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Avian pathogenic Escherichia coli (APEC) poses a global threat to poultry health and public safety due to its high lethality, limited treatment options, and potential for zoonotic transmission via the food chain. However, long-term genomic surveillance remains limited, especially in countries like China where poultry farming is highly intensive. This study aimed to characterize the population structure, virulence traits, and antimicrobial resistance of 81 APEC isolates from diseased chickens collected over 16 years from Shandong and neighboring provinces in eastern China. The isolates were grouped into seven Clermont phylogroups, with A and B1 being dominant. MLST revealed 27 STs, and serotyping identified 29 O and 16 H antigens, showing high genetic diversity. The minor phylogroups (B2, C, D, E, G) encoded more virulence genes and had higher virulence-plasmid ColV carriage, with enrichment for iron-uptake, protectins, and extraintestinal toxins. In contrast, the dominant phylogroups A and B1 primarily carried adhesin and enterotoxin genes. Antimicrobial resistance was widespread: 76.5% of isolates were multidrug-resistant. The minor phylogroups exhibited higher tetracycline resistance (mediated by tet(A)), whereas the major phylogroups showed increased resistance to third- and fourth-generation cephalosporins (due to bla_CTX-M-type ESBL genes). These findings offer crucial data for APEC prevention and control, safeguarding the poultry industry and public health. Full article

Contamination of coastal-marine environment with multidrug-resistant Escherichia coli has resulted in such bacteria increasingly being detected in the seafood chain. This study aimed to determine the quinolone and colistin resistance genes in extended spectrum-β-lactamase (ESBL)-producing E. coli from seafood. ESBL-producing E. coli isolates (n = 269) were tested for quinolones and colistin resistance phenotypes by disk diffusion and broth microdilution methods, respectively. The isolates were further PCR screened for the plasmid-mediated quinolone resistance (PMQR) genes qnrA, qnrB, and qnrS, genomic mutations in gyrA and parC genes, and the colistin resistance genes mcr-1 and mcr-2. Phylogroup was determined by PCR using the Clermont E. coli phylotyping method. Of 269 isolates tested, 73.60% of E. coli isolates were resistant to moxifloxacin and 8.55% to ofloxacin, the least of all the quinolones tested. Further, 150 (55.76%) E. coli isolates carried at least one of the three PMQR genes tested, where qnrS was the most prevalent gene (53.90%). The colistin resistance gene (mcr-2) was detected in 38 (14.12%) isolates. Twenty-one of these isolates (55.26%) had a colistin minimum inhibitory concentration (MIC) of 16 µg/mL. Based on the Clermont E. coli phylotyping of the isolates harboring at least one of the qnr genes, 66 (44%) belonged to the phylogroup B1, followed by 23 (15.33%) to phylogroup A. Among 38 E. coli isolates carrying colistin resistance gene mcr-2, 27 (71.05%) isolates belonged to phylogroup B1, followed by 4 (10.52%) isolates to phylogroup A. The results suggest that E. coli phylogroups B1 and A harboring plasmid-mediated quinolone and colistin resistance genes are predominant in the seafood supply chain. Full article

Background/Objectives: According to the One Health concept, wild birds can be indicators of ecosystem pollution and disease incidence. Escherichia coli strains are widespread worldwide, but there are still few reports on the association of human infections with a potential reservoir of highly pathogenic human strains in wild birds. Fecal E. coli with uropathogenic potential (UPEC) can be transmitted between birds and humans and may be a risk factor for urinary tract infections (UTIs). Results: The results showed that above 50% of the isolates were grouped as highly pathogenic, according to Clermont phylogroup classification. Such strains were found to be stronger biofilm producers, with a higher adherence of monocytes than low pathogenic. However, the highest cytotoxicity was observed for strains described as aquatic environmental. Convergence of the results of the analysis of monocyte activation by E. coli strains and the ability to form biofilm by individual phylogroups of the strains tested was demonstrated. Genetic determinants of the uropathogenicity of E. coli (UPEC) correlate with the evidence of strain pathogenicity during monocyte activation in in vitro assays. Methods: In this study, we assessed the virulence potential of environmental strains isolated from wild waterfowl using genetic analysis (Clermont phylogroup classification) and phenotypic methods, including analysis of the human monocyte response to biofilm formation. The estimation of the ability to form biofilms was tested using crystal violet, and the pathogenic potential of strains by monocyte activation assay including changes in morphology, adhesion and cytotoxicity. Conclusions: In conclusion, the virulence of E. coli strains isolated from free-living birds is significant, and they can be considered environmental reservoirs of pathogenic strains. According to our observations, they can be responsible for the dissemination of uropathogenic strains among humans. Full article

