# Assessing the Genomic Landscape of Salmonella enterica Isolated From Cattle Faeces on a Nigerian Farm

## TL;DR

This study found low antibiotic resistance in Salmonella from Nigerian cattle, suggesting good antibiotic use practices on the farm.

## Contribution

The study reports rare Salmonella serovars and minimal AMR gene carriage in a low-income African setting.

## Key findings

- All Salmonella isolates showed 100% phenotypic susceptibility to tested antibiotics.
- Most sequenced strains lacked AMR genes except for a few with resistance genes like fosA7 and aph(3′)‐lb.

## Abstract

Antibiotic resistance is a global menace, particularly in low‐ and middle‐income countries where antimicrobial resistance (AMR) in zoonotic pathogens like Salmonella is on the rise. This study investigates the phenotypic and genotypic AMR in Salmonella enterica. isolated from cattle faeces collected by faecal grab method on a Nigerian dairy farm. Salmonella enterica was cultured from the faecal samples of 138 individual cattle at the University of Ibadan dairy farm, with identification done through MALDI‐TOF‐MS, genus‐specific PCR, and Microbact 24E. The minimum inhibitory concentration (MIC) of selected antibiotics was determined by Vitek 2 compact system. Whole genome sequencing was conducted on eighteen isolates that met pre‐sequencing quality standards, utilizing the Illumina HiSeq platform. Sequence types and AMR genes were determined using publicly available tools. Interestingly, all isolates showed 100% phenotypic susceptibility to the tested antibiotics. Notably, several rare Salmonella enterica serovars were identified among the sequenced strains; Koketime (n = 2), Hadar (n = 3), Banalia|Tounouma (n = 10), Hermannswerder (n = 2), and Chomedey|Glostrup (n = 1). While most of the sequenced Salmonella enterica strains (15 out of 18) lacked AMR genes besides efflux transporter gene, a strain of Chomedey|Glostrup serovar exhibited genes associated with reduced susceptibility to aminoglycosides (aph(3′)‐lb, aph(6)‐Id), quinolones (qnrB), sulphonamides (sul2), and tetracycline (tet(A)), while Koketime strains possessed fosfomycin resistance genes (fosA7) besides the efflux genes. The absence of phenotypic and genotypic AMR in most of the isolates highlights the possibility that AMR could be controlled in livestocks in developing countries.

This study examined Salmonella enterica isolated from cattle faeces on a Nigerian farm. All isolates exhibited complete susceptibility to tested antibiotics, and whole‐genome sequencing revealed minimal antimicrobial resistance gene carriage. These findings demonstrate a notably low resistance burden which is an uncommon observation in many low‐and middle‐ income African settings, underscoring the crucial role of prudent antibiotic use in livestock management.