Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing

Abstract

BackgroundUnderstanding the emergence and spread of multidrug-resistant tuberculosis (MDR-TB) is crucial for its control. MDR-TB in previously treated patients is generally attributed to the selection of drug resistant mutants during inadequate therapy rather than transmission of a resistant strain. Traditional genotyping methods are not sufficient to distinguish strains in populations with a high burden of tuberculosis and it has previously been difficult to assess the degree of transmission in these settings. We have used whole genome analysis to investigate M. tuberculosis strains isolated from treatment experienced patients with MDR-TB in Uganda over a period of four years.Methods and FindingsWe used high throughput genome sequencing technology to investigate small polymorphisms and large deletions in 51 Mycobacterium tuberculosis samples from 41 treatment-experienced TB patients attending a TB referral and treatment clinic in Kampala. This was a convenience sample representing 69% of MDR-TB cases identified over the four year period. Low polymorphism was observed in longitudinal samples from individual patients (2-15 SNPs). Clusters of samples with less than 50 SNPs variation were examined. Three clusters comprising a total of 8 patients were found with almost identical genetic profiles, including mutations predictive for resistance to rifampicin and isoniazid, suggesting transmission of MDR-TB. Two patients with previous drug susceptible disease were found to have acquired MDR strains, one of which shared its genotype with an isolate from another patient in the cohort. ConclusionsWhole genome sequence analysis identified MDR-TB strains that were shared by more than one patient. The transmission of multidrug-resistant disease in this cohort of retreatment patients emphasises the importance of early detection and need for infection control. Consideration should be given to rapid testing for drug resistance in patients undergoing treatment to monitor the emergence of resistance and permit early intervention to avoid onward transmission.

A brief primer on genomic epidemiology: lessons learned fromMycobacterium tuberculosis

“…With the ever-decreasing cost of bacterial genome sequencing-a recent review noted that, in some extreme cases, the cost of generating a single draft assembly is now less than one dollar 35 -it can be tempting to see sequencing as the hammer for every nail. However, before deciding to launch 26 2 Schürch et al 159 3 Gardy et al 27 36 Bryant et al 160 199 Bryant et al 143 94 Clark et al 161 51 Kato-Maeda et al 162 9 Roetzer et al 139 86 Torok et al 163 2 Walker et al 29 390 Jamieson et al 19 36 Kohl et al 164 26 Luo et al 165 32 Mehaffy et al 166 61 Pérez-Lago et al 148 36 Walker et al 167 247 Coscolla et al 168 46 Glynn et al 169 170 Guerra-Assunção et al 170 1687 Guerra-Assunção et al 144 1933 Lee et al 171 120 Lee et al 172 163 Regmi et al 173 9 Stucki et al 174 3 Witney et al 175 16 Arnold et al 138 2 Outhred et al 176 22 a genomic epidemiology study, several questions must be answered. First, is sequencing even possible?…”

A Microbiological Revolution Meets an Ancient Disease: Improving the Management of Tuberculosis with Genomics

“…In the case of ethambutol resistance, a study showed that a low-level resistance that would be undetected by current phenotypic antibiotic susceptibility testing may accumulate within the genome of M. tuberculosis (41). In contrast, another study reported that phenotypic testing indicated isoniazid resistance, but WGS failed to identify the mutation responsible (45). Mutations conferring drug resistance are known to come at the cost of a loss in an organism's fitness; however, recent genomic studies revealed that compensatory mutations can occur which overcome the loss of fitness and create a "perfect storm" of resistant isolates without reduced fitness (42,(46)(47)(48).…”

Le séquençage haut-débit

“…Des difficultés demeurent quant à la généralisation de l'approche du séquençage haut-débit dans l'élucidation de maladies infectieuses, excluant dans l'immédiat une utilisation en routine. Malgré tout, pour des applications particulières, telles que la prise en charge d'infections à bactéries multirésistantes, le recours au séquençage haut-débit est envisagé à large échelle [8,9]. • L'élucidation des cas de co-infections ; le séquençage haut-débit permet de séquencer le microorganisme prédominant ainsi que les microorganismes minoritaires, rendant possible l'identification et la caractérisation de variants rares.…”