Genome-Wide Analysis of Escherichia coli Isolated from Dairy Animals Identifies Virulence Factors and Genes Enriched in Multidrug-Resistant Strains

Escherichia coli Isolated from Bovine Sources Encoding the Fosfomycin Resistance Gene fosA7.5

Dairy animals are reservoirs of antimicrobial-resistant Escherichia coli that are frequently resistant to tetracycline, aminoglycoside, β-lactam, sulfonamide, and macrolide-lincosamide-streptogramin B antibiotics. However, resistance to other classes of antimicrobials is less frequently observed, and resistance to fosfomycin is rarely observed in E. coli. In this study, we describe the genomic characteristics of E. coli encoding fosA7.5 that have been recovered from bovine sources in the United States. Most isolates only encoded the fosA7.5 gene, whereas 37% encoded at least one other resistance gene, and 25% were genotypically multidrug-resistant. Most (112 isolates, 93%) belonged to phylogenetic group B1 and were assigned to 19 sequence types (STs), the most frequently identified being ST1727, ST2307, and ST3234. Results of this study indicate that fosA-encoding E. coli from bovine sources is very rare in the United States with isolates demonstrating a high level of similarity across a broad geographic region.

Molecular Epidemiology and Antibiotic Resistance Associated with Avian Pathogenic Escherichia coli in Shanxi Province, China, from 2021 to 2023

Avian Pathogenic Escherichia coli (APEC) constitutes a major etiological agent of avian colibacillosis, which significantly hinders the development of the poultry industry. Conducting molecular epidemiological studies of APEC plays a crucial role in its prevention and control. This study aims to elucidate the molecular epidemiological characteristics of Avian Pathogenic Escherichia coli in Shanxi Province. In this study, 135 APEC strains were isolated and identified from 150 liver samples of diseased and deceased chickens exhibiting clinical symptoms, which were collected from farms in Shanxi Province between 2021 and 2023. The isolates were then analyzed for phylogenetic clustering, drug resistance, resistance genes, virulence genes, and biofilm formation capabilities. The results revealed that the proportions of the A, B1, B2, and D evolutionary subgroups were 26.67%, 32.59%, 17.78%, and 15.56%, respectively. The drug resistance testing results indicated that 92% of the isolates exhibited resistance to cotrimoxazole, kanamycin, chloramphenicol, amoxicillin, tetracycline, and other antibiotics. In contrast, 95% of the strains were sensitive to ofloxacin, amikacin, and ceftazidime. The most prevalent resistance genes included tetracycline-related (tetA) at 88.15%, followed by beta-lactam-related (bla-TEM) at 85.19%, and peptide-related (mcr1) at 12.59%. The virulence gene analysis revealed that ibeB, ompA, iucD, and mat were present in more than 90% of the isolates. The results revealed that 110 strains were biofilm-positive, corresponding to a detection rate of 81.48%. No significant correlation was found between the drug resistance genes, virulence genes, and the drug resistance phenotype. A moderate negative correlation was observed between the adhesion-related gene tsh and biofilm formation ability (r = -0.38). This study provides valuable insights into the prevention and control of avian colibacillosis in Shanxi Province.

Genotypic Antimicrobial Resistance Profiles of Diarrheagenic Escherichia coli and Nontyphoidal Salmonella Strains Isolated from Children with Diarrhea and Their Exposure Environments in Ethiopia

Background

Antimicrobial resistance (AMR) poses a significant global threat, particularly in low- and middle-income countries, such as Ethiopia, where surveillance is limited. This study aimed to predict and characterize the AMR profiles of diarrheagenic Escherichia coli (DEC) and nontyphoidal Salmonella (NTS) strains isolated from human, animal, food, and environmental samples using whole genome sequencing.

Methods

A total of 57 NTS and 50 DEC isolates were sequenced on an Illumina NextSeq 550. The ResFinder and PointFinder tools were employed to identify antimicrobial resistance genes (ARGs) and point mutations. Salmonella serotypes were determined using SeqSero.

Results

The analysis identified at least one ARG in every NTS sample and 78% of the DEC isolates, with 22 distinct ARGs in the NTS samples and 40 in the DEC samples. The most prevalent ARGs were aac(6')-Iaa and aph(3')-Ib, which predict aminoglycoside resistance in 100% of NTS and 54% of DEC isolates, respectively. Other commonly identified ARGs include sul2, aph(6)-Id, blaTEM-1B , and tet(A), which confer resistance to folate inhibitors, aminoglycosides, β-lactams, and tetracycline. Some ARGs predicted phenotypic multidrug resistance in both DEC and NTS isolates. All identified β-lactam ARGs, except for blaTEM -1D, conferred resistance to more than three antibiotics. Interestingly, blaCTX- M-15 was found to confer resistance to nine antibiotics, including third-generation cephalosporins, in 18% of DEC and 3.5% of NTS isolates. DEC isolates from children exhibited the highest ARG diversity. Notably, genes such as aph(3″)-Ib, aph(6)-Id, sul2, and tet(A) were detected across all sample types, including water sources, although some ARGs were exclusive to specific sample types. Point mutations mediating AMR were detected in several genes, with mutations associated with nucleotide substitution being the most frequent.

