Detection of the epidemic Pseudomonas aeruginosa AUST-03 (ST242) strain in people with cystic fibrosis in South Africa.

INTRODUCTION: Pseudomonas aeruginosa AUST-03 (ST242) has been reported to cause epidemics in people with CF (pwCF) from Australia and has been associated with multidrug resistance and increased morbidity and mortality. Here, we report an epidemic P. aeruginosa (AUST-03) strain in South African pwCF detected at a public hospital and characterize the genomic antibiotic resistance determinants. METHODS: The P. aeruginosa AUST-03 (ST242) study isolates were analysed with whole genome sequencing using the Illumina NextSeq2000 platform. Raw sequencing reads were processed using the Jekesa pipeline and multilocus sequence typing and genomic antibiotic resistance characterization was performed using public databases. Genetic relatedness between the study isolates and global P. aeruginosa ST242 from public databases was determined using a maximum-likelihood phylogenetic tree. Antibiotic susceptibility testing was performed using the disk diffusion and broth microdilution techniques. RESULTS: A total of 11 P. aeruginosa AUST-03 isolates were isolated from two children with CF. The majority (8/11) of these isolates were multidrug-resistant (MDR) or extensively drug resistant; and the multidrug efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM were the most clinically relevant antibiotic resistance determinants and were detected in all of the isolates. The study isolates were the most closely related to a 2020 P. aeruginosa AUST-03 (ST242) CF isolate from Russia. CONCLUSION: Epidemic MDR P. aeruginosa strains are present at South African public CF clinics and need to be considered when implementing segregation and infection control strategies to prevent possible spread and outbreaks.

Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa.

Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes (mefC, msrE, mphG and mphE) were in highest abundance at a WWTW serving an urban high-income area; while sul1, sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which blaKPC-2 and blaKPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.

Epidemiology and antimicrobial resistance profiles of pathogenic Escherichia coli from commercial swine and poultry abattoirs and farms in South Africa: A One Health approach.

Pathogenic Escherichia coli (PEC) are important foodborne bacteria that can cause severe illness in humans. The PECs thrive within the intestines of humans as well as animals and may contaminate multiple ecosystems, including food and water, via faecal transmission. Abattoir and farm employees are at high risk of PEC exposure, which could translate to community risk through person-to-person contact. To determine the epidemiology and resistome of PECs in Gauteng and Limpopo provinces of South Africa, 198 swine faecal samples, 220 poultry cloacal swabs, 108 human hand swabs, 11 run-off water samples from abattoirs and farms were collected from four swine and five poultry commercial abattoirs and two swine farms. One effluent sample each was collected from four wastewater treatment plants (WWTP) and a tertiary hospital setting. Phenotypic and genotypic techniques were used including polymerase chain reaction, pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Results showed EHEC and EPEC prevalence was 4.1 % (22/542) and 20.8 % (113/542), respectively, with the O26 serogroup detected the most in PEC isolates. According to the PFGE dendrogram, isolates from poultry, human hand swabs and run-off water clustered together. Diverse virulence factors such as the novel stx2k subtype and eae genes were detected among the 36 representative PEC isolates according to WGS. The results showed that 66.7 % (24/36) of sequenced PECs presented with multi-drug resistance (MDR) to ß-lactamase 13.9 % (5/36), aminoglycoside 61.1 % (22/36), tetracycline 41.7 % (15/36) and quinolones 38.9 % (14/36). No colistin nor carbapenem resistance was detected. Sequence types (STs) associated with MDR in this study were: ST752, ST189, ST206, ST10, ST48 and ST38. The findings highlight the threat of zoonotic pathogens to close human contacts and the need for enhanced surveillance to mitigate the spread of MDR foodborne PECs.

Whole-Genome Sequencing of Human and Porcine Escherichia coli Isolates on a Commercial Pig Farm in South Africa.

