Mobile Genetic Elements Drive Drug Resistance Spread Across Swine and Humans

A genomic investigation of Escherichia coli isolates recovered from swine and human populations across Sichuan Province, China, has demonstrated that the spread of critically important antibiotic resistance genes at the animal-human interface is driven primarily by horizontal gene transfer rather than the clonal expansion of bacterial lineages. The surveillance study, published in Animal Diseases, evaluated 1,001 fecal samples gathered from 103 pig farms and neighboring communities to characterize the distribution and mobility of genes conferring resistance to extended-spectrum cephalosporins and last-resort carbapenems. Among the collected samples, researchers identified 110 Escherichia coli isolates exhibiting extended-spectrum beta-lactamase production, carbapenem resistance, or both phenotypes, representing an overall recovery rate of 11.0 percent. Notably, core-genome single-nucleotide polymorphism analysis revealed that while clonal transmission occurred within swine herds, no direct cross-species clonal transfer occurred between pigs and farm workers. Instead, the presence of identical resistance determinants across human and animal isolates pointed to mobile genetic elements as the primary mechanisms driving cross-compartment resistance dissemination.

The sample cohort comprised 808 fecal specimens from domestic pigs, 96 specimens from occupationally exposed farm workers, and 97 specimens from local community residents without farm exposure. Laboratory screening identified 106 extended-spectrum beta-lactamase producers among the 110 confirmed resistant isolates, with the majority originating from swine production stages. Piglets accounted for the largest share of extended-spectrum beta-lactamase strains at 45.3 percent with 48 isolates, followed by fattening pigs at 17.9 percent with 19 isolates, and sows at 17.0 percent with 18 isolates. Farm workers yielded 11 resistant strains, representing 10.4 percent of the beta-lactamase cohort, while unexposed community residents contributed 10 strains, representing 9.4 percent. In contrast to the wide distribution of cephalosporin resistance across human and swine cohorts, phenotypic carbapenem resistance was detected in 11 isolates recovered exclusively from pigs. These carbapenem-resistant strains originated from five fattening pigs, three piglets, and three sows, demonstrating an apparent restriction of phenotypic carbapenem insensitivity to animal housing facilities rather than human participants.

Antimicrobial susceptibility profiling conducted via standard Kirby-Bauer disk diffusion against 16 antimicrobial agents confirmed widespread multidrug resistance across the bacterial collection. High levels of non-susceptibility were recorded against cephalosporins, with resistance rates reaching 98.2 percent for cefotaxime, 97.3 percent for cefazolin, and 86.4 percent for ceftazidime. The isolates also displayed extensive co-resistance to older veterinary and human therapeutic classes, including tetracycline at 90.0 percent, chloramphenicol at 89.1 percent, florfenicol at 87.3 percent, trimethoprim-sulfamethoxazole at 84.5 percent, and ciprofloxacin at 82.7 percent. Moderate resistance rates were documented for azithromycin at 38.2 percent and gentamicin at 37.3 percent. Conversely, the isolates remained largely susceptible to select reserve therapies, showing lower resistance frequencies for imipenem at 15.5 percent, amikacin at 15.5 percent, ampicillin-sulbactam at 8.2 percent, cefoxitin at 7.3 percent, polymyxin B at 7.3 percent, and tigecycline at 3.6 percent. Overall, 106 of the 110 isolates, or 96.4 percent, met the criteria for multidrug resistance by displaying non-susceptibility to at least three distinct antimicrobial classes.

Whole-genome sequencing of the 110 isolates revealed an average bacterial genome size of 4.95 megabases, ranging from 4.48 to 5.46 megabases, with an average GC content of 50.6 percent. Multilocus sequence typing resolved the bacterial collection into 42 distinct sequence types, reflecting substantial genetic diversity among circulating strains. ST648 was the predominant lineage at 14.5 percent, followed by ST10 at 9.1 percent, ST617 at 7.3 percent, and ST542 at 5.5 percent, with ST48, ST206, and ST744 each accounting for 4.5 percent. Core-genome single-nucleotide polymorphism clustering applying a threshold of five or fewer differences partitioned the isolates into 70 distinct groups. Maximum-likelihood phylogenetic reconstruction revealed 10 putative clonal transmission events, including four horizontal transfers among fattening pigs, three among piglets, one among sows, one vertical transmission event between a sow and piglet, and one cross-stage transmission involving piglets, fattening pigs, and sows. All identified clonal clusters were confined strictly within swine herds, confirming the absence of direct bacterial clone sharing across human-animal boundaries.

