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
Tolbert SondaFrank M Aarestrup

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 cef...Continue Reading

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Citations

Aug 15, 2019·Implementation Science : IS·Nina Van GoethemAnnie Robert
Aug 12, 2020·The Journal of Antimicrobial Chemotherapy·Valeria BortolaiaFrank M Aarestrup
Dec 25, 2021·Journal of the Pediatric Infectious Diseases Society·Alexander L Greninger, Danielle M Zerr

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Datasets Mentioned

BETA
PRJEB26616

Methods Mentioned

BETA
Assay
PCR

Software Mentioned

FastQC
PlasmidFinder
ResFinder
VirulenceFinder
pMLST
QUAST
Stata
SPAdes
MLST

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