Escherichia coli is an indicator micro-organism in One Health antibiotic resistance surveillance programs. The purpose of the study was to describe and compare E. coli isolates obtained from pigs and human contacts from a commercial farm in South Africa using conventional methods and whole-genome sequencing (WGS). Porcine E. coli isolates were proportionally more resistant phenotypically and harbored a richer diversity of antibiotic resistance genes as compared to human E. coli isolates. Different pathovars, namely ExPEC (12.43%, 21/169), ETEC (4.14%, 7/169), EPEC (2.96%, 5/169), EAEC (2.96%, 5/169) and STEC (1.18%, 2/169), were detected at low frequencies. Sequence type complex (STc) 10 was the most prevalent (85.51%, 59/169) among human and porcine isolates. Six STcs (STc10, STc86, STc168, STc206, STc278 and STc469) were shared at the human-livestock interface according to multilocus sequence typing (MLST). Core-genome MLST and hierarchical clustering (HC) showed that human and porcine isolates were overall genetically diverse, but some clustering at HC2-HC200 was observed. In conclusion, even though the isolates shared a spatiotemporal relationship, there were still differences in the virulence potential, antibiotic resistance profiles and cgMLST and HC according to the source of isolation.

A One Health Perspective on Salmonella enterica Serovar Infantis, an Emerging Human Multidrug-Resistant Pathogen.

Salmonella enterica serovar Infantis presents an ever-increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole-genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989-2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster. The levels of AMR varied by Salmonella Infantis cluster and by isolation source; 73% of poultry isolates were multidrug resistant, compared with 35% of human isolates. This finding correlated with the presence of the pESI megaplasmid; 71% of poultry isolates contained pESI, compared with 32% of human isolates. This study provides key information for public health teams engaged in reducing the spread of this pathogen.

The genomic epidemiology of shigellosis in South Africa.

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.

Characterization of Salmonella enterica serovar Isangi from South Africa, 2020-2021.

BACKGROUND: We describe the genotypic characteristics and antimicrobial resistance (AMR) determinants of Salmonella enterica serovar Isangi (Salmonella Isangi) clinical isolates in South Africa from 2020 through 2021. METHODS: During the years 2020 to 2021, the Centre for Enteric Diseases of the National Institute for Communicable Diseases, a national reference centre in South Africa for human infections resulting from enteric bacterial pathogens, investigated a total of 3549 clinical isolates of Salmonella species. Whole genome sequencing (WGS) was performed using Illumina NextSeq Technology. WGS data was analyzed using Centre for Genomic Epidemiology-based tools and EnteroBase web-based platform. Genotypic relatedness and cluster analysis was investigated based on core-genome multilocus sequence typing. RESULTS: Forty-nine isolates were confirmed to be Salmonella Isangi, with most submitted from Gauteng Province (24/49, 49%). The most prevalent sequence type was ST335 (48/49, 98%), and the remaining 1 isolate was ST216. All ST335 isolates were genotypically multidrug-resistant (MDR), with resistance to fluoroquinolones, chloramphenicol, trimethoprim-sulfamethoxazole and tetracycline; the ST216 isolate was resistant only to aminoglycosides. All ST335 isolates carried ESBL genes, the most common being blaCTX-M-15. Five clusters (consisting of isolates related within five allele differences) were detected, all being ST335. CONCLUSIONS: Most Salmonella Isangi isolates in South Africa are MDR and ESBL-positive. Ongoing monitoring of the epidemiology and AMR profile of this serovar is important for public health and treatment guidelines.

Imported Cholera Cases, South Africa, 2023.

Since February 2022, Malawi has experienced a cholera outbreak of >54,000 cases. We investigated 6 cases in South Africa and found that isolates linked to the outbreak were Vibrio cholerae O1 serotype Ogawa from seventh pandemic El Tor sublineage AFR15, indicating a new introduction of cholera into Africa from south Asia.

Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization.

The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention's Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.

