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

AVAILABILITY OF DATA AND MATERIALS : All sequencing data were uploaded to the public EnteroBase platform (http:// enter obase. warwi ck. ac. uk/ speci es/ index/ sente rica) and so are freely available to access at the EnteroBase platform. In addition, sequencing data are deposited in the European Nucleotide Archive under the project accession numbers PRJEB39546 and PRJEB39988.SUPPLEMENTARY INFORMATION : Map of South Africa, showing the different provinces of the country. Provinces (regions) are indicated in different colors.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 coregenome 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.The SEQAFRICA project which is funded by the Department of Health and Social Care’s Fleming Fund using UK aid.https://bmcinfectdis.biomedcentral.comam2024Medical MicrobiologySDG-03:Good heatlh and well-bein

Odyssean malaria outbreaks in Gauteng Province, South Africa, 2007 - 2013

Background. Odyssean malaria refers to malaria transmitted by translocated mosquitoes and is a diagnosis of exclusion, as the probability of finding the responsible vector is miniscule. We believe that road traffic from endemic areas in and around South Africa is the source of most of the infected mosquitoes. Because of the unexpected nature of the disease, diagnosis is often delayed and severe and complicated malaria is common.Objectives. To describe outbreaks of odyssean malaria during the period 2007 through 2013 in Gauteng Province, South Africa, and to educate healthcare workers about this form of malaria.Methods. Site visits, environmental hygiene inspections, patient interviews, and entomological investigations for adult mosquitoes and larvae in potential breeding sites were done in each identified outbreak.Results. Over the period, 14 laboratory-proven and 7 probable cases of odyssean malaria were investigated. There were 2 deaths (9.5% case fatality rate, approximately 10 times higher than the national fatality rate for malaria). We describe two recent clusters of cases in detail, and emphasise the importance of clinician awareness of this rare but frequently severe form of malaria.Conclusion. Odyssean malaria cases are inevitable in South Africa, given the volume of road, rail and air traffic from malaria risk areas into Gauteng and other non-endemic provinces. It is likely that many cases are missed, owing to the rare and sporadic nature of the condition. Malaria should always be kept in mind as a cause of unexplained fever and thrombocytopenia, even in the absence of a travel history.

Diagnostic testing practices for diarrhoeal cases in South African public hospitals

BACKGROUND : Stool samples submitted for diagnostic testing represent a proportion of diarrhoeal cases seeking healthcare, and an even smaller proportion of diarrhoeal cases in the community. Despite this, surveillance relies heavily on these laboratory results. This study described diarrhoeal diagnostic practices and aetiological agents of diarrhoea in patients admitted to three South African public hospitals in order to understand biases in surveillance data, and inform guidelines, diagnostic and laboratory practices to improve clinical management. METHODS : A doctors’ survey was conducted to determine sample submission, diarrhoeal treatment and barriers to submitting samples for testing. Results for all samples submitted for routine diagnostics were obtained from the NHLS Central Data Warehouse. An enhanced surveillance study enrolled patients with acute diarrhoea at the same hospitals over the same period. Differences between routine culture results and molecular testing from the surveillance study were described. RESULTS : Stool samples were seldom submitted for diagnostic testing (median of 10% of admitted cases). Current diagnostic guidelines were not useful, hence most doctors (75.1%) relied on their own clinical judgement or judgement of a senior clinician. Although most doctors (90.3%) agreed that diagnostics were helpful for clinical management, they reported patients being unwilling to provide samples and long laboratory turnaround times. Routine diagnostic data represent cases with chronic diarrhoea and dysentery since doctors are most likely to submit specimens for these cases. Pathogen yield (number of pathogens detected for samples tested for specific pathogens) was significantly higher in the surveillance study, which used molecular methods, than through routine diagnostic services (73.3% versus 8.2%, p < 0.001), including for viruses (48.9% versus 2.6%, p < 0.001), bacteria (40.1% versus 2.2%, p < 0.001) and parasites (16.2% versus 3.6%, p < 0.001). Despite viruses being commonly detected in the surveillance study, viral testing was seldom requested in routine diagnostic investigations. CONCLUSIONS : Comprehensive diagnostic and treatment guidelines are required for diarrhoeal diseases. These guidelines should be informed by local epidemiological data, where diagnostic testing is reserved for cases most likely to benefit from specific treatment. Optimisation of current diagnostic processes and methods are required for these cases, specifically in terms of minimising turnaround times while maximising diagnostic acumen.The ANDEMIA study was supported by the German Federal Ministry of Education and Research.http://www.biomedcentral.com/bmcinfectdisam2023Medical VirologyPaediatrics and Child Healt

State-Level Policy Environments, Discrimination, and Victimization among Sexual and Gender Minority People

