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Kekana D, Naicker SD, Shuping L, Velaphi S, Nakwa FL, Wadula J, Govender NP. Candida auris Clinical Isolates Associated with Outbreak in Neonatal Unit of Tertiary Academic Hospital, South Africa. Emerg Infect Dis 2023; 29:2044-2053. [PMID: 37735719 PMCID: PMC10521600 DOI: 10.3201/eid2910.230181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Candida auris was first detected at a university-affiliated hospital in Johannesburg, South Africa, in 2009. We used whole-genome sequencing to describe the molecular epidemiology of C. auris in the same hospital during 2016-2020; the neonatal unit had a persistent outbreak beginning in June 2019. Of 287 cases with culture-confirmed C. auris infection identified through laboratory surveillance, 207 (72%) had viable isolates and 188 (66%) were processed for whole-genome sequencing. Clade III (118/188, 63%) and IV (70/188, 37%) isolates co-circulated in the hospital. All 181/188 isolates that had a fluconazole MIC >32 µg/mL had ERG11 mutations; clade III isolates had VF125AL substitutions, and clade IV isolates had K177R/N335S/E343D substitutions. Dominated by clade III, the neonatal unit outbreak accounted for 32% (91/287) of all cases during the study period. The outbreak may have originated through transmission from infected or colonized patients, colonized healthcare workers, or contaminated equipment/environment.
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Shuping L, Maphanga TG, Naicker SD, Mpembe R, Ngoma N, Velaphi S, Nakwa F, Wadula J, Jaglal P, Govender NP. High Prevalence of Candida auris Colonization during Protracted Neonatal Unit Outbreak, South Africa. Emerg Infect Dis 2023; 29:1913-1916. [PMID: 37610276 PMCID: PMC10461653 DOI: 10.3201/eid2909.230393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023] Open
Abstract
One third of patients were colonized by Candida auris during a point-prevalence survey in a neonatal unit during an outbreak in South Africa. The sensitivity of a direct PCR for rapid colonization detection was 44% compared with culture. The infection incidence rate decreased by 85% after the survey and implementation of isolation/cohorting.
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Paccoud O, Shuping L, Mashau R, Greene G, Quan V, Meiring S, Govender NP. Impact of prior cryptococcal antigen screening on in-hospital mortality in cryptococcal meningitis or fungaemia among HIV-seropositive individuals in South Africa: a cross-sectional observational study. Clin Microbiol Infect 2023; 29:1063-1069. [PMID: 37086780 DOI: 10.1016/j.cmi.2023.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 04/24/2023]
Abstract
OBJECTIVES We investigated whether patients with cryptococcal meningitis (CM) or fungaemia detected through South Africa's laboratory cryptococcal antigen (CrAg) screening programme had better outcomes than those presenting directly to the hospital. METHODS We compared 14-day in-hospital case-fatality ratios of HIV-seropositive individuals with CD4 counts below 100 cells/μL and laboratory-confirmed CM/fungaemia from 2017-2021, with or without evidence of a positive blood CrAg test within 14 days prior to diagnosis. We evaluated whether the impact of prior CrAg screening on mortality varied according to the study period (pre-COVID-19: before March 2020 vs. COVID-19: after March 2020). RESULTS Overall, 24.5% (830/3390) of patients had a prior positive CrAg test within 14 days of diagnosis. CrAg-screened patients were less likely to have an altered mental status at baseline than non-CrAg-screened patients (38.1% [296/776] vs. 42.6% [1010/2372], p = 0.03), and had a lower crude 14-day case-fatality ratio (24.7% [205/830] vs. 28.3% [724/2560]; OR, 0.83 [95% CI, 0.69-0.99]; p = 0.045). Previous CrAg screening was associated with a greater reduction in the crude 14-day mortality during the COVID-19 period (OR, 0.64 [0.47-0.87]; p = 0.005) compared with before (OR, 0.95 [0.76-1.19]; p = 0.68). After adjustment, previous CrAg screening within 14 days was associated with increased survival only during the COVID-19 period (adjusted OR, 0.70 [0.51-0.96]; p = 0.03). DISCUSSION Previous CrAg screening was associated with a survival benefit in patients hospitalized with CM/fungaemia during the COVID-19 period, with fewer patients having an altered mental status at baseline, suggesting that these patients may have been diagnosed with cryptococcosis earlier.
