Molecular characterization of multidrug-resistant Shiga toxin-producing Escherichia coli harboring antimicrobial resistance genes obtained from a farmhouse

Epidemiological Characterization of Isolates of Salmonella enterica and Shiga Toxin-Producing Escherichia coli from Backyard Production System Animals in the Valparaíso and Metropolitana Regions

Backyard production systems (BPS) are distributed worldwide, rearing animals recognized as reservoirs of Salmonella enterica and Shiga toxin-producing Escherichia coli (STEC), both zoonotic pathogens. The aim of this study was to characterize isolates of both pathogens obtained from animals raised in BPS from two central Chile regions. The presence of pathogens was determined by bacterial culture and confirmatory PCR for each sampled BPS, calculating positivity rates. Multivariate logistic regression was used to determine risk factors. Additionally, phenotypic antimicrobial resistance was determined. A positivity rate of 2.88% for S. enterica and 14.39% for STEC was determined for the complete study region (Valparaíso and Metropolitana regions). Risk factor analysis suggests that the presence of ruminants (OR = 1.03; 95% CI = 1.002-1.075) increases the risk of STEC-positive BPS, and the presence of ruminants (OR = 1.05; 95% CI = 1.002-1.075) and the animal handlers being exclusively women (OR = 3.54; 95% CI = 1.029-12.193) increase the risk for S. enterica/STEC positivity. Eighty percent of S. enterica isolates were multidrug resistant, and all STEC were resistant to Cephalexin. This study evidences the circulation of multidrug-resistant zoonotic bacterial strains in animals kept in BPS and the presence of factors that modify the risk of BPS positivity for both pathogens.

Antimicrobial resistomes in food chain microbiomes

The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.

Microbial Resistance to Antibiotics and Biofilm Formation of Bacterial Isolates from Different Carp Species and Risk Assessment for Public Health

The aim of this research was to investigate the effects of biofilm on antibiotic resistance of the bacterial isolates present in fish meat and to assess the risk of antibiotic residues for public health. Common carp, silver carp and grass carp fishes were purchased from retail stores for an in vitro biofilm investigation and a drug-resistant pattern determination. In all samples, up to 10⁴ CFU/g of bacteria, such as Escherichia coli, Aeromonas hydrophila, Shewanella putrefaciens, Vibrio spp. and Staphylococcus spp., were observed. Isolates from the samples and their biofilms were subjected to an antibiogram assay using antibiotics such as amoxicillin, ampicillin, cefotaxime, ciprofloxacin, chloramphenicol, gentamicin, streptomycin, tetracycline and trimethoprim. Obtained results showed that some of the isolates were sensitive to antibiotics and some were resistant. Results of LC-MS/MS analysis showed that antibiotics residues were present in fish samples in the range between 4.9 and 199.4 µg/kg, with a total sum of 417.1 µg/kg. Estimated daily intake (EDI) was established to be 0.274 μg/kg of body weight/day for men and 0.332 μg/kg of body weight/day for women, with an acceptable daily intake (ADI) of 8.5 and 7.0 µg/kg of body weight/day for men and women, respectively. The results of the present study, therefore, highlight the safe consumption of fresh fish.

Isolation and characterization of bacteriophage Ib_pec2 against shigatoxigenic Escherichia coli

