Hospital and Environmental Transmission of XDR <i>Salmonella</i> Isangi Revealed by Genomic Surveillance in Malawi and South Africa

ABSTRACT Background Salmonella Isangi is an under-characterised serovar repeatedly associated with antimicrobial resistant hospital infections. Outbreaks of extensively drug-resistant (XDR) Salmonella Isangi occurred in close succession within hospitals in Malawi and South Africa, prompting us to characterise the serovar using epidemiologic, phenotypic, and genomic perspectives. Methods In Malawi, we integrated hospital blood culture surveillance with environmental sampling from neonatal wards and urban waterways. In South Africa, we analysed isolates from five hospitals involved in a regional outbreak. We used whole genome sequencing (Illumina and MinION) to characterise AMR genes and plasmids, assessed biofilm formation, disinfectant susceptibility, in vivo virulence, and analysed all publicly available Salmonella Isangi genomes. Findings 224 / 345 (65%) of genomes in the global collection belonged to Salmonella Isangi sequence type (ST) 335. Of these, 221 (99%) originated from Malawi and South Africa, including the isolates recovered from both outbreaks. 199 (89%) ST335 genomes carried determinants of resistance to fluoroquinolones and third-generation cephalosporins, consistent with an XDR profile. In Malawi, a single ST335 clade caused the outbreak and was simultaneously present in both the hospital environment and nearby rivers. Inter-hospital transmission of a separate ST335 clade sustained the outbreak in South Africa. Closely related Malawian and South African isolates carried distinct plasmids encoding similar resistance determinants; evidence from our study and public databases suggests gene transfer via a cointegrate intermediate. Five non-outbreak South African ST335 isolates harboured additional carbapenem and macrolide resistance genes. Phenotypically, Salmonella Isangi ST335 resembled Salmonella Typhimurium in biofilm formation and disinfectant tolerance but was less virulent in mice. Interpretation Salmonella Isangi ST335 combines a locally untreatable XDR profile with nosocomial transmission and environmental persistence, suggesting a high potential for future outbreaks. A distinct and potentially greater threat lies in the horizontal spread of its resistance determinants to Salmonella Typhimurium and Salmonella Enteritidis, the two dominant invasive serovars in the region. Strengthened surveillance, integrating phenotypic testing with targeted genomics, is urgently needed. Its absence in Malawi, in contrast to South Africa, underscores inequities in preparedness for emerging AMR threats. Funding This work was supported by the Wellcome Trust through the Core Grant (206545/Z/17/Z) and the COVID-19 Sequencing Grant (220757/Z/20/Z) awarded to MLW. Additional support was provided by the Global Health Research Professorship to Melita Gordon from the UK National Institute for Health and Care Research (NIHR) (NIHR300039). Peter Johnston is funded by the Liverpool Clinical PhD Programme for Health Priorities in the Global South, supported by the Wellcome Trust (223502/Z/21/Z). For open access, the author has applied a CC BY public copyright license to any author-accepted manuscript version arising from this submission. Whole-genome sequencing of Salmonella isolates from South Africa was made possible by support from the SEQAFRICA project which is funded by the Department of Health and Social Care’s Fleming Fund using UK aid. The views expressed in this publication are those of the authors and not necessarily those of the UK Department of Health and Social Care or its Management Agent, Mott MacDonald. Analyses in this study were supported in part through use of software and workflows developed under National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH) grant R21AI178369. The NIH had no role in study design, data collection, analysis/interpretation, or publication decisions. Research in Context Evidence before this study Salmonella Isangi is a recurrent cause of antimicrobial resistant hospital outbreaks. We searched PubMed for Salmonella Isangi and related synonyms (to February 23rd, 2026) and identified 39 articles. No prior studies have examined transmission routes or provided phenotypic characterisation beyond antimicrobial resistance testing. Outbreaks have been reported from five hospitals on three continents, as well as a foodborne outbreak in China. Two major sequence types (STs) consistently appeared: ST335 and ST216. ST216 was widely geographically distributed and recovered from a variety of animal, meat, and environmental sources. ST335 was primarily associated with human clinical cases. Added value of this study This investigation was motivated by an outbreak of extensively drug-resistant (XDR) Salmonella Isangi at a hospital in Malawi. The Malawian outbreak occurred shortly before a multi-centre nosocomial outbreak in South Africa, and we provide insights from both in our analysis. We combined local epidemiology, phenotypic analyses, and global genomic characterisation to deliver a comprehensive description of the serovar. Both outbreaks were caused by ST335, which is the dominant sequence type in South Africa and Malawi, but by distinguishable clades in each country. In Malawi, genetically indistinguishable isolates were simultaneously circulating among patients, the hospital environment, and rivers throughout Blantyre City. Transfer of patients between hospitals is likely to have sustained the outbreak in South Africa. Recombination through a cointegrate intermediate may explain why the same resistance determinants are carried on distinct plasmid backbones within the Malawian and South African ST335 clades. We identify five ST335 isolates in South Africa that were not related to either outbreak and which harbour carbapenem and macrolide resistance genes in addition to an XDR genotype. Implications of all available evidence XDR Salmonella Isangi ST335 is a major threat in Malawi because effective therapy requires antibiotics that are seldom accessible in routine care. The ability of ST335 to transmit in hospitals and to persist in the environment may increase the risk of future outbreaks. Salmonella Isangi readily acquires and maintains antimicrobial resistance determinants through diverse plasmid backbones and recombination, raising concern for transfer to locally prevalent invasive Salmonella serovars. National genomic surveillance of the kind that exists in South Africa is essential to track and contain further resistance emergence, but such surveillance does not exist in Malawi. There is an urgent need to expand genomic surveillance in low-income countries if the threat posed by Salmonella Isangi and other pathogens that drive antimicrobial resistance is to be recognised early and effectively contained.