Genomic diversity and antimicrobial susceptibility of invasive Neisseria meningitidis in South Africa, 2016-2021

Rito L Mikhari; Susan Meiring; Linda de Gouveia; Wai Yin Chan; Keith A Jolley; Daria Van Tyne; Lee H Harrison; Henju Marjuki; Arshad Ismail; Vanessa Quan; Cheryl Cohen; Sibongile Walaza; Anne von Gottberg; Mignon du Plessis

doi:10.1093/infdis/jiae225

Genomic diversity and antimicrobial susceptibility of invasive Neisseria meningitidis in South Africa, 2016-2021

J Infect Dis. 2024 Apr 30:jiae225. doi: 10.1093/infdis/jiae225. Online ahead of print.

Authors

Rito L Mikhari^{1

2}, Susan Meiring³, Linda de Gouveia¹, Wai Yin Chan^{4

5

6}, Keith A Jolley⁷, Daria Van Tyne⁸, Lee H Harrison⁹, Henju Marjuki¹⁰, Arshad Ismail^{4

11

12}, Vanessa Quan³, Cheryl Cohen^{1

13}, Sibongile Walaza^{1

13}, Anne von Gottberg^{1

2}, Mignon du Plessis^{1

2}

Affiliations

¹ Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.
² School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
³ Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa.
⁴ Sequencing Core Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
⁵ Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
⁶ Right to Care, Pretoria, South Africa.
⁷ Department of Biology, University of Oxford, Oxford, United Kingdom.
⁸ Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States.
⁹ Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States.
¹⁰ Meningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States.
¹¹ Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou, South Africa.
¹² Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa.
¹³ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.

PMID: 38687883
DOI: 10.1093/infdis/jiae225

Abstract

Background: Invasive meningococcal isolates in South Africa have in previous years (<2008) been characterized by serogroup B, C, W and Y lineages over time, with penicillin intermediate resistance (peni) at 6%. We describe the population structure and genomic markers of peni among invasive meningococcal isolates in South Africa, 2016-2021.

Methods: Meningococcal isolates were collected through national, laboratory-based invasive meningococcal disease (IMD) surveillance. Phenotypic antimicrobial susceptibility testing and whole-genome sequencing were performed, and the mechanism of reduced penicillin susceptibility was assessed in silico.

Results: Of 585 IMD cases reported during the study period, culture and PCR-based capsular group was determined for 477/585 (82%); and 241/477 (51%) were sequenced. Predominant serogroups included NmB (210/477; 44%), NmW (116/477; 24%), NmY (96/477; 20%) and NmC (48/477; 10%). Predominant clonal complexes (CC) were CC41/44 in NmB (27/113; 24%), CC11 in NmW (46/56; 82%), CC167 in NmY (23/44; 53%), and CC865 in NmC (9/24; 38%). Peni was detected in 16% (42/262) of isolates, and was due to the presence of a penA mosaic, with the majority harboring penA7, penA9 or penA14.

Conclusion: IMD lineages circulating in South Africa were consistent with those circulating prior to 2008, however peni was higher than previously reported, and occurred in a variety of lineages.

Keywords: FetA; MLST; PorA; antimicrobial resistance; genomic surveillance; invasive meningococcal disease; penicillin-binding protein; whole-genome sequencing.