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.
Highlights
Bacterial strains are genetic variants of a bacterial species or subspecies
We investigated the relationship between these two strains with conventional and whole genome sequence-based methods of strain differentiation
The bacilli were acid-fast with the Ziehl-Neelson stain and were negative for the MPB64 antigen in the Tibilia test for M. tuberculosis
Summary
Bacterial strains are genetic variants of a bacterial species or subspecies. Strain differentiation is usually carried out to establish clonal transmission in disease outbreaks, to confirm cross-infection in healthcare settings, or to study evolutionary diversity among bacteria. The more frequently used techniques include multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP) studies, and repetitive sequence-based PCR (rep-PCR) typing These methods have been effectively used in the investigation of tuberculosis transmission and reactivation in human patients (Gori et al, 2005) and animals (Aranaz et al, 2010). 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. 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. Detailed epidemiological tracking revealed that the elephants shared a common habitat eight years apart, strengthening the possibility of a clonal relationship between the two strains
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