Search Results (87)

This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The bla_NDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes bla_NDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (bla_TEM-1B), aminoglycosides (aph(6)-Id, aph(3′)-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding bla_NDM-19 includes ISAba125-IS5-bla_NDM-19-ble_MBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of bla_NDM and its related variants. To our knowledge, this is the first genomic report of a bla_NDM-19/IncX3-carrying E. coli isolate of animal origin globally. Full article

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

Diarrhea in alpaca crias significantly impacts livestock health in high-altitude regions, with Escherichia coli as a common pathogen. This study analyzed 10 E. coli isolates from diarrheic and healthy alpacas using whole-genome sequencing to assess genetic diversity, virulence factors, and antibiotic resistance. Predominant sequence types (ST73, ST29), serotypes (O22:H1, O109:H11), and phylogroups (B2, B1, A) were identified. Virulence profiling revealed ExPEC-like and EPEC pathotypes, while resistance genes for β-lactams (blaEC-15), fosfomycin (glpT_E448K), and colistin (pmrB) were prevalent. These findings highlight the need for genomic surveillance and antimicrobial stewardship to manage E. coli infections in alpacas and reduce public health risks. Full article

In the past two decades, Shiga toxin-producing Escherichia coli (STEC) has been responsible for multiple large-scale outbreaks worldwide, affecting thousands of individuals. While surveillance systems in developed countries such as the United States, the United Kingdom, Europe, Australia, Japan, and Canada are well-established, data on STEC prevalence in developing nations remain sparse, partly due to the absence of well-structured molecular diagnostic networks or surveillance systems. This review analyzed 250 studies published between 2014 and 2024 across 39 developing countries in Africa, Asia, Latin America, and the Caribbean, yielding 8986 STEC isolates. Detailed serogroup and serotype data were available for 55.9% of these, with O111, O157, and O26 being most common in humans. In animals, O157:H7 was most frequent, while food isolates mirrored global trends with O157 and O111 dominance. Notably, O145, a serogroup frequently reported in the U.S. and Europe, was absent from the ‘’Top Seven’’ serogroups. Shiga toxin subtypes stx1a and stx2a were most prevalent in human cases. In animal isolates, stx2e was the most prevalent subtype, while stx2c was most commonly found in food samples. We recommend establishing reference laboratories in these regions to improve data quality, strengthen monitoring efforts, and reduce the burden of STEC infections globally. Full article

Enterotoxigenic Escherichia coli (ETEC) poses a critical threat to livestock health and food safety, particularly in regard to misuse of antimicrobial agents, which have accelerated the evolution of multidrug-resistant (MDR) ETEC strains, reshaping their virulence landscapes and epidemiological trajectories. In this study, 24 ETEC isolates from porcine diarrheal samples undergo genomic and phenotypic profiling, including virulence genotyping, bacterial adhesion, and antimicrobial resistance (AMR) analysis. Results show that multi-locus sequence typing (MLST) outputs (ST88, ST100) and serotypes (O9:H19, O116:H11, O149:H10) exhibited enhanced virulence, with F18ab-fimbriated strains carrying Shiga toxin genes (stx2A) demonstrating higher cytotoxicity than non-stx strains. There exists a significant negative correlation between bacterial growth rates and intestinal epithelial adhesion, with the expression of ETEC adhesion and virulence genes being growth-time-dependent. These relationships suggest evolutionary trade-offs favoring either rapid proliferation or virulence. Among these isolates, 95.8% were MDR, with alarming resistance to quinolones and aminoglycosides. Geospatial analysis identified region-specific AMR gene clusters, notably oqxB-aac(3) co-occurrence networks in 79% of ETEC isolates. These results highlight the urgent need for precision interventions, including vaccines targeting epidemic serotypes and AMR monitoring systems to disrupt resistance propagation across swine production networks. By underscoring the importance of current virulence and AMR profiles, this study provides actionable strategies to mitigate ETEC-associated threats to both animal welfare and meat safety ecosystems. Full article

