The genomic epidemiology of multi-drug resistant invasive non-typhoidal in selected sub-Saharan African countries.

Background: Invasive non-typhoidal (iNTS) is one of the leading causes of bacteraemia in sub-Saharan Africa. We aimed to provide a better understanding of the genetic characteristics and transmission patterns associated with multi-drug resistant (MDR) iNTS serovars across the continent.

Methods: A total of 166 iNTS isolates collected from a multi-centre surveillance in 10 African countries (2010-2014) and a fever study in Ghana (2007-2009) were genome sequenced to investigate the geographical distribution, antimicrobial genetic determinants and population structure of iNTS serotypes-genotypes.

The Typhoid Fever Surveillance in Africa Program: Geospatial Sampling Frames for Household-based Studies: Lessons Learned From a Multicountry Surveillance Network in Senegal, South Africa, and Sudan.

Background: Robust household sampling, commonly applied for population-based investigations, requires sampling frames or household lists to minimize selection bias. We have applied Google Earth Pro satellite imagery to constitute structure-based sampling frames at sites in Pikine, Senegal; Pietermaritzburg, South Africa; and Wad-Medani, Sudan. Here we present our experiences in using this approach and findings from assessing its applicability by determining positional accuracy.

Laboratory characterisation of Salmonella enterica serotype Typhi isolates from Zimbabwe, 2009-2017.

Background: Typhoid fever remains a major public health problem in Zimbabwe with recurrent outbreaks reported since 2009. To provide guidance on appropriate treatment choice in order to minimise the morbidity and mortality of typhoid fever and prevent large scale outbreaks, we investigated the antimicrobial susceptibility patterns, prevalence of Salmonella enterica serotype Typhi (S. Typhi) H58 haplotype and molecular subtypes of S.

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa.

There is paucity of data regarding the geographical distribution, incidence, and phylogenetics of multi-drug resistant (MDR) Salmonella Typhi in sub-Saharan Africa. Here we present a phylogenetic reconstruction of whole genome sequenced 249 contemporaneous S. Typhi isolated between 2008-2015 in 11 sub-Saharan African countries, in context of the 2,057 global S.

The Burden of Typhoid Fever in South Africa: The Potential Impact of Selected Interventions.

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.

Clinical and microbiological features of invasive nontyphoidal Salmonella associated with HIV-infected patients, Gauteng Province, South Africa.

The aim of this study was to define factors associated with HIV-infected versus uninfected patients with invasive nontyphoidal Salmonella (iNTS) and factors associated with mortality, which are inadequately described in Africa.Laboratory-based surveillance for iNTS was undertaken. At selected sentinel sites, clinical data (age, sex, HIV status, severity of illness, and outcome) were collected.

An association between decreasing incidence of invasive non-typhoidal salmonellosis and increased use of antiretroviral therapy, Gauteng Province, South Africa, 2003-2013.

Background: HIV-infected persons are at increased risk of opportunistic infections, including invasive nontyphoidal Salmonella (iNTS) infections; antiretroviral therapy (ART) reduces this risk. We explored changing iNTS incidence associated with increasing ART availability in South Africa.

Methods: Laboratory-based surveillance for iNTS was conducted in Gauteng Province, South Africa, with verification using the National Health Laboratory Service's Central Data Warehouse (CDW), between 2003 and 2013.

Incidence of invasive salmonella disease in sub-Saharan Africa: a multicentre population-based surveillance study.

Background: Available incidence data for invasive salmonella disease in sub-Saharan Africa are scarce. Standardised, multicountry data are required to better understand the nature and burden of disease in Africa. We aimed to measure the adjusted incidence estimates of typhoid fever and invasive non-typhoidal salmonella (iNTS) disease in sub-Saharan Africa, and the antimicrobial susceptibility profiles of the causative agents.

Typhoid Fever in South Africa in an Endemic HIV Setting.

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.

Genome Sequences for a Cluster of Human Isolates of Listeria monocytogenes Identified in South Africa in 2015.

Listeria monocytogenesis a Gram-positive bacterium with a ubiquitous presence in the environment. There is growing concern about the increasing prevalence ofL. monocytogenesassociated with food-borne outbreaks.

The Relationship Between Invasive Nontyphoidal Salmonella Disease, Other Bacterial Bloodstream Infections, and Malaria in Sub-Saharan Africa.

Background: Country-specific studies in Africa have indicated that Plasmodium falciparum is associated with invasive nontyphoidal Salmonella (iNTS) disease. We conducted a multicenter study in 13 sites in Burkina Faso, Ethiopia, Ghana, Guinea-Bissau, Kenya, Madagascar, Senegal, South Africa, Sudan, and Tanzania to investigate the relationship between the occurrence of iNTS disease, other systemic bacterial infections, and malaria.

