A highly rifampicin resistant Mycobacterium tuberculosis strain emerging in Southern Brazil

Abstract

Here we described phenotypical, molecular and epidemiological features of a highly rifampicin-resistant Mycobacterium tuberculosis strain emerging in Southern Brazil, that carries an uncommon insertion of 12 nucleotides at the codon 435 in the rpoB gene. Employing a whole-genome sequencing-based study on drug-resistant Mycobacterium tuberculosis strains, we identified this emergent strain in 16 (9.19%) from 174 rifampicin-resistant clinical strains included. Nine of these 16 strains were available to minimum inhibitory concentration determination and for all of them was found a high rifampicin-resistance level (≥ to 32 mg/L). This high resistance level could be explained by structural changes into the RIF binding site of RNA polymerase caused by the insertions, and consequent low-affinity interaction with rifampicin complex confirmed through protein modeling and molecular docking simulations. Epidemiological investigation showed that most of the individuals (56.25%) infected by the studied strains were prison inmate individuals or that spent some time in prison. The phylogenomic approach revealed that all strains carrying on the 12 nucleotide insertion belonged to the same genomic cluster, evidencing a communal transmission chain involving inmate individuals and community. We stress the importance of tuberculosis genomic surveillance and the introduction of measures to interrupt the Mycobacterium tuberculosis transmission chain in this region.

Genomic-based surveillance reveals high ongoing transmission of multi-drug-resistant Mycobacterium tuberculosis in Southern Brazil

“…In GC2, 10/21 strains were isolated from prison inmates, and in GC3, 8/17 of the clustered strains came from prison inmates or individuals with a recent history of incarceration, along with a prison worker. Thus, GC3 represents an important active transmission chain involving the inmate population and the community [6] , similar to that found in other regions in Brazil [39] and worldwide [40] .…”

“…RIF resistance was mainly caused by variants carrying the rpoB S450L (in 54.6%) and rpoB S450L + A286V (in 10.9%) mutations, and by the 12-nucleotide insertion at codon 435 of the rpoB gene (in 9.2%), stressing the significant spread of these highly RIFresistant strains (MIC ≥32 mg/L) in the population [6] . In the same way, most common resistance-associated mutations were found among clinical strains that were phenotypically resistant to EMB ( embB M306V in 83.3% of resistant strains) and STR ( rrs 492 C > T in 14.9% and rpsL K43R in 14.9% of resistant strains), similar to results in global collections [14] .…”

“…Amino acid changes in codon 450 were the most frequent, occurring in 73.6% of the resistant isolates. An uncommon insertion ( rpoB 435 QNNP > QNNPQNNP) [6] was identified in 16/174 isolates (9.2%), and two isolates (1.1%) had deletion of two amino acids ( rpoB 435 FMD > F) ( Figure 1 ). Disputed mutations occurring in the rpoB gene were found in 22 RIF-susceptible (according to MGIT) strains: 14 of them were INH-monoresistant strains, seven were resistant to INH and STR, and one was susceptible to first-line drugs.…”

Metagenomic insights for antimicrobial resistance surveillance in soils with different land uses in Brazil

“…The genetic product is an RNA-binding protein that has demonstrated to confer low levels of rifamycin resistance in Streptomyces coelicolor [85] and it might influence the response of Mycobacterium tuberculosis against rifamycin antibiotics [86]. In 2019, 73,000 new cases of tuberculosis (TB) and 4,500 deaths due to this disease have been reported, being several of them related to rifampicin-resistant strains, in a way that TB treatment with 82% chance of success decreases to 60% when associated with isoniazid and rifampicin resistant M. tuberculosis strains [87,88]. Additionally, genomic characterization of the zoonotic and human-opportunistic pathogens Rhodococcus equi and Mycolicibacterium peregrinum obtained from human, pig and soil samples indicated that all the isolates’ genomes contained rbpA genes, suggesting that infections caused by these antibiotic resistant bacteria might have an environmental source [89,90].…”