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Affiliation(s)
- Olivier Paccoud
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; Université Paris Cité, Necker-Pasteur Center for Infectious Diseases and Tropical Medicine, Hospital Necker-Enfants Maladies, Assistance Publique-Hopitaux de Paris, Paris, France
| | - Liliwe Shuping
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Rudzani Mashau
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Greg Greene
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Vanessa Quan
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nelesh P Govender
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Institute of Infection and Immunity, St George's University of London, London, UK; Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK; Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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Naicker SD, Shuping L, Zulu TG, Mpembe RS, Mhlanga M, Tsotetsi EM, Maphanga TG, Govender NP. Epidemiology and susceptibility of Nakaseomyces (formerly Candida) glabrata bloodstream isolates from hospitalised adults in South Africa. Med Mycol 2023; 61:myad057. [PMID: 37336590 DOI: 10.1093/mmy/myad057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023] Open
Abstract
During 2016-2017, Nakaseomyces glabrata (formerly Candida glabrata) caused 14% of cases of candidaemia in South Africa. We aimed to describe the clinical characteristics of adults with N. glabrata candidaemia at 20 sentinel hospitals (accounting for 20% (172/917) of cases) and the antifungal susceptibility of the corresponding isolates. A higher proportion of patients with N. glabrata candidaemia were older (median age: 55 years [interquartile range (IQR): 41-65 years] vs. 49 years [IQR: 35-63 years]; p = 0.04), female (87/164, 53% vs. 283/671, 42%; p = 0.01), admitted to a public-sector hospital (152/172, 88% vs. 470/745, 63%; p < 0.001), treated with fluconazole only (most with suboptimal doses) (51/95, 54% vs. 139/361, 39%; p < 0.001), and had surgery (47/172, 27% vs. 123/745, 17%; p = 0.001) and a shorter hospital stay (median 7 days [IQR: 2-20 days] vs. 13 days [IQR: 4-27 days]; p < 0.001) compared to patients with other causes of candidaemia. Eight N. glabrata isolates (6%, 8/131) had minimum inhibitory concentrations in the intermediate or resistant range for ≥ 1 echinocandin and a R1377K amino acid substitution encoded by the hotspot 2 region of the FKS2 gene. Only 11 isolates (8%, 11/131) were resistant to fluconazole. Patients with confirmed N. glabrata candidaemia are recommended to be treated with an echinocandin (or polyene), thus further guideline training is required.
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Affiliation(s)
- Serisha D Naicker
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Liliwe Shuping
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Thokozile G Zulu
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ruth S Mpembe
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mabatho Mhlanga
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ernest M Tsotetsi
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Tsidiso G Maphanga
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nelesh P Govender
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infection and Immunity, St George's University of London, London and Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, United Kingdom
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Kufa T, Jassat W, Cohen C, Tempia S, Masha M, Wolter N, Walaza S, von Gottburg A, Govender NP, Hunt G, Shonhiwa AM, Ebonwu J, Ntshoe G, Maruma W, Bapela P, Ndhlovu N, Mathema H, Modise M, Shuping L, Manana PN, Moore D, Dangor Z, Verwey C, Madhi SA, Saloojee H, Zar HJ, Blumberg L. Epidemiology of SARS-CoV-2 infection and SARS-CoV-2 positive hospital admissions among children in South Africa. Influenza Other Respir Viruses 2021; 16:34-47. [PMID: 34796674 PMCID: PMC9664941 DOI: 10.1111/irv.12916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/15/2022] Open
Abstract
Introduction We describe epidemiology and outcomes of confirmed SARS‐CoV‐2 infection and positive admissions among children <18 years in South Africa, an upper‐middle income setting with high inequality. Methods Laboratory and hospital COVID‐19 surveillance data, 28 January ‐ 19 September 2020 was used. Testing rates were calculated as number of tested for SARS‐CoV‐2 divided by population at risk; test positivity rates were calculated as positive tests divided by total number of tests. In‐hospital case fatality ratio (CFR) was calculated based on hospitalized positive admissions with outcome data who died in‐hospital and whose death was judged SARS‐CoV‐2 related by attending physician. Findings 315 570 children aged <18 years were tested for SARS‐CoV‐2; representing 8.9% of all 3 548 738 tests and 1.6% of all children in the country. Of children tested, 46 137 (14.6%) were positive. Children made up 2.9% (n = 2007) of all SARS‐CoV‐2 positive admissions to sentinel hospitals. Among children, 47 died (2.6% case‐fatality). In‐hospital deaths were associated with male sex [adjusted odds ratio (aOR) 2.18 (95% confidence intervals [CI] 1.08–4.40)] vs female; age <1 year [aOR 4.11 (95% CI 1.08–15.54)], age 10–14 years [aOR 4.20 (95% CI1.07–16.44)], age 15–17 years [aOR 4.86 (95% 1.28–18.51)] vs age 1–4 years; admission to a public hospital [aOR 5.07(95% 2.01–12.76)] vs private hospital and ≥1 underlying conditions [aOR 12.09 (95% CI 4.19–34.89)] vs none. Conclusions Children with underlying conditions were at greater risk of severe SARS‐CoV‐2 outcomes. Children > 10 years, those in certain provinces and those with underlying conditions should be considered for increased testing and vaccination.