The presence of antibiotic-resistant Escherichia coli in food is a serious and persistent problem worldwide. In this study, 68 E. coli strains isolated from Thai food samples were characterized. Based on antibiotic susceptibility assays, 31 of these isolates (45.59%) showed multiple antibiotic resistance (MAR) index values > 0.2, indicating high exposure to antibiotics. Among these, strain CM24E showed the highest resistance (it was resistant to ten antibiotics, including colistin and imipenem). Based on genome sequencing, we identified four isolates (namely, CF25E, EF37E, NM10E1, and SF50E) with novel Achtman-scheme multi-locus sequence types (STs) (ST14859, ST14866, ST14753, and ST14869, respectively). Clermont phylogrouping was used to subtype the 68 researched isolates into five Clermont types, mainly A (51.47%) and B1 (41.18%). The bla_EC gene was found only in Clermont type A, while the bla_EC-13 gene was predominant in Clermont type B1. A correlation between genotypes and phenotypes was found only in Clermont type B1, which showed a strong positive correlation between the presence of an afa operon and yersiniabactin-producing gene clusters with the colistin resistance phenotype. Strain SM47E1, of Clermont type B2, carried the highest number of predicted virulence genes. In summary, this study demonstrates the pressing problems posed by the prevalence and potential transmission of antimicrobial resistance and virulence genes in the food matrix. Full article

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

Animals, humans and food are all interconnected sources of antimicrobial resistance (AMR), allowing extensive and rapid exchange of AMR bacteria and genes. Whole genome sequencing (WGS) was used to characterize 279 Escherichia coli isolates obtained from animals (livestock, companion animals, wildlife), food and humans in Italy. E. coli predominantly belonged to commensal phylogroups B1 (46.6%) and A (29%) using the original Clermont criteria. One hundred and thirty-six sequence types (STs) were observed, including different pandemic (ST69, ST95, ST131) and emerging (ST10, ST23, ST58, ST117, ST405, ST648) extraintestinal pathogenic Escherichia coli (ExPEC) lineages. Eight antimicrobial resistance genes (ARGs) and five chromosomal mutations conferring resistance to highest priority critically important antimicrobials (HP-CIAs) were identified (qnrS1, qnrB19, mcr-1, bla_CTX-M1,15,55, bla_CMY-2, gyrA/parC/parE, ampC and pmrB). Twenty-two class 1 integron arrangements in 34 strains were characterized and 11 ARGs were designated as intI1 related gene cassettes (aadA1, aadA2, aadA5, aad23, ant2_Ia, dfrA1, dfrA7, dfrA14, dfrA12, dfrA17, cmlA1). Notably, most intI1 positive strains belonged to rabbit (38%) and poultry (24%) sources. Three rabbit samples carried the mcr-1 colistin resistance gene in association with IS6 family insertion elements. Poultry meat harbored some of the most prominent ExPEC STs, including ST131, ST69, ST10, ST23, and ST117. Wildlife showed a high average number of virulence-associated genes (VAGs) (mean = 10), mostly associated with an ExPEC pathotype and some predominant ExPEC lineages (ST23, ST117, ST648) were identified. Full article