Conclusion

This genotypic AMR profiling revealed the presence of widespread drug-resistant NTS and DEC strains in Ethiopia. Robust and sustained AMR surveillance is essential for monitoring the emergence and spread of these resistant pathogens.

Dissemination and characterization of Escherichia coli resistant to extended-cephalosporins in feedlot lambs: A two-year two-population study

Dissemination of antimicrobial resistance in food animals is a One Health concern, but sheep production has been overlooked. This study aimed to explore the dissemination of Escherichia coli resistant to extended-spectrum cephalosporins (ESC) in feedlot lambs. Two pens were sampled on two occasions, and carcasses and other mammals living around were also tested. E. coli were recovered and antibiotic resistance determined. blaCTX-M/CMY genes and their genetic localization were characterized. Whole genome sequencing (WGS) was performed to confirm clonal relationship. The most prevalent ESC-resistance genes in the 108 E. coli isolates were blaCTX-M-55 (53.7 %), blaCTX-M-2 (14.8 %) and blaCMY-2 (13.9 %). Most blaCTX-M-55 genes were found on the chromosome, but IncA/C, IncHI1, IncHI2 and IncF plasmids were also identified. Genetic diversity was observed even though ST6448 was by far the most frequent ST. WGS analysis showed high similarity among isolates recovered from feedlot lambs, animals in the surroundings and lambs' carcasses, proving the clonal and plasmidic dissemination.

Four New Sequence Types and Molecular Characteristics of Multidrug-Resistant Escherichia coli Strains from Foods in Thailand

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 blaEC gene was found only in Clermont type A, while the blaEC-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.

Whole genome sequence analysis reveals high genomic diversity and potential host-driven adaptations among multidrug-resistant Escherichia coli from pre-weaned dairy calves

Food-producing animals such as dairy cattle are potential reservoirs of antimicrobial resistance (AMR), with multidrug-resistant (MDR) organisms such as Escherichia coli observed in higher frequency in young calves compared to older cattle. In this study, we characterized the genomes of enteric MDR E. coli from pre-weaned dairy calves with and without diarrhea and evaluated the influence of host-level factors on genomic composition. Whole genome sequence comparative analysis of E. coli (n = 43) revealed substantial genomic diversity that primarily clustered by sequence type and was minimally driven by calf diarrheal disease status (healthy, diarrheic, or recovered), antimicrobial exposure, and dietary zinc supplementation. Diverse AMR genes (ARGs)-including extended-spectrum beta-lactamase genes and quinolone resistance determinants-were identified (n = 40), with unique sets of ARGs co-occurring in gene clusters with large AMR plasmids IncA/C2 and IncFIB(AP001918). Zinc supplementation was not significantly associated with the selection of individual ARGs in E. coli, however analysis of ARG and metal resistance gene pairs identified positive associations between certain aminoglycoside, beta-lactam, sulfonamide, and trimethoprim ARGs with acid, tellurium and mercury resistance genes. Although E. coli in this study lacked the typical virulence factors of diarrheagenic strains, virulence genes overlapping with those in major pathotypes were identified. Among the 103 virulence genes detected, the highest abundance and diversity of genes corresponded to iron acquisition (siderophores and heme uptake). Our findings indicate that the host-level factors evaluated in this study were not key drivers of genomic variability, but that certain accessory genes in enteric MDR E. coli may be enriched. Collectively, this work provides insight into the genomic diversity and host-microbe interface of MDR E. coli from pre-weaned dairy calves.

Epidemiology, Virulence and Antimicrobial Resistance of Escherichia coli Isolated from Small Brazilian Farms Producers of Raw Milk Fresh Cheese

This study aimed to identify contamination sources in raw milk and cheese on small farms in Brazil by isolating Escherichia coli at various stages of milk production and cheese manufacturing. The study targeted EAEC, EIEC, ETEC, EPEC, STEC, and ExPEC pathotypes, characterizing isolates for the presence of virulence genes, phylogroups, antimicrobial susceptibility, and phylogenetic relationships using PFGE and MLST. The presence of antimicrobial resistance genes and serogroups was also determined. Three categories of E. coli were identified: pathogenic, commensal, and ceftriaxone-resistant (ESBL) strains. Pathogenic EPEC, STEC, and ExPEC isolates were detected in milk and cheese samples. Most isolates belonged to phylogroups A and B1 and were resistant to antimicrobials such as nalidixic acid, ampicillin, kanamycin, streptomycin, sulfisoxazole, and tetracycline. Genetic analysis revealed that E. coli with identical virulence genes were present at different stages within the same farm. The most frequently identified serogroup was O18, and MLST identified ST131 associated with pathogenic isolates. The study concluded that E. coli was present at multiple points in milk collection and cheese production, with significant phylogroups and high antimicrobial resistance. These findings highlight the public health risk posed by contamination in raw milk and fresh cheese, emphasizing the need to adopt hygienic practices to control these microorganisms.

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.