This study was aimed to isolate and characterize bacteriophage against drug-resistant, shigatoxigenic Escherichia coli (STEC), one of the zoonotic, food-borne organisms associated with ruminants, mainly cattle. STEC were isolated (n = 35) from neonatal calves, dairy workers, and the surrounding environment and their antimicrobial resistance pattern was studied. Out of the 35 isolates tested, 17 isolates were found to be multidrug resistant to important antibiotics like ampicillin, amoxicillin-clavulanate, ciprofloxacin, streptomycin, and tetracycline. Bacteriophage namely Ib_pec2 was isolated against one of the STEC isolates and its morphology, genetic and proteomic characterization was done. Morphological analysis by TEM revealed bacteriophages belonging to myoviridae family. The genetic characterization of g23 gene revealed that the bacteriophage belonged to Tequatrovirus of myoviridae family. Proteomic analysis was able to identify five proteins identical to Tequatrovirus of myoviridae family. One-step growth curve experiment revealed a latency period of 40 min and a burst size of 893 pfu/bacteria. Temperature and pH ranging from 40°C to 50°C, pH 6-8, respectively. Phage could able to lyse majority of the STEC isolates. STEC are commensal organisms in the gastrointestinal tract of ruminants but are pathogenic in humans. Bacteriophages can be used as alternatives to antibiotics to control bacterial growth in ruminants and prevent its further spillage in the environment.

Occurrence and genetic characteristics of multidrug-resistant Escherichia coli isolates co-harboring antimicrobial resistance genes and metal tolerance genes in aquatic ecosystems

Multidrug-resistant (MDR) Escherichia coli isolates (n = 50) were recovered from aquatic ecosystems, which presented high counts of E. coli and metal values within the recommended range. These isolates showed different multidrug resistance profiles, highlighting the resistance to extended-spectrum cephalosporins, polymyxins, and fluoroquinolones. Several antimicrobial resistance genes (ARGs) were found, spotlighting the presence of at least one β-lactamase-encoding gene in each E. coli isolate. Substitutions in the quinolone resistance-determining regions and the two-component systems involving PhoP/PhoQ and PmrA/PmrB were also found. The metal tolerance gene rcnA (nickel and cobalt efflux pump) was the most prevalent. In this regard, 94% of E. coli isolates presented the co-occurrence of at least one ARG and metal tolerance gene. Furthermore, virulence genes and genetic diversity were found among MDR E. coli isolates. The emergence of potentially pathogenic isolates exhibiting multidrug resistance and metal tolerance emerged as a global health problem at the human-animal-environment interface.

Prevalence and Whole-Genome Sequence-Based Analysis of Shiga Toxin-Producing Escherichia coli Isolates from the Recto-Anal Junction of Slaughter-Age Irish Sheep

Shiga toxin-producing Escherichia coli (STEC) organisms are a diverse group of pathogenic bacteria capable of causing serious human illness, and serogroups O157 and O26 are frequently implicated in human disease. Ruminant hosts are the primary STEC reservoir, and small ruminants are important contributors to STEC transmission. This study investigated the prevalence, serotypes, and shedding dynamics of STEC, including the supershedding of serogroups O157 and O26, in Irish sheep. Recto-anal mucosal swab samples (n = 840) were collected over 24 months from two ovine slaughtering facilities. Samples were plated on selective agars and were quantitatively and qualitatively assessed via real-time PCR (RT-PCR) for Shiga toxin prevalence and serogroup. A subset of STEC isolates (n = 199) were selected for whole-genome sequencing and analyzed in silico. In total, 704/840 (83.8%) swab samples were Shiga toxin positive following RT-PCR screening, and 363/704 (51.6%) animals were subsequently culture positive for STEC. Five animals were shedding STEC O157, and three of these were identified as supershedders. No STEC O26 was isolated. Post hoc statistical analysis showed that younger animals are more likely to harbor STEC and that STEC carriage is most prevalent during the summer months. Following sequencing, 178/199 genomes were confirmed as STEC. Thirty-five different serotypes were identified, 15 of which were not yet reported for sheep. Serotype O91:H14 was the most frequently reported. Eight Shiga toxin gene variants were reported, two stx₁ and six stx₂, and three novel Shiga-toxin subunit combinations were observed. Variant stx_1c was the most prevalent, while many strains also harbored stx_2b. IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) bacteria are foodborne, zoonotic pathogens of significant public health concern. All STEC organisms harbor stx, a critical virulence determinant, but it is not expressed in most serotypes. Sheep shed the pathogen via fecal excretion and are increasingly recognized as important contributors to the dissemination of STEC. In this study, we have found that there is high prevalence of STEC circulating within sheep and that prevalence is related to animal age and seasonality. Further, sheep harbor a variety of non-O157 STEC, whose prevalence and contribution to human disease have been underinvestigated for many years. A variety of Stx variants were also observed, some of which are of high clinical importance.

