# Third-Generation Cephalosporin-Resistant Enterobacterales and Methicillin-Resistant Staphylococcus aureus (MRSA) in Pigs in Rwanda

## TL;DR

This study found antibiotic-resistant bacteria in pigs and their environment in Rwanda, highlighting a public health risk due to close human-animal interactions.

## Contribution

The study identifies MRSA and third-generation cephalosporin-resistant Enterobacterales in pigs and their environment in Rwanda for the first time.

## Key findings

- 32 third-generation cephalosporin-resistant Enterobacterales were detected, mostly Escherichia coli and Klebsiella pneumoniae.
- Four MRSA isolates were found, all belonging to clonal complex 398, a livestock-associated strain.
- Multidrug resistance and virulence factors were commonly observed in the resistant bacteria.

## Abstract

This study explored the presence of antibiotic-resistant bacteria in pigs and their surroundings on farms in Rwanda. Antibiotic resistance occurs when bacteria change and become harder to kill with medicines, which is a serious problem for both human and animal health worldwide. We collected samples from pigs and their environment, such as nasal swabs, feces, manure, and dust, to check for two types of resistant bacteria: one called MRSA, which can cause tough infections in people and animals, and another group that resists important antibiotics often used to treat infections. Resistant bacteria were especially common in pig droppings and nasal samples. The study highlights the risk of sharing such bacteria where people and animals live closely together, as is common in Rwanda. These findings show the need to carefully watch for and control antibiotic resistance in animals and their environment, not just in people. This work supports efforts to protect health by promoting safer farming practices and responsible use of antibiotics in Rwanda.

This pilot study investigated the presence of methicillin-resistant Staphylococcus aureus (MRSA) and third-generation cephalosporin-resistant (3GC-R) Enterobacterales in conventionally kept domestic pigs and their environment across four districts in Rwanda. A total of 114 swabs (nasal, rectal, manure, dust) from 29 farms were collected and processed to isolate resistant bacteria. Thirty-two 3GC-R Enterobacterales were detected. Escherichia coli predominantly harboring blaCTX-M group 1 β-lactamase genes, alongside Klebsiella pneumoniae isolates, all displaying extended-spectrum β-lactamase (ESBL) phenotypes. Four MRSA isolates, all belonging to clonal complex 398 and SCCmec type IV, the typical livestock MRSA, were recovered from nasal and environmental samples. Multidrug resistance was frequently observed. The co-occurrence of β-lactamase genes, non-β-lactam resistance genes, and virulence factors such as fimH and loci associated with extraintestinal pathogenic and enteropathogenic E. coli. The detection of both MRSA and 3GC-R Enterobacterales in the present study indicates pigs and their farm environments as reservoirs of WHO priority pathogens in Rwanda, highlighting a potential public health risk in the context of extensive human–animal–environment interaction. These findings emphasize the urgent need for integrated One Health surveillance and comprehensive AMR control strategies addressing both animal and environmental reservoirs to support Rwanda’s National Action Plan on Antimicrobial Resistance.