Genetic characterization of Salmonella Infantis from South Africa, 2004-2016.

Salmonella Infantis is presenting an increasing risk to public health. Of particular concern are the reports of pESI, a multidrug resistance (MDR) encoding megaplasmid, in isolates from multiple countries, but little is known about its presence or diversity in South Africa. Whole genome sequences of 387 S. Infantis isolates from South Africa (2004-2020) were analysed for genetic phylogeny, recombination frequency, antimicrobial resistance (AMR) determinants, plasmid presence and overall gene content. The population structure of South African S. Infantis was substantially different to S. Infantis reported elsewhere; only two thirds of isolates belonged to eBG31, while the remainder were identified as eBG297, a much rarer group globally. Significantly higher levels of recombination were observed in the eBG297 isolates, which was associated with the presence of prophages. The majority of isolates were putatively susceptible to antimicrobials (335/387) and lacked any plasmids (311/387); the megaplasmid pESI was present in just one isolate. A larger proportion of eBG31 isolates, 19% (49/263), contained at least one AMR determinant, compared to eBG297 at 2% (3/124). Comparison of the pan-genomes of isolates from either eBG identified 943 genes significantly associated with eBG, with 43 found exclusively in eBG31 isolates and 34 in eBG297 isolates. This, along with the single nucleotide polymorphism distance and difference in resistance profiles, suggests that eBG31 and eBG297 isolates occupy different niches within South Africa. If antibiotic-resistant S. Infantis emerges in South Africa, probably through the spread of the pESI plasmid, treatment of this infection would be compromised.

Characterisation and epidemiological subtyping of Shiga toxin-producing Escherichia coli isolated from the beef production chain in Gauteng, South Africa.

In South Africa, there is a shortage of epidemiologic data on Shiga toxin-producing Escherichia coli (STEC) in the beef production chain. This study was conducted to characterise STEC isolates originating from three studies conducted in a cattle feedlot, beef abattoirs and retail outlets in Gauteng province, South Africa. Polymerase chain reaction was used to detect virulence genes, the Epsilometer test to assess antimicrobial susceptibility, pulsed-field gel electrophoresis (PFGE) to investigate genetic relatedness of isolates, and conventional serotyping for phenotypic identification. Amongst the 86 STEC isolates, the eaeA gene was detected in 20 (23%), and 26 different serogroups were identified, including the clinically important O8, O174, O2, 020 and O117. The majority of the isolates (95%; 82/86) exhibited resistance to one or more antimicrobial agents, and 30 of the isolates (35%) exhibited multi-drug resistance (MDR), being resistant to at least three antimicrobial classes. The PFGE patterns showed a highly diverse but related STEC population, with 45 distinct patterns and evidence of horizontal transmission along the beef production chain. This is significant because it demonstrates continual environmental contamination and risk of contamination along the beef production chain and the food chain. To our knowledge, this is the first study that provides evidence of horizontal transmission of STEC along the beef production chain in South Africa. This epidemiological information could facilitate the development of a proactive strategy for reducing potential foodborne outbreaks and transmission of antimicrobial resistant pathogens in the food chain.

PulseNet International Survey on the Implementation of Whole Genome Sequencing in Low and Middle-Income Countries for Foodborne Disease Surveillance.