Legislation has been passed in some states to reduce discrimination and victimization toward sexual and gender minority people (SGM; people who are not solely heterosexual and/or whose gender identity is not equal to what is socially associated with sex assigned at birth). The purpose of these analyses is to test whether state-level policy environments are associated with past-year discrimination and victimization among SGM people. Cross-sectional data from The Population Research in Identity and Disparities for Equality (PRIDE) Study annual questionnaire (collected 2018–2019), a national study of the health of SGM adults in the USA, were used for these analyses. Measures included related to discrimination, victimization, and demographic characteristics. State-level policy environments were measured using data from the Movement Advancement Project. Logistic regression analyses evaluated state-level policy environment scores and past-year discrimination and victimization among gender identity categories. In this sample, 7044 people (gender minority n = 2530) were included. Cisgender sexual minority (odds ratio [OR] = 1.007, p = 0.041) and the gender expansive subgroup of gender minority people (OR = 1.010, p = 0.047) in states with more protective policy environments had greater odds of discrimination. The gender expansive subgroup was found to have greater odds of victimization in states with more protective policy environments (OR = 1.003, p \u3c 0.05). There was no relationship between state-level policy environments and victimization among any other study groups. SGM people may experience increased risk for discrimination and victimization despite legislative protections, posing continued risks for poor health outcomes and marginalization. Evaluation of factors (e.g., implementation strategies, systems of accountability) that influence the effectiveness of state-level polices on the reported experiences of discrimination and victimization among SGM people is needed

Identifying gaps in hand hygiene practice to support tailored target audience messaging in Soweto : a cross-sectional community survey

Effective risk communication is essential for outbreak mitigation, as recently highlighted during the coronavirus disease 2019 (COVID-19) pandemic. Hand hygiene is one of the proposed public health interventions to protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) acquisition and transmission along with social distancing, improved ventilation, environmental cleaning, and wearing of masks. Improving hand hygiene practices in the community requires an understanding of the socio-behavioural context. This cross-sectional community survey in Soweto identified gaps in hand hygiene, which can inform appropriate messaging at the community level. Only 42% of survey respondents practiced adequate hand hygiene. Tailored educational messaging should be targeted at young adults in particular, and the importance of soap for hand hygiene must be emphasised for all age groups. Risk communication should expand to focus on preventing multiple infectious diseases during and beyond the COVID-19 pandemic.GlaxoSmithKline and the German Federal Ministry of Education and Research. The CHAMPS programme is funded by the Bill & Melinda Gates Foundation.https://sajid.co.za/index.php/sajiddm2022Medical Virolog

Diarrhoeal diseases in Soweto, South Africa, 2020 : a cross-sectional community survey

BACKGROUND : In South Africa, there are limited data on the burden of diarrhoea at a community level, specifically in older children and adults. This community survey estimated rates of and factors associated with diarrhoea across all ages and determined the proportion of cases presenting to healthcare facilities. METHODS : Households were enrolled from an existing urban health and demographic surveillance site. A household representative was interviewed to determine associated factors and occurrence of diarrhoea in the household, for all household members, in the past 2 weeks (including symptoms and health seeking behaviour). Diarrhoeal rate of any severity was calculated for 15 years age groups. Factors associated with diarrhoea and health seeking behaviour were investigated using binomial logistic regression. RESULTS : Diarrhoeal rate among respondents (2.5 episodes/person-year (95% CI, 1.8–3.5)) was significantly higher than for other household members (1.0 episodes/person-year (95% CI, 0.8–1.4); IRR = 2.4 (95% CI, 1.5–3.7) p < 0.001). Diarrhoeal rates were similar between age groups, however younger children (< 5 years) were more likely to present to healthcare facilities than adults (OR = 5.9 (95% CI, 1.1–31.4), p = 0.039). Oral rehydration solution was used in 44.8% of cases. Having a child between 5 and 15 years in the household was associated with diarrhoea (OR = 2.3 (95% CI, 1.3–3.9), p = 0.003) and, while 26.4% of cases sought healthcare, only 4.6% were hospitalised and only 3.4% of cases had a stool specimen collected. While the majority of cases were mild, 13.8% of cases felt they required healthcare but were unable to access it. CONCLUSION : Diarrhoeal rate was high across all age groups in this community; however, older children and adults were less likely to present to healthcare, and are therefore underrepresented through facility-based clinical surveillance. Current diarrhoeal surveillance represents a fraction of the overall cases occurring in the community.SUPPLEMENTARY MATERIAL: FIGURE S1. Health seeking for reported diarrhoeal episodes. TABLE S1. Factors associated with ORS knowledge.This work was supported by GlaxoSmithKline [E-Track 200238] and the German Federal Ministry of Education and Research [grant number 81203616] to SLJ. The CHAMPS program is funded by the Bill & Melinda Gates Foundation (Grant OPP1126780).http://www.biomedcentral.com/bmcpublichealtham2022Medical Virolog

Erratum: Investigation of two suspected diarrhoeal-illness outbreaks in Northern Cape and KwaZulu-Natal provinces, South Africa, April–July 2013: The role of rotavirus

No abstract available

Serum levels of inflammatory cytokines in Rift Valley fever patients are indicative of severe disease