Methods: Febrile patients received a blood culture and a malaria test.

Comparative Characterization of Vibrio cholerae O1 from Five Sub-Saharan African Countries Using Various Phenotypic and Genotypic Techniques.

We used standardized methodologies to characterize Vibrio cholerae O1 isolates from Guinea, Democratic Republic of the Congo (DRC), Togo, Côte d'Ivoire and Mozambique. We investigated 257 human isolates collected in 2010 to 2013. DRC isolates serotyped O1 Inaba, while isolates from other countries serotyped O1 Ogawa.

Bloodstream Infections and Frequency of Pretreatment Associated With Age and Hospitalization Status in Sub-Saharan Africa.

Background: The clinical diagnosis of bacterial bloodstream infections (BSIs) in sub-Saharan Africa is routinely confused with malaria due to overlapping symptoms. The Typhoid Surveillance in Africa Program (TSAP) recruited febrile inpatients and outpatients of all ages using identical study procedures and enrollment criteria, thus providing an opportunity to assess disease etiology and pretreatment patterns among children and adults.

Methods: Inpatients and outpatients of all ages with tympanic or axillary temperatures of ≥38.

Clinical and Microbiological Features of Salmonella Meningitis in a South African Population, 2003-2013.

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.

Nosocomial outbreak of Salmonella enterica serovar Typhimurium primarily affecting a pediatric ward in South Africa in 2012.

We describe a nosocomial outbreak of diarrheal disease caused by extended-spectrum β-lactamase-producing multidrug-resistant Salmonella enterica serovar Typhimurium, focused on a pediatric ward in South Africa. The outbreak peaked between May 2012 and July 2012. Person-to-person transmission was the most likely mechanism of spread of the infection, expedited due to a breakdown in hand-washing and hygiene, suboptimal infection control practices, overcrowding of hospital wards, and an undesirable nurse-to-patient ratio.

Cholera outbreak in South Africa, 2008-2009: laboratory analysis of Vibrio cholerae O1 strains.

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.

Diagnosis of Vibrio cholerae O1 infection in Africa.

Isolation of Vibrio cholerae O1 is necessary for cholera outbreak confirmation. Rapid diagnostic testing of fecal specimens, based on lipopolysaccharide detection of V. cholerae O1 or O139, may assist in early outbreak detection and surveillance.

Human infections due to Salmonella Blockley, a rare serotype in South Africa: a case report.

Background: Infections due to nontyphoidal Salmonella have increased worldwide over the last couple of decades. Salmonella enterica serotype Blockley (Salmonella Blockley) infections is associated with chickens and is a rarely isolated serotype in human infections in most countries.

Case Presentation: We report a case of human infections due to Salmonella Blockley in KwaZulu-Natal, South Africa in 2011.

Escherichia coli O104 associated with human diarrhea, South Africa, 2004-2011.

To determine the origin of >4,000 suspected diarrheagenic Escherichia coli strains isolated during 2004-2011 in South Africa, we identified 7 isolates as serotype O104; 5 as enteroaggregative E. coli O104:H4, and 2 as enteropathogenic E. coli O104:non-H4.

Systemic shigellosis in South Africa.

Background: Systemic disease due to shigellae is associated with human immunodeficiency virus (HIV), malnutrition, and other immunosuppressed states. We examined the clinical and microbiologic characteristics of systemic shigellosis in South Africa, where rates of HIV infection are high.

Methods: From 2003 to 2009, 429 cases of invasive shigellosis were identified through national laboratory-based surveillance.

Possible laboratory contamination leads to incorrect reporting of Vibrio cholerae O1 and initiates an outbreak response.

Vibrio cholerae O1 in a river water specimen in South Africa was reported, and a public health response followed in order to prevent an outbreak. Further investigation determined this to be a pseudoalert of V. cholerae O1, possibly linked to laboratory contamination.

Sensitivity and specificity of typhoid fever rapid antibody tests for laboratory diagnosis at two sub-Saharan African sites.

Objective: To evaluate three commercial typhoid rapid antibody tests for Salmonella Typhi antibodies in patients suspected of having typhoid fever in Mpumalanga, South Africa, and Moshi, United Republic of Tanzania.

Methods: The diagnostic accuracy of Cromotest(®) (semiquantitative slide agglutination and single tube Widal test), TUBEX(®) and Typhidot(®) was assessed against that of blood culture. Performance was modelled for scenarios with pretest probabilities of 5% and 50%.