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Affiliation(s)
- Tendesayi Kufa
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of Public HealthUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Waasila Jassat
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Cheryl Cohen
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of Public HealthUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Stefano Tempia
- School of Public HealthUniversity of the WitwatersrandJohannesburgSouth Africa
- Influenza Division, National Center for Immunization and Respiratory DiseasesUS Centers for Disease Control and PreventionAtlantaGeorgiaUSA
- MassGenicsDuluthGeorgiaUSA
| | - Maureen Masha
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Nicole Wolter
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of PathologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Sibongile Walaza
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Anne von Gottburg
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of PathologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Nelesh P. Govender
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of PathologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Gillian Hunt
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of PathologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | | | - Joy Ebonwu
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Genevie Ntshoe
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of Health Systems and Public Health, Faculty of Health SciencesUniversity of PretoriaPretoriaSouth Africa
| | - Wellington Maruma
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Poncho Bapela
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Nomathamsanqa Ndhlovu
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Hlengani Mathema
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Motshabi Modise
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Liliwe Shuping
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
| | - Pinky N. Manana
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
- School of PathologyUniversity of the WitwatersrandJohannesburgSouth Africa
| | - David Moore
- Department of Pediatrics and Child HealthUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Ziyaad Dangor
- Department of Pediatrics and Child HealthUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Charl Verwey
- Department of Pediatrics and Child HealthUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Shabir A. Madhi
- South African Medical Research Council: Vaccines and Infectious Diseases Analytical Research Unit (VIDA), Faculty of Health Science JohannesburgUniversity of the WitwatersrandJohannesburgSouth Africa
- Department of Science/National Research Foundation: Vaccine Preventable Diseases, Faculty of Health Science JohannesburgUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Haroon Saloojee
- Department of Pediatrics and Child HealthUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Heather J. Zar
- Dept of Paediatrics and Child Health, Red Cross Children's Hospital, and SA‐MRC Unit on Child and Adolescent HealthUniversity of Cape TownCape TownSouth Africa
| | - Lucille Blumberg
- National Institute for Communicable DiseasesNational Health Laboratory ServicesJohannesburgSouth Africa
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Shuping L, Mpembe R, Mhlanga M, Naicker SD, Maphanga TG, Tsotetsi E, Wadula J, Velaphi S, Nakwa F, Chibabhai V, Mahabeer P, Moncho M, Prentice E, Bamford C, Reddy K, Maluleka C, Mawela D, Modise M, Govender NP. Epidemiology of Culture-confirmed Candidemia Among Hospitalized Children in South Africa, 2012-2017. Pediatr Infect Dis J 2021; 40:730-737. [PMID: 33872278 DOI: 10.1097/inf.0000000000003151] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND We aimed to describe the epidemiology of candidemia among children in South Africa. METHODS We conducted laboratory-based surveillance among neonates (≤28 days), infants (29 days to <1 year), children (1-11 years) and adolescents (12-17 years) with Candida species cultured from blood during 2012-2017. Identification and antifungal susceptibility of viable isolates were performed at a reference laboratory. We used multivariable logistic regression to determine the association between Candida parapsilosis candidemia and 30-day mortality among neonates. RESULTS Of 2996 cases, neonates accounted for 49% (n = 1478), infants for 27% (n = 806), children for 20% (n = 589) and adolescents for 4% (n = 123). The incidence risk at tertiary public sector hospitals was 5.3 cases per 1000 pediatric admissions (range 0.39-119.1). Among 2943 cases with single-species infections, C. parapsilosis (42%) and Candida albicans (36%) were most common. Candida auris was among the 5 common species with an overall prevalence of 3% (n = 47). Fluconazole resistance was more common among C. parapsilosis (55% [724/1324]) versus other species (19% [334/1737]) (P < 0.001). Of those with known treatment (n = 1666), 35% received amphotericin B deoxycholate alone, 32% fluconazole alone and 30% amphotericin B deoxycholate with fluconazole. The overall 30-day in-hospital mortality was 38% (n = 586) and was highest among neonates (43% [323/752]) and adolescents (43% [28/65]). Compared with infection with other species, C. parapsilosis infection was associated with a reduced mortality among neonates (adjusted odds ratio 0.41, 95% confidence interval: 0.22-0.75, P = 0.004). CONCLUSIONS Candidemia in this setting mainly affected neonates and infants and was characterized by fluconazole-resistant C. parapsilosis with no increased risk of death.