PulseNet International (PNI) is a global network of 88 countries who work together through their regional and national public health laboratories to track foodborne disease around the world. The vision of PNI is to implement globally standardized surveillance using whole genome sequencing (WGS) for real-time identification and subtyping of foodborne pathogens to strengthen preparedness and response and lower the burden of disease. Several countries in North America and Europe have experienced significant benefits in disease mitigation after implementing WGS. To broaden the routine use of WGS around the world, challenges and barriers must be overcome. We conducted this study to determine the challenges and barriers countries are encountering in their attempts to implement WGS and to identify how PNI can provide support to improve and become a better integrated system overall. A survey was designed with a set of qualitative questions to capture the status, challenges, barriers, and successes of countries in the implementation of WGS and was administered to laboratories in Africa, Asia-Pacific, Latin America and the Caribbean, and Middle East. One-third of respondents do not use WGS, and only 8% reported using WGS for routine, real-time surveillance. The main barriers for implementation of WGS were lack of funding, gaps in expertise, and training, especially for data analysis and interpretation. Features of an ideal system to facilitate implementation and global surveillance were identified as an all-in-one software that is free, accessible, standardized and validated. This survey highlights the minimal use of WGS for foodborne disease surveillance outside the United States, Canada, and Europe to date. Although funding remains a major barrier to WGS-based surveillance, critical gaps in expertise and availability of tools must be overcome. Opportunities to seek sustainable funding, provide training, and identify solutions for a globally standardized surveillance platform will accelerate implementation of WGS worldwide.

Emergence of Vibrio cholerae O1 Sequence Type 75, South Africa, 2018-2020.

We describe the molecular epidemiology of cholera in South Africa during 2018-2020. Vibrio cholerae O1 sequence type (ST) 75 recently emerged and became more prevalent than the V. cholerae O1 biotype El Tor pandemic clone. ST75 isolates were found across large spatial and temporal distances, suggesting local ST75 spread.

Whole-genome sequencing to investigate two concurrent outbreaks of Salmonella Enteritidis in South Africa, 2018.

Salmonella enterica serotype Enteritidis (Salmonella Enteritidis) is a major cause of foodborne disease outbreaks worldwide. In 2018, two concurrent outbreaks of Salmonella Enteritidis gastroenteritis in one district of South Africa were investigated. We describe the use of whole-genome sequencing (WGS) analysis of bacterial isolates to assist with the investigation of these outbreaks. Outbreak A affected children (n=27) attending a day-care centre, while outbreak B affected adults (n=16) who ate breakfast at the same restaurant. Salmonella Enteritidis was isolated from stool samples in both outbreaks (four children in outbreak A; 12 restaurant customers and three restaurant food-handlers in outbreak B). In outbreak B, Salmonella Enteritidis was isolated from three food retention samples (raw chicken egg, hollandaise sauce and rocket-herb). Available isolates from both outbreaks (n=13) were investigated using WGS analysis. Sequencing data for isolates were analysed at the EnteroBase web-based platform and included core-genome multi-locus sequence typing (cgMLST). Isolates with epidemiological links to the restaurant (n=10) and day-care centre (n=3), were shown by cgMLST to be highly genetically related, with no more than five allele differences when comparing one isolate against another. On food history, eggs and hollandaise sauce were the common food items consumed by ill restaurant customers. Unfortunately, Salmonella Enteritidis isolated from the egg and hollandaise sauce were not available for WGS analysis. Our investigation concluded that the two concurrent outbreaks were caused by a highly related strain of Salmonella Enteritidis, suggesting the possibility of a common contaminated food source, of which contaminated eggs are strongly implicated.

Outbreak of Listeriosis in South Africa Associated with Processed Meat.