Genomic interrogation identified 82 distinct antimicrobial resistance genes across the bacterial collection, revealing marked contrasts between animal and human resistomes. Isolates obtained from pigs carried a significantly higher average resistance gene burden, harboring 16.86 resistance genes per isolate compared to an average of 11.42 genes observed in human strains. Distinct host-associated distribution patterns emerged for several determinants, including oqxA, oqxB, tet(A), sul3, dfrA12, and mph(A). Among the 106 isolates possessing blaCTX-M alleles, nine distinct variants were resolved, dominated by blaCTX-M-55 in 59 isolates, blaCTX-M-14 in 17 isolates, and blaCTX-M-15 in 15 isolates, with two individual strains simultaneously harboring two CTX-M variants. The metallo-beta-lactamase gene blaNDM occurred in 11 isolates, comprising eight blaNDM-5 alleles, two blaNDM-1 alleles, and one blaNDM-4 allele. Furthermore, seven strains demonstrated co-occurrence of both blaNDM and blaCTX-M determinants. The authors noted that this discrepancy in resistance gene burdens between hosts aligns with historical selective pressures exerted by veterinary antimicrobial regimens administered throughout swine production cycles.

The authors contextualized these genetic disparities within the framework of intensive animal husbandry practices, where veterinary pharmaceuticals exert selective pressure across distinct production phases. In commercial swine farming, antimicrobial compounds including doxycycline, olaquindox, and tylosin are frequently administered for therapeutic management, directly contributing to the enrichment of corresponding resistance determinants such as tet, oqxAB, and mph(A). The piglet stage represents a particularly vulnerable physiological window characterized by an immature intestinal microbiome and an underdeveloped immune system. During the critical weaning period, therapeutic doses of cephalosporins and sulfonamides are routinely administered via feed and water to prevent diarrhea and enteric infections. This targeted exposure creates an optimal ecological niche for the colonization and expansion of resistant Enterobacteriaceae. Furthermore, the routine use of third-generation cephalosporins in fattening pigs and sows sustains selective pressure, perpetuating high baseline resistance frequencies and driving the maintenance of multidrug-resistant bacterial reservoirs throughout the production continuum.

To uncover the structural foundations of gene mobility, the researchers examined the flanking genetic environments of blaCTX-M and blaNDM using colocalization network analyses. Mobilization of blaCTX-M alleles was predominantly linked to insertion sequences ISEc9, IS903B, and IS26, which frequently flanked the resistance cassettes. In parallel, blaNDM alleles exhibited close structural associations with insertion sequences IS3000 and IS26. Complete plasmid sequences resolved via Oxford Nanopore long-read sequencing across nine non-duplicate blaNDM-carrying isolates identified four plasmid replicon types: IncX3, IncHI2, IncFIB, and IncY. In IncX3 plasmids harboring blaNDM-1, designated pF86F3 and pF86F4, the resistance gene was situated within a Tn3000-like transposon structure flanked upstream by IS3000 and ISAba125 and downstream by IS26. In blaNDM-5-positive IncX3 plasmids, including pF24S1P, pF93P1, and pF70F2, an additional IS5 element was inserted between ISAba125 and the resistance gene. This precise IS5 insertion was consistently retained across all blaNDM-5-bearing plasmids, appearing universally in IncX3, IncY, and IncHI2 replicons.

