Population structure and circulating genotypes of drug-sensitive and drug-resistant Mycobacterium tuberculosis clinical isolates in São Paulo state, Brazil

Abstract

São Paulo is the most populous Brazilian state and reports the largest number of tuberculosis cases in the country annually (over 18,500). This study included 193 isolates obtained during the 2nd Nationwide Survey on Mycobacterium tuberculosis Drug Resistance that was conducted in São Paulo state and 547 isolates from a laboratory based study of drug resistance that were analyzed by the Mycobacteria Reference Laboratory at the Institute Adolfo Lutz. Both studies were conducted from 2006 to 2008 and sought to determine the genetic diversity and pattern of drug resistance of M. tuberculosis isolates (MTC) circulating in São Paulo. The patterns obtained from the spoligotyping analysis demonstrated that 51/740 (6.9%) of the isolates corresponded to orphan patterns and that 689 (93.1%) of the isolates distributed into 144 shared types, including 119 that matched a preexisting shared type in the SITVIT2 database and 25 that were new isolates. A total of 77/144 patterns corresponded to unique isolates, while the remaining 67 corresponded to clustered patterns (n = 612 isolates clustered into groups of 2-84 isolates each). The evolutionarily ancient PGG1 lineages (Beijing, CAS1-DEL, EAI3-IND, and PINI2) were rarely detected in São Paulo and comprised only 13/740, or 1.76%, of the total isolates; all of the remaining 727/740, or 98.24%, of the MTC isolates from São Paulo state were from the recent PGG2/3 evolutionary isolates belonging to the LAM, T, S, X, and Haarlem lineages, i.e., the Euro-American group. This study provides the first overview of circulating genotypes of M. tuberculosis in São Paulo state and demonstrates that the clustered shared types containing seven or more M. tuberculosis isolates that are spread in São Paulo state included both resistant and susceptible isolates.

Clonality and genetic profiles of drug‐resistant Mycobacterium tuberculosis in the Eastern Cape Province, South Africa

“…Of noteworthy, LAM6 was absent in our study. This was in contrast to the report elsewhere (Martins et al, 2013).…”

A systematic review of East African-Indian family of Mycobacterium tuberculosis in Brazil

“…3 A). 14 , 20 , 21 , 22 , 23 Furthermore, the spoligotyping patterns EAI3-IND SIT 11 and EAI1-SOM SIT 48 were also present in more than one study ( Table 2 and Fig. 3 A).…”

“…The EAI family is rare in Brazil, occurring typically at frequencies below 2% of the datasets analyzed ( Table 2 ). While EAI family isolates were found in the North, 22 , 24 Northeast, 19 , 22 South, 14 , 16 , 26 and Southeast of Brazil, 15 , 17 , 18 , 20 , 21 , 22 , 23 , 27 the highest circulation of this family was reported in the North (Pará) 22 ( Table 2 ). The number of EAI isolates varied from only one to as many as 15 in the studies reviewed ( Table 2 ).…”

“…2 and Table 2 ). 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 Most of these were either based on bacterial collections maintained in reference laboratories that perform culturing for species identification and phenotypic drug-susceptibility testing, 14 , 16 , 17 , 18 , 20 , 21 , 24 , 26 , 27 or on convenience sampling of TB patients at reference health care units responsible for TB diagnosis. 15 , 22 , 23 , 25 One report consisted of a case-control study involving drug-sensitive versus drug-resistant TB patients.…”

Distribution of Mycobacterium tuberculosis lineages in South America

“…The lineages 3, 4 and 6 have been incorporated into a variety of MTB lineages found in Brazil by the migration of people (Esteves et al, 2018;Salvato et al, 2019). Brazil has a low incidence of unidentified strains (10.5%), which is due to the implementation of molecular techniques such as spoligotyping, MIRU-VNTR (24 and 12 loci) and WGS to determine the transmission routes of TB (Cardoso Oelemann et al, 2011;Dalla Costa et al, 2013;Gomes et al, 2012;Luiz et al, 2013;Machado et al, 2014;Martins et al, 2013;Medeiros et al, 2018;Nogueira et al, 2016;Noguti et al, 2010;Soares et al, 2013;Vasconcellos et al, 2014).…”