I D Olaru1, H Patel2, K Kranzer3, N Perera2. 1. Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK. Electronic address: ioanad_olaru@yahoo.co.uk. 2. Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester, UK. 3. National Mycobacterium Reference Laboratory, Research Center Borstel, Borstel, Germany; London School of Hygiene and Tropical Medicine, London, UK.
Abstract
OBJECTIVES: Until recently whole genome sequencing (WGS) for mycobacteria has been restricted mostly to the research setting. However, in 2017 Public Health England has implemented WGS for routine mycobacterial identification and susceptibility testing for Mycobacterium tuberculosis. Our objective was to evaluate the impact of this change on the laboratory turnaround times and availability of results. METHODS: Over the years 2016 and 2017, the period 1 January to 30 April was selected to represent before and after implementation of WGS. Prior to 2017, line probe assays were used for mycobacterial species identification. Turnaround times for the different steps of the diagnostic process were evaluated for all positive mycobacterial cultures that were sent from our hospital to the Reference Laboratory during the study period. RESULTS: A total of 161 positive mycobacterial cultures were sent to the Reference Laboratory. Half of the isolates (n=81/161, 50%) were M. tuberculosis and 80/161 (50%) were non-tuberculous mycobacteria. The median number of workdays for mycobacterial species identification was 1 day (interquartile range (IQR) 1-3) in 2016 and 6 days (IQR 5-7) in 2017, p <0.001. For M. tuberculosis complex, the median time to drug susceptibility testing results, either molecular or phenotypic, was 12 days (IQR 11-18) in 2016 and 8 days (IQR 7-10) in 2017, p <0.001. CONCLUSIONS: Routine WGS performed well in this setting for mycobacterial identification and susceptibility testing for M. tuberculosis and decreased time to drug susceptibility testing results. There was an increase in turnaround times for species identification using WGS, when compared with the previous methods.
OBJECTIVES: Until recently whole genome sequencing (WGS) for mycobacteria has been restricted mostly to the research setting. However, in 2017 Public Health England has implemented WGS for routine mycobacterial identification and susceptibility testing for Mycobacterium tuberculosis. Our objective was to evaluate the impact of this change on the laboratory turnaround times and availability of results. METHODS: Over the years 2016 and 2017, the period 1 January to 30 April was selected to represent before and after implementation of WGS. Prior to 2017, line probe assays were used for mycobacterial species identification. Turnaround times for the different steps of the diagnostic process were evaluated for all positive mycobacterial cultures that were sent from our hospital to the Reference Laboratory during the study period. RESULTS: A total of 161 positive mycobacterial cultures were sent to the Reference Laboratory. Half of the isolates (n=81/161, 50%) were M. tuberculosis and 80/161 (50%) were non-tuberculous mycobacteria. The median number of workdays for mycobacterial species identification was 1 day (interquartile range (IQR) 1-3) in 2016 and 6 days (IQR 5-7) in 2017, p <0.001. For M. tuberculosis complex, the median time to drug susceptibility testing results, either molecular or phenotypic, was 12 days (IQR 11-18) in 2016 and 8 days (IQR 7-10) in 2017, p <0.001. CONCLUSIONS: Routine WGS performed well in this setting for mycobacterial identification and susceptibility testing for M. tuberculosis and decreased time to drug susceptibility testing results. There was an increase in turnaround times for species identification using WGS, when compared with the previous methods.
Authors: Iris Finci; Audrey Albertini; Matthias Merker; Sönke Andres; Nino Bablishvili; Ivan Barilar; Tatiana Cáceres; Valeriu Crudu; Eduardo Gotuzzo; Nchimunya Hapeela; Harald Hoffmann; Christine Hoogland; Thomas A Kohl; Katharina Kranzer; Anna Mantsoki; Florian P Maurer; Mark P Nicol; Ecaterina Noroc; Sara Plesnik; Timothy Rodwell; Morten Ruhwald; Theresa Savidge; Max Salfinger; Elizabeth Streicher; Nestani Tukvadze; Robin Warren; Widaad Zemanay; Anna Zurek; Stefan Niemann; Claudia M Denkinger Journal: Lancet Microbe Date: 2022-07-27
Authors: Annelies Van Rie; Elise De Vos; Emilyn Costa; Lennert Verboven; Felex Ndebele; Tim H Heupink; Steven Abrams; Boitumelo Fanampe; Anneke Van der Spoel Van Dyk; Salome Charalambous; Gavin Churchyard; Rob Warren Journal: Trials Date: 2022-10-08 Impact factor: 2.728