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Third-Generation Cephalosporin-Resistant Enterobacterales and Methicillin-Resistant Staphylococcus aureus (MRSA) in Pigs in Rwanda
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Emmanuel Irimaso
1,2
,
Valens Hagenimana
2,
Emmanuel Nzabamwita
2,
Michael Blümlinger
1,3,
Otto W. Fischer
4,
Lukas Schwarz
3
,
Michael P. Szostak
1,
Olga Makarova
5,
Adriana Cabal Rosel
6,
Werner Ruppitsch
7,8,
Elke Müller
9,10,11,
Andrea T. Feßler
12,13,
Sascha D. Braun
9,10,11,
Stefan Schwarz
12,13
,
Stefan Monecke
9,10,11,
Ralf Ehricht
9,10,11,14,
Suzana Tkalcic
15,
Christophe Ntakirutimana
4,
Joachim Spergser
1,
Doris Verhovsek
3 and
Igor Loncaric
1,*add
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1
Institute of Microbiology, University of Veterinary Medicine, 1210 Vienna, Austria
2
The College of Veterinary Medicine and Animal Sciences (CVAS), University of Rwanda, Nyagatare P.O. Box 57, Rwanda
3
Clinical Center for Population Medicine in Fish, Pig and Poultry, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210 Vienna, Austria
4
New Vision Veterinary Hospital (NVVH), RN 4 Kigali—Musanze Road, Musanze, Rwanda
5
Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210 Vienna, Austria
6
Institute for Surveillance & Infectious Disease Epidemiology, Division Public Health, Austrian Agency for Health and Food Safety, 1200 Vienna, Austria
7
Institute of Hygiene and Medical Microbiology, Medical University Innsbruck, 6020 Innsbruck, Austria
8
Faculty of Food Technology, Food Safety and Ecology, University of Donja Gorica, 81000 Podgorica, Montenegro
9
Leibniz-Institute of Photonic Technology (Leibniz-IPHT), Member of the Leibniz Center for Photonics in Infection Research (LPI), 07745 Jena, Germany
10
InfectoGnostics Research Campus, 07743 Jena, Germany
11
Center for Translational Medicine (CETRAMED), Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany
12
Institute of Microbiology and Epizootics, School of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
13
Veterinary Centre for Resistance Research (TZR), School of Veterinary Medicine, Freie Universität Berlin, Robert-von-Ostertag-Straße 8, 14163 Berlin, Germany
14
Institute of Physical Chemistry, Friedrich-Schiller-University, 07743 Jena, Germany
15
College of Veterinary Medicine, Western University of Health Sciences, Pomona, CA 91766-1854, USA
*
Author to whom correspondence should be addressed.
Animals 2026, 16(1), 122; https://doi.org/10.3390/ani16010122
Submission received: 15 October 2025
/
Revised: 25 December 2025
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Accepted: 29 December 2025
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Published: 31 December 2025
(This article belongs to the Special Issue Antimicrobial Resistance and Innovative Strategies in Veterinary Medicine)
Simple Summary
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.
Abstract
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.
