Journal Article

Five-year microevolution of a multidrug-resistant Mycobacterium tuberculosis strain within a patient with inadequate compliance to treatment

Martí, Marcelo, Paul, Roxana, Fernandez Do Porto, Darío A., Poklepovich, Tomás, Matteo, Mario, Castello, Florencia, Monteserin, Johana, Simboli, Norberto, Benevento, Andrés Fernández, Campos, Josefina, López, Beatriz, Turjanski, Adrián, Yokobori, Noemí, Pardo, Agustín, Serral, Federico, Wainmayer, Ingrid, Ritacco, Viviana, Sosa, Ezequiel J.

2021

Overview

Background Whole-genome sequencing has shown that the Mycobacterium tuberculosis infection process can be more heterogeneous than previously thought. Compartmentalized infections, exogenous reinfections, and microevolution are manifestations of this clonal complexity. The analysis of the mechanisms causing the microevolution —the genetic variability of M. tuberculosis at short time scales— of a parental strain into clonal variants with a patient is a relevant issue that has not been yet completely addressed. To our knowledge, a whole genome sequence microevolution analysis in a single patient with inadequate adherence to treatment has not been previously reported. Case presentation In this work, we applied whole genome sequencing analysis for a more in-depth analysis of the microevolution of a parental Mycobacterium tuberculosis strain into clonal variants within a patient with poor treatment compliance in Argentina. We analyzed the whole-genome sequence of 8 consecutive Mycobacterium tuberculosis isolates obtained from a patient within 57-months of intermittent therapy . Nineteen mutations (9 short-term, 10 fixed variants) emerged, most of them associated with drug resistance. The first isolate was already resistant to isoniazid, rifampicin, and streptomycin, thereafter the strain developed resistance to fluoroquinolones and pyrazinamide. Surprisingly, isolates remained susceptible to the pro-drug ethionamide after acquiring a frameshift mutation in ethA, a gene required for its activation. We also found a novel variant, (T-54G), in the 5′ untranslated region of whiB7 (T-54G), a region allegedly related to kanamycin resistance. Notably, discrepancies between canonical and phage-based susceptibility testing to kanamycin were previously found for the isolate harboring this mutation. In our patient, microevolution was mainly driven by drug selective pressure. Rare short-term mutations fixed together with resistance-conferring mutations during therapy. Conclusions This report highlights the relevance of whole-genome sequencing analysis in the clinic for characterization of pre-XDR and MDR resistance profile, particularly in patients with incomplete and/or intermittent treatment.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: 5' Untranslated regions / Adult / Antibiotics / Antitubercular Agents - pharmacology / Antitubercular Agents - therapeutic use / Argentina / Case Report / Clonal evolution / Cloning / Drug resistance / Drug Resistance, Multiple, Bacterial - drug effects / Drug Resistance, Multiple, Bacterial - genetics / Drug resistant tuberculosis / Ethionamide / Female / Fluoroquinolones / Frameshift mutation / Gene sequencing / Genetic variability / Genomes / High-throughput nucleotide sequencing / Humans / Infectious Diseases / Internal Medicine / Isoniazid / Isoniazid - therapeutic use / Kanamycin / Medical Microbiology / Medication Adherence / Medicine / Medicine & Public Health / Microbial Sensitivity Tests / Multidrug resistance / Multidrug resistant organisms / Mutation / Mycobacterium tuberculosis / Mycobacterium tuberculosis - drug effects / Mycobacterium tuberculosis - genetics / Mycobacterium tuberculosis - isolation & purification / Nucleotide sequence / Parasitology / Phages / Phylogeny / Pyrazinamide / Pyrazinamide - therapeutic use / Rifampin / Rifampin - therapeutic use / Streptomycin / Streptomycin - pharmacology / Tropical Medicine / Tuberculosis / Tuberculosis and other mycobacterial diseases / Tuberculosis, Multidrug-Resistant - drug therapy / Tuberculosis, Multidrug-Resistant - microbiology / Tuberculosis, Pulmonary - drug therapy / Tuberculosis, Pulmonary - microbiology / Whole Genome Sequencing