We report whole-genome sequences for 10 Listeria monocytogenes sequence type 6 isolates associated with a large listeriosis outbreak in South Africa, which occurred over the period of 2017 to 2018. The possibility of listeriosis spreading beyond South Africa's borders as a result of exported contaminated food products prompted us to make the genome sequences publicly available.
A dissertation submitted to the Faculty of Health Sciences, University of the Witwatersrand,
Johannesburg, in fulfillment of requirements of the degree of Master of Science.
Johannesburg, 2017
Background Typhoid fever remains an important disease in Africa, associated with outbreaks and the emerging multidrug resistant Salmonella enterica serotype Typhi (Salmonella Typhi) haplotype, H58. This study describes the incidence of, and factors associated with mortality due to, typhoid fever in South Africa, where HIV prevalence is high. Methods and Findings Nationwide active laboratory-based surveillance for culture-confirmed typhoid fever was undertaken from 2003–2013. At selected institutions, additional clinical data from patients were collected including age, sex, HIV status, disease severity and outcome. HIV prevalence among typhoid fever patients was compared to national HIV seroprevalence estimates. The national reference laboratory tested Salmonella Typhi isolates for antimicrobial susceptibility and haplotype. Unadjusted and adjusted logistic regression analyses were conducted determining factors associated with typhoid fever mortality. We identified 855 typhoid fever cases: annual incidence ranged from 0.11 to 0.39 per 100,000 population. Additional clinical data were available for 369 (46.8%) cases presenting to the selected sites. Among typhoid fever patients with known HIV status, 19.3% (29/150) were HIV-infected. In adult females, HIV prevalence in typhoid fever patients was 43.2% (19/44) versus 15.7% national HIV seroprevalence (P < .001); in adult males, 16.3% (7/43) versus 12.3% national HIV seroprevalence (P = .2). H58 represented 11.9% (22/185) of Salmonella Typhi isolates tested. Increased mortality was associated with HIV infection (AOR 10.7; 95% CI 2.3–50.3) and disease severity (AOR 9.8; 95% CI 1.6–60.0) on multivariate analysis. Conclusions Typhoid fever incidence in South Africa was largely unchanged from 2003–2013. Typhoid fever mortality was associated disease severity. HIV infection may be a contributing factor. Interventions mandate improved health care access, including to HIV management programmes as well as patient education. Further studies are necessary to clarify relationships between HIV infection and typhoid fever in adults.
ABSTRACT Listeria monocytogenes is a Gram-positive bacterium with a ubiquitous presence in the environment. There is growing concern about the increasing prevalence of L. monocytogenes associated with food-borne outbreaks. Here we report genome sequences for a cluster of human isolates of L. monocytogenes identified in South Africa in 2015.
Background. A total of 720 Vibrio cholerae O1 strains were recovered for investigation from an outbreak of cholera in South Africa between November 2008 and April 2009. Methods. Strains were characterized by serotype testing. Antimicrobial susceptibility testing. Genetic diversity of 248 strains was investigated using pulsed-field gel electrophoresis (PFGE) analysis. Extended characterization was performed on 90 strains. Molecular analysis included: polymerase chain reaction (PCR) identification of ctxA and tcpA genes, sequencing the ctxAB gene, and investigation of molecular mechanisms conferring antimicrobial resistance. Results. The majority of strains were characterized as serotype Ogawa. Strains showed multidrug resistance. Approximately 1.0% of strains displayed extended-spectrum β-lactamase (ESBL) activity. Strains showed very similar PFGE patterns. Ninety strains selected for extended characterization showed the following results: Strains possessed the cholera toxin (CT) and all were PCR positive for the tcpA-El Tor variant. Sequencing of the ctxB gene matched the B-1 allele. Strains harbored the SXT element. Strains that displayed ESBL activity possessed a 140-kilobase-pair plasmid that produced the TEM-63 β-lactamase. Nalidixic acid–resistant strains harbored mutations in GyrA (Ser83-Ile) and ParC (Ser85-Leu). Conclusions. These data highlight the rapid development of antimicrobial resistance and spread of V. cholerae O1 El Tor variants expressing the classical CT within South Africa.