BACKGROUND: An outbreak of listeriosis was identified in South Africa in 2017. The source was unknown. METHODS: We conducted epidemiologic, trace-back, and environmental investigations and used whole-genome sequencing to type Listeria monocytogenes isolates. A case was defined as laboratory-confirmed L. monocytogenes infection during the period from June 11, 2017, to April 7, 2018. RESULTS: A total of 937 cases were identified, of which 465 (50%) were associated with pregnancy; 406 of the pregnancy-associated cases (87%) occurred in neonates. Of the 937 cases, 229 (24%) occurred in patients 15 to 49 years of age (excluding those who were pregnant). Among the patients in whom human immunodeficiency virus (HIV) status was known, 38% of those with pregnancy-associated cases (77 of 204) and 46% of the remaining patients (97 of 211) were infected with HIV. Among 728 patients with a known outcome, 193 (27%) died. Clinical isolates from 609 patients were sequenced, and 567 (93%) were identified as sequence type 6 (ST6). In a case-control analysis, patients with ST6 infections were more likely to have eaten polony (a ready-to-eat processed meat) than those with non-ST6 infections (odds ratio, 8.55; 95% confidence interval, 1.66 to 43.35). Polony and environmental samples also yielded ST6 isolates, which, together with the isolates from the patients, belonged to the same core-genome multilocus sequence typing cluster with no more than 4 allelic differences; these findings showed that polony produced at a single facility was the outbreak source. A recall of ready-to-eat processed meat products from this facility was associated with a rapid decline in the incidence of L. monocytogenes ST6 infections. CONCLUSIONS: This investigation showed that in a middle-income country with a high prevalence of HIV infection, L. monocytogenes caused disproportionate illness among pregnant girls and women and HIV-infected persons. Whole-genome sequencing facilitated the detection of the outbreak and guided the trace-back investigations that led to the identification of the source.

Epidemiological investigation of a typhoid fever outbreak in Sekhukhune District, Limpopo province, South Africa - 2017.

BACKGROUND: Typhoid fever remains a public health concern in South Africa, where the risk of transmission is high because of poor access to safe water and sanitation. This study describes the investigation of typhoid fever outbreak in Limpopo province. METHODOLOGY: Following notification of laboratory-confirmed cases, a descriptive study was conducted at Sekhukhune District, Limpopo province. A suspected case was defined as any person residing in Makhuduthamaga Municipality from November 2017 to January 2018, presenting with fever and gastrointestinal symptoms. Data were collected using case investigation forms. Whole-genome sequencing (WGS) was carried out on Salmonella Typhi isolates and polymerase chain reaction (PCR) test was done for Salmonella species from water samples. Location of cases and water sources were mapped using ArcGIS mapping tool. RESULTS: Amongst 122 cases, 54% (n = 66) were female and 6% (n = 7) laboratory-confirmed. The median age of the cases was 11 years (range 2-83 years), with 79% (n = 102) being children under the age of 14 years. Salmonella species were detected in 37% (10/27) of water samples and geographic information system (GIS) mapping showed clustering of cases in Tswaing-Kgwaripe and Vlakplaas villages. Six isolates were available for WGS analysis, with resulting data showing that five of the six isolates were genetically related. Phylogenetic analysis showed that the five isolates clustered together were genetically related showing < 22 single nucleotide polymorphisms when compared to each other. CONCLUSION: Molecular epidemiology of isolates suggests a common source outbreak, supported by the detection of Salmonella species from water sources. Consumption of water from contaminated open water sources, because of ongoing interruption of municipal water supply, was the likely cause of the outbreak. The investigation highlights the importance of consistent safe water supply and the ability of district surveillance systems to identify and contain outbreaks.

Prevalence and antibiotic susceptibility patterns of enteric bacterial pathogens in human and non-human sources in an urban informal settlement in Cape Town, South Africa.

BACKGROUND: In light of rampant childhood diarrhoea, this study investigated bacterial pathogens from human and non-human sources in an urban informal settlement. Meat from informal abattoirs (n = 85), river water (n = 64), and diarrheic stool (n = 66) were collected between September 2015 and May 2016. A duplex real-time PCR, gel-based PCR, and CHROMagar™STEC were used to screen Tryptic Soy Broth (TSB) for diarrheic E. coli. Standard methods were used to screen for other selected food and waterborne bacterial pathogens. RESULTS: Pathogens isolated from stool, meat, and surface water included Salmonella enterica (6, 5, 0%), Plesiomonas shigelloides (9, 0, 17%), Aeromonas sobria (3, 3, 0%), Campylobacter jejuni (5, 5, 0%), Shigella flexneri (17, 5, 0%), Vibrio vulnificus (0, 0, 9%), and diarrheic E. coli (21, 3, 7%) respectively. All the isolates were resistant to trimethoprim-sulphamethoxazole. CONCLUSIONS: There was a high burden of drug resistant diarrheal pathogens in the stool, surface water and meat from informal slaughter. Integrated control measures are needed to ensure food safety and to prevent the spread of drug resistant pathogens in similar settings.

