Molecular characterization of multidrug-resistant Mycobacterium tuberculosis isolates from high prevalence tuberculosis states in Mexico

Whole genomic sequencing as a tool for diagnosis of drug and multidrug-resistance tuberculosis in an endemic region in Mexico

“…Such variations in the occurrence of mutations associated with resistance 13 to E are similar to those reported previously [49]. Resistant isolates lacking in mutations 14 and the presence of mutations related to resistance in sensitive isolates show the possibility 15 of failures in the BACTEC MGIT phenotypic assay, and further analysis is required in 16 order to identify the factors that cause this low sensitivity and to improve the efficiency of 17 WGS in predicting resistance against this drug among the isolates from the setting.…”

“…Moreover, increasing numbers of XDR-TB 12 cases are reported every year [22]. These figures make Mexico the country in the Americas 13 with the third highest contribution of tuberculosis, including aggravated forms of TB such 14 as DR-TB, MDR-TB and possibly XDR-TB. [23] Previous studies using Sanger 15 sequencing protocols have shown that Mexico presents a considerable diversity of 16 mutations associated with DR-TB, as well as variations related to geographical regions 17 [24][25][26][27][28][29][30][31], which act to limit the utility of new genotypic diagnostic procedures and make 18 WGS a very attractive alternative.…”

“…We classified all of 12 the strains according to the presence of the specific lineages or sub-lineages of phylogenetic 13 variants proposed by Coll et al 2014 [36] and Stucki et al 2016 [37]. In order to detect 14 highly likely genomic transmission clusters, we performed a pairwise genetic distance 15 analysis based on a concatenated SNP alignment obtained from every constant-SNP from 16 every isolate. A ≤12 SNP threshold was applied to delineate the transmission clusters, as 17 proposed by Walker et al 2013 [38].…”

“…In relation to the phenotypic drug resistance profile of the 81 isolates determined by 14 BACTEC MGIT assay, S resistance was observed in 47% (38) of the isolates, while H 15 resistance was presented in 75% (61), R resistance in 62% (n=51), E resistance in 29% (24) 16 and Z resistance in 34% (28). A total of 25% (21) of the isolates were classified as mono-17 resistant, 14% (12) as poly-resistant, 56% (46) as MDR-TB and 16% (13) as resistant to all 18 first-line drugs.…”

“…The sensitivity of 96% and specificity of 94% observed for the diagnostic of R by 13 WGS coincides with previous reports [8][9][10][11]21] (Table 7). Two isolates were notable for 14 being phenotypically susceptible to rifampicin, despite the fact that they were carriers of the 15 mutations rpoB432Q/L and rpoB430L/P respectively, which have been considered as 16 "disputed mutations" [47] that confers low-level R resistance [48]. Isolates carrying this 1 type of mutation are phenotypically misclassified as rifampicin susceptible, and routine 2 genotypic tests fail in terms of their detection [47].…”