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

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Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. / Sonda, Tolbert; Kumburu, Happiness; van Zwetselaar, Marco; Alifrangis, Michael; Mmbaga, Blandina T; Lund, Ole; Kibiki, Gibson S; Aarestrup, Frank M.

In: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, Vol. 37, No. 10, 2018, p. 1901-1914.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Sonda, T, Kumburu, H, van Zwetselaar, M, Alifrangis, M, Mmbaga, BT, Lund, O, Kibiki, GS & Aarestrup, FM 2018, 'Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania', European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, vol. 37, no. 10, pp. 1901-1914. https://doi.org/10.1007/s10096-018-3324-5

APA

Sonda, T., Kumburu, H., van Zwetselaar, M., Alifrangis, M., Mmbaga, B. T., Lund, O., Kibiki, G. S., & Aarestrup, F. M. (2018). Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 37(10), 1901-1914. https://doi.org/10.1007/s10096-018-3324-5

Vancouver

Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Lund O et al. Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology. 2018;37(10):1901-1914. https://doi.org/10.1007/s10096-018-3324-5

Author

Sonda, Tolbert ; Kumburu, Happiness ; van Zwetselaar, Marco ; Alifrangis, Michael ; Mmbaga, Blandina T ; Lund, Ole ; Kibiki, Gibson S ; Aarestrup, Frank M. / Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania. In: European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology. 2018 ; Vol. 37, No. 10. pp. 1901-1914.

Bibtex

@article{2c3eefa538004e02a9ac0c6622de051c,
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.",
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",
doi = "10.1007/s10096-018-3324-5",
language = "English",
volume = "37",
pages = "1901--1914",
journal = "European Journal of Clinical Microbiology & 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

Y1 - 2018

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.

U2 - 10.1007/s10096-018-3324-5

DO - 10.1007/s10096-018-3324-5

M3 - Journal article

C2 - 30030694

VL - 37

SP - 1901

EP - 1914

JO - European Journal of Clinical Microbiology & Infectious Diseases

JF - European Journal of Clinical Microbiology & Infectious Diseases

SN - 0934-9723

IS - 10

ER -

ID: 203129837