Extraintestinal pathogenic Escherichia coli (ExPEC) is a group of Escherichia coli strains that can cause severe infectious diseases outside the gastrointestinal tract, such as urinary tract infections, meningitis, septicemia, etc. We report a case of a calf herd infection by ExPEC with high rates of morbidity and mortality. The research purpose of this study was to thoroughly investigate the characteristics of the ExPEC responsible for the calf herd infection. Specifically, we aimed to understand the mechanisms underlying its multidrug resistance and high pathogenicity. Clinical samples were collected for the isolation and identification of ExPECs, cultured on MacConkey agar, and further tested by PCR for the uidA gene, 16S rRNA gene sequencing, and adhesion patterns on HEp-2 cells. The antimicrobial activity was determined using the disk diffusion method according to Clinical & Laboratory Standards Institute (CLSI) guidelines. The pathogenicity was assessed through the experimental infection of Kunming mice, tracking their survival and weight changes, and performing autopsies for bacterial counts and histopathological analysis. Additionally, whole-genome sequencing (WGS) and a comprehensive analysis were performed, including multilocus sequence typing (MLST), serotyping, drug-resistance gene analysis, virulence factor analysis, metabolic pathway analysis, and enrichment analysis, using various online tools and databases. An ExPEC strain named RZ-13 was responsible for this case and was identified as ST345 and O134: H21. Among the 14 antibiotics tested, 13 showed resistance, indicating that the RZ-13 strain is a multidrug-resistant (MDR) bacterium. The experimental infection of Kunming mice proved the greater pathogenicity of RZ-13 than that of CICC 24186. The comprehensive WGS revealed the presence of 28 antibiotic resistance genes and 86 virulence-related genes in the genome of the strain, corroborating its clinical manifestations of MDR and high pathogenicity. Our study isolated a MDR ExPEC strain, RZ-13, with a strong pathogenicity. This is the first case report of ExPEC leading to severe mortality in calf herds in China, underscoring the need for the rational use of antibiotics to reduce the risk of the generation and transmission of MDR bacteria from food-producing animals to ensure food safety and public health. Full article

Antimicrobial resistant (AMR) Escherichia coli (E. coli) isolated from animals may lead to antibiotic treatment failure and economic losses to farmers. The co-existence of antimicrobial resistant genes (ARGs) in the same isolate presents a major challenge for the prevention and control of infection in multidrug-resistant (MDR) Gram-negative organisms. There have been a lot of studies on the antibiotic resistance of E. coli in livestock and poultry, but few of them have focused on clinical pathogens. Objective: The aim of this study was to explore the genetic characteristics, co-occurrence, and correlations between ARGs of E. coli isolated from the pathological tissues of livestock and poultry in Shandong Province, East China during 2015–2020. Methods: A total of 158 E. coli strains were collected and subjected to antimicrobial susceptibility testing and sequencing by whole-genome Next Generation Sequencing (NGS). Results: MDR strains accounted for 46.20% of the 158 E. coli strains with the highest resistant rate of ciprofloxacin (71.52%). In addition, strains with bla_NDM-5/mcr-1.1 and mcr-1.1/mcr-3.24 were found in chickens, while three strains with Tet(X4) were found in pigs. In addition, the most common serotypes detected were the O serotype (76/158) and H serotype (36/158). Moreover, seventy-one STs were found and the most common STs were ST10 (6.33%), ST155 (6.33%), and ST101 (5.69%). The genetic environment analysis of the phylogroups revealed that E. coli belonging to phylogroup B1, phylogroup A, and phylogroup C constituted 39.87%, 27.85%, and 15.19%, respectively. Through the correlation analysis, mcr genes were observed to have certain relationships with ARGS such as bla_TEM, floR, catA/B, and oqx. Conclusions: This study demonstrates the high prevalence and gene diversity of MDR E. coli isolated from a clinic in Shandong Province, East China. We predicted the transmission risk of animal-borne Tet(X4)-bearing and mcr-harboring E. coli to public health and provided insight into the relationship of co-existence or co-transfer between mcr with ARGS. These relationships present a great challenge for the infection control of MDR Gram-negative organisms. Full article

Escherichia coli O157:H7, a Shiga-toxin-producing E. coli (STEC), is an important pathogen related to foodborne disease that is responsible for a growing number of outbreaks worldwide and has been detected in processed meats, dairy, and fresh vegetables. Although culturing is the gold standard method for detection of this bacterium, molecular methods based on nucleic acid amplification techniques such as PCR are becoming more common because of their rapidity, sensitivity, and specificity. However, to ensure reliable results among the several alternative PCR protocols (e.g., commercial kits and reference methods), different measurement assurance tools, including validated methods, reference materials, and proficiency tests, among others, are required. Herein, we present a digital PCR method validation for E. coli O157:H7 detection and quantification using seven specific gene sequences; this method quantified nucleic acids from different E. coli serotypes, with a detection range of 6.6 to 7900 copies/µL and a repeatability standard deviation over the concentration range of 1% to 13.6%. The relative standard uncertainty was 3.5–14.6%, and the detection limit was 0.27 copies/µL. Subsequently, two batches of a candidate reference material based on E. coli O157:H7 genomic DNA were then produced and characterized for evaluation of copy number concentration with the validated ddPCR method, with assigned values of 164,770 ± 9251 and 172 ± 9 copies/μL. Thus, this study demonstrated the development of a validated method and reference material for dPCR and qPCR detection of E. coli O157:H7, a key STEC responsible for food poisoning. Full article