Draft genome sequence of colistin-resistant and extended-spectrum β-lactamase (ESBL)-producing multidrug-resistant Escherichia coli isolated from poultry meat

OBJECTIVES

The presence of multidrug-resistant bacteria in the food chain represents a major public-health concern and has significant economic repercussions. Here we describe the draft genome sequence of serotype O21:H16, multilocus sequence typing (MLST) ST3270 and ribosomal MLST rST120701, multidrug-resistant Escherichia coli Ch7_4SIAU, which was isolated from poultry meat collected from a local market in Jeddah, Saudi Arabia.

METHODS

Ch7_4SIAU was grown on MacConkey agar and was identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). An Illumina MiSeq platform was used to generate 2.4 million paired-end reads of 150 bp.

RESULTS

The draft genome of Ch7_4SIAU is ∼5.1 Mb with a GC content of ∼50% and contains five plasmid replicons [ColpVC, IncFII, IncHI2, IncI(Gamma) and IncX1]. The isolate is resistant to third- and fourth-generation cephalosporins. It carries the mobile colistin resistance gene mcr-1.1 and the extended-spectrum β-lactamase (ESBL) gene bla_CTXM-15 as well as the astA gene encoding enteroaggregative E. coli heat-stable enterotoxin 1 (EAST-1).

CONCLUSION

This report presents the first draft genome of ESBL-positive E. coli isolated from poultry meat in Saudi Arabia. The findings can be used as a reference for genomic epidemiological studies of antimicrobial resistance in Enterobacteriaceae in the local food chain.

Emergence of Plasmid-Mediated Resistance Genes tet(X) and mcr-1 in Escherichia coli Clinical Isolates from Pakistan

The emergence of tet(X) represents a significant threat to human health. In this study, we aimed to investigate the genomic characterizations of tet(X)-positive clinical Escherichia coli isolates and provide genomic insight into the dissemination of antibiotic-resistant bacteria in clinical settings. Four tet(X)-positive E. coli isolates, PK5074, PK5086, PK5095, and PK5097, from 100 human clinical isolates were identified by PCR and were resistant to tigecycline. tet(X) genes were in IncFII plasmids in 4 E. coli isolates. Worryingly, PK5074 also carried an mcr-1-bearing IncHI2 plasmid. Notably, a relatively high cotransfer frequency of tet(X) and mcr-1 in PK5074 was found. PK5086, PK5095, and PK5097 were categorized into sequence type 410 (ST410) and indicated clonal dissemination of tet(X)-positive strains in hospitals, but tet(X)-bearing plasmids in PK5086, PK5095, and PK5097 were nontransferable. We present the first report of clinical E. coli isolates harboring tet(X) in South Asia. Our results support the implication of humans as a potential reservoir for tet(X)-harboring E. coli. We provide insight into the dissemination of tet(X) and mcr-1 in a clinical setting and highlight the current transmission of both critical resistance genes globally.

IMPORTANCE Global transmission of plasmid-mediated tigecycline resistance gene tet(X)-bearing Escherichia coli strains incurs a public health concern. However, the research focusing on the prevalence of tet(X)-positive isolates in clinical specimens is still rare, and to our knowledge, there is no such report from South Asia. Here, we characterized four E. coli clinical isolates harboring tet(X) of human origin in Pakistan and demonstrated clonal dissemination of tet(X)-positive isolates in hospitals. We report the emergence of an mcr-1-bearing IncHI2 plasmid together with a tet(X)-positive IncFII plasmid in one clinical isolate. Cotransfer of tet(X)- and mcr-1-carrying plasmids is worrying and warrants further investigations.

