Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome

Autor: T Goolam Mahomed, RPH Peters, GHJ Pretorius, A Goolam Mahomed, V Ueckermann, MM Kock, MM Ehlers

Publikováno v: BMC Microbiology, Vol 21, Iss 1, Pp 1-13 (2021)

Abstract Background Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagen

Externí odkaz: https://doaj.org/article/5ba1048412f24edb977237c64fb86502

Epidemiology and antimicrobial resistance profiles of pathogenic Escherichia coli from commercial swine and poultry abattoirs and farms in South Africa: A One Health approach.

Autor: Ogundare ST; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa. Electronic address: stogundare@gmail.com., Fasina FO; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa; Food and Agriculture Organisation of the United Nations, FAO Headquarters, Rome, Italy., Makumbi JP; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa., van der Zel GA; Gauteng Department of Agriculture, Rural Development and Environment, Pretoria, South Africa., Geertsma PF; Gauteng Department of Agriculture, Rural Development and Environment, Pretoria, South Africa., Kock MM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Department of Medical Microbiology, National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa., Smith AM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa., Ehlers MM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa; Department of Medical Microbiology, National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa.

Publikováno v: The Science of the total environment [Sci Total Environ] 2024 Nov 15; Vol. 951, pp. 175705. Date of Electronic Publication: 2024 Aug 22.

Klebsiella pneumoniae with carbapenemases: high prevalence of sequence type 307 with bla OXA181 in South African community hospitals.

Autor: Salvador-Oke KT; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa., Pitout JDD; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.; Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada.; Alberta Precision Laboratories, Calgary, Canada., Peirano G; Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada.; Alberta Precision Laboratories, Calgary, Canada., Strydom KA; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa.; Ampath National Reference Laboratory, Centurion, Pretoria, South Africa., Kingsburgh C; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa.; Ampath National Reference Laboratory, Centurion, Pretoria, South Africa., Ehlers MM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa., Kock MM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa. marleen.kock@up.ac.za.; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa. marleen.kock@up.ac.za.

Publikováno v: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology [Eur J Clin Microbiol Infect Dis] 2024 Nov; Vol. 43 (11), pp. 2239-2244. Date of Electronic Publication: 2024 Sep 17.

Detection of the epidemic Pseudomonas aeruginosa AUST-03 (ST242) strain in people with cystic fibrosis in South Africa.

Autor: Hamiwe T; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa., White DA; Department of Paediatric Pulmonology, Charlotte Maxeke Johannesburg Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa., Kwenda S; Division of the National Health Laboratory Service, Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, South Africa., Ismail A; Division of the National Health Laboratory Service, Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, South Africa.; Department of Biochemistry and Microbiology, University of Venda, Thohoyandou, South Africa.; Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa., Klugman S; Department of Paediatric Pulmonology, Charlotte Maxeke Johannesburg Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa., Van Bruwaene L; Department of Paediatric Pulmonology, Steve Biko Academic Hospital/University of Pretoria, Pretoria, South Africa.; Department of Pediatrics, Centre Hospitalier Universitaire Saint-Pierre Hospital, Brussels, Belgium., Goga A; Department of Paediatric Pulmonology, Steve Biko Academic Hospital/University of Pretoria, Pretoria, South Africa.; South African Medical Research Council, Pretoria, South Africa., Kock MM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.; Department of Microbiology, National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa., Smith AM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.; Division of the National Health Laboratory Service, Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa., Ehlers MM; Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.; Department of Microbiology, National Health Laboratory Service, Tshwane Academic Division, Pretoria, South Africa.

Publikováno v: Pediatric pulmonology [Pediatr Pulmonol] 2024 Aug 07. Date of Electronic Publication: 2024 Aug 07.

Genomic epidemiology and molecular characteristics of bla NDM-1 -positive carbapenem-resistant Pseudomonas aeruginosa belonging to international high-risk clone ST773 in the Gauteng region, South Africa.

Autor: Jung H; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa., Pitout JDD; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.; Division of Microbiology, Alberta Public Laboratories, Cummings School of Medicine, University of Calgary, Calgary, Canada., Matsumura Y; Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan., Strydom KA; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.; Ampath National Reference Laboratory, Centurion, South Africa., Kingsburgh C; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.; Ampath National Reference Laboratory, Centurion, South Africa., Ehlers MM; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service (NHLS), Pretoria, South Africa., Kock MM; Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. marleen.kock@up.ac.za.; Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service (NHLS), Pretoria, South Africa. marleen.kock@up.ac.za.

Publikováno v: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology [Eur J Clin Microbiol Infect Dis] 2024 Apr; Vol. 43 (4), pp. 627-640. Date of Electronic Publication: 2024 Jan 24.