dThe emergence of drug-resistant forms of tuberculosis (TB) represents a major public health concern. Understanding the transmission routes of the disease is a key factor for its control and for the implementation of efficient interventions. Mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) marker typing is a well-described method for lineage identification and transmission tracking. However, the conventional manual genotyping technique is cumbersome and time-consuming and entails many risks for errors, thus hindering its implementation and dissemination. We describe here a new approach using the QIAxcel system, an automated high-throughput capillary electrophoresis system that also carries out allele calling. This automated method was assessed on 1,824 amplicons from 82 TB isolates and tested with sets of markers of 15 or 24 loci. Overall allele-calling concordance between the methods from 140 to 1,317 bp was 98.9%. DNA concentrations and repeatability and reproducibility performances showed no biases in allele calling. Furthermore, turnaround time using this automated system was reduced by 81% compared to the conventional manual agarose gel method. In sum, this new automated method facilitates MIRU-VNTR genotyping and provides reliable results. Therefore, it is well suited for field genotyping. The implementation of this method will help to achieve accurate and cost-effective epidemiological studies, especially in countries with a high prevalence of TB, where the high number of strains complicates the surveillance of circulating lineages and requires efficient interventions to be carried out in an urgent manner.T uberculosis (TB) remains a major public health concern worldwide. The widespread emergence of multidrug resistant (MDR-TB) strains and extensively and extremely drug-resistant (XDR-TB and XXDR-TB) strains has hampered the management of treatment of the disease and the control of TB outbreaks (1). Many epidemiological questions remain unresolved, particularly in regard to the risk factors associated with the transmission of the bacilli to the host and to the prevalence of strain reactivation versus exogenous reinfection. Various genotype lineages of Mycobacterium tuberculosis have been described that can be associated with drug resistance, a higher rate of transmission, a higher rate of progression to disease, virulence, and vaccine escape (2, 3). The emergence of whole-genome sequencing (WGS) technologies can provide a complete genomic picture of lineage characterization and drug-resistant mutations. However, these technologies are presently not affordable for most laboratories, considering the costs and specialized skills required for data analysis. Thus, methods on the bench still have their value, as they have a faster turnaround time and can handle a higher batch capacity at a lower cost. One of these in particular, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) marker typing, is commonly used for effective genotyping. There ...
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