TY - JOUR
T1 - MIRU-VNTR genotype diversity and indications of homoplasy in M. avium strains isolated from humans and slaughter pigs in Latvia
AU - Kalvisa, Adrija
AU - Tsirogiannis, Constantinos
AU - Silamikelis, Ivars
AU - Skenders, Girts
AU - Broka, Lonija
AU - Zirnitis, Agris
AU - Jansone, Inta
AU - Ranka, Renate
N1 - Funding Information:
This work was funded by ESF 2013/0039/1DP/1.1.1.2.0/13/APIA/VIAA/038 and Latvian National Research Program VPP “BIOMEDICINE” (Project No. 5.7.3 ). Authors thank Ilva Pole for the DNA samples from clinical M. avium isolates and Liana Pliss for the fruitful discussion.
Publisher Copyright:
© 2016 Elsevier B.V..
PY - 2016/9/1
Y1 - 2016/9/1
N2 - 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.
AB - 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.
KW - Homoplasy
KW - IS1245 RFLP
KW - MIRU-VNTR
KW - Non-tuberculous mycobacteria
UR - http://www.scopus.com/inward/record.url?scp=84969240234&partnerID=8YFLogxK
U2 - 10.1016/j.meegid.2016.05.013
DO - 10.1016/j.meegid.2016.05.013
M3 - Article
C2 - 27178993
AN - SCOPUS:84969240234
SN - 1567-1348
VL - 43
SP - 15
EP - 21
JO - Infection, Genetics and Evolution
JF - Infection, Genetics and Evolution
ER -
