Evidence map›Paper›PMID 38687883›Full record

ArticleThe Journal of infectious diseases2024

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 and 4 more

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Article in The Journal of infectious diseases, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Rito L MikhariCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.ORCID 0000-0002-6608-9162
Susan MeiringDivision of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
Linda de GouveiaCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
Wai Yin ChanSequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
Keith A JolleyDepartment of Biology, University of Oxford, Oxford, United Kingdom.
Daria Van TyneDivision of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.ORCID 0000-0001-7284-0103
Lee H HarrisonMicrobial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA.
Henju MarjukiMeningitis and Vaccine Preventable Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Arshad IsmailSequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.ORCID 0000-0003-4672-5915
Vanessa QuanDivision of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
Cheryl CohenCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
Sibongile WalazaCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
Anne von GottbergCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
Mignon du PlessisCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.

Funding

Southern African-Pittsburgh Public Health Genomic Epidemiology Training Program (SAPPHGenE)D43TW011255 · FIC · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Lee H Harrison, Anne von Gottberg · 2019 to 2026
$1.7M
CDC HHSDepartment of Health and Social CareFIC NIH HHS D43 TW011255National Health Laboratory ServiceNIH HHS D43TW011255US Agency for International DevelopmentWellcome TrustWellcome Trust 218205/Z/19/Z
6 · The paper itself

Abstract

backgroundInvasive 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.

methodsMeningococcal 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.

resultsOf 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.

conclusionsIMD 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.

Indexed as

Anti-Bacterial AgentsGenetic VariationMeningococcal InfectionsMicrobial Sensitivity TestsNeisseria meningitidisSerogroupWhole Genome SequencingAdolescentAdultChildChild, PreschoolFemaleGenome, BacterialHumansInfantMaleAnti-Bacterial Agentsantimicrobial resistanceFetAgenomic surveillanceinvasive meningococcal diseaseMLSTpenicillin-binding proteinPorAwhole-genome sequencing

Identifiers

PMID38687883
PMCPMC11646611

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LicenceCC BY-NC-ND
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.