Genomic Epidemiology of Shiga Toxin-Producing Escherichia coli Isolated from the Livestock-Food-Human Interface in South America

Simple Summary

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens that cause food-borne diseases in humans, where cattle and derived products play a key role as reservoirs and vehicles. We analyzed the genomic data of STEC strains circulating at the livestock-food-human interface in South America, extracting clinically and epidemiologically relevant information (serotypes, virulome, resistance genes, sequence types, and phylogenomics). This study included 130 STEC genomes obtained from cattle (n = 51), beef (n = 48), and human (n = 31) samples. The successful expansion of O157:H7 (ST11) and non-O157 (ST16, ST21, ST223, ST443, ST677, ST679, ST2388) clones is highlighted, suggesting common activities, such as multilateral trade and travel. Circulating STEC strains analyzed exhibit high genomic diversity and harbor several genetic determinants associated with severe illness in humans, highlighting the need to establish official surveillance of this pathogen that should be focused on detecting molecular determinants of virulence and clonal relatedness, in the whole beef production chain.

Abstract

Shiga toxin-producing Escherichia coli (STEC) are zoonotic pathogens responsible for causing food-borne diseases in humans. While South America has the highest incidence of human STEC infections, information about the genomic characteristics of the circulating strains is scarce. The aim of this study was to analyze genomic data of STEC strains isolated in South America from cattle, beef, and humans; predicting the antibiotic resistome, serotypes, sequence types (STs), clonal complexes (CCs) and phylogenomic backgrounds. A total of 130 whole genome sequences of STEC strains were analyzed, where 39.2% were isolated from cattle, 36.9% from beef, and 23.8% from humans. The ST11 was the most predicted (20.8%) and included O-:H7 (10.8%) and O157:H7 (10%) serotypes. The successful expansion of non-O157 clones such as ST16/CC29-O111:H8 and ST21/CC29-O26:H11 is highlighted, suggesting multilateral trade and travel. Virulome analyses showed that the predominant stx subtype was stx2a (54.6%); most strains carried ehaA (96.2%), iha (91.5%) and lpfA (77.7%) genes. We present genomic data that can be used to support the surveillance of STEC strains circulating at the livestock-food-human interface in South America, in order to control the spread of critical clones “from farm to table”.

Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli

Introduction

Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants.

Objectives

In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources.

Results

The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers.

Conclusion

This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.

Genomic features and antimicrobial resistance patterns of Shiga toxin-producing Escherichia coli strains isolated from food in Chile

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen that causes severe illness in humans, often associated with foodborne outbreaks. Antimicrobial resistance among foodborne E. coli has increased over the last decades becoming a public health issue. In this study, the presence and features of STEC were investigated in samples of meat, seafood, vegetables and ready-to-eat street-vended food collected in Chile, using a genomic and microbiological approach. Phenotypic and genotypic antimicrobial resistance profiles were determined, and serotype, phylogroup, sequence type (ST) and phylogenomics were predicted using bioinformatic tools. Three thousand three hundred samples collected in 2019 were screened, of which 18 were positive for STEC strains (0.5%), with stx2a (61.1%) being the predominant stx subtype. The presence of the virulence genes lpfA (100%), iha and ehaA (94.4%), and ehxA, hlyA and saa (83.3%) was confirmed among the STEC strains; the Locus of adhesion and autoaggregation (LAA) was predicted in 14 (77.8%) strains. Strains displayed resistance to colistin (100%), and intermediate resistance to enrofloxacin (11.1%) and chloramphenicol (5.6%). In this regard, mutations in the two-component regulatory system genes pmrA (S29G), pmrB (D283G) and phoP (I44L), and the presence of the qnrB19 gene were confirmed. STEC strains belonged to ST11231 (38.9%), ST297 and ST58 (16.7% each), and ST1635, ST11232, ST446, ST442 and ST54 (5.6% each), and the most frequently detected serotypes were O113:H21 (44.4%), O130:H11 and O116:H21 (16.7% each), and O174:H21 (11.1%). Strains belonging to the international ST58 showed genomic relatedness with worldwide strains from human and non-human sources. Our study reports for the first time the genomic profile of STEC strains isolated from food in Chile, highlighting the presence of international clones and sequence types commonly associated with human infections in different geographical regions, as well as the convergence of virulence and resistance in STEC lineages circulating in this country.