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Affiliation(s)
- Liliwe Shuping
- From the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ruth Mpembe
- From the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mabatho Mhlanga
- From the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Serisha D Naicker
- From the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Tsidiso G Maphanga
- From the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Ernest Tsotetsi
- From the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- Department of Microbiology, National Health Laboratory Service, Chris Hani Baragwanath Hospital, Johannesburg, South Africa
| | - Sithembiso Velaphi
- Department of Paediatrics and Child Health, Chris Hani Baragwanath Hospital, Johannesburg, South Africa
| | - Firdose Nakwa
- Department of Paediatrics and Child Health, Chris Hani Baragwanath Hospital, Johannesburg, South Africa
| | - Vindana Chibabhai
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- Department of Microbiology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Prasha Mahabeer
- Department of Microbiology, National Health Laboratory Service, King Edward VIII Hospital, KZN Academic Complex, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Masego Moncho
- Department of Medical Microbiology, Faculty of Health Sciences, Universitas Hospital, National Health Laboratory Service, University of Free State, Bloemfontein, South Africa
| | - Elizabeth Prentice
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Groote Schuur Microbiology Laboratory, National Health Laboratory Service, Cape Town, South Africa
| | - Colleen Bamford
- Division of Medical Microbiology and Immunology, Department of Pathology, Faculty of Health Sciences, Stellenbosch University/National Health Laboratory Services, Tygerberg, Cape Town, South Africa
| | - Kessendri Reddy
- Division of Medical Microbiology and Immunology, Department of Pathology, Faculty of Health Sciences, Stellenbosch University/National Health Laboratory Services, Tygerberg, Cape Town, South Africa
| | - Caroline Maluleka
- Department of Microbiology, National health Laboratory Service, Dr George Mukhari Hospital, Johannesburg, South Africa
- Department of Paediatrics and Child Health, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Dini Mawela
- Department of Microbiology, National health Laboratory Service, Dr George Mukhari Hospital, Johannesburg, South Africa
- Department of Paediatrics and Child Health, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Motshabi Modise
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, a Division of National Health Laboratory Service, Johannesburg, South Africa
| | - Nelesh P Govender
- From the Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a Division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
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Zwane T, Shuping L, Perovic O. Etiology and Antimicrobial Susceptibility of Pathogens Associated with Urinary Tract Infections among Women Attending Antenatal Care in Four South African Tertiary-Level Facilities, 2015-2019. Antibiotics (Basel) 2021; 10:669. [PMID: 34199691 PMCID: PMC8229093 DOI: 10.3390/antibiotics10060669] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/23/2021] [Accepted: 05/31/2021] [Indexed: 12/29/2022] Open
Abstract
In South Africa, uncomplicated community-acquired UTIs (CA-UTIs) are treated empirically; however, the extent of antibiotic resistance among these pathogens is not well known. We conducted a descriptive cross-sectional study of women attending ANCs at four tertiary public-sector hospitals in Gauteng. Female patients aged 15-49 years, with urine cultures performed between January 2015 and December 2019, were included. A case of culture-confirmed UTI was defined as any woman with ≤2 uropathogens with a bacterial count of ≥105 colony-forming units per ml for at least one pathogen. We identified 3558 cases of culture-confirmed UTIs in women with a median age of 30 years (interquartile range; 25-35). E. coli accounted for most infections (56% (1994/3558)), followed by E. faecalis, with a prevalence of 17% (609/3558). The prevalence of K. pneumoniae was 5% (193/3558), 5% (186/3558) for S. agalactiae, and 5% (179/3558) for P. mirabilis. Ninety-five percent (1827/1927) of the E. coli and 99% of the E. faecalis (301/305) isolates were susceptible to nitrofurantoin. Common uropathogens showed high susceptibility to first-line antibiotics, gentamicin and nitrofurantoin, as recommended for use in primary healthcare settings. Overall, our study provided an indication of the level of antimicrobial resistance in the four facilities.
