Sequence-Based Typing of Clinical Isolates of Mycobacterium xenopi Isolated from Ontario, Canada

Samia Mirza, David J. Farrell, Theodore K. Marras, Jennifer Ma, Daniel Liu, David C. Alexander, Julianne V. Kus, Frances B. Jamieson

Abstract


Mycobacterium xenopiis an environmental pathogen responsible for pulmonary infections and tuberculosis-like disease typically found in patients with previous pulmonary disease. A sequence typing (ST) scheme was developed to classify and analyze sixteen isolates obtained from a prospective clinical study and subsequently extended to include five additional clinical isolates. Twenty housekeeping genes were sequenced and inspected for single nucleotide polymorphisms (SNPs). Seven targets including atpD, fusA1, glnA1, pheT, secA1, topA, and the internal transcribed spacer (ITS) region were selected for continuing ST analysis, using the type strain ATCC 19250T as reference. Three isolates contained SNPs in glnA1 and pheT while the remaining 13 isolates displayed SNPs in topA. Consistency was observed with topA SNPs exclusively present in ITS subgroups B, C, and BC whereas glnA1and pheT SNPs were only evident in ITS A. Among the sixteen clinical isolates obtained from the prospective study, strain types (ST) ST4 and ST7 were most prevalent. Two patients with pulmonary symptoms, each with two isolates collected three months apart, displayed identical sequences in all target genes suggesting persistence of the strain causing infection rather than reinfection. We have described seven SNPs in six targets (atpD, secA1, fusA1, glnA1, pheT and topA) and ITS, which provide a typing tool to analyze relatedness between strains and a foundation for a genotypic phylogenetic comparison. This typing scheme represents a basic tool that facilitates the comparison of
M. xenopi strains to investigate the source and transmission dynamics between patients and their environment.

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