Two distinct stx_2f-carrying Escherichia coli (E. coli) strains, isolated from a child with uncomplicated diarrhea fifteen weeks apart, were characterized by combining short- and long-read sequencing to compare their genetic relatedness. One strain was characterized as Shiga toxin-producing E. coli (STEC)/typical enteropathogenic E. coli (tEPEC) O63:H6 with a repertoire of virulence genes including stx_2f, eae (α2-subtype), cdt, and bfpA. The other STEC with serotype O157:H16, reported for the first time as stx_2f-carrying Escherichia coli in this study, possessed, in addition, eae (ε-subtype) and cdt, amongst other virulence-related genes. BLAST comparison showed that the stx_2f-harboring prophage sequences of both strains were highly homologous (99.6% identity and 96.1% coverage). These results were corroborated by core Stx2f phage Multilocus Sequence Typing (cpMLST) as the stx_2f-harboring prophages of both isolates clustered together when compared to those of 167 other human stx_2f-carrying Escherichia coli. Overall, the stx_2f-harboring prophages of the two distinct E. coli strains isolated from the present case were highly similar, suggesting that the stx_2f-harboring phage might have been transferred from the STEC/tEPEC O63:H6 strain to the atypical EPEC (aEPEC) O157:H16 strain in the gut of the child. Full article

Shiga toxin-producing Escherichia coli (STEC) can cause severe clinical disease in humans, particularly in young children. Recent advances have led to greater availability of sequencing technologies. We sought to use whole genome sequencing data to identify the presence or absence of known virulence factors in all clinical isolates submitted to our laboratory from Southern Alberta dated 2020–2022 and correlate these virulence factors with clinical outcomes obtained through chart review. Overall, the majority of HUS and hospitalizations were seen in patients with O157:H7 serotypes, and HUS cases were primarily in young children. The frequency of virulence factors differed between O157:H7 and non-O157 serotypes. Within the O157:H7 cases, certain virulence factors, including espP, espX1, and katP, were more frequent in HUS cases. The number of samples was too low to determine statistical significance. Full article

Escherichia coli is a frequent pathogen isolated from bloodstream infections. This study aimed to characterize the genetic features of EC092, an E. coli strain isolated from bacteremia that harbors enteroaggregative E. coli (EAEC) genetic markers, indicating its hybrid pathogenic potential. Whole-genome sequencing showed that EC092 belongs to phylogroup B1, ST278, and serotype O165:H4. Genes encoding virulence factors such as fimbriae, toxins, iron-uptake systems, autotransporter proteins (Pet, Pic, Sat, and SepA), and secretion systems were detected, as well as EAEC virulence genes (aggR, aatA, aaiC, and aap). EC092 was found to be closely related to the other EAEC prototype strains and highly similar in terms of virulence to three EAEC strains isolated from diarrhea. The genomic neighborhood of pet, pic, sat, sepA, and the EAEC virulence genes of EC092 and its three genetically related fecal EAEC strains showed an identical genomic organization and nucleotide sequences. Also, EC092 produced and secreted Pet, Pic, Sat, and SepA in the culture supernatant and resisted the bactericidal activity of normal human serum. Our results demonstrate that the strain EC092, isolated from bacteremia, is a hybrid pathogenic extraintestinal E. coli (ExPEC)/EAEC with virulence features that could mediate both extraintestinal and intestinal infections. Full article

Escherichia coli serotype O157:H7 is a diarrheal agent and a significant cause of hemorrhagic colitis and the development of hemolytic uremic syndrome (HUS), mainly in infants. Early detection of contaminated food and water using reliable and fast tests is one of the strategies to prevent infections from E. coli O157:H7. Methods: Four quantitative polymerase chain reaction protocols (SYBR Green qPCR) were developed and validated to determine the presence of the bacteria according to its rfbE, stx₁, and stx₂ genes. Results: The results of the efficiencies were between 80% and 97% with a high linearity (R² 0.99). The cut-off limits for each primer sequence were 3.1667 × 10⁻² ng µL⁻¹ for two sequences of the serogroup O157 (primers rfbE and O157), 1.7228 × 10⁻³ ng µL⁻¹ for stx₁, and 3.5185 × 10⁻³ ng µL⁻¹ for stx₂. The inclusivity and the exclusivity of each gene, as well as the analytical precision and the positive and negative predictive value, were 100%. A contaminated meat matrix was evaluated, detecting up to 4 CFU g⁻¹. Conclusions: SYBR Green qPCR protocols could be implemented to trace the presence of E. coli O157 in a routine analysis of ground beef or as an easy, rapid, sensitive, and specific diagnostic test while still considering microbiological tests to validate any inconclusive results. Full article