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Affiliation(s)
- Thembekile Zwane
- Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Private Bag 3 Wits, Johannesburg 2050, South Africa
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa;
- South African Field Epidemiology Training Program, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa
| | - Liliwe Shuping
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa;
| | - Olga Perovic
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Private Bag X4 Sandringham, Johannesburg 2131, South Africa;
- Department of Clinical Microbiology and Infectious Disease, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Private Bag 3 Wits, Johannesburg 2050, South Africa
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Naicker SD, Magobo RE, Maphanga TG, Firacative C, van Schalkwyk E, Monroy-Nieto J, Bowers J, Engelthaler DM, Shuping L, Meyer W, Govender NP. Genotype, Antifungal Susceptibility, and Virulence of Clinical South African Cryptococcus neoformans Strains from National Surveillance, 2005-2009. J Fungi (Basel) 2021; 7:jof7050338. [PMID: 33925754 PMCID: PMC8146981 DOI: 10.3390/jof7050338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
In South Africa, Cryptococcus neoformans is the most common cause of adult meningitis. We performed multi locus sequence typing and fluconazole susceptibility testing of clinical C. neoformans isolates collected from 251 South African patients with cryptococcosis through national surveillance from 2005 to 2009. We examined the association between clinical characteristics of patients and genotype, and the effect of genotype on in-hospital mortality. We performed whole genome phylogenetic analysis of fifteen C. neoformans isolates with the molecular type VNB and tested their virulence in a Galleria mellonella model. Most isolates had the molecular type VNI (206/251, 82%), followed by VNII (25/251, 10%), VNB (15/251, 6%), and VNIV (5/251, 2%); 67 sequence types were identified. There were no differences in fluconazole minimum inhibitory concentration (MIC) values among molecular types and the majority of strains had low MIC values (MIC50 of 1 µg/mL and MIC90 of 4 µg/mL). Males were almost twice as likely of being infected with a non-VNI genotype (adjusted odds ratio [OR]: 1.65, 95% confidence interval [CI]: 0.25–10.99; p = 0.61). Compared to patients infected with a VNI genotype, those with a non-VNI genotype had a 50% reduced adjusted odds of dying in hospital (95% CI: 0.03–7.57; p = 0.62). However, for both these analyses, our estimates had wide confidence intervals spanning 1 with large p-values. Fifteen VNB strains were not as virulent in a G. mellonella larval model as the H99 reference strain. A majority of these VNB strains belonged to the VNBII clade and were very closely related by phylogenetic analysis.
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Affiliation(s)
- Serisha D. Naicker
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
- Correspondence: ; Tel.: +27-11-555-0491
| | - Rindidzani E. Magobo
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Tsidiso G. Maphanga
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Carolina Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad del Rosario, 111611 Bogota, Colombia;
| | - Erika van Schalkwyk
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Juan Monroy-Nieto
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; (J.M.-N.); (J.B.); (D.M.E.)
| | - Jolene Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; (J.M.-N.); (J.B.); (D.M.E.)
| | - David M. Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA; (J.M.-N.); (J.B.); (D.M.E.)
| | - Liliwe Shuping
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Center for Infectious Diseases and Microbiology, Westmead Clinical School, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia;
- Marie Bashir Institute for Emerging Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW 2006, Australia
- Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
- Research and Educational Network, Westmead Hospital, Western Sydney Local Health District, Westmead, NSW 2145, Australia
| | - Nelesh P. Govender
- Center for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, A Division of the National Health Laboratory Service, Johannesburg 2192, South Africa; (R.E.M.); (T.G.M.); (E.v.S.); (L.S.); (N.P.G.)
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2001, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town 7701, South Africa
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9
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Ismail H, Govender NP, Singh-Moodley A, van Schalkwyk E, Shuping L, Moema I, Feller G, Mogokotleng R, Strasheim W, Lowe M, Mpembe R, Naicker S, Maphanga TG, De Abreu C, Ismail F, Ismail N, Allam M, Ismail A, Singh T, Matuka O, Duba T, Perovic O. An outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin-producing methicillin-susceptible Staphylococcus aureus among gold mine workers, South Africa, November 2017 to March 2018. BMC Infect Dis 2020; 20:621. [PMID: 32831057 PMCID: PMC7446146 DOI: 10.1186/s12879-020-05352-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 08/16/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND We aimed to describe an outbreak of cutaneous abscesses caused by Panton-Valentine leukocidin (PVL)-producing methicillin-susceptible Staphylococcus aureus (MSSA) among gold mine workers. METHODS In February 2018, we retrospectively reviewed a random sample of 50 medical records from 243 cases and conducted face-to-face interviews using a structured questionnaire. Pus aspirates were sent to the National Institute for Communicable Diseases from prospectively-identified cases (November 2017-March 2018). Nasopharyngeal swabs were collected during a colonisation survey in February 2018. Staphylococcus aureus isolates were screened with a conventional PCR for lukS/F-PV. Pulsed-field gel electrophoresis (PFGE) was performed to determine the genetic relatedness among the isolates. A sample of isolates were selected for whole genome sequencing (WGS). We conducted an assessment on biological risks associated with mining activities. RESULTS From January 2017 to February 2018, 10% (350/3582) of mine workers sought care for cutaneous abscesses. Forty-seven medical files were available for review, 96% were male (n = 45) with a mean age of 43 years (SD = 7). About 52% (24/46) were involved in stoping and 28% (13/47) worked on a particular level. We cultured S. aureus from 79% (30/38) of cases with a submitted specimen and 14% (12/83) from colonisation swabs. All isolates were susceptible to cloxacillin. Seventy-one percent of S. aureus isolates (30/42) were PVL-PCR-positive. Six PFGE clusters were identified, 57% (21/37) were closely related. WGS analysis found nine different sequence types. PFGE and WGS analysis showed more than one cluster of S. aureus infections involving closely related isolates. Test reports for feed and product water of the mine showed that total plate counts were above the limits of 1000 cfu/ml, coliform counts > 10 cfu/100 ml and presence of faecal coliforms. Best practices were poorly implemented as some mine workers washed protective clothing with untreated water and hung them for drying at the underground surface. CONCLUSIONS PVL-producing MSSA caused an outbreak of cutaneous abscesses among underground workers at a gold mining company. To our knowledge, no other outbreaks of PVL-producing S. aureus involving skin and soft tissue infections have been reported in mining facilities in South Africa. We recommend that worker awareness of infection prevention and control practices be strengthened.
