title: MIRU-VNTR genotype diversity and indications of homoplasy in M. avium strains isolated from humans and slaughter pigs in Latvia.
abstract: Diseases which are caused by non-tuberculous mycobacteria (NTM) are an increasing problem in the developed countries. In Latvia, one of the most clinically important members of NTM is Mycobacterium avium (M. avium), an opportunistic pathogen which has been isolated from several lung disease patients and tissue samples of slaughter pigs. This study was designed to characterize the genetic diversity of the M. avium isolates in Latvia and to compare the distribution of genotypic patterns among humans and pigs. Eleven (Hall and Salipante, 2010) clinical M. avium samples, isolated from patients of Center of Tuberculosis and Lung Diseases (years 2003-2010), and 32 isolates from pig necrotic mesenterial lymph nodes in different regions (years 2003-2007) were analyzed. The majority (42 of 43) of samples were identified as M. avium subsp. hominissuis; one porcine isolate belonged to M. avium subsp. avium. MIRU-VNTR genotyping revealed 13 distinct genotypes, among which nine genotype patterns, including M. avium subsp. avium isolate, were newly identified. IS1245 RFLP fingerprinting of 25 M. avium subsp. hominissuis samples yielded 17 different IS1245 RFLP patterns, allowing an efficient discrimination of isolates. Clusters of identical RFLP profiles were observed within host species, geographical locations and time frame of several years. Additional in silico analysis on simulated MIRU-VNTR genotype population datasets showed that the MIRU-VNTR pattern similarity could partly arise due to probabilistic increase of acquiring homoplasy among subpopulations, thus the similar MIRU-VNTR profiles of M. avium strains even in close geographical proximity should be interpreted with caution.
authors.affiliation: Latvian Biomedical Research and Study Centre (LV BMC), Riga, Latvia; Riga Stradins University (RSU), Riga, Latvia.
authors.forename: Adrija
authors.initials: A
authors.lastname: Kalvisa
authors.affiliation: Center for Massive Data Algorithmics (MADALGO), Aarhus University, Aarhus, Denmark.
authors.forename: Constantinos
authors.initials: C
authors.lastname: Tsirogiannis
authors.affiliation: Latvian Biomedical Research and Study Centre (LV BMC), Riga, Latvia.
authors.forename: Ivars
authors.initials: I
authors.lastname: Silamikelis
authors.affiliation: Riga East University Hospital, Tuberculosis and Lung Diseases Center, Latvia.
authors.forename: Girts
authors.initials: G
authors.lastname: Skenders
authors.affiliation: Riga East University Hospital, Tuberculosis and Lung Diseases Center, Latvia.
authors.forename: Lonija
authors.initials: L
authors.lastname: Broka
authors.affiliation: Department of Veterinary Medicine, Latvia University of Agriculture, Jelgava, Latvia.
authors.forename: Agris
authors.initials: A
authors.lastname: Zirnitis
authors.affiliation: Latvian Biomedical Research and Study Centre (LV BMC), Riga, Latvia.
authors.forename: Inta
authors.initials: I
authors.lastname: Jansone
authors.affiliation: Latvian Biomedical Research and Study Centre (LV BMC), Riga, Latvia; Riga Stradins University (RSU), Riga, Latvia. Electronic address: renate_r@biomed.lu.lv.
authors.forename: Renate
authors.initials: R
authors.lastname: Ranka
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D007844:Latvia; D018598:Minisatellite Repeats; D009162:Mycobacterium avium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D013552:Swine; D013553:Swine Diseases / Q000382:microbiology; D014376:Tuberculosis / Q000382:microbiology* / Q000662:veterinary
chemical_list: D004269:DNA, Bacterial
keywords: Homoplasy; IS1245 RFLP; MIRU-VNTR; Non-tuberculous mycobacteria