Evidence map›Paper›PMID 31789384›Full record

ArticleThe Journal of antimicrobial chemotherapy2020

A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa.

Stephanie W Lo, Rebecca A Gladstone, Andries J van Tonder, Mignon Du Plessis, Jennifer E Cornick, Paulina A Hawkins, Shabir A Madhi, Susan A Nzenze, Rama Kandasamy, K L Ravikumar and 19 more

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In one paragraph

Article in The Journal of antimicrobial chemotherapy, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed, 2 pooled it
–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

12 citing papers in PubMed, 2 syntheses or guidelines pooled it.

  1. Pooled it
  2. Pooled it
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  6. Review
  7. Article
  8. Article
  9. Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022
    Review
  10. Review
  11. The Emergence of InvasiveFrontiers in microbiology · 2021
    Article
  12. 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

29 authors.

Stephanie W LoParasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Rebecca A GladstoneParasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Andries J van TonderParasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Mignon Du PlessisCentre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.
Jennifer E CornickMalawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.
Paulina A HawkinsHubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
Shabir A MadhiMedical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
Susan A NzenzeMedical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
Rama KandasamyOxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford OX3 9DU, UK.
K L RavikumarDepartment of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Centre, Bangalore, India.
Naima ElmdaghriDepartment of Microbiology, Faculty of Medicine and Pharmacy, B.P. 9154, Hassan II University of Casablanca, Casablanca, Morocco.
Brenda Kwambana-AdamsNIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.
Samanta Cristine Grassi AlmeidaNational Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz (IAL), São Paulo, Brazil.
Anna SkoczynskaDepartment of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland.
Ekaterina EgorovaLaboratory of Clinical Microbiology and Biotechnology, Moscow Research Institute for Epidemiology and Microbiology, Moscow, Russian Federation.
Leonid TitovLaboratory of Clinical and Experimental Microbiology, The Republican Research and Practical Center for Epidemiology and Microbiology, Minsk, Belarus.
Samir K SahaDepartment of Microbiology, Dhaka Shishu (Children's) Hospital, Child Health Research Foundation, Dhaka, Bangladesh.
Metka ParagiDepartment for Public Health Microbiology, National Laboratory of Health, Environment and Food, Maribor, Slovenia.
Dean B EverettMalawi Liverpool Wellcome Trust Clinical Research Programme, PO Box 30096, Blantyre, Malawi.
Martin AntonioWHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit, The Gambia at The London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
Keith P KlugmanCentre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.
Yuan LiRespiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
Benjamin J MetcalfRespiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
Bernard BeallRespiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
Lesley McGeeRespiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
Robert F BreimanHubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
Stephen D BentleyParasites and Microbes Programme, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Anne von GottbergCentre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa.
Global Pneumococcal Sequencing Consortium

Funding

Wellcome TrustWellcome Trust 098051Wellcome Trust 206194
6 · The paper itself

Abstract

objectivesWe reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions.

methodsWe whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth-death model.

resultsWe identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth-death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage.

conclusionsThe prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era.

Indexed as

Pneumococcal InfectionsStreptococcus pneumoniaeAnti-Bacterial AgentsChildChild, PreschoolDrug Resistance, BacterialHumansMultilocus Sequence TypingPneumococcal VaccinesSerogroupSouth AfricaTetracycline ResistanceAnti-Bacterial AgentsPneumococcal Vaccines

Identifiers

PMID31789384
PMCPMC7021099

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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.