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Affiliation(s)
- Husna Ismail
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.
| | - Nelesh P Govender
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
| | - Ashika Singh-Moodley
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
| | - Erika van Schalkwyk
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Liliwe Shuping
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Itumeleng Moema
- South African Field Epidemiology Training Programme, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Gal Feller
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Ruth Mogokotleng
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Wilhelmina Strasheim
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Michelle Lowe
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Ruth Mpembe
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Serisha Naicker
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Tsidiso G Maphanga
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Cecilia De Abreu
- Centre for Tuberculosis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Farzana Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Tanusha Singh
- Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa.,Immunology and Microbiology, National Institute for Occupational Health, a division of the National Health Laboratory Service, 25 Hospital Street, Constitution Hill, Johannesburg, 2000, South Africa
| | - Onnicah Matuka
- Immunology and Microbiology, National Institute for Occupational Health, a division of the National Health Laboratory Service, 25 Hospital Street, Constitution Hill, Johannesburg, 2000, South Africa
| | - Thabang Duba
- Immunology and Microbiology, National Institute for Occupational Health, a division of the National Health Laboratory Service, 25 Hospital Street, Constitution Hill, Johannesburg, 2000, South Africa
| | - Olga Perovic
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, 1 Modderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Faculty of Health Sciences, University of Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
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van Schalkwyk E, Mpembe RS, Thomas J, Shuping L, Ismail H, Lowman W, Karstaedt AS, Chibabhai V, Wadula J, Avenant T, Messina A, Govind CN, Moodley K, Dawood H, Ramjathan P, Govender NP. Epidemiologic Shift in Candidemia Driven by Candida auris, South Africa, 2016-2017 1. Emerg Infect Dis 2020; 25:1698-1707. [PMID: 31441749 PMCID: PMC6711229 DOI: 10.3201/eid2509.190040] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Candida auris is an invasive healthcare-associated fungal pathogen. Cases of candidemia, defined as illness in patients with Candida cultured from blood, were detected through national laboratory-based surveillance in South Africa during 2016–2017. We identified viable isolates by using mass spectrometry and sequencing. Among 6,669 cases (5,876 with species identification) from 269 hospitals, 794 (14%) were caused by C. auris. The incidence risk for all candidemia at 133 hospitals was 83.8 (95% CI 81.2–86.4) cases/100,000 admissions. Prior systemic antifungal drug therapy was associated with a 40% increased adjusted odds of C. auris fungemia compared with bloodstream infection caused by other Candida species (adjusted odds ratio 1.4 [95% CI 0.8–2.3]). The crude in-hospital case-fatality ratio did not differ between Candida species and was 45% for C. auris candidemia, compared with 43% for non–C. auris candidemia. C. auris has caused a major epidemiologic shift in candidemia in South Africa.
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11
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Lumngwena EN, Abrahams B, Shuping L, Cicala C, Arthos J, Woodman Z. Selective transmission of some HIV-1 subtype C variants might depend on Envelope stimulating dendritic cells to secrete IL-10. PLoS One 2020; 15:e0227533. [PMID: 31978062 PMCID: PMC6980567 DOI: 10.1371/journal.pone.0227533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/20/2019] [Indexed: 11/21/2022] Open
Abstract
Envelope (Env) phenotype(s) that provide transmitted founders (TF) with a selective advantage during HIV-1 transmission would be the ideal target for preventative therapy. We generated Env clones from four individuals infected with a single virus and one participant infected with multiple variants at transmission and compared phenotype with matched Envs from chronic infection (CI). When we determined whether pseudovirus (PSV) of the five TF and thirteen matched CI Env clones differed in their ability to 1) enter TZM-bl cells, 2) bind DC-SIGN, and 3) trans-infect CD4+ cells there was no association between time post-infection and variation in Env phenotype. However, when we compared the ability of PSV to induce monocyte-derived dendritic cells (MDDCs) to secrete Interleukin-10 (IL-10), we found that only TF Envs from single variant transmission cases induced MDDCs to secrete either higher or similar levels of IL-10 as the CI clones. Furthermore, interaction between MDDC DC-SIGN and Env was required for secretion of IL-10. When variants were grouped according to time post-infection, TF PSV induced the release of higher levels of IL-10 than their CI counterparts although this relationship varied across MDDC donors. The selection of variants during transmission is therefore likely a complex event dependent on both virus and host genetics. Our findings suggest that, potentially due to overall variation in N-glycosylation across variants, nuanced differences in binding of TF Env to DC-SIGN might trigger alternative DC immune responses (IRs) in the female genital tract (FGT) that favour HIV-1 survival and facilitate transmission.
