Evidence map›Paper›PMID 41668110›Full record

ArticleTropical medicine and health2026

Genomic analysis of the genetic background underlying Streptococcus pneumoniae beta-lactam nonsusceptibility in central Vietnam: increased beta-lactam nonsusceptibility and dynamics of the pbp2x gene.

Hiroshi Fujii, Mitsuhiko Sato, Hien Anh Thi Nguyen, Huong Thi Thu Vu, Satoshi Kakiuchi, Bhim Gopal Dhoubhadel, Shota Nakamura, Daisuke Motooka, Yoshitoshi Ogura, Satoshi Nakano and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Tropical medicine and health, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

17 authors.

Hiroshi FujiiDepartment of Infection Research, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8102, Japan.
Mitsuhiko SatoDepartment of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
Hien Anh Thi NguyenDepartment of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, 100000, Vietnam.
Huong Thi Thu VuDepartment of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, 100000, Vietnam.
Satoshi KakiuchiDepartment of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.
Bhim Gopal DhoubhadelSchool of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, 852-8523, Japan.
Shota NakamuraDepartment of Infection Metagenomics, Bioinformatics Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan.
Daisuke MotookaDepartment of Infection Metagenomics, Bioinformatics Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan.
Yoshitoshi OguraDepartment of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
Satoshi NakanoAntimicrobial Resistance Research Center, Japan Institute for Health Security, National Institute of Infectious Diseases, Tokyo, 162-0052, Japan.
Christopher M ParrySchool of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, 852-8523, Japan.
Konosuke MorimotoDepartment of Infection Research, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8102, Japan.
Lay-Myint YoshidaSchool of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, 852-8523, Japan.
Dang Duc AnhDepartment of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, 100000, Vietnam.
Tetsuya HayashiDepartment of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
Tetsuya IidaDepartment of Infection Metagenomics, Bioinformatics Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan.
Koya AriyoshiDepartment of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. kari@nagasaki-u.ac.jp.

Funding

Institute of Tropical Medicine, Nagasaki University 2014-Ippan-10, 2015-Ippan-25
6 · The paper itself

Abstract

backgroundWe previously reported alarmingly high carriage rates of Streptococcus pneumoniae (SP) serotype 19F and serogroup 6 isolates, which were not susceptible to multiple beta-lactams among children under five years of age in Vietnam. Multilocus sequence typing analysis revealed the predominance of two major lineages, ST320 and ST13223, among serotype 19F and serogroup 6 isolates, respectively. Investigating the association between nonsusceptible genotypes and clinical outcomes could help optimize patient care or lead to the development of new diagnostic tests.

methodsWe performed WGS on SP isolates randomly selected from the two major lineages and their related strains. FASTQ quality control and de novo assembly were performed using CLC Genomics Workbench ver. 7.5.1. Draft genome sequences were annotated using DFAST (DDBJ Fast Annotation and Submission Tool), which revealed the serogroups/serotypes and the sequences of the three major penicillin-binding protein genes and the sequence types. Draft sequences were aligned using MUMmer ver. 3.23, and putative recombination events and phylogenetic relationships excluding recombination regions were identified using Gubbins ver. 2.4.1. Finally, the association between a detected nonsusceptible genotype and the duration of hospital stay was evaluated in patients with acute respiratory infection.

resultsWGS analysis (serotype 19F/ST320, n = 22; serogroup 6/ST13223, n = 13; and isolates closely related to ST13223, n = 4) revealed substantial differences in genomic diversity and antimicrobial susceptibility between serogroup 6/ST13223 and serotype 19F/ST320 isolates, particularly the recombination-prone nature of serogroup 6/ST13223. Among the 23 recombination events observed in serogroup 6/ST13223, only those spanning the pbp2x region (15.5 kb and 6.4 kb) were associated with high MICs for multiple beta-lactams. A subset of ST13223 isolates and all ST320 isolates carried the identical pbp2x allele 16, which was significantly associated with a lack of susceptibility to the combination of penicillin, cefotaxime, and meropenem (p < 0.0001; odds ratio 11.5; 95% confidence interval [CI] 3.35-39.3). No significant association was demonstrated between the presence of this pbp2x allele and prolonged hospitalization (p = 0.6123).

conclusionsWe revealed that the widespread nonsusceptibility to multiple beta-lactams among SP isolates circulating in central Vietnam was primarily driven by the dynamics of the pbp2x gene. However, the nonsusceptible pbp2x allele had little effect on clinical outcome.

Indexed as

Antimicrobial nonsusceptibilityMolecular epidemiologyPenicillin-binding proteinPneumococcal conjugate vaccineStreptococcus pneumoniaeWhole-genome sequencing

Identifiers

PMID41668110
PMCPMC12961782

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.