Dairy products from ovine milk are very popular in the Mediterranean countries and are gaining a large portion of the market in EU countries and worldwide. EU legislation permits the dairy processing of raw ovine milk under certain conditions. To study the ecology and prevalence of E. coli in raw ewes’ milk and assess thus the public health risk, samples of milk were taken from 75 different sheep farms in the rural area of Epirus, Greece. The initial sampling was conducted in clinically healthy animals which were noted as controls (group A). From the same farms, samples were taken from animals with clinical mastitis and before treatment (group B). For therapeutic purposes, to some animals, a combination of penicillin and streptomycin was administrated (group C1), or tetracycline (group C2), or enrofloxacin (group C3). Finally, samples of raw milk were taken from the C groups, on the first day after the withdrawal period of the antibiotics used, when the milk is permitted to enter the food chain. In total, 97 isolates of Escherichia coli were recovered from all groups. Analysis revealed an impressive increase in E. coli strains in the milk of group B (39.33%) with respect to group A (5%). Even after treatment, although the prevalence was decreased, it was still found to be higher in the C groups than group A. E. coli O157:H7 strains absent from group A were detected in all other groups in relatively low occurrence rates with respect to other “O” serotypes but non-O157:H7 strains. Virulence factors such as the production of toxins (32.60% for serotoxin 1 and 18.47% for serotoxin 2) and hemolysin (42.39%) as well as biofilm formation capacity (52.17% of the total) and ESDL production (43.47% of the total) were also studied. All strains were also tested for susceptibility against 12 antibiotics by the MIC method and the results showed a high prevalence of resistance and multi-resistance. The presence of various resistant strains to antibiotics and pathogenic “O” serotype strains in the milk when it can enter the food chain again is an alarming conclusion. Full article

The emerging heteropathotype shigatoxigenic (STEC) and extra-intestinal pathogenic Escherichia coli (ExPEC) O80:H2 has been the second leading cause of pediatric HUS in France since the mid-2010s. In contrast with other highly pathogenic STEC serotypes, for which ruminants have clearly been identified as the main human infection source, this heteropathotype’s reservoir remains unknown. In this context, we describe for the first time the isolation of seven STEC O80:H2 strains from healthy cattle on a single cattle farm in France. This study aimed at (i) characterizing the genome and (ii) investigating the phylogenetic positions of these O80:H2 STEC strains. The virulomes, resistomes, and phylogenetic positions of the seven bovine isolates were investigated using in silico typing tools, antimicrobial susceptibility testing and cgMLST analysis after short-read whole genome sequencing (WGS). One representative isolate (A13P112V1) was also subjected to long-read sequencing. The seven isolates possessed ExPEC-related virulence genes on a pR444_A-like mosaic plasmid, previously described in strain RDEx444 and known to confer multi-drug resistance. All isolates were clonally related and clustered with human clinical strains from France and Switzerland with a range of locus differences of only one to five. In conclusion, our findings suggest that healthy cattle in France could potentially act as a reservoir of the STEC-ExPEC O80:H2 pathotype. Full article

Enterohemorrhagic Escherichia coli (EHEC) serotype O157:H7 is a commonly encountered foodborne pathogen that can cause hemorrhagic enteritis and lead to hemolytic uremic syndrome (HUS) in severe cases. Bifidobacterium is a beneficial bacterium that naturally exists in the human gut and plays a vital role in maintaining a healthy balance in the gut microbiota. This study investigated the protective effects of B. longum K5 in a mouse model of EHEC O157:H7 infection. The results indicated that pretreatment with B. longum K5 mitigated the clinical symptoms of EHEC O157:H7 infection and attenuated the increase in myeloperoxidase (MPO) activity in the colon of the mice. In comparison to the model group, elevated serum D-lactic acid concentrations and diamine oxidase (DAO) levels were prevented in the K5-EHEC group of mice. The reduced mRNA expression of tight junction proteins (ZO-1, Occludin, and Claudin-1) and mucin MUC2, as well as the elevated expression of virulence factors Stx1A and Stx2A, was alleviated in the colon of both the K5-PBS and K5-EHEC groups. Additionally, the increase in the inflammatory cytokine levels of TNF-α and IL-1β was inhibited and the production of IL-4 and IL-10 was promoted in the K5-EHEC group compared with the model group. B. longum K5 significantly prevented the reduction in the abundance and diversity of mouse gut microorganisms induced by EHEC O157:H7 infection, including blocking the decrease in the relative abundance of Roseburia, Lactobacillus, and Oscillibacter. Meanwhile, the intervention with B. longum K5 promoted the production of acetic acid and butyric acid in the gut. This study provides insights into the use of B. longum K5 for developing probiotic formulations to prevent intestinal diseases caused by pathogenic bacterial infections. Full article