TY - JOUR
T1 - Outbreak of multidrug-resistant tuberculosis in South Africa undetected by WHO-endorsed commercial tests
T2 - an observational study
AU - Makhado, Ndivhuho A.
AU - Matabane, Edith
AU - Faccin, Mauro
AU - Pinçon, Claire
AU - Jouet, Agathe
AU - Boutachkourt, Fairouz
AU - Goeminne, Léonie
AU - Gaudin, Cyril
AU - Maphalala, Gugu
AU - Beckert, Patrick
AU - Niemann, Stefan
AU - Delvenne, Jean Charles
AU - Delmée, Michel
AU - Razwiedani, Lufuno
AU - Nchabeleng, Maphoshane
AU - Supply, Philip
AU - de Jong, Bouke C.
AU - André, Emmanuel
N1 - Funding Information:
This study was funded by VLIR-UOS (to NAM), National Research Foundation (South Africa; to NAM [81974]), and Innoviris (to EA, J-CD, MF, FB, and MD). BCdJ was supported by a European Research Council starting grant for INTERRUPTB (311725), and Genoscreen was supported by the French governmental programme Investing for the Future. EA was an employee of Cliniques Universitaires Saint-Luc (UC Louvain, Belgium) at the start of this study. We thank all colleagues at the Department of Medical Microbiology, National Health Laboratory Service–Dr George Mukhari Tertiary Laboratory; the Department of Microbiological Pathology, Sefako Makgatho Health Sciences University; the Mycobacteriology Unit, Institute of Tropical Medicine (Antwerp, Belgium); and the Global Health Institute, University of Antwerp. We thank all patients who were part of this study and the respective clinics and hospitals in Gauteng, North West, and Mpumalanga provinces; Elisabeth Sanchez-Padilla and Maryline Bonnet (Epicentre, Médecins Sans Frontières, Paris); and Rosine Gros (UC Louvain, Belgium, and Université Claude Bernard Lyon 1, France) and Stéphanie Duthoy (Genoscreen, Lille, France) for their technical assistance.
Publisher Copyright:
© 2018 Elsevier Ltd
PY - 2018/12
Y1 - 2018/12
N2 - Background: Global roll-out of rapid molecular assays is revolutionising the diagnosis of rifampicin resistance, predictive of multidrug-resistance, in tuberculosis. However, 30% of the multidrug-resistant (MDR) strains in an eSwatini study harboured the Ile491Phe mutation in the rpoB gene, which is associated with poor rifampicin-based treatment outcomes but is missed by commercial molecular assays or scored as susceptible by phenotypic drug-susceptibility testing deployed in South Africa. We evaluated the presence of Ile491Phe among South African tuberculosis isolates reported as isoniazid-monoresistant according to current national testing algorithms. Methods: We screened records of 37 644 Mycobacterium tuberculosis positive cultures from four South African provinces, diagnosed at the National Health Laboratory Service–Dr George Mukhari Tertiary Laboratory, to identify isolates with rifampicin sensitivity and isoniazid resistance according to Xpert MTB/RIF, GenoType MTBDRplus, and BACTEC MGIT 960. Of 1823 isolates that met these criteria, 277 were randomly selected and screened for Ile491Phe with multiplex allele-specific PCR and Sanger sequencing of rpoB. Ile491Phe-positive strains (as well as 17 Ile491Phe-bearing isolates from the eSwatini study) were then tested by Deeplex-MycTB deep sequencing and whole-genome sequencing to evaluate their patterns of extensive resistance, transmission, and evolution. Findings: Ile491Phe was identified in 37 (15%) of 249 samples with valid multiplex allele-specific PCR and sequencing results, thus reclassifying them as MDR. All 37 isolates were additionally identified as genotypically resistant to all first-line drugs by Deeplex-MycTB. Six of the South African isolates harboured four distinct mutations potentially associated with decreased bedaquiline sensitivity. Consistent with Deeplex-MycTB genotypic profiles, whole-genome sequencing revealed concurrent silent spread in South Africa of a MDR tuberculosis strain lineage extending from the eSwatini outbreak and at least another independently emerged Ile491Phe-bearing lineage. Whole-genome sequencing further suggested acquisition of mechanisms compensating for the Ile491Phe fitness cost, and of additional bedaquiline resistance following the introduction of this drug in South Africa. Interpretation: A substantial number of MDR tuberculosis cases harbouring the Ile491Phe mutation in the rpoB gene in South Africa are missed by current diagnostic strategies, resulting in ineffective first-line treatment, continued amplification of drug resistance, and concurrent silent spread in the community. Funding: VLIR-UOS, National Research Foundation (South Africa), and INNOVIRIS.
AB - Background: Global roll-out of rapid molecular assays is revolutionising the diagnosis of rifampicin resistance, predictive of multidrug-resistance, in tuberculosis. However, 30% of the multidrug-resistant (MDR) strains in an eSwatini study harboured the Ile491Phe mutation in the rpoB gene, which is associated with poor rifampicin-based treatment outcomes but is missed by commercial molecular assays or scored as susceptible by phenotypic drug-susceptibility testing deployed in South Africa. We evaluated the presence of Ile491Phe among South African tuberculosis isolates reported as isoniazid-monoresistant according to current national testing algorithms. Methods: We screened records of 37 644 Mycobacterium tuberculosis positive cultures from four South African provinces, diagnosed at the National Health Laboratory Service–Dr George Mukhari Tertiary Laboratory, to identify isolates with rifampicin sensitivity and isoniazid resistance according to Xpert MTB/RIF, GenoType MTBDRplus, and BACTEC MGIT 960. Of 1823 isolates that met these criteria, 277 were randomly selected and screened for Ile491Phe with multiplex allele-specific PCR and Sanger sequencing of rpoB. Ile491Phe-positive strains (as well as 17 Ile491Phe-bearing isolates from the eSwatini study) were then tested by Deeplex-MycTB deep sequencing and whole-genome sequencing to evaluate their patterns of extensive resistance, transmission, and evolution. Findings: Ile491Phe was identified in 37 (15%) of 249 samples with valid multiplex allele-specific PCR and sequencing results, thus reclassifying them as MDR. All 37 isolates were additionally identified as genotypically resistant to all first-line drugs by Deeplex-MycTB. Six of the South African isolates harboured four distinct mutations potentially associated with decreased bedaquiline sensitivity. Consistent with Deeplex-MycTB genotypic profiles, whole-genome sequencing revealed concurrent silent spread in South Africa of a MDR tuberculosis strain lineage extending from the eSwatini outbreak and at least another independently emerged Ile491Phe-bearing lineage. Whole-genome sequencing further suggested acquisition of mechanisms compensating for the Ile491Phe fitness cost, and of additional bedaquiline resistance following the introduction of this drug in South Africa. Interpretation: A substantial number of MDR tuberculosis cases harbouring the Ile491Phe mutation in the rpoB gene in South Africa are missed by current diagnostic strategies, resulting in ineffective first-line treatment, continued amplification of drug resistance, and concurrent silent spread in the community. Funding: VLIR-UOS, National Research Foundation (South Africa), and INNOVIRIS.
UR - http://www.scopus.com/inward/record.url?scp=85058180561&partnerID=8YFLogxK
U2 - 10.1016/S1473-3099(18)30496-1
DO - 10.1016/S1473-3099(18)30496-1
M3 - Article
C2 - 30342828
AN - SCOPUS:85058180561
SN - 1473-3099
VL - 18
SP - 1350
EP - 1359
JO - The Lancet Infectious Diseases
JF - The Lancet Infectious Diseases
IS - 12
ER -