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Affiliation(s)
- Evelyn Ngwa Lumngwena
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute for Medical Research and Medicinal Plants studies (IMPM), Ministry of Scientific Research and Innovation (MINRESI), Yaounde, Cameroon
- * E-mail: (ZW); (ENL)
| | - Bianca Abrahams
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Liliwe Shuping
- National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa
| | - Claudia Cicala
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, United States of America
| | - James Arthos
- National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, United States of America
| | - Zenda Woodman
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail: (ZW); (ENL)
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12
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Nana T, Moore C, Boyles T, Brink AJ, Cleghorn J, Devenish LM, du Toit B, Fredericks ES, Lekalakala-Mokaba MR, Maluleka C, Rajabally MN, Reubenson G, Shuping L, Swart K, Swe Han KS, Wadula J, Wojno J, Lowman W. South African Society of Clinical Microbiology Clostridioides difficile infection diagnosis, management and infection prevention and control guideline. S Afr J Infect Dis 2020; 35:219. [PMID: 34485483 PMCID: PMC8378053 DOI: 10.4102/sajid.v35i1.219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile infection (CDI) is a problem in both developed and developing countries and is a common hospital-acquired infection. This guideline provides evidence-based practical recommendations for South Africa and other developing countries. The scope of the guideline includes CDI diagnostic approaches; adult, paediatric and special populations treatment options; and surveillance and infection prevention and control recommendations.
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Affiliation(s)
- Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Charlotte Maxeke Johannesburg Academic Hospital Microbiology Laboratory, National Health Laboratory Services, Johannesburg, South Africa
| | | | - Tom Boyles
- Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Adrian J. Brink
- Department of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Joy Cleghorn
- Life Healthcare Group, Johannesburg, South Africa
| | - Lesley M. Devenish
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Infection Control Services Laboratory, National Health Laboratory Services, Johannesburg, South Africa
| | | | - Ernst S. Fredericks
- Department of Physiology, Faculty of Science, Nelson Mandela University, Port Elizabeth, South Africa
| | - Molebogeng R. Lekalakala-Mokaba
- Department of Microbiology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- Dr George Mukhari Academic Hospital Microbiology Laboratory, National Health Laboratory Services, Pretoria, South Africa
| | - Caroline Maluleka
- Department of Microbiology, Faculty of Health Sciences, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- Dr George Mukhari Academic Hospital Microbiology Laboratory, National Health Laboratory Services, Pretoria, South Africa
| | | | - Gary Reubenson
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Liliwe Shuping
- Centre for Healthcare-Associated Infections, National Institute for Communicable Diseases, a division of National Health Laboratory Service, Johannesburg, South Africa
| | - Karin Swart
- Netcare Hospitals Limited, Johannesburg, South Africa
| | - Khine Swe Swe Han
- Medical Microbiology Department, Inkosi Albert Luthuli Central Hospital Academic Complex, National Health Laboratory Services, Durban, South Africa
- Department of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Chris Hani Baragwanath Hospital Microbiology Laboratory, National Health Laboratory Services, Johannesburg, South Africa
| | | | - Warren Lowman
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Clinical Microbiology, PathCare/Vermaak Pathologists, Johannesburg, South Africa
- Department of Clinical Microbiology and Infection Prevention and Control, WITS Donald Gordon Medical Centre, Johannesburg, South Africa
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13
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van Schalkwyk E, Mpembe RS, Thomas J, Shuping L, Ismail H, Lowman W, Karstaedt AS, Chibabhai V, Wadula J, Avenant T, Messina A, Govind CN, Moodley K, Dawood H, Ramjathan P, Govender NP. Epidemiologic Shift in Candidemia Driven by Candida auris, South Africa, 2016–20171. Emerg Infect Dis 2019. [DOI: 10.3201/eid2509190040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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14
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Lumngwena EN, Shuping L, Bernitz N, Woodman Z. HIV-1 subtype C Envelope function becomes less sensitive to N-glycosylation deletion during disease progression. BMC Res Notes 2019; 12:340. [PMID: 31208438 PMCID: PMC6580609 DOI: 10.1186/s13104-019-4375-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 12/27/2022] Open
