title: Multiphasic strain differentiation of atypical mycobacteria from elephant trunk wash.
abstract: 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.
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia.
authors.forename: Kok-Gan
authors.initials: KG
authors.lastname: Chan
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia.
authors.forename: Mun Fai
authors.initials: MF
authors.lastname: Loke
authors.affiliation: Faculty of Veterinary Medicine, Universiti Malaysia Kelantan , Kelantan , Malaysia.
authors.forename: Bee Lee
authors.initials: BL
authors.lastname: Ong
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia.
authors.forename: Yan Ling
authors.initials: YL
authors.lastname: Wong
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia.
authors.forename: Kar Wai
authors.initials: KW
authors.lastname: Hong
authors.affiliation: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya , Kuala Lumpur , Malaysia.
authors.forename: Kian Hin
authors.initials: KH
authors.lastname: Tan
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia.
authors.forename: Sargit
authors.initials: S
authors.lastname: Kaur
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia.
authors.forename: Hien Fuh
authors.initials: HF
authors.lastname: Ng
authors.affiliation: Department of Wildlife and National Parks, Peninsular Malaysia , Kuala Lumpur , Malaysia.
authors.forename: Mfa
authors.initials: M
authors.lastname: Abdul Razak
authors.affiliation: Department of Medical Microbiology, Faculty of Medicine, University of Malaya , Kuala Lumpur , Malaysia ; Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman , Kajang , Malaysia.
authors.forename: Yun Fong
authors.initials: YF
authors.lastname: Ngeow
keywords: Biolog phenotyping; Genomic analysis; Genotyping; Mass spectrometry; Mycobacterium; Rep-PCR