Shiga toxin-producing Escherichia coli (STEC) strains are primarily foodborne pathogens that may cause diarrheal outbreaks and are associated with severe complications, specifically hemolytic-uremic syndrome (HUS). We report here genome sequence data for STEC O26:H11, which is associated with a cluster of cases of HUS, a rarely described syndrome in South Africa.
Background. The clinical and microbiological characteristics of nontyphoidal Salmonella (NTS) meningitis in South Africa, where human immunodeficiency virus (HIV) prevalence is high (approximately 15% in persons ≥15 years of age), were reviewed. Methods. From 2003 through 2013, 278 cases were identified through national laboratory-based surveillance. Clinical information (age, sex, outcome, Glasgow Coma Scale [GCS], and HIV status) was ascertained at selected sites. Isolates were serotyped; susceptibility testing and multilocus sequence typing on Salmonella enterica serovar Typhimurium isolates was performed. Multivariable logistic regression was used to determine factors associated with mortality outcome, using Stata software, version 13. Results. Where age was ascertained, 139 of 256 (54.3%) patients were <15 years. Males represented 151 of 267 (56.6%). Mortality outcome was recorded for 112 of 146 (76.7%) enhanced surveillance patients; 53 of 112 (47.3%) died. Death was associated with GCS ≤13 (adjusted odds ratio [OR], 18.7; 95% confidence interval [CI], 3.0–118.5; P = .002) on multivariable analysis. Where data were available, all 45 patients aged >15 years were HIV infected, compared with 24 of 46 (52.2%) patients aged <5 years. Neonates were less likely to be HIV infected than infants aged 2–12 months (OR, 4.8; 95% CI, 1.1–21.1; P = .039). Salmonella Typhimurium represented 106 of 238 (44.5%) serotyped isolates: 65 of 95 (68.4%) were ST313 vs ST19, respectively, and significantly associated with HIV-infected patients (P = .03) and multidrug resistance (OR, 6.6; 95% CI, 2.5–17.2; P < .001). Conclusions. NTS meningitis in South Africa is highly associated with HIV in adults, with neonates (irrespective of HIV status), and with Salmonella Typhimurium ST313. GCS is the best predictor of mortality: early diagnosis and treatment are critical. Focused prevention requires further studies to understand the sources and transmission routes.
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.
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.
Typhoid fever is notifiable in South Africa but clinical notification is notoriously poor. South Africa has an estimated annual incidence rate of 0.1 cases per 100,000 population of culture-confirmed typhoid fever, decreased from 17 cases per 100,000 population in the 1980s. This work was undertaken to identify the reasons for this decrease and identify potential weaknesses that may result in an increase of observed cases. Culture-confirmed cases, with additional demographic and clinical data have been collected from selected sentinel sites since 2003. Data on contextual factors (gross domestic product [GDP], sanitation, female education, and childhood diarrhea mortality) were collected. National incidence rates of culture-confirmed typhoid fever have remained constant for the past 13 years, with the exception of an outbreak in 2005: incidence was 0.4 per 100,000 population. Paratyphoid fever remains a rare disease. Antimicrobial susceptibility data suggest resistance to ciprofloxacin and azithromycin is emerging. The South African population increased from 27.5 million in 1980 to 55.0 million in 2015: urbanization increased from 50% to 65%, GDP increased from United States Dollar (USD) $2,910 to USD $6,167, access to sanitation improved from 64.4% to 70.0% in the urban population and 26.4% to 60.5% in rural areas. Female literacy levels improved from 74.8% to 92.6% over the period. Improved socioeconomic circumstances in South Africa have been temporally associated with decreasing incidence rates of typhoid fever over a 35-year period. Ongoing challenges remain including potential for large outbreaks, a large immigrant population, and emerging antimicrobial resistance. Continued active surveillance is mandatory.
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