Long-read assemblies further demonstrated striking differences in structural complexity and resistance gene cargo among plasmid backbones carrying carbapenemase genes. IncHI2 plasmids, represented by pF24S2 and pF81P2, embedded the core IS3000-ISAba125-IS5-blaNDM-5 cassette within extensive multidrug resistance regions containing elements such as IS1 and TnEc1. Structural alignments between these two plasmids revealed that while the immediate blaNDM-5 genetic environment remained intact, peripheral flanking regions underwent rearrangements, inversions, and deletions mediated by insertion elements. In contrast, blaNDM-4 carried on the IncFIB plasmid pF29F1 was flanked exclusively by IS26 without IS3000 or ISAba125 involvement, indicating mobilization via an independent composite transposon pathway. Plasmid incompatibility groups exhibited contrasting functional specializations: IncX3 plasmids maintained minimal resistance burdens limited strictly to blaNDM and bleMBL, functioning as streamlined low-burden vectors, whereas IncHI2 and IncY plasmids served as broad multi-resistance platforms accumulating up to 19 and 17 resistance determinants, while IncFIB plasmids carried an intermediate burden of six resistance genes.

In vitro filter mating experiments using rifampin-resistant Escherichia coli C600 recipients evaluated the functional conjugative potential of the different blaNDM-bearing plasmids. Conjugative transfer was exclusively detected for IncHI2 and IncX3 plasmids, whereas IncFIB and IncY plasmids failed to yield transconjugants under standard laboratory conditions. Among IncHI2-bearing strains, successful transfer occurred only in strain F24_S2 at a conjugation frequency of 1.08 × 10⁻⁵ transconjugants per recipient, while strain F81_P2 exhibited no transfer. In contrast, IncX3 plasmids demonstrated conjugative mobility across four distinct donor strains, with transfer frequencies spanning four orders of magnitude from 1.54 × 10⁻⁸ in strain F70F2 to 3.33 × 10⁻⁴ in strain F93P1. The failure of IncFIB, IncY, and certain IncHI2 plasmids to conjugate suggests they may lack critical transfer genes such as relaxases or type IV coupling proteins, or transfer at frequencies beneath detection thresholds. Nevertheless, transposons like Tn3000 and translocatable units formed by IS26 permit blaNDM modules to transpose between replicons, facilitating genetic exchange independent of whole-plasmid conjugation.

The epidemiological dynamics identified in Sichuan reflect broader national patterns documented across China, where blaCTX-M-55 and blaNDM-5 have become established as dominant beta-lactamase subtypes circulating in commercial swine operations. Similar dissemination patterns mediated by mobile elements have been confirmed in swine populations in Guangxi and Zhejiang provinces, underscoring a cohesive cross-regional trend within intensive animal production. The study authors emphasized that from a One Health perspective, the absence of shared bacterial clones does not diminish the substantial public health risk posed by mobile resistance determinants traversing the swine-human boundary. Agricultural reservoirs provide an expansive matrix for mobile genetic elements to shuttle critical resistance genes into human-associated bacteria, presenting an occupational exposure hazard for livestock handlers. The authors acknowledged key limitations in their study, including geographic confinement to Sichuan Province, reliance on in vitro mating assays that may underestimate complex in vivo transfer dynamics, and the lack of newly discovered mobile elements, highlighting the need for wider geographical surveillance and in vivo horizontal transfer models.

Subject of Research: Horizontal gene transfer of blaCTX-M and blaNDM in Escherichia coli from pigs and humans

Article Title: Horizontal gene transfer facilitates the dissemination of blaCTX-M and blaNDM in Escherichia coli isolates from humans and pigs in Sichuan Province, China

Article References: Liu, L., Li, X., Kang, R., Zhou, Y., Wang, Q., Zhang, T., Wang, X., Yang, X., Wang, H., & Lei, C. (2026). Horizontal gene transfer facilitates the dissemination of blaCTX-M and blaNDM in Escherichia coli isolates from humans and pigs in Sichuan Province, China. Animal Diseases, 6(1), Article 39. https://doi.org/10.1186/s44149-026-00250-w

Image Credits: AI Generated

DOI: 10.1186/s44149-026-00250-w

Keywords: Escherichia coli, Antibiotic Resistance, Horizontal Gene Transfer, blaCTX-M, blaNDM, One Health, Plasmids, Swine, Horizontal, gene, transfer, facilitates