Association of specific mutations in katG, rpoB, rpsL and rrs genes with spoligotypes of multidrug-resistant Mycobacterium tuberculosis isolates in Russia

Abstract

Most multidrug-resistant (MDR) Mycobacterium tuberculosis isolates in Russia belong to the Beijing or Latino-American and Mediterranean (LAM) spoligotype families. The objective of this study was to investigate possible associations between genotype and the frequencies of mutations that confer drug resistance in a population that has two large families of circulating strains. Spoligotyping, IS6110 restriction fragment length polymorphism typing, and sequencing of the katG and rpoB genes, were performed for 217 consecutive MDR M. tuberculosis isolates from patients. The rpsL and rrs genes were also sequenced for selected streptomycin-resistant isolates. Of the 217 MDR isolates, 99 (46%) belonged to the LAM family, 92 (42%) to the Beijing family, 21 (10%) to the Haarlem family and four (2%) to the T family. There was one unique spoligotype. Mutations in the katG gene were identified in 207 (95%) isolates, all of which had mutations in codon 315. Mutations in the rpoB gene were identified in 200 (92%) isolates; 75% of LAM isolates carried a mutation in codon 516, whereas 71% of Beijing isolates carried a mutation in codon 531. In the 33 isolates resistant to streptomycin 50 mg/L, the 43AGG rpsL mutation was found in 27% of Haarlem, 75% of Beijing and 0% of LAM isolates, and rrs mutations were found in 17% (516C-->T) of Beijing and 100% (513A-->C) of LAM isolates. Overall, there appeared to be a correlation between the genotype and specific mutations conferring resistance to rifampicin or streptomycin in the Beijing and LAM families. The biological implications of this correlation remain to be explored.

Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis

“…The mutation frequency and type vary in function of different parameters, such as the geographic region, the drug resistance pattern and genetic background (Fenner et al., 2012; Hillemann, Kubica, Rusch‐Gerdes, & Niemann, 2005; Lipin, Stepanshina, Shemyakin, & Shinnick, 2007; Qian et al., 2002). Despite the large diversity of mutation patterns globally, only few specific mutations are predominant (Table 2) (Sandgren et al., 2009; Zhang & Yew, 2015).…”

“…Despite the large diversity of mutation patterns globally, only few specific mutations are predominant (Table 2) (Sandgren et al., 2009; Zhang & Yew, 2015). For instance, in the case of rifampicin resistance, hundreds of rpo B mutations have been described (not all were associated with rifampicin resistance), but more than 80% of rifampicin‐resistant isolates display mutations in three codons rpo B531, 526 and 516 (Campbell et al., 2011; Lipin et al., 2007; Pozzi et al., 1999; Telenti et al., 1993). Similar to that, among the approximately 300 mutations found in the kat G gene, the prevalence of kat G S315T mutation can vary between 32% and 95% in isoniazid‐resistant clinical isolates depending on the geographic regions and drug resistance patterns (Hazbon et al., 2006; Lipin et al., 2007; Mokrousov et al., 2002; Vilcheze & Jacobs, 2014).…”

“… Notes aNucleotide change.bSee the following studies for reference (Campbell et al., 2011; Duong et al., 2009; Hazbon et al., 2006; Hillemann et al., 2005; Lipin et al., 2007; Mokrousov et al., 2002; Müller et al., 2011; Niehaus et al., 2015; Perdigao et al., 2010; Pozzi et al., 1999; Qian et al., 2002; Shi et al., 2011; van Soolingen et al., 2000; Sreevatsan et al., 1996, 1997; Telenti et al., 1993; Von Groll et al., 2009). …”

“…For instance, the kat G S315T is prevalent in lineage 2, conversely the inh A‐15 mutation is associated mostly with lineage 1 (Casali et al., 2014; Fenner et al., 2012; Gagneux, Burgos, et al., 2006; Mokrousov et al., 2002; Nguyen, Nguyen, et al., 2017). Similar to that, the rpo B S531L mutation is observed mainly in lineage 2 compared with other lineages, while the rpo B D516V mutation is more frequent in lineage 4 (LAM family) (Casali et al., 2014; Hillemann et al., 2005; Lipin et al., 2007). In particular, the prevalence of specific drug resistance‐associated mutations also varies within the lineage, such as the frequencies of the rpo B S531L and kat G S315T mutations are greater in the modern (typical) Beijing strains than in ancient (atypical) ones (Hillemann et al., 2005; Lipin et al., 2007; Qian et al., 2002).…”

“…Similar to that, the rpo B S531L mutation is observed mainly in lineage 2 compared with other lineages, while the rpo B D516V mutation is more frequent in lineage 4 (LAM family) (Casali et al., 2014; Hillemann et al., 2005; Lipin et al., 2007). In particular, the prevalence of specific drug resistance‐associated mutations also varies within the lineage, such as the frequencies of the rpo B S531L and kat G S315T mutations are greater in the modern (typical) Beijing strains than in ancient (atypical) ones (Hillemann et al., 2005; Lipin et al., 2007; Qian et al., 2002). These differences could be the result of epistatic interactions (see Box 1 and below) and might reflect the adaptation of M. tuberculosis sublineages to the different human populations and the efficiency of treatment and public health strategies (Bañuls et al., 2015; Comas et al., 2013; Eldholm et al., 2016).…”