Antimicrobial Usage Factors and Resistance Profiles of Shiga Toxin-Producing Escherichia coli in Backyard Production Systems From Central Chile

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen and important cause of foodborne disease worldwide. Many animal species in backyard production systems (BPS) harbor STEC, systems characterized by low biosecurity and technification. No information is reported on STEC circulation, antimicrobial resistance (AMR) and potential drivers of antimicrobial usage in Chilean BPS, increasing the risk of maintenance and transmission of zoonotic pathogens and AMR generation. Thus, the aim of this study was to characterize phenotypic and genotypic AMR and to study the epidemiology of STEC isolated in BPS from Metropolitana region, Chile. A total of 85 BPS were sampled. Minimal inhibitory concentration and whole genome sequencing was assessed in 10 STEC strain isolated from BPS. All strains were cephalexin-resistant (100%, n = 10), and five strains were resistant to chloramphenicol (50%). The most frequent serotype was O113:H21 (40%), followed by O76:H19 (40%), O91:H14 (10%), and O130:H11 (10%). The stx1 type was detected in all isolated strains, while stx2 was only detected in two strains. The Stx subtype most frequently detected was stx1c (80%), followed by stx1a (20%), stx2b (10%), and stx2d (10%). All strains harbored chromosomal bla_AmpC. Principal component analysis shows that BPS size, number of cattle, pet and horse, and elevation act as driver of antimicrobial usage. Logistic multivariable regression shows that recognition of diseases in animals (p = 0.038; OR = 9.382; 95% CI: 1.138–77.345), neighboring poultry and/or swine BPS (p = 0.006; OR = 10.564; 95% CI: 1.996–55.894), visit of Veterinary Officials (p = 0.010; OR = 76.178; 95% CI: 2.860–2029.315) and close contact between animal species in the BPS (p = 0.021; OR = 9.030; 95% CI: 1.385–58.888) increase significantly the risk of antimicrobial use in BPS. This is the first evidence of STEC strains circulating in BPS in Chile, exhibiting phenotypic AMR, representing a threat for animal and public health. Additionally, we identified factors acting as drivers for antimicrobial usage in BPS, highlighting the importance of integration of these populations into surveillance and education programs to tackle the potential development of antimicrobial resistance and therefore the risk for ecosystemic health.

An Overview of Shiga-Toxin Producing Escherichia coli Carriage and Prevalence in the Ovine Meat Production Chain

Shiga-toxin producing Escherichia coli (STEC) are zoonotic foodborne pathogens that are capable of causing serious human illness. Ovine ruminants are recognized as an important source of STEC and a notable contributor to contamination within the food industry. This review examined the prevalence of STEC in the ovine food production chain from farm-to-fork, reporting carriage in sheep herds, during abattoir processing, and in raw and ready-to-eat meats and meat products. Factors affecting the prevalence of STEC, including seasonality and animal age, were also examined. A relative prevalence can be obtained by calculating the mean prevalence observed over multiple surveys, weighted by sample number. A relative mean prevalence was obtained for STEC O157 and all STEC serogroups at multiple points along the ovine production chain by using suitable published surveys. A relative mean prevalence (and range) for STEC O157 was calculated: for feces 4.4% (0.2-28.1%), fleece 7.6% (0.8-12.8%), carcass 2.1% (0.2-9.8%), and raw ovine meat 1.9% (0.2-6.3%). For all STEC independent of serotype, a relative mean prevalence was calculated: for feces 33.3% (0.9-90.0%), carcass 58.7% (2.0-81.6%), and raw ovine meat 15.4% (2.7-35.5%). The prevalence of STEC in ovine fleece was reported in only one earlier survey, which recorded a prevalence of 86.2%. Animal age was reported to affect shedding in many surveys, with younger animals typically reported as having a higher prevalence of the pathogen. The prevalence of STEC decreases significantly along the ovine production chain after the application of postharvest interventions. Ovine products pose a small risk of potential STEC contamination to the food supply chain.