Virulence Characteristics and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Humans in South Africa: 2006-2013.

Shiga toxin-producing Escherichia coli (STEC) isolates (N = 38) that were incriminated in human disease from 2006 to 2013 in South Africa were characterized by serotype, virulence-associated genes, antimicrobial resistance and pulsed-field gel electrophoresis (PFGE). The isolates belonged to 11 O:H serotypes. STEC O26:H11 (24%) was the most frequent serotype associated with human disease, followed by O111:H8 (16%), O157:H7 (13%) and O117:H7 (13%). The majority of isolates were positive for key virulence-associated genes including stx1 (84%), eaeA (61%), ehxA (68.4%) and espP (55%), but lacked stx2 (29%), katP (42%), etpD (16%), saa (16%) and subA (3%). stx2 positive isolates carried stx2c (26%) and/or stx2d (26%) subtypes. All pathogenicity island encoded virulence marker genes were detected in all (100%) isolates except nleA (47%), nleC (84%) and nleD (76%). Multidrug resistance was observed in 89% of isolates. PFGE revealed 34 profiles with eight distinct clusters that shared ≥80% intra-serotype similarity, regardless of the year of isolation. In conclusion, STEC isolates that were implicated in human disease between 2006 and 2013 in South Africa were mainly non-O157 strains which possessed virulence genes and markers commonly associated with STEC strains that have been incriminated in mild to severe human disease worldwide. Improved STEC monitoring and surveillance programs are needed in South Africa to control and prevent STEC disease in humans.

Review of molecular subtyping methodologies used to investigate outbreaks due to multidrug-resistant enteric bacterial pathogens in sub-Saharan Africa.

BACKGROUND: In sub-Saharan Africa, molecular epidemiological investigation of outbreaks caused by antimicrobial-resistant enteric bacterial pathogens have mostly been described for Salmonella species, Vibrio cholerae, Shigella species and Escherichia coli. For these organisms, I reviewed all publications describing the use of molecular subtyping methodologies to investigate outbreaks caused by multidrug-resistant (MDR) enteric bacterial infections. OBJECTIVES: To describe the use of molecular subtyping methodologies to investigate outbreaks caused by MDR enteric bacterial pathogens in sub-Saharan Africa and to describe the current status of molecular subtyping capabilities in the region. METHODS: A PubMed database literature search (English language only) was performed using the search strings: 'Africa outbreak MDR', 'Africa outbreak multi', 'Africa outbreak multidrug', 'Africa outbreak multi drug', 'Africa outbreak resistance', 'Africa outbreak resistant', 'Africa outbreak drug', 'Africa outbreak antibiotic', 'Africa outbreak antimicrobial'. These search strings were used in combination with genus and species names of the organisms listed above. All results were included in the review. RESULTS: The year 1991 saw one of the first reports describing the use of molecular subtyping methodologies in sub-Saharan Africa; this included the use of plasmid profiling to characterise Salmonella Enteritidis. To date, several methodologies have been used; pulsed-field gel electrophoresis analysis and multilocus sequence typing have been the most commonly used methodologies. Investigations have particularly highlighted the emergence and spread of MDR clones; these include Salmonella Typhi H58 and Salmonella Typhimurium ST313 clones. In recent times, whole-genome sequencing (WGS) analysis approaches have increasingly been used. CONCLUSION: Traditional molecular subtyping methodologies are still commonly used and still have their place in investigations; however, WGS approaches have increasingly been used and are slowly gaining a stronghold. African laboratories need to start adapting their molecular surveillance methodologies to include WGS, as it is foreseen that WGS analysis will eventually replace all traditional methodologies.