Abstract
Objective As part of a larger study to understand how Envelope N-glycosylation influences HIV-1 pathogenesis, we selected a participant infected with a single Subtype C variant and determined whether deletion of specific potential N-glycan sites (PNGs) impacted Envelope function longitudinally. Results We deleted five PNGs previously linked to HIV-1 transmission of two matched Envelope clones representing variants at 5 and 173 weeks post-infection. The transmitted founder (TF) had significantly better pseudovirus entry efficiency than the chronic infection (CI) variant. Deletion of all PNGs significantly reduced TF entry efficiency, binding to dendritic cell-specific intracellular adhesion molecule 3 grabbing non-integrin (DC-SIGN) receptor and trans-infection. However, mutational analysis did not affect the phenotype of the CI Envelope to the same extent. Notably, deletion of the PNGs at N241 and N448 had no effect on CI Envelope function, suggesting that some PNGs might only be important during acute infection. Therefore, vaccines that elicit antibodies against N-glycans important for TF Envelope function could drive the loss of PNGs during immune escape, abrogating viral replication. Conversely, changes in N-glycosylation might have no effect on some variants, reducing vaccine efficacy. This finding highlights the need for further investigation into the role of Envelope N-glycosylation in HIV-1 pathogenesis.
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Affiliation(s)
- Evelyn Ngwa Lumngwena
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Centre for the Study of Emerging and Re-Emerging Infections (CREMER), Institute for Medical Research and Medicinal Plants Studies (IMPM), Ministry of Scientific Research and Innovation (MINRESI), Yaoundé, Cameroon
| | - Liliwe Shuping
- Division of the National Laboratory Service, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Netanya Bernitz
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Zenda Woodman
- Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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Smith A, Naicker P, Bamford C, Shuping L, McCarthy K, Sooka A, Smouse S, Tau N, Keddy K. Whole-genome sequencing analysis of Listeria monocytogenes isolated in South Africa. Int J Infect Dis 2016. [DOI: 10.1016/j.ijid.2016.11.178] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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16
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Lumngwena EN, Shuping L, Bertniz N, Cicala C, Arthos J, Woodman Z. The Role of N-glycosylation in DC-SIGN Interactions with Transmitted Founder Variants of HIV-1 Subtype C Envelope. AIDS Res Hum Retroviruses 2014. [DOI: 10.1089/aid.2014.5494.abstract] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Evelyn N. Lumngwena
- University of Cape Town, Molecular and Cell Biology, Cape Town, South Africa
| | - Liliwe Shuping
- University of Cape Town, Molecular and Cell Biology, Cape Town, South Africa
| | - Netanya Bertniz
- University of Cape Town, Molecular and Cell Biology, Cape Town, South Africa
| | - Claudia Cicala
- National Institutes of Health, Laboratory of Immunoregulation, NIAID, Bethesda, MD, United States
| | - James Arthos
- National Institutes of Health, Laboratory of Immunoregulation, NIAID, Bethesda, MD, United States
| | - Zenda Woodman
- University of Cape Town, Molecular and Cell Biology, Cape Town, South Africa
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Fujimoto N, Matsubayashi K, Miyahara T, Murai A, Matsuda M, Shio H, Suzuki H, Kameyama M, Saito A, Shuping L. The risk factors for ischemic heart disease in Tibetan highlanders. Jpn Heart J 1989; 30:27-34. [PMID: 2724529 DOI: 10.1536/ihj.30.27] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The risk factors for ischemic heart disease (IHD) in 35 Tibetan highlanders were investigated and compared with those in 30 age- and sex-matched healthy Japanese controls. Although Tibetans had remarkably high hematocrit values, and a decrease of eicosapentaenoic acid in both serum total lipids and serum phospholipid (PL) possibly due to their diet, they were considered to have a low incidence of IHD from our door-to-door study. These positive risk factors are likely counteracted by other negative risk factors as follows; Tibetans rarely exhibited systolic hypertension, and had lower levels of serum cholesterol and serum apolipoprotein (apo) B, and apo B/apo A-I ratio. In addition, Tibetan highlanders showed a decreased level of palmitic acid and an increased level of linoleic acid in serum PL which may protect against atherosclerosis.
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Affiliation(s)
- N Fujimoto
- Department of Neurology, Medical Center for Adult Diseases, Shiga, Japan
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