Prevalence of ESBL-associated resistance genes and antimicrobial resistance in Escherichia coli from pigs and cattle slaughtered at urban abattoirs in Lilongwe District, Malawi.

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in food-producing animals represents a priority public health concern because of its capacity for zoonotic transmission through the food chain and frequent co-carriage of multidrug resistance (MDR) determinants. Surveillance in sub-Saharan Africa remains disproportionately limited, and no published data characterize ESBL prevalence or resistance gene profiles in slaughter animals in Malawi. This study investigated the prevalence of E. coli harboring ESBL-associated resistance genes (blaCTX-M, blaSHV) and characterized antimicrobial resistance and MDR profiles in pigs and cattle slaughtered at urban abattoirs in Lilongwe District, Malawi. Rectal swabs were collected from 50 pigs and 50 cattle (n = 100) at four urban abattoirs. Following exclusion of six samples with no bacterial growth, 94 confirmed isolates were analyzed. E. coli was identified by MALDI-TOF MS. Antimicrobial susceptibility testing was performed by disk diffusion (CLSI) against gentamicin, chloramphenicol, ciprofloxacin, sulfamethoxazole-trimethoprim, cefotaxime, and tetracycline. blaCTX-M and blaSHV genes were detected by conventional PCR. Of 94 confirmed E. coli isolates (48 pig, 46 cattle), pig isolates showed significantly higher resistance to gentamicin (50.0% vs. 15.2%; p = 0.0008) and tetracycline (85.4% vs. 56.5%; p = 0.004). Chloramphenicol resistance was high in both species (77.1% pigs; 63.0% cattle). blaCTX-M was detected in 12.5% of pig and 21.7% of cattle isolates; blaSHV in 20.8 and 6.5%, respectively (all p > 0.05). MDR was significantly more prevalent in pig isolates (70.8%, 34/48) than in cattle isolates (41.3%, 19/46; crude OR = 3.40, 95% CI 1.35-8.90; p = 0.004). Pigs had a mean resistance count of 3.17 antibiotic classes per isolate compared with 2.26 in cattle. E. coli harboring targeted ESBL-associated genes circulates in both species at urban abattoirs in Lilongwe District, with pig isolates carrying a significantly higher MDR burden. These results provide an initial baseline for monitoring E. coli harboring targeted ESBL-associated genes at the livestock-food chain interface in Malawi. While stewardship practices were not directly assessed, the findings raise important implications for species-stratified antibiotic stewardship and highlight the value of systematic antimicrobial resistance monitoring within a One Health framework.