Practical approach to detection and surveillance of emerging highly resistant Mycobacterium tuberculosis Beijing 1071-32-cluster
Mokrousov I. Vyazovaya A. Sinkov V. Gerasimova A. Ioannidis P. Jiao W. Khromova P. Papaventsis D. Pasechnik O. Perdigão J. Rastogi N. Shen A. Skiba Y. Solovieva N. Suffys P. Tafaj S. Umpeleva T. Vakhrusheva D. Yarusova I. Zhdanova S. Zhuravlev V. Ogarkov O.
December 2021Nature Research
Scientific Reports
2021#11Issue 1
Ancient sublineage of the Mycobacterium tuberculosis Beijing genotype is endemic and prevalent in East Asia and rare in other world regions. While these strains are mainly drug susceptible, we recently identified a novel clonal group Beijing 1071-32 within this sublineage emerging in Siberia, Russia and present in other Russian regions. This cluster included only multi/extensive drug resistant (MDR/XDR) isolates. Based on the phylogenetic analysis of the available WGS data, we identified three synonymous SNPs in the genes Rv0144, Rv0373c, and Rv0334 that were specific for the Beijing 1071-32-cluster and developed a real-time PCR assay for their detection. Analysis of the 2375 genetically diverse M. tuberculosis isolates collected between 1996 and 2020 in different locations (European and Asian parts of Russia, former Soviet Union countries, Albania, Greece, China, Vietnam, Japan and Brazil), confirmed 100% specificity and sensitivity of this real-time PCR assay. Moreover, the epidemiological importance of this strain and the newly developed screening assay is further stressed by the fact that all identified Beijing 1071-32 isolates were found to exhibit MDR genotypic profiles with concomitant resistance to additional first-line drugs due to a characteristic signature of six mutations in rpoB450, rpoC485, katG315, katG335, rpsL43 and embB497. In conclusion, this study provides a set of three concordant SNPs for the detection and screening of Beijing 1071-32 isolates along with a validated real-time PCR assay easily deployable across multiple settings for the epidemiological tracking of this significant MDR cluster.
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St. Petersburg Pasteur Institute, 14 Mira Street, St. Petersburg, 197101, Russian Federation
Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russian Federation
National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
Omsk State Medical University, Omsk, Russian Federation
Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou Children’s Hospital, Zhengzhou, China
Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
University Hospital “Shefqet Ndroqi”, Tirana, Albania
Ural Research Institute for Phthisiopulmonology, National Medical Research Center of Tuberculosis and Infectious Diseases of Ministry of Health of the Russian Federation, Yekaterinburg, Russian Federation
Clinical Tuberculosis Dispensary, Omsk, Russian Federation
St. Petersburg Pasteur Institute
Scientific Centre of the Family Health and Human Reproduction Problems
National Reference Laboratory for Mycobacteria
National Clinical Research Center for Respiratory Diseases
Omsk State Medical University
Research Institute for Medicines (iMed.ULisboa)
WHO Supranational TB Reference Laboratory
Children’s Hospital Affiliated to Zhengzhou University
Almaty Branch of National Center for Biotechnology in Central Reference Laboratory
St. Petersburg Research Institute of Phthisiopulmonology
Fundação Oswaldo Cruz
University Hospital “Shefqet Ndroqi”
Ural Research Institute for Phthisiopulmonology
Clinical Tuberculosis Dispensary
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