Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants

Background: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts...

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Main Authors: Rendani I. Manenzhe, Felix S. Dube, Meredith Wright, Katie Lennard, Stephanie Mounaud, Stephanie W. Lo, Heather J. Zar, William C. Nierman, Mark P. Nicol, Clinton Moodley
Format: Article
Language:English
Published: Frontiers Media S.A. 2020-09-01
Series:Frontiers in Public Health
Subjects:
Online Access:https://www.frontiersin.org/article/10.3389/fpubh.2020.543898/full
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language English
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author Rendani I. Manenzhe
Felix S. Dube
Felix S. Dube
Meredith Wright
Katie Lennard
Stephanie Mounaud
Stephanie W. Lo
Heather J. Zar
William C. Nierman
Mark P. Nicol
Mark P. Nicol
Clinton Moodley
Clinton Moodley
spellingShingle Rendani I. Manenzhe
Felix S. Dube
Felix S. Dube
Meredith Wright
Katie Lennard
Stephanie Mounaud
Stephanie W. Lo
Heather J. Zar
William C. Nierman
Mark P. Nicol
Mark P. Nicol
Clinton Moodley
Clinton Moodley
Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants
Frontiers in Public Health
nasopharyngeal
Streptococcus pneumoniae
pneumococcal conjugate vaccine
serotypes
shotgun metagenomic sequencing
resistance determinants
author_facet Rendani I. Manenzhe
Felix S. Dube
Felix S. Dube
Meredith Wright
Katie Lennard
Stephanie Mounaud
Stephanie W. Lo
Heather J. Zar
William C. Nierman
Mark P. Nicol
Mark P. Nicol
Clinton Moodley
Clinton Moodley
author_sort Rendani I. Manenzhe
title Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants
title_short Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants
title_full Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants
title_fullStr Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants
title_full_unstemmed Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African Infants
title_sort characterization of pneumococcal colonization dynamics and antimicrobial resistance using shotgun metagenomic sequencing in intensively sampled south african infants
publisher Frontiers Media S.A.
series Frontiers in Public Health
issn 2296-2565
publishDate 2020-09-01
description Background: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal (NP) samples at 2-weekly intervals from birth through the first year of life from 137 infants. As a proof of concept, 196 NP samples were retrieved from a subset of 23 infants to explore strain-level pneumococcal colonization patterns and associated antimicrobial-resistance determinants. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of pneumococcal and non-pneumococcal bacterial reads. Pneumococcal contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. In silico pneumococcal capsular and multilocus sequence typing were performed.Results: Of the 196 samples sequenced, 174 had corresponding positive cultures for pneumococci, of which, 152 were assigned an in silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of the samples. Twenty-two different pneumococcal serotypes were identified, with 15B/15C and 16F being the most common non-PCV13 serotypes, while 23F and 19A were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including four novel STs were identified in silico. Mutations in the folA and folP genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci, as well as in the pbp1a and pbp2x genes, in penicillin non-susceptible ST705215B/15C isolates.Conclusions: Metagenomic sequencing of NP samples is a valuable culture-independent technique for a detailed evaluation of the pneumococcal component and resistome of the NP microbiome. This method allowed for the detection of novel STs, as well as co-colonization, with a predominance of non-PCV13 serotypes in this cohort. Forty-eight resistance genes, as well as mutations associated with resistance were detected, but the correlation with phenotypic non-susceptibility was lower than expected.
topic nasopharyngeal
Streptococcus pneumoniae
pneumococcal conjugate vaccine
serotypes
shotgun metagenomic sequencing
resistance determinants
url https://www.frontiersin.org/article/10.3389/fpubh.2020.543898/full
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spelling doaj-6958a484f2fd49ca9af8fe768d92e0f62020-11-25T03:47:02ZengFrontiers Media S.A.Frontiers in Public Health2296-25652020-09-01810.3389/fpubh.2020.543898543898Characterization of Pneumococcal Colonization Dynamics and Antimicrobial Resistance Using Shotgun Metagenomic Sequencing in Intensively Sampled South African InfantsRendani I. Manenzhe0Felix S. Dube1Felix S. Dube2Meredith Wright3Katie Lennard4Stephanie Mounaud5Stephanie W. Lo6Heather J. Zar7William C. Nierman8Mark P. Nicol9Mark P. Nicol10Clinton Moodley11Clinton Moodley12Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South AfricaDivision of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South AfricaDepartment of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South AfricaJ. Craig Venter Institute, Rockville, MD, United StatesDivision of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South AfricaJ. Craig Venter Institute, Rockville, MD, United StatesParasites and Microbes Program, The Wellcome Sanger Institute, Cambridge, United KingdomDepartment of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and South African - Medical Research Council Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South AfricaJ. Craig Venter Institute, Rockville, MD, United StatesDivision of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South AfricaDivision of Infection and Immunity, University of Western Australia, Perth, WA, AustraliaDivision of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South AfricaNational Health Laboratory Service, Groote Schuur Hospital, Cape Town, South AfricaBackground: There remains a significant proportion of deaths due to pneumococcal pneumonia in infants from low- and middle-income countries despite the marginal global declines recorded in the past decade. Monitoring changes in pneumococcal carriage is key to understanding vaccination-induced shifts in the ecology of carriage, patterns of antimicrobial resistance, and impact on health. We longitudinally investigated pneumococcal carriage dynamics in PCV-13 vaccinated infants by collecting nasopharyngeal (NP) samples at 2-weekly intervals from birth through the first year of life from 137 infants. As a proof of concept, 196 NP samples were retrieved from a subset of 23 infants to explore strain-level pneumococcal colonization patterns and associated antimicrobial-resistance determinants. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of pneumococcal and non-pneumococcal bacterial reads. Pneumococcal contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. In silico pneumococcal capsular and multilocus sequence typing were performed.Results: Of the 196 samples sequenced, 174 had corresponding positive cultures for pneumococci, of which, 152 were assigned an in silico serotype. Metagenomic sequencing detected a single pneumococcal serotype in 85% (129/152), and co-colonization in 15% (23/152) of the samples. Twenty-two different pneumococcal serotypes were identified, with 15B/15C and 16F being the most common non-PCV13 serotypes, while 23F and 19A were the most common PCV13 serotypes. Twenty-six different sequence types (STs), including four novel STs were identified in silico. Mutations in the folA and folP genes, associated with cotrimoxazole resistance, were detected in 89% (87/98) of cotrimoxazole-non-susceptible pneumococci, as well as in the pbp1a and pbp2x genes, in penicillin non-susceptible ST705215B/15C isolates.Conclusions: Metagenomic sequencing of NP samples is a valuable culture-independent technique for a detailed evaluation of the pneumococcal component and resistome of the NP microbiome. This method allowed for the detection of novel STs, as well as co-colonization, with a predominance of non-PCV13 serotypes in this cohort. Forty-eight resistance genes, as well as mutations associated with resistance were detected, but the correlation with phenotypic non-susceptibility was lower than expected.https://www.frontiersin.org/article/10.3389/fpubh.2020.543898/fullnasopharyngealStreptococcus pneumoniaepneumococcal conjugate vaccineserotypesshotgun metagenomic sequencingresistance determinants