Livestock are a source of zoonotic pathogens and bacteria harbouring antimicrobial resistance (AMR) that can pose a threat to public health. This study assessed the burden of antimicrobial resistance (AMR) and genomic diversity of Salmonella and Escherichia coli at 25 poultry farms in Oyo State, Nigeria. The farm-level occurrence of Salmonella was 48%, with 12 serovars identified, including S. Kentucky Sequence Type 198. Notably, 70% of Salmonella isolates were resistant to fluoroquinolones, and multidrug resistance was observed in S. Kentucky and S. Derby. The study also found a 52% farm-level occurrence of extended-spectrum beta-lactamase-producing E. coli, with four bla_CTX-M variants detected (bla_CTX-M-15, bla_CTX-M-27, bla_CTX-M-55, and bla_CTX-M-65). A genomic analysis revealed the dissemination of bacterial clones between farms, indicating potential routes of transmission. The high occurrence of AMR in both Salmonella and E. coli presents a potential public health risk, mainly through the consumption of contaminated poultry products. The study highlights the need for improved farm biosecurity and appropriate antimicrobial use to reduce the spread of resistant strains and combat AMR. These findings contribute to the Nigerian National Action Plan for AMR and underscore the importance of ongoing research and interventions in the poultry sector.

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are resistant to the critically important third- and fourth-generation cephalosporin antibiotics and present a risk to animal and human health. In Zimbabwe, there is an evidence gap concerning the prevalence and diversity of ESBL-producing E. coli in poultry. In this study, we screened for ESBL-E. coli at farms (n=50) and markets (n=10) using MacConkey agar supplemented with 4 µg ml⁻¹ ceftriaxone. ESBL-E. coli were detected at every market and at 21 farms, giving a farm-level prevalence of 42%. Seventy isolates were obtained and tested for antimicrobial susceptibility, whilst 69 of these were further analysed by whole-genome sequencing. A total of eight distinct bla _CTX-M variants were identified, and 69 out of 70 isolates were multidrug-resistant. Genomic analysis revealed evidence for clonal expansion of an ESBL-producing clone and horizontal gene transfer via plasmids being responsible for the dissemination of ESBL-E. coli. Geographic Information System mapping was used to visualize the distribution of the ESBL-producing clones. For example, ST1141 isolates were clonal, having a highly conserved core genome, and harboured bla _CTX-M-15 and 11 additional antimicrobial resistance genes on a ~338 kbp IncHI2 plasmid which was not present in other isolates. This clone was present at nine farms. In contrast, a conserved ~93 kbp IncFII plasmid harbouring bla _CTX-M-55 was present in isolates from three different multilocus sequence types obtained from six farms. This study provides insight into the burden and distribution of ESBL-E. coli at poultry farms in Zimbabwe and provides molecular genetic evidence for clonal expansion and plasmid transfer as being important mechanisms for the dissemination of ESBL-E. coli in this setting. This study underscores the importance of adopting measures, such as prudent antimicrobial use and farm biosecurity, that can limit the development and dissemination of ESBL-producing E. coli.

Salmonella enterica is a significant zoonotic pathogen, posing a serious public health threat through its presence in the food supply chain, particularly in poultry production facilities. This study aimed to investigate the genetic diversity, antimicrobial resistance (AMR) profiles and phylogenetic relationships of S. enterica serovars isolated from various stages of the broiler supply chain in Harare, Zimbabwe. Whole-genome sequencing was employed to analyse 28 Salmonella isolates from broiler farms, slaughter facilities and retail markets. The overall prevalence of Salmonella was 5.1% out of 552 samples tested. Contamination rates were higher at slaughter facilities, where 11% of 100 samples tested positive and at retail markets, where 20% of 20 samples were contaminated. In contrast, farms had a significantly lower prevalence, with only 3.0% of 432 samples showing Salmonella presence. Eight serovars were identified, with S. enterica subsp. enterica serovar Typhimurium being the most prevalent at 27.6%. Notably, 34.5% of the isolates harboured resistance genes, including fosA3 , fosA7.2 and qnrB19 , and exhibited mutations in the gyrA and parC regions. An extended-spectrum beta-lactamase-producing S. enterica subsp. enterica serovar Kentucky ST198 strain was isolated from retail chicken cuts. All isolates carried virulence genes such as iroC , iroB and sinH , with sodC1 present in 47.4% of the isolates. Approximately 31% of the isolates co-harboured antimicrobial, stress tolerance and virulence genes. Genomic analysis identified distinct sequence types while also revealing identical core SNPs in genomes across various stages of the supply chain. This study highlights the transmission of Salmonella and AMR in the broiler supply chain, emphasizing the urgent need for improved surveillance and intervention strategies to reduce public health risks from contaminated poultry products.

Escherichia coli (E. coli) and Salmonella spp are bacteria commonly found in the intestinal flora of humans, other mammals, animals, and birds. These two pathogens are the most important food-borne pathogens of public health importance in poultry globally. This study was designed to determine the antibiotics resistance patterns, identify resistance genes and ESBL production in E. coli and Salmonella species isolated from commercial poultry farms across Nigeria. A subset of 101 isolates (24 putative Salmonella and 77 putative E. coli) from a collection obtained at poultry farms in Nigeria , were analysed in this study. Of the 24 confirmed Salmonella, 7 isolates were fully susceptible and had no resistance genes, these were the two Dugbe’s and five Isangi serovars. The antimicrobial class with the highest prevalence of resistance was the quinolones with 71% of isolates having resistance to Ciprofloxacin and Nalidixic Acid. None of the Salmonella isolates had resistance to Amikacin, Azithromycin, Cephalosporins (2nd – 4th generation), Colistin, Meropenem, Tigecycline and Trimethoprim. There was a much higher resistance frequency in the E. coli compared to the Salmonella. Over 80% of isolates have resistance to Fluoroquinolones (Ciprofloxacin and Nalidixic Acid) with a similar percentage having resistance to tetracyclines. No isolates had an AmpC phenotype. The MIC distribution for the E. coli is also far greater than the Salmonella with a higher prevalence of MDR strains. Notable genes identified in isolates include: sul2, aph(3'')-Ib, aph(6)-Id, blaCTX-M, blaOXA, blaCTX-M-15, CTX-M-15, CTX-M-27, CTX-M-65 and the most prevalent been CTX-M-55. The study revealed that Salmonella and E. coli from in Oyo State are becoming more resistant to antibiotics.