The results suggested zoonotic potential of ST117 APEC/ExPEC between birds and humans. Moreover, genomic analysis showed that a pool of diverse plasmids drove the virulence and multidrug resistance of ST117 APEC/ExPEC. Several types of large plasmids were scattered across the ST117 isolates, but there was no strong plasmid-clade adaptation. Combined with the pan-genome analysis, a double polymerase chain reaction (PCR) method was designed for rapid and cost-effective detection of ST117 isolates from various avian and human APEC/ExPEC isolates. Overall, this study addressed a gap in current knowledge about the ST117 APEC/ExPEC genome, with significant implications to understand the success and spread of ST117 APEC/ExPEC.

Synergistic effect of high hydrostatic pressure, allyl isothiocyanate, and acetic acid on the inactivation and survival of pathogenic Escherichia coli in ground chicken

Meat and poultry are prone to contamination with foodborne pathogens sourced from the livestock or introduced from the processing environments. In this study, for retention of meat quality while assuring microbial food safety, mild levels of high hydrostatic pressure were hurdled with food-grade additives (i.e., allyl isothiocyanate [AITC] and acetic acid [AA], functioned as antimicrobials) to inactivate pathogenic Escherichia coli in ground chicken. The reductions of Shiga toxin-producing E. coli (STEC) O157:H7 and uropathogenic E. coli (UPEC) were described as a function of high hydrostatic pressure (200-350 MPa), process-holding time (10-25 min), AITC concentration (0.05-0.20% w/w), and AA concentration (0.10--0.30% w/w) using a full factorial design. The antimicrobials had little influence on bacterial inactivation without high pressure. Without the antimicrobials, a high-pressure treatment at 300 MPa and 4°C for 15 min reduced E. coli O157:H7 and UPEC by 1.52 and 2.52 log, respectively. A 5-log reduction was achieved when AITC and AA were combined with high pressure, indicating a synergistic effect. The survivors were further reduced to below the detection limit of 1 log CFU/g after subsequent storage tests at 4 and 10°C for 10 days. The STEC O157:H7 was found slightly more resistant than UPEC in our test matrix. The developed models showed good fits with experimental data (R²  > 0.95 for linear models; Pr > F (<0.0001) for dimensionless nonlinear models); which may help processors find/optimize the processing parameters to achieve target foodborne pathogens reduction for food safety requirement. PRACTICAL APPLICATION: Models were developed to predict the inactivation of pathogenic Escherichia coli in ground chicken by high-pressure processing (HPP) in combination with natural antimicrobial compounds. These models can be used to estimate/determine the HPP operation parameters and antimicrobial usage levels (i.e., allyl isothiocyanate and acetic acid) needed to achieve a specific microbial log reduction within the selected factor ranges. The operation parameters and clean-label ingredients are of interest in the food industry, which may benefit from the application of the models in achieving microbial safety, process optimization, and operation cost reduction.

Virulence potential of faecal <i>Escherichia coli</i> strains isolated from healthy cows and calves on farms in Perm Krai

Cattle are a reservoir of pathogenic and potentially pathogenic Escherichia coli (E. coli) strains, which can pose a threat to human and animal health. The aim of the study was to evaluate the occurrence of 22 virulence-associated genes (VAGs), as well as the prevalence of antimicrobial drug resistance and three different bla-genes among 49 E. coli strains isolated from healthy cattle. The presence of VAGs that are common among diarrheagenic E. coli (DEC) strains and/or extraintestinal pathogenic E. coli (ExPEC) strains was determined by amplifying specific gene sequences by PCR. The following VAGs associated with DEC were found: east1 in 24.5 % of the studied E. coli strains, estI in 10.2 %, ehxA in 8.2 %, stx2 in 6.1 %, eltA in 4.1 %, estII and stx1 in 2.0 % of the studied strains. The prevalence of ExPEC VAGs was: fimH – 91.8 %, afa/draBC – 61.2 %, iutA – 44.9 %, flu – 32.7 %, sfaDE and hlyF – 30.6 %, iroN – 22.4 %, ompT and papC – 20.4 %, kpsMTII and hlyA – 18.4 %, iss – 14.3 %, usp – 2.0 %, cnf1 and iha were not detected among the studied strains. Based on the found co-occurrence of VAGs “classical”, hetero-pathogenic and hybrid-pathogenic E. coli strains were found. E. coli strains isolated from cows had a higher diarrheagenic potential, whereas E. coli strains isolated from calves more frequently contained genes associated with the ExPEC pathotype. Among the studied E. coli strains, 77.6 % were resistant to ampicillin, 49.0 % to tetracycline, 20.4 % to chloramphenicol, 16.3 % to cefoperazone, 16.3 % to ceftriaxone, 16.3 % to aztreonam, 14.3 % to cefepime, 10.2 % to norfloxacin, 10.2 % to ciprofloxacin, 6.1 % to levofloxacin and 2.0 % to gentamicin. All strains were sensitive to meropenem and amikacin. 32.7 % of the studied E. coli strains were found to be multidrug resistant, as they were resistant to at least three groups of antibiotics. With PCR, the blaTEM, blaSHV, and blaCTX-M genes were detected in 100, 31.6, and 26.3 %, respectively, of strains resistant to at least one of the beta-lactam antibiotics. Thus, it was shown that the studied faecal E. coli of healthy cows and calves had a high hetero-pathogenic potential, therefore in the future molecular genetic characterization of these bacteria shall be an important part of the epizootic monitoring.