BACKGROUND : Rift Valley fever (RVF) is a mosquito-borne viral zoonosis affecting domestic and wild ruminants, camels and humans. Outbreaks of RVF are characterized by a sudden onset of abortions and high mortality amongst domestic ruminants. Humans develop disease ranging from a mild flu-like illness to more severe complications including hemorrhagic syndrome, ocular and neurological lesions and death. During the RVF outbreak in South Africa in 2010/11, a total of 278 human cases were laboratory confirmed, including 25 deaths. The role of the host inflammatory response to RVF pathogenesis is not completely understood. METHODS : Virus load in serum from human fatal and non-fatal cases was determined by standard tissue culture infective dose 50 (TCID50) titration on Vero cells. Patient serum concentration of chemokines and cytokines involved in inflammatory responses (IL-8, RANTES, CXCL9, MCP-1, IP-10, IL-1β, IL-6, IL-10, TNF and IL-12p70) was determined using cytometric bead assays and flow cytometry. RESULTS : Fatal cases had a 1-log10 higher TCID50/ml serum concentration of RVF virus (RVFV) than survivors (p < 0.05). There were no significant sequence differences between isolates recovered from fatal and non-fatal cases. Chemokines and pro- and anti-inflammatory cytokines were detected at significantly increased (IL-8, CXCL9, MCP-1, IP-10, IL-10) or decreased (RANTES) levels when comparing fatal cases to infected survivors and uninfected controls, or when comparing combined infected patients to uninfected controls. CONCLUSIONS : The results suggest that regulation of the host inflammatory responses plays an important role in the outcome of RVFV infection in humans. Dysregulation of the inflammatory response contributes to a fatal outcome. The cytokines and chemokines identified in this study that correlate with fatal outcomes warrant further investigation as markers for disease severity.The Poliomyelitis Research Foundation (PRF), grant number 12/10. PJvV is further supported by a grant from the Incentive Funding for Rated Researchers program of the National Research Foundation (NRF), South Africa. This work is based on the research supported in part by the National Research Foundation of South Africa (Grant specific unique reference number UID 85544).http://www.virologyj.comam201

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

Epidemiology and aetiology of moderate to severe diarrhoea in hospitalised patients ≥5 years old living with HIV in South Africa, 2018- 2021 : a case-control analysis

DATA AVAILABILITY STATEMENT : The dataset has been made available in the supplementary material.SUPPORTING INFORMATION : DATA S1. (DTA) TABLE S1. Pathogens included in molecular testing. TABLE S2. Clinical presentation for cases among PLHIV, stratified by CD4+ cell counts. TABLE S3. Pathogen detection in specimens of cases among PLHIV, stratified by CD4+ cell count. TABLE S4. Clinical presentation of cases among PLHIV, stratified by treatment. TABLE S5. Pathogens detected in cases among PLHIV, stratified by treatment.Diarrhoea is a recognised complication of HIV-infection, yet there are limited local aetiological data in this high-risk group. These data are important for informing public health interventions and updating diagnostic and treatment guidelines. This study aimed to determine the pathogenic causes of diarrhoeal admissions in people living with HIV (PLHIV) compared to hospital controls between July 2018 and November 2021. Admitted diarrhoeal cases (n = 243) and non-diarrhoeal hospital controls (n = 101) 5 years of age were enrolled at Kalafong, Mapulaneng and Matikwana hospitals. Stool specimens/rectal swabs were collected and pathogen screening was performed on multiple platforms. Differences in pathogen detections between cases and controls, stratified by HIV status, were investigated. The majority (n = 164, 67.5%) of enrolled diarrhoeal cases with known HIV status were HIVinfected. Pathogens could be detected in 66.3% (n = 228) of specimens, with significantly higher detection in cases compared to controls (72.8% versus 50.5%, p0.001). Amongst PLHIV, prevalence of Cystoisospora spp. was significantly higher in cases than controls (17.7% versus 0.0%, p = 0.028), while Schistosoma was detected more often in controls than cases (17.4% versus 2.4%, p = 0.009). Amongst the HIV-uninfected participants, prevalence of Shigella spp., Salmonella spp. and Helicobacter pylori was significantly higher in cases compared to controls (36.7% versus 12.0%, p = 0.002; 11.4% versus 0.0%, p = 0.012; 10.1% versus 0.0%, p = 0.023). Diarrhoeal aetiology differed by HIV status, with Shigella spp. (36.7%) and Salmonella spp. (11.4%) having the highest prevalence amongst HIV-uninfected cases and Shigella spp. (18.3%), Cystoisospora (17.7%), and Cryptosporidium spp. (15.9%) having the highest prevalence in cases amongst PLHIV. These differences should be considered for the development of diagnostic and treatment guidelines.https://journals.plos.org/globalpublichealth/am2024Internal MedicineMedical VirologyPaediatrics and Child HealthSDG-03:Good heatlh and well-bein