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

  • Tolbert SondaEmail author
  • Happiness Kumburu
  • Marco van Zwetselaar
  • Michael Alifrangis
  • Blandina T. Mmbaga
  • Ole Lund
  • Gibson S. Kibiki
  • Frank M. Aarestrup
Original Article


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.


K. pneumoniae Whole-genome sequencing Virulence Antimicrobial resistance Tanzania 



We thank the management of Kilimanjaro Christian Medical Centre and all patients who consented to participate in this study.

Authors’ contributions

TS conceived the initial idea; FA, OL, MA, BTM and GK refined the idea. TS and HK performed the laboratory analyses. TS and MZ analysed the data and prepared the manuscript draft. TS, HK, MZ, FA, OL, MA, BTM and GK read, revised and approved the final manuscript.


This study was supported by DANIDA through Danida Fellowship Centre award number DFC no. 12-007DTU.

Compliance with ethical standards

Ethical approval and participant’s consent

This study was granted ethical approval by the KCMUCo Research Ethics Committee and the National Institute for Medical Research with approval numbers 893 and NIMR/HQ/R.8a/Vol.IX/2080, respectively. A written informed consent was obtained from each participant or from parents or guardians of children before enrolment into the study.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no conflicts of interest.

Availability of Data and Materials

Genome assemblies have been submitted to the European Nucleotide Archive with project accession number PRJEB26616. Other data are available on request to the authors.

Supplementary material

10096_2018_3324_MOESM1_ESM.xls (35 kb)
ESM 1 (XLS 35 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Kilimanjaro Clinical Research InstituteKilimanjaro Christian Medical CentreMoshiTanzania
  2. 2.Kilimanjaro Christian Medical University CollegeMoshiTanzania
  3. 3.Centre for Medical Parasitology, Department of Immunology and MicrobiologyCopenhagen University HospitalCopenhagenDenmark
  4. 4.Centre for Biological Sequence AnalysisTechnical University of DenmarkLyngbyDenmark
  5. 5.East African Health Research CommissionBujumburaBurundi
  6. 6.DTU-Food, Centre for Genomic EpidemiologyTechnical University of DenmarkLyngbyDenmark

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