title: Evaluation of Semiautomated IS6110-Based Restriction Fragment Length Polymorphism Typing for Mycobacterium tuberculosis in a High-Burden Setting.
abstract: The manual IS6110-based restriction fragment length polymorphism (RFLP) typing method is highly discriminatory; however, it is laborious and technically demanding, and data exchange remains a challenge. In an effort to improve IS6110-based RFLP to make it a faster format, DuPont Molecular Diagnostics recently introduced the IS6110-PvuII kit for semiautomated typing of Mycobacterium tuberculosis using the RiboPrinter microbial characterization system. This study aimed to evaluate the semiautomated RFLP typing against the standard manual method. A total of 112 isolates collected between 2013 and 2014 were included. All isolates were genotyped using manual and semiautomated RFLP typing methods. Clustering rates and discriminatory indexes were compared between methods. The overall performance of semiautomated RFLP compared to manual typing was excellent, with high discriminatory index (0.990 versus 0.995, respectively) and similar numbers of unique profiles (72 versus 74, respectively), numbers of clustered isolates (33 versus 31, respectively), cluster sizes (2 to 6 and 2 to 5 isolates, respectively), and clustering rates (21.9% and 17.1%, respectively). The semiautomated RFLP system is technically simple and significantly faster than the manual RFLP method (8 h versus 5 days). The analysis is fully automated and generates easily manageable databases of standardized fingerprints that can be easily exchanged between laboratories. Based on its high-throughput processing with minimal human effort, the semiautomated RFLP can be a very useful tool as a first-line method for routine typing of M. tuberculosis isolates, especially where Beijing strains are highly prevalent, followed by manual RFLP typing if resolution is not achieved, thereby saving time and labor.
authors.affiliation: Centre for Tuberculosis, National Institute of Communicable Diseases, Johannesburg, South Africa Department of Medical Microbiology, Faculty of Health Science, University of Free State, Bloemfontein, South Africa halimas@nicd.ac.za.
authors.forename: Halima M
authors.initials: HM
authors.lastname: Said
authors.affiliation: DuPont Nutrition and Health, Geneva, Switzerland.
authors.forename: Keshav
authors.initials: K
authors.lastname: Krishnamani
authors.affiliation: Centre for Tuberculosis, National Institute of Communicable Diseases, Johannesburg, South Africa.
authors.forename: Shaheed V
authors.initials: SV
authors.lastname: Omar
authors.affiliation: Centre for Tuberculosis, National Institute of Communicable Diseases, Johannesburg, South Africa.
authors.forename: Andries W
authors.initials: AW
authors.lastname: Dreyer
authors.affiliation: Centre for Tuberculosis, National Institute of Communicable Diseases, Johannesburg, South Africa.
authors.forename: Bianca
authors.initials: B
authors.lastname: Sansom
authors.affiliation: Public Health Research Institute, Rutgers University, Newark, New Jersey, USA.
authors.forename: Dorothy
authors.initials: D
authors.lastname: Fallows
authors.affiliation: Centre for Tuberculosis, National Institute of Communicable Diseases, Johannesburg, South Africa Department of Medical Microbiology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa.
authors.forename: Nazir A
authors.initials: NA
authors.lastname: Ismail
mesh_terms: D057205:Automation, Laboratory / Q000379:methods*; D016000:Cluster Analysis; D004251:DNA Transposable Elements; D006801:Humans; D017720:Molecular Epidemiology / Q000379:methods; D058889:Molecular Typing / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000145:classification* / Q000235:genetics*; D012150:Polymorphism, Restriction Fragment Length; D013997:Time Factors
chemical_list: D004251:DNA Transposable Elements