Whole-Genome Sequence Analysis of Streptococcus pneumoniae Strains That Cause Hospital-Acquired Pneumonia Infections

Chang, Bin; Morita, Masatomo; Lee, Ken-ichi; Ohnishi, Makoto

doi:10.1128/jcm.01822-17

Cited by 22 publications

(19 citation statements)

References 39 publications

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“…In Taiwan, while ST338 and ST166 accounted for the majority (74.5%, 35/47) and minority (6.4%, 3/47) of serotype 23A isolates, respectively, during 2012-2014 in one hospital (Su et al, 2015), we observed an increase of a serotype 23A-ST166 MDR meropenem-resistant clone in patients from different hospitals during 2016-2018. ST166 has been associated with serotype 9V isolates in Taiwan, Japan, and Korea before 2014 (Hsieh et al, 2009;Su et al, 2015;Chang et al, 2018;Yun et al, 2018), and in serotype 11A isolates from Korea and Japan more recently (Chang et al, 2018;Kim et al, 2019). However, only one isolate from Japan and two ceftriaxone-nonsusceptible isolates from Korea with the serotype 23A-ST166 combination have been described so far but their meropenem susceptibility is unknown (Chang et al, 2018;Choi et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

“…ST166 has been associated with serotype 9V isolates in Taiwan, Japan, and Korea before 2014 (Hsieh et al, 2009;Su et al, 2015;Chang et al, 2018;Yun et al, 2018), and in serotype 11A isolates from Korea and Japan more recently (Chang et al, 2018;Kim et al, 2019). However, only one isolate from Japan and two ceftriaxone-nonsusceptible isolates from Korea with the serotype 23A-ST166 combination have been described so far but their meropenem susceptibility is unknown (Chang et al, 2018;Choi et al, 2019). Together, these observations suggested emergence of MDR meropenem-non-susceptible serotype 15A-ST63 isolates in different countries, and possible capsular switching of ST166 to serotype 23A isolates followed by local spread of MDR meropenem-resistant serotype 23A-ST166 clone in Taiwan, both of which raise concern since neither serotype is included in the current PCV13.…”

Section: Discussionmentioning

confidence: 99%

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Serotype Distribution and Antimicrobial Susceptibility of Streptococcus pneumoniae in Pre- and Post- PCV7/13 Eras, Taiwan, 2002–2018

Lai

Huang

et al. 2020

Front. Microbiol.

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In Taiwan, the 7-valent pneumococcal conjugate vaccine (PCV7) was introduced in 2006 and a PCV13 national childhood catchup program was implemented in 2013. To delineate the trend of serotype distribution and antimicrobial susceptibility following vaccination programs, we investigated a total of 1845 Streptococcus pneumoniae isolates collected biennially between 2002 and 2018 over a 3-month period from 25 hospitals. The number of isolates collected over the years decreased significantly in all age groups, from a total of 320 isolates in 2002 (pre-PCV), to 196 in 2010 (post-PCV7/pre-PCV13), to 89 in 2018 (post-PCV13). Overall, PCV7/PCV13 serotypes comprised 66.9%/76.3%, 53.1%/78.1%, and 15.7%/31.5% of isolates in 2002, 2010, and 2018, respectively. The leading serotypes in the pre-PCV era were 23F, 19F, 6B, and 14, while serotype 19A predominated in the post-PCV7/pre-PCV13 era, but nonvaccine serotypes (NVT) 15A (18.0%) and 23A (15.7%) surpassed 19A (10.1%) to become the top two leading serotypes in 2018. All the major serotypes, including the emergent serotypes 15A and 23A, were multidrug-resistant with high rates of nonsusceptibility to β-lactam (except serotype 3) and several non-β-lactam agents. PFGE and MLST revealed that while meropenem-susceptible serotype 15A-ST3058 isolates and a serotype 23A-ST338 clone existed in earlier years, rise and spread of meropenemnon-susceptible serotype 15A-ST63 and serotype 23A-ST166 clones occurred in recent years. We conclude that successive implementation of PCVs has led to a marked decrease in pneumococcal isolate burden, but the replacement by meropenem-nonsusceptible NVT 15A and 23A highlights the need for continued local surveillance to track pneumococcal evolution in each region to help vaccine polyvalency decisions.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Serotype Distribution and Antimicrobial Susceptibility of Streptococcus pneumoniae in Pre- and Post- PCV7/13 Eras, Taiwan, 2002–2018

Lai

Huang

et al. 2020

Front. Microbiol.

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“…Indeed, WGS has increased power to establish the evolutionary relationships between close strains across the species [9]. Multiple studies have used the high-throughput WGS to investigate PCV impact and clustering pneumococcal populations into groups using genomic variation that reflect a recent evolutionary history [10][11][12][13]. The objectives of this study, as part of the Pneumococcal African Genome project (PAGe), were to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca, compared to isolates from other African countries (Egypt, Ethiopia, Ghana, Malawi, Mozambique, Niger, Nigeria, South Africa and The Gambia), and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype.…”

Section: Introductionmentioning

confidence: 99%

Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco

et al. 2021

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Background Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype. Results The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa. Conclusions The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan invasive isolates.

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“…Indeed, the WGS has increased power to establish the evolutionary relationships between close strains across the species [9]. Multiple studies have used the high-throughput WGS to investigate PCV impact and clustering pneumococcal populations into groups using genomic variation that re ect a recent evolutionary history [10][11][12][13]. The objectives of this study, as part of the Pneumococcal African Genome project (PAGe), were to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca, compared to isolates from other African countries (Egypt, Ethiopia, Ghana, Malawi, Mozambique, Niger, Nigeria, South Africa and The Gambia), and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype.…”

Section: Introductionmentioning

confidence: 99%

Whole Genomic Comparative Analysis of Streptococcus Pneumoniae Serotype 1 Isolates Causing Invasive and Non-Invasive Infections Among Children Under 5 years in Casablanca, Morocco

Nzoyikorera

Diawara

Fresia

et al. 2020

Preprint

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Background: Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype.Results: The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa.Conclusions: The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan isolates.

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Whole-Genome Sequence Analysis of Streptococcus pneumoniae Strains That Cause Hospital-Acquired Pneumonia Infections

Cited by 22 publications

References 39 publications

Serotype Distribution and Antimicrobial Susceptibility of Streptococcus pneumoniae in Pre- and Post- PCV7/13 Eras, Taiwan, 2002–2018

Serotype Distribution and Antimicrobial Susceptibility of Streptococcus pneumoniae in Pre- and Post- PCV7/13 Eras, Taiwan, 2002–2018

Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco

Whole Genomic Comparative Analysis of Streptococcus Pneumoniae Serotype 1 Isolates Causing Invasive and Non-Invasive Infections Among Children Under 5 years in Casablanca, Morocco

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