Affiliations 

  • 1 Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia
  • 2 National Public Health Laboratory, Disease Control Division, Ministry of Health, Malaysia
  • 3 Disease Control Division, Ministry of Health, Malaysia
  • 4 Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
  • 5 Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA Selangor (UiTM), Puncak Alam, Selangor, Malaysia
  • 6 Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA Selangor (UiTM), Puncak Alam, Selangor, Malaysia; Faculty of Sports Science and Recreation, Universiti Teknologi MARA Selangor (UiTM), Shah Alam, Selangor, Malaysia
  • 7 Division of Genetics and Molecular Biology, Institute of Biological Sciences, University of Malaya, Kuala Lumpur, Malaysia. Electronic address: kokgan@um.edu.my
Infect Genet Evol, 2017 Oct;54:263-270.
PMID: 28711373 DOI: 10.1016/j.meegid.2017.07.015

Abstract

In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile. In the context of CRISPR-Cas system, which confers adaptive immunity against re-invading DNA, 73 out of 86 spacer sequences were found to be unique to Malaysian strains which harboured only type-II-C and/or type-I-E-a systems. A total of 48 tox genes which code for the diphtheria toxin were retrieved from the 74 genomes and with the exception of one truncated gene, only nucleotide substitutions were detected when compared to the tox gene sequence of PW8. More than half were synonymous substitution and only two were nonsynonymous substitutions whereby H24Y was predicted to have a damaging effect on the protein function whilst T262V was predicted to be tolerated. Both toxigenic and non-toxigenic toxin-gene bearing strains have been isolated in Malaysia but the repeated isolation of toxigenic strains with the same MLST profile suggests the possibility of some of these strains may be circulating in the population. Hence, efforts to increase herd immunity should be continued and supported by an effective monitoring and surveillance system to track, manage and control outbreak of cases.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.