Evidence map›Paper›PMID 41381572›Full record

ArticleScientific reports2025

Real-time PCR assay for robust detection and global surveillance of the Mycobacterium tuberculosis Haarlem genotype.

Daria Tkachuk, Anna Vyazovaya, Irina Kostyukova, David Couvin, Svetlana Zhdanova, Zofia Bakuła, Weiwei Jiao, Natalia Solovieva, Platon Eliseev, Maria Badleeva and 23 more

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Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

33 authors.

Daria TkachukSt. Petersburg Pasteur Institute, St. Petersburg, Russia.
Anna VyazovayaSt. Petersburg Pasteur Institute, St. Petersburg, Russia.
Irina KostyukovaClinical Tuberculosis Dispensary, Omsk, Russia.
David CouvinInstitut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France.
Svetlana ZhdanovaInstitute of Epidemiology and Microbiology, Scientific Centre for the Family Health and Human Reproduction Problems, Irkutsk, Russia.
Zofia BakułaDepartment of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
Weiwei JiaoBeijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Laboratory of Respiratory Diseases, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
Natalia SolovievaSt. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
Platon EliseevNorthern State Medical University, Arkhangelsk, Russia.
Maria BadleevaDepartment of Infectious Diseases, Dorji Banzarov Buryat State University, Ulan-Ude, Buryatia, Russia.
Nikolai KobesovRepublican Clinical Center of Phthisiopulmonology, Vladikavkaz, North Ossetia-Alania, Russia.
Valentin DzagoevRepublican Clinical Center of Phthisiopulmonology, Vladikavkaz, North Ossetia-Alania, Russia.
Valentine B WuyepPlateau State College of Health Technology, Zawan, Jos, Nigeria.
Eugene I IkehDepartment of Medical Microbiology, School of Medical and Health Sciences, College of Medical Sciences, University of Jos, Jos, Nigeria.
Dinara NayzabaevaM.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan.
Ilya KondratovInstitute of Epidemiology and Microbiology, Scientific Centre for the Family Health and Human Reproduction Problems, Irkutsk, Russia.
Mikhail BezruchkoSt. Petersburg Pasteur Institute, St. Petersburg, Russia.
Sergei ChekryginResource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia.
Dmitrii PolevSt. Petersburg Pasteur Institute, St. Petersburg, Russia.
Ivan GorokhovSt. Petersburg Pasteur Institute, St. Petersburg, Russia.
Grigorii SergeevSt. Petersburg Pasteur Institute, St. Petersburg, Russia.
Alena ChilikinaSt. Petersburg Pasteur Institute, St. Petersburg, Russia.
Oksana PasechnikDepartment of Public Health, Omsk State Medical University, Omsk, Russia.
Yakov SchwartzNovosibirsk Tuberculosis Research Institute, Novosibirsk, Russia.
Viacheslav ZhuravlevSt. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
Oleg OgarkovInstitute of Epidemiology and Microbiology, Scientific Centre for the Family Health and Human Reproduction Problems, Irkutsk, Russia.
Andrei MariandyshevNorthern State Medical University, Arkhangelsk, Russia.
Adong ShenBeijing Key Laboratory of Core Technologies for the Prevention and Treatment of Emerging Infectious Diseases in Children, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Laboratory of Respiratory Diseases, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
Tomasz JagielskiDepartment of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
Urvashi SinghAll Indian Institute of Medical Sciences, Delhi and Head of National TB, Program, India.
Violeta ValchevaLaboratory of Molecular Genetics of Mycobacteria, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
Yuriy SkibaM.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan.
Igor MokrousovSt. Petersburg Pasteur Institute, St. Petersburg, Russia. imokrousov@mail.ru.

Funding

Bio-bank Center, Research Park of St. Petersburg State University 125022803066-3Russian Science Foundation 23-15-00280Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan STP No BR27195585St. Petersburg Pasteur Institute AAAA-A21-121021600206-5
6 · The paper itself

Abstract

The Haarlem genotype is a significant yet understudied part of the Euro-American lineage of Mycobacterium tuberculosis, characterized by unique pathogenetic features. Spoligotyping is a primary method for its detection, but it is not suitable for isolates with long blocks of deleted spacers. We have developed a simple and robust method to detect the Haarlem genotype. The real-time PCR (RT-PCR) assay with LNA probes was designed to detect the Rv0282 211 C > T mutation that was shown to be specific for the Haarlem genotype. The developed RT-PCR assay was optimized with 68 isolates with known whole-genome sequencing (WGS) data and applied to the geographically and genetically diverse collection of 428 isolates. As a result, 396 isolates were concordantly assigned to either Haarlem or non-Haarlem genotypes by both methods, whereas 32 isolates were discrepant cases. Twenty-two isolates of "unknown genotype" (Russia, Belarus, and Poland) were assigned to Haarlem by SNP-based assay. WGS of these isolates confirmed the results of the RT-PCR assay. To conclude, the developed RT-PCR method provides a reliable detection of the Haarlem genotype in retrospective collections and under prospective epidemiological surveillance. Its actual proportion in M. tuberculosis populations in certain world regions is higher than previously thought. Abridged spoligoprofiles with large deleted blocks of spacers require caution in interpretation.

Indexed as

Mycobacterium tuberculosisReal-Time Polymerase Chain ReactionTuberculosisGenotypeHumansPolymorphism, Single NucleotideWhole Genome SequencingHaarlem genotypeMycobacterium tuberculosisSpoligotypingWhole-genome sequencing

Identifiers

PMID41381572
PMCPMC12699029

What Socratic holds

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.