Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Introduction . Shiga toxin-producing Escherichia coli (STEC) are foodborne pathogens that may cause diarrhoeal outbreaks and occasionally are associated with haemolytic-uraemic syndrome (HUS). We report on STEC O26:H11 associated with a cluster of four HUS cases in South Africa in 2017. Methodology . All case-patients were female and aged 5 years and under. Standard microbiological tests were performed for culture and identification of STEC from specimens (human stool and food samples). Further analysis of genomic DNA extracted from bacterial cultures and specimens included PCR for specific virulence genes, whole-genome sequencing and shotgun metagenomic sequencing. Results . For 2/4 cases, stool specimens revealed STEC O26:H11 containing eae , stx2a and stx2b virulence genes. All food samples were found to be negative for STEC. No epidemiological links could be established between the HUS cases. Dried meat products were the leading food item suspected to be the vehicle of transmission for these cases, as 3/4 case-patients reported they had eaten this. However, testing of dried meat products could not confirm this. Conclusion . Since STEC infection does not always lead to severe symptoms, it is possible that many more cases were associated with this cluster and largely went unrecognized.
Purpose: There is growing concern about the increasing prevalence of Listeria monocytogenes associated with foodborne outbreaks. Data concerning the prevalence and epidemiology of L. monocytogenes in South Africa are lacking. To prevent, investigate and control Listeria outbreaks, molecular epidemiological data are critical for understanding strain relatedness and defining source attribution. This present study describes the first whole-genome sequencing data for L. monocytogenes isolates from South Africa. Methods & Materials: A cluster of human cases of L. monocytogenes was recently reported from the Western Cape Province (WCP) of South Africa. This initiated our inaugural whole-genome sequencing (WGS) analysis of L. monocytogenes. To date, 11 isolates have been analyzed; WCP [n=9], Gauteng Province (GP) [n=1] and Eastern Cape Province (ECP) [n=1]. For WGS analysis, raw sequencing data generated on Illumina MiSeq equipment (2 x 300 paired-end sequencing runs) was analyzed using tools available in the CLC Genomics Workbench Software; trimmed reads were assembled using the 'De novo Assembly Tool'. Assembled WGS data was analyzed using bioinformatics tools and on-line analysis pipelines available at the Center for Genomic Epidemiology (CGE), Technical University of Denmark (http://cge.cbs.dtu.dk/services/). Results: Single nucleotide polymorphism (SNP) analysis separated our 11 isolates into 6 branches of a SNP phylogenetic tree. In particular, SNP analysis determined that the cluster of WCP isolates was not the result of a single strain, but rather that several strains were involved. Multi-locus sequence typing (MLST) data concurred with SNP results in differentiating the isolates. MLST subtype data were as follows: ST6 (n=4, WCP), ST1 (n=2, WCP), ST876 (n=2, WCP), ST54 (n=1, WCP), ST3 (n=1, GP), ST820 (n=1, ECP). In particular, our largest group was associated with MLST subtype ST6, a subtype commonly associated with unfavourable outcomes in patients. Conclusion: Analysis of WGS data using bioinformatics tools and on-line analysis pipelines at the CGE provided a single, rapid and cost-effective approach to investigate the molecular epidemiology of L. monocytogenes. This study has initiated a larger surveillance project for L. monocytogenes in South Africa. In future, all South African L. monocytogenes isolates will routinely be investigated using WGS.
The National Institute for Communicable Diseases in South Africa participates in national laboratory-based surveillance for human isolates of Salmonella species. Laboratory analysis includes whole-genome sequencing (WGS) of isolates. We report on WGS-based surveillance of Salmonella enterica serovar Typhi ( Salmonella Typhi) in South Africa from 2020 through 2021. We describe how WGS analysis identified clusters of enteric fever in the Western Cape Province of South Africa and describe the epidemiological investigations associated with these clusters. A total of 206 Salmonella Typhi isolates were received for analysis. Genomic DNA was isolated from bacteria and WGS was performed using Illumina NextSeq technology. WGS data were investigated using multiple bioinformatics tools, including those available at the Centre for Genomic Epidemiology, EnteroBase and Pathogenwatch. Core-genome multilocus sequence typing was used to investigate the phylogeny of isolates and identify clusters. Three major clusters of enteric fever were identified in the Western Cape Province; cluster one ( n =11 isolates), cluster two ( n =13 isolates), and cluster three ( n =14 isolates). To date, no likely source has been identified for any of the clusters. All isolates associated with the clusters, showed the same genotype (4.3.1.1.EA1) and resistome (antimicrobial resistance genes: bla TEM-1B , catA1 , sul1 , sul2 , dfrA7 ). The implementation of genomic surveillance of Salmonella Typhi in South Africa has enabled rapid detection of clusters indicative of possible outbreaks. Cluster identification allows for targeted epidemiological investigations and a timely, coordinated public health response.
Abstract Salmonell a Infantis presents an ever-increasing threat to public health due to its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). Whole genome sequences of 5,284 S . Infantis strains from 74 countries, isolated between 1989 and 2020 from a wide variety of sources including humans, animals, and food, were analysed to compare genetic phylogeny, AMR determinants and plasmid presence. The global S . Infantis population structure diverged into three clusters: a North American cluster, European cluster and a global cluster. The levels of AMR varied between the S . Infantis clusters and by isolation source; 73% of poultry isolates had multidrug resistance (MDR) compared to 35% of human isolates. This correlated with plasmid of emerging S . Infantis (pESI) presence; 71% of poultry isolates contained pESI versus 32% of human isolates. This provides important information for public health teams engaged in reducing the spread of this pathogen.
In South Africa, a progressive increase in listeriosis cases was noted from mid-June 2017, heralding what was to become the world's largest listeriosis outbreak. A total of 1060 cases were reported for the period January 1, 2017 to July 17, 2018. We describe laboratory activities, experiences, and results of whole-genome sequencing (WGS) analysis of Listeria monocytogenes isolates associated with this outbreak. Bacteria were identified using the VITEK-2 COMPACT 15 microbial identification system. WGS was performed using Illumina MiSeq technology. WGS data were analyzed using CLC Genomics Workbench Software and free-to-use on-line analysis tools/pipelines. Multilocus sequence typing (MLST) showed that 91% of clinical isolates were sequence type 6 (ST6), determining that the outbreak was largely associated with L. monocytogenes ST6. Epidemiological and laboratory findings led to investigation of a large ready-to-eat processed meat production facility in South Africa, named Enterprise Foods. L. monocytogenes ST6 was found in environmental sampling swabs of the production facility and in ready-to-eat processed meat products (including polony, a product similar to bologna sausage) manufactured at the facility. ST6 isolates, sourced at the Enterprise Foods production facility and from Enterprise food products, were shown by single nucleotide polymorphism (SNP) analysis to be highly related to clinical isolates; these nonclinical ST6 isolates showed <10 SNP differences when compared to clinical ST6 isolates. Core-genome MLST showed that clinical ST6 isolates and Enterprise-related ST6 isolates had no more than 4 allele differences between each other, suggestive of a high probability of epidemiological relatedness. WGS data interpreted together with epidemiological data concluded that the source of the listeriosis outbreak was ready-to-eat processed meat products manufactured by Enterprise Foods. Listeriosis has now been added to the South African list of mandatory notifiable medical conditions. Surveillance systems have been strengthened to facilitate prevention and early detection of listeriosis outbreaks.
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.
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
Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
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