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Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania

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@article{fe4d74027f3c4c06a01fe289eaa4f6cc,
title = "Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania",
abstract = "This study aimed to use whole-genome sequencing to determine virulence and antimicrobial resistance genes in K. pneumoniae isolated from patients in a tertiary care hospital in Kilimanjaro. K. pneumoniae isolates from patients attending Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced and analysed locally. Sequence analysis was done for identification of virulence and AMR genes. Plasmid and multi-locus sequence typing and capsular or capsular (K) typing were performed and phylogeny was done to ascertain K. pneumoniae relatedness. Stata 13 (College Station, TX, 77845, USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and sequence-predicted resistance. A total of 16 (47.1{\%}) sequence types (STs) and 10 (29.4{\%}) K types were identified in 30 (88.2{\%}) and 17 (50.0{\%}) of all analysed isolates, respectively. K. pneumoniae ST17 were 6 (17.6{\%}). The commonest determinants were blaCTX-M-15 in 16 (47.1{\%}) isolates, blaSHV in 30 (88.2{\%}), blaOXA-1 in 8 (23.5{\%}) and blaTEM-1 in 18 (52.9{\%}) isolates. Resistance genes for aminoglycosides were detected in 21 (61.8{\%}) isolates, fluoroquinolones in 13 (38.2{\%}) and quinolones 34 (100{\%}). Ceftazidime and ceftriaxone showed the strongest agreement between phenotype- and sequence-based resistance results: 93.8{\%}, kappa = 0.87 and p = 0.0002. Yersiniabactin determinant was detected in 12 (35.3{\%}) of K. pneumoniae. The proportion of AMR and virulence determinants detected in K. pneumoniae is alarming. WGS-based diagnostic approach has showed promising potentials in clinical microbiology, hospital outbreak source tracing virulence and AMR detection at KCMC.",
keywords = "Adult, Aged, Aged, 80 and over, Anti-Bacterial Agents/pharmacology, Child, Cross-Sectional Studies, Drug Resistance, Bacterial/drug effects, Female, Hospitals, Humans, Klebsiella Infections/drug therapy, Klebsiella pneumoniae/drug effects, Male, Middle Aged, Molecular Epidemiology, Phylogeny, Plasmids/genetics, Tanzania, Virulence/genetics, beta-Lactamases/genetics",
author = "Tolbert Sonda and Happiness Kumburu and {van Zwetselaar}, Marco and Michael Alifrangis and Mmbaga, {Blandina T} and Ole Lund and Kibiki, {Gibson S} and Aarestrup, {Frank M}",
year = "2018",
month = "10",
doi = "10.1007/s10096-018-3324-5",
language = "English",
volume = "37",
pages = "1901--1914",
journal = "European Journal of Clinical Microbiology and Infectious Diseases",
issn = "0934-9723",
publisher = "Springer",
number = "10",

}

RIS

TY - JOUR

T1 - Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania

AU - Sonda, Tolbert

AU - Kumburu, Happiness

AU - van Zwetselaar, Marco

AU - Alifrangis, Michael

AU - Mmbaga, Blandina T

AU - Lund, Ole

AU - Kibiki, Gibson S

AU - Aarestrup, Frank M

PY - 2018/10

Y1 - 2018/10

N2 - This study aimed to use whole-genome sequencing to determine virulence and antimicrobial resistance genes in K. pneumoniae isolated from patients in a tertiary care hospital in Kilimanjaro. K. pneumoniae isolates from patients attending Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced and analysed locally. Sequence analysis was done for identification of virulence and AMR genes. Plasmid and multi-locus sequence typing and capsular or capsular (K) typing were performed and phylogeny was done to ascertain K. pneumoniae relatedness. Stata 13 (College Station, TX, 77845, USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and sequence-predicted resistance. A total of 16 (47.1%) sequence types (STs) and 10 (29.4%) K types were identified in 30 (88.2%) and 17 (50.0%) of all analysed isolates, respectively. K. pneumoniae ST17 were 6 (17.6%). The commonest determinants were blaCTX-M-15 in 16 (47.1%) isolates, blaSHV in 30 (88.2%), blaOXA-1 in 8 (23.5%) and blaTEM-1 in 18 (52.9%) isolates. Resistance genes for aminoglycosides were detected in 21 (61.8%) isolates, fluoroquinolones in 13 (38.2%) and quinolones 34 (100%). Ceftazidime and ceftriaxone showed the strongest agreement between phenotype- and sequence-based resistance results: 93.8%, kappa = 0.87 and p = 0.0002. Yersiniabactin determinant was detected in 12 (35.3%) of K. pneumoniae. The proportion of AMR and virulence determinants detected in K. pneumoniae is alarming. WGS-based diagnostic approach has showed promising potentials in clinical microbiology, hospital outbreak source tracing virulence and AMR detection at KCMC.

AB - This study aimed to use whole-genome sequencing to determine virulence and antimicrobial resistance genes in K. pneumoniae isolated from patients in a tertiary care hospital in Kilimanjaro. K. pneumoniae isolates from patients attending Kilimanjaro Christian Medical Centre between August 2013 and August 2015 were fully genome-sequenced and analysed locally. Sequence analysis was done for identification of virulence and AMR genes. Plasmid and multi-locus sequence typing and capsular or capsular (K) typing were performed and phylogeny was done to ascertain K. pneumoniae relatedness. Stata 13 (College Station, TX, 77845, USA) was used to determine Cohen's kappa coefficient of agreement between the phenotypically tested and sequence-predicted resistance. A total of 16 (47.1%) sequence types (STs) and 10 (29.4%) K types were identified in 30 (88.2%) and 17 (50.0%) of all analysed isolates, respectively. K. pneumoniae ST17 were 6 (17.6%). The commonest determinants were blaCTX-M-15 in 16 (47.1%) isolates, blaSHV in 30 (88.2%), blaOXA-1 in 8 (23.5%) and blaTEM-1 in 18 (52.9%) isolates. Resistance genes for aminoglycosides were detected in 21 (61.8%) isolates, fluoroquinolones in 13 (38.2%) and quinolones 34 (100%). Ceftazidime and ceftriaxone showed the strongest agreement between phenotype- and sequence-based resistance results: 93.8%, kappa = 0.87 and p = 0.0002. Yersiniabactin determinant was detected in 12 (35.3%) of K. pneumoniae. The proportion of AMR and virulence determinants detected in K. pneumoniae is alarming. WGS-based diagnostic approach has showed promising potentials in clinical microbiology, hospital outbreak source tracing virulence and AMR detection at KCMC.

KW - Adult

KW - Aged

KW - Aged, 80 and over

KW - Anti-Bacterial Agents/pharmacology

KW - Child

KW - Cross-Sectional Studies

KW - Drug Resistance, Bacterial/drug effects

KW - Female

KW - Hospitals

KW - Humans

KW - Klebsiella Infections/drug therapy

KW - Klebsiella pneumoniae/drug effects

KW - Male

KW - Middle Aged

KW - Molecular Epidemiology

KW - Phylogeny

KW - Plasmids/genetics

KW - Tanzania

KW - Virulence/genetics

KW - beta-Lactamases/genetics

U2 - 10.1007/s10096-018-3324-5

DO - 10.1007/s10096-018-3324-5

M3 - Journal article

VL - 37

SP - 1901

EP - 1914

JO - European Journal of Clinical Microbiology and Infectious Diseases

JF - European Journal of Clinical Microbiology and Infectious Diseases

SN - 0934-9723

IS - 10

ER -

ID: 56461873