Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates
In South Africa, Candida auris was the third most common cause of candidemia in 2016–2017. We performed single nucleotide polymorphism (SNP) genome-wide analysis of 115 C. auris isolates collected between 2009 and 2018 from national laboratory-based surveillance, an environmental survey at four hosp...
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2021-01-01
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| Series: | Emerging Microbes and Infections |
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| Online Access: | https://www.tandfonline.com/doi/10.1080/22221751.2021.1944323 |
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| author | Serisha D. Naicker Tsidiso G. Maphanga Nancy A. Chow Mushal Allam Stanford Kwenda Arshad Ismail Nelesh P. Govender |
| author_facet | Serisha D. Naicker Tsidiso G. Maphanga Nancy A. Chow Mushal Allam Stanford Kwenda Arshad Ismail Nelesh P. Govender |
| author_sort | Serisha D. Naicker |
| collection | DOAJ |
| description | In South Africa, Candida auris was the third most common cause of candidemia in 2016–2017. We performed single nucleotide polymorphism (SNP) genome-wide analysis of 115 C. auris isolates collected between 2009 and 2018 from national laboratory-based surveillance, an environmental survey at four hospitals and a colonization study during a neonatal unit outbreak. The first known South African C. auris strain from 2009 clustered in clade IV. Overall, 98 strains clustered within clade III (85%), 14 within clade I (12%) and three within clade IV (3%). All environmental and colonizing strains clustered in clade III. We also identified known clade-specific resistance mutations in the ERG11 and FKS1 genes. Identification of clade I strains between 2016 and 2018 suggests introductions from South Asia followed by local transmission. SNP analysis characterized most C. auris strains into clade III, the clade first reported from South Africa, but the presence of clades I and IV strains also suggest early introductions from other regions. |
| first_indexed | 2024-12-10T20:22:31Z |
| format | Article |
| id | doaj.art-eb57bab164104c27989d1917634b1d49 |
| institution | Directory Open Access Journal |
| issn | 2222-1751 |
| language | English |
| last_indexed | 2024-12-10T20:22:31Z |
| publishDate | 2021-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Emerging Microbes and Infections |
| spelling | doaj.art-eb57bab164104c27989d1917634b1d492022-12-22T01:34:58ZengTaylor & Francis GroupEmerging Microbes and Infections2222-17512021-01-011011300130810.1080/22221751.2021.1944323Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolatesSerisha D. Naicker0Tsidiso G. Maphanga1Nancy A. Chow2Mushal Allam3Stanford Kwenda4Arshad Ismail5Nelesh P. Govender6National Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South AfricaNational Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South AfricaMycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USANational Institute for Communicable Diseases (Core Sequencing Facility), a Division of the National Health Laboratory Service, Johannesburg, South AfricaNational Institute for Communicable Diseases (Core Sequencing Facility), a Division of the National Health Laboratory Service, Johannesburg, South AfricaNational Institute for Communicable Diseases (Core Sequencing Facility), a Division of the National Health Laboratory Service, Johannesburg, South AfricaNational Institute for Communicable Diseases (Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses), a Division of the National Health Laboratory Service, Johannesburg, South AfricaIn South Africa, Candida auris was the third most common cause of candidemia in 2016–2017. We performed single nucleotide polymorphism (SNP) genome-wide analysis of 115 C. auris isolates collected between 2009 and 2018 from national laboratory-based surveillance, an environmental survey at four hospitals and a colonization study during a neonatal unit outbreak. The first known South African C. auris strain from 2009 clustered in clade IV. Overall, 98 strains clustered within clade III (85%), 14 within clade I (12%) and three within clade IV (3%). All environmental and colonizing strains clustered in clade III. We also identified known clade-specific resistance mutations in the ERG11 and FKS1 genes. Identification of clade I strains between 2016 and 2018 suggests introductions from South Asia followed by local transmission. SNP analysis characterized most C. auris strains into clade III, the clade first reported from South Africa, but the presence of clades I and IV strains also suggest early introductions from other regions.https://www.tandfonline.com/doi/10.1080/22221751.2021.1944323Candida auriswhole genome sequencingcladesSouth Africasingle nucleotide polymorphisms |
| spellingShingle | Serisha D. Naicker Tsidiso G. Maphanga Nancy A. Chow Mushal Allam Stanford Kwenda Arshad Ismail Nelesh P. Govender Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates Emerging Microbes and Infections Candida auris whole genome sequencing clades South Africa single nucleotide polymorphisms |
| title | Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates |
| title_full | Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates |
| title_fullStr | Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates |
| title_full_unstemmed | Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates |
| title_short | Clade distribution of Candida auris in South Africa using whole genome sequencing of clinical and environmental isolates |
| title_sort | clade distribution of candida auris in south africa using whole genome sequencing of clinical and environmental isolates |
| topic | Candida auris whole genome sequencing clades South Africa single nucleotide polymorphisms |
| url | https://www.tandfonline.com/doi/10.1080/22221751.2021.1944323 |
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