Antimicrobial Resistance, Virulence Factor-Encoding Genes, and Biofilm-Forming Ability of Community-Associated Uropathogenic Escherichia coli in Western Saudi Arabia

To explore the prevalence of multidrug-resistant community-associated uropathogenic Escherichia coli (UPEC) and their virulence factors in Western Saudi Arabia. A total of 1,000 urine samples were examined for the presence of E. coli by selective plating on MacConkey, CLED, and sheep blood agar. Antimicrobial susceptibility patterns were determined using Vitek^® 2 Compact (MIC) and the disc diffusion method with Mueller-Hinton agar. Genes encoding virulence factors (kpsMTII, traT, sat, csgA, vat, and iutA) were detected by PCR. The overall prevalence of UTI-associated E. coli was low, and a higher prevalence was detected in samples of female origin. Many of the isolates exhibited resistance to norfloxacin, and 60% of the isolates showed resistance to ampicillin. No resistance to imipenem, meropenem, or ertapenem was detected. In general, half of the isolates showed multiple resistance patterns. UPEC exhibited a weak ability to form biofilms, where no correlation was observed between multidrug resistance and biofilm-forming ability. All uropathogenic E. coli isolates carried the kpsMTII, iutA, traT, and csgA genes, whereas the low number of the isolates harbored the sat and vat genes. The diversity of virulence factors harbored by community-associated UPEC may render them more virulent and further explain the recurrence/relapse cases among community-associated UITs. To the best of our knowledge, this study constitutes the first exploration of virulence, biofilm-forming ability, and its association with multidrug resistance among UPEC isolates in Saudi Arabia. Further investigations are needed to elucidate the epidemiology of community-associated UPEC in Saudi Arabia.

Positive biofilms to control surface-associated microbial communities in a broiler chicken production system - a field study

In the One Health concept, the use of beneficial bacteria to form positive biofilms that prevent the settlement of undesirable bacteria is a promising solution to limit the use of antimicrobials on farms. However, there is a lack of field studies reporting the onset of these beneficial bacteria after application and the effects on autochthonous surface microbiota. In the study reported here, the inner surfaces of commercial broiler chicken houses were treated or not with a bacterial consortium composed of Bacillus spp. and Pediococcus spp. strains, able to form covering biofilms in different laboratory models. Preinstalled coupons were sampled over time to capture microbial biofilm dynamics on-farm surfaces. The results showed that the bacterial consortium can establish on the farm surfaces, modulate microbial communities, and limit the implantation of Enterobacteriaceae and Enterococcaceae, two families containing potential pathogens.

Highly Virulent and Multidrug-Resistant Escherichia coli Sequence Type 58 from a Sausage in Germany

Studies have previously described the occurrence of multidrug-resistant (MDR) Escherichia coli in human and veterinary medical settings, livestock, and, to a lesser extent, in the environment and food. While they mostly analyzed foodborne E. coli regarding phenotypic and sometimes genotypic antibiotic resistance and basic phylogenetic classification, we have limited understanding of the in vitro and in vivo virulence characteristics and global phylogenetic contexts of these bacteria. Here, we investigated in-depth an E. coli strain (PBIO3502) isolated from a pork sausage in Germany in 2021. Whole-genome sequence analysis revealed sequence type (ST)58, which has an internationally emerging high-risk clonal lineage. In addition to its MDR phenotype that mostly matched the genotype, PBIO3502 demonstrated pronounced virulence features, including in vitro biofilm formation, siderophore secretion, serum resilience, and in vivo mortality in Galleria mellonella larvae. Along with the genomic analysis indicating close phylogenetic relatedness of our strain with publicly available, clinically relevant representatives of the same ST, these results suggest the zoonotic and pathogenic character of PBIO3502 with the potential to cause infection in humans and animals. Additionally, our study highlights the necessity of the One Health approach while integrating human, animal, and environmental health, as well as the role of meat products and food chains in the putative transmission of MDR pathogens.

Comparative Characteristics and Pathogenic Potential of Escherichia coli Isolates Originating from Poultry Farms, Retail Meat, and Human Urinary Tract Infection

The pathogenicity of many bacterial strains is determined by the acquisition of virulence genes and depends on many factors. The aim of this study was to analyse the phylogenetic background, virulence patterns, and drug susceptibility of 132 E. coli isolates tested in the context of the ExPEC (Extraintestinal Pathogenic E. coli) pathotype and the correlation of these features with bacterial isolation source: food (retail meat), poultry farms (AFEC—Avian Faecal E. coli), and patients with UTI (urinary tract infection) symptoms. The drug-susceptibility results of tested E. coli isolates obtained indicate that the resistance profile—ampicillin/tetracycline/trimethoprim+sulfamethoxazole/ciprofloxacin (AMP/TE/SXT/CIP)—was most frequently observed. The multidrug resistance (MDR) phenotype was found in 31.8% of isolates from poultry farms, 36.8% of strains isolated from food, and 20% of clinical samples. The greatest similarity of virulence profiles applied to isolates derived from poultry farms and food. Most of the AFEC from poultry farms and food-derived isolates belonged to commensals from phylogroups A and B1, while among the isolates from patients with UTI symptoms, the most common was the B2 phylogroup. The collective analysis showed similarity of the three studied groups of E. coli isolates in terms of the presented patterns of antimicrobial resistance, while the virulence profiles of the isolates studied showed great diversity. The phylogroup analysis showed no similarity between the poultry/food isolates and the UTI isolates, which had significant pathogenic potential.