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Multiphasic strain differentiation of atypical mycobacteria from elephant trunk wash


Kok-Gan Chan and Mun Fai Loke and Bee Lee Ong and Yan Ling Wong and Kar Wai Hong and Kian Hin Tan and Sargit Kaur and Hien Fuh Ng and MFA Abdul Razak and Yun Fong Ngeow (2015) Multiphasic strain differentiation of atypical mycobacteria from elephant trunk wash. PeerJ. ISSN 2167-8359


Background. Two non-tuberculous mycobacterial strains, UM_3 and UM_11, were isolated from the trunk wash of captive elephants in Malaysia. As they appeared to be identical phenotypes, they were investigated further by conventional and whole genome sequence-based methods of strain differentiation.

Methods. Multiphasic investigations on the isolates included species identification with hsp65 PCR-sequencing, conventional biochemical tests, rapid biochemical profiling using API strips and the Biolog Phenotype Microarray analysis, protein profiling with liquid chromatography-mass spectrometry, repetitive sequence-based PCR typing and whole genome sequencing followed by phylogenomic analyses.

Results. The isolates were shown to be possibly novel slow-growing schotochromogens with highly similar biological and genotypic characteristics. Both strains have a genome size of 5.2 Mbp, G+C content of 68.8%, one rRNA operon and 52 tRNAs each. They qualified for classification into the same species with their average nucleotide identity of 99.98% and tetranucleotide correlation coefficient of 0.99999. At the subspecies level, both strains showed 98.8% band similarity in the Diversilab automated repetitive sequence-based PCR typing system, 96.2% similarity in protein profiles obtained by liquid chromatography mass spectrometry, and a genomic distance that is close to zero in the phylogenomic tree constructed with conserved orthologs. Detailed epidemiological tracking revealed that the elephants shared a common habitat eight years apart, thus, strengthening the possibility of a clonal relationship between the two strains.

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Additional Metadata

Item Type: Non-Indexed Article
Collection Type: Institution
Date: 2015
Journal or Publication Title: PeerJ
ISSN: 2167-8359
Uncontrolled Keywords: Biolog phenotyping; Genomic analysis; Genotyping; Mass spectrometry; Mycobacterium; Rep-PCR
Faculty/Centre/Office: Faculty of Veterinary Medicine
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