Coexistence of blaKPC-2-IncN and mcr-1-IncX4 plasmids in a ST48 Escherichia coli strain in China

OBJECTIVES

The aim of this study was to explore the genomic content of a bla_KPC-2- and mcr-1-harbouring Escherichia coli strain and to clarify the molecular mechanism for the transmission of multidrug resistance.

METHODS

Antimicrobial susceptibility testing was conducted by the broth microdilution method to determine the resistance profile. Filter-mating conjugation assays were performed to confirm the plasmid transfer ability. Whole-genome sequence data were acquired by a combination of Illumina paired-end reads and Nanopore long-read sequencing.

RESULTS

Escherichia coli strain QE11-421 was an mcr-1-positive colistin-resistant isolate that co-harboured the bla_KPC-2 gene conferring carbapenem resistance. Genome sequence data confirmed QE11-421 as a sequence type 48 (ST48) E. coli that harboured five large conjugative plasmids encoding several multidrug resistance genes. The bla_KPC-2 gene was located on a Tn3-Tn4401 composite transposon, which is part of a 65-kb multidrug-resistant IncN plasmid. The mcr-1 gene was harboured on another 33-kb IncX4 plasmid that was more conserved and presented few antimicrobial resistance determinants. No copies of insertion sequence ISApl1 were found flanking the mcr-1 gene, decreasing the mobility of mcr-1 based on its original Tn6330 transposon.

CONCLUSIONS

Horizontal transfer of multidrug resistance plasmids or resistance-related transposon units was responsible for the emergence of this notorious superbug. The coexistence of bla_KPC-2-IncN and mcr-1-IncX4 plasmids in a ST48 E. coli strain in humans poses a great threat.

Genetic Diversity of Multidrug-Resistant CMY-Producing Escherichia coli from Feces and Soil in a Small-Scale Pig Farm

Diarrheagenic Escherichia coli cause diarrheal diseases, which are a public health concern and affect mainly developing countries. Multidrug-resistant (MDR) pathogens have been spreading in different sources, including animals and the environment. E. coli strains were obtained from a small-scale pig farm and 33 antimicrobials were tested. All strains were classified as MDR and harbored several antimicrobial resistance genes (ARGs) [bla_CMY, bla_OXA-1-like, bla_SHV, tet(A), tet(B), aadA, aac(6')-Ib, aph(3')-Ia, sul1, sul2, sul3, floR, and cmlA] and plasmids. Besides, mutations in quinolone resistance-determining region of GyrA (Ser83Leu and Asp87Asn) and ParC (Glu84Asp) were detected. Among the MDR E. coli, nine strains (52%) presented diarrheagenic virulence genes, including genes related to Shiga toxin-producing E. coli (STEC), enteroinvasive E. coli (EIEC), and enteroaggregative E. coli (EAEC). The pulsed-field gel electrophoresis results showed a high genetic diversity among the MDR E. coli strains. Multilocus sequence typing (MLST) analyses revealed different sequence types phylogenetically related to each other, including ST10 and ST56. Subtyping of MLST by fimH gene showed different fimH type. This study shows a high genetic diversity among MDR ARG-producing E. coli belonging to STEC, EIEC, and EAEC pathotypes obtained from a small-scale pig farm and contributes to the monitoring of antimicrobial-resistant pathogens worldwide, mainly in environmental samples, which are associated with One Health framework.