Journal article
Molecular epidemiology of virulence and antimicrobial resistance determinants in Klebsiella pneumoniae from hospitalised patients in Kilimanjaro, Tanzania
Kilimanjaro Christian Medical University College1
Kilimanjaro Christian Medical Centre2
University of Copenhagen3
Department of Bio and Health Informatics, Technical University of Denmark4
Genomic Epidemiology, Department of Bio and Health Informatics, Technical University of Denmark5
Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark6
Technical University of Denmark7
National Food Institute, Technical University of Denmark8
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.
| Language: | English |
|---|---|
| Publisher: | Springer Berlin Heidelberg |
| Year: | 2018 |
| Pages: | 1901-1914 |
| ISSN: | 14354373 and 09349723 |
| Types: | Journal article |
| DOI: | 10.1007/s10096-018-3324-5 |
| ORCIDs: | 0000-0001-5279-5421 , Lund, Ole , Møller Aarestrup, Frank and 0000-0002-3835-3333 |
Adult Aged Aged, 80 and over Anti-Bacterial Agents Biomedical and Life Sciences Biomedicine Child Cross-Sectional Studies Drug Resistance, Bacterial Female Hospitals Humans Internal Medicine Klebsiella Infections Klebsiella pneumoniae Male Medical Microbiology Middle Aged Molecular Epidemiology Phylogeny Plasmids beta-Lactamases beta-lactamase CTX-M-15 beta-lactamase OXA-2 beta-lactamase TEM-1
