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Blankson HNA, Kamara RF, Barilar I, Andres S, Conteh OS, Dallenga T, Foray L, Maurer F, Kranzer K, Utpatel C, Niemann S. Molecular determinants of multidrug-resistant tuberculosis in Sierra Leone. Microbiol Spectr 2024; 12:e0240523. [PMID: 38289066 PMCID: PMC10923214 DOI: 10.1128/spectrum.02405-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/28/2023] [Indexed: 03/06/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) management has become a serious global health challenge. Understanding its epidemic determinants on the regional level is crucial for developing effective control measures. We used whole genome sequencing data of 238 of Mycobacterium tuberculosis complex (MTBC) strains to determine drug resistance profiles, phylogeny, and transmission dynamics of MDR/rifampicin-resistant (RR) MTBC strains from Sierra Leone. Forty-two strains were classified as RR, 196 as MDR, 5 were resistant to bedaquiline (BDQ) and clofazimine (CFZ), but none was found to be resistant to fluoroquinolones. Sixty-one (26%) strains were resistant to all first-line drugs, three of which had additional resistance to BDQ/CFZ. The strains were classified into six major MTBC lineages (L), with strains of L4 being the most prevalent, 62% (n = 147), followed by L6 (Mycobacterium africanum) strains, (21%, n = 50). The overall clustering rate (using ≤d12 single-nucleotide polymorphism threshold) was 44%, stratified into 31 clusters ranging from 2 to 16 strains. The largest cluster (n = 16) was formed by sublineage 2.2.1 Beijing Ancestral 3 strains, which developed MDR several times. Meanwhile, 10 of the L6 strains had a primary MDR transmission. We observed a high diversity of drug resistance mutations, including borderline resistance mutations to isoniazid and rifampicin, and mutations were not detected by commercial assays. In conclusion, one in five strains investigated was resistant to all first-line drugs, three of which had evidence of BDQ/CFZ resistance. Implementation of interventions such as rapid diagnostics that prevent further resistance development and stop MDR-TB transmission chains in the country is urgently needed. IMPORTANCE A substantial proportion of MDR-TB strains in Sierra Leone were resistant against all first line drugs; however this makes the all-oral-six-month BPaLM regimen or other 6-9 months all oral regimens still viable, mainly because there was no FQ resistance.Resistance to BDQ was detected, as well as RR, due to mutations outside of the hotspot region. While the prevalence of those resistances was low, it is still cause for concern and needs to be closely monitored.
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Affiliation(s)
- Harriet N. A. Blankson
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- School of Biomedical and Allied Health Sciences, College of Health Sciences, University of Ghana, Korle-Bu, Accra, Ghana
| | - Rashidatu Fouad Kamara
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Ousman S. Conteh
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Tobias Dallenga
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- Cellular Microbiology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Lynda Foray
- National Leprosy and Tuberculosis Control Programme Sierra Leone, Freetown, Sierra Leone
| | - Florian Maurer
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Reims, Borstel, Germany
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel Leibniz Lung Center, Borstel, Germany
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Barilar I, Fernando T, Utpatel C, Abujate C, Madeira CM, José B, Mutaquiha C, Kranzer K, Niemann T, Ismael N, de Araujo L, Wirth T, Niemann S, Viegas S. Emergence of bedaquiline-resistant tuberculosis and of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis strains with rpoB Ile491Phe mutation not detected by Xpert MTB/RIF in Mozambique: a retrospective observational study. Lancet Infect Dis 2024; 24:297-307. [PMID: 37956677 DOI: 10.1016/s1473-3099(23)00498-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND In 2021, an estimated 4800 people developed rifampicin-resistant tuberculosis in Mozambique, 75% of which went undiagnosed. Detailed molecular data on rifampicin-resistant and multidrug-resistant (MDR) tuberculosis are not available. Here, we aimed at gaining precise data on the determinants of rifampicin-resistant and MDR tuberculosis in Mozambique. METHODS In this retrospective observational study, we performed whole-genome sequencing of 704 rifampicin-resistant Mycobacterium tuberculosis complex (Mtbc) strains submitted to the National Tuberculosis Reference Laboratory (NTRL) in Maputo, Mozambique, between 2015 and 2021. Phylogenetic strain classification, genomic resistance prediction, and cluster analysis were performed. FINDINGS Between Jan 1, 2015, and July 31, 2021, 2606 Mtbc isolates with an isoniazid or rifampicin resistance were identified in the NTRL biobank, of which, 1483 (56·9%) were from men, 1114 (42·7%) from women, and nine (0·4%) were unknown. Genome-based drug-resistant prediction classified 704 Mtbc strains as rifampicin resistant. 628 (89%) of the 704 Mtbc strains were classified MDR; of those, 146 (23%) were pre-extensively drug resistant (pre-XDR; additional fluoroquinolone resistance), and 24 (4%) extensively drug resistant (XDR; combined fluoroquinolone and bedaquiline resistance). Overall, 61 (9%) of 704 strains revealed resistance to bedaquiline: five (7%) of 76 rifampicin resistant plus bedaquiline resistant, 32 (7%) of 458 MDR plus bedaquiline resistant, and 24 (100%) of 24 XDR. Prevalence of bedaquiline resistance increased from 3% in 2016 to 14% in 2021. The cluster rate (12 single-nucleotide polymorphism threshold) was 42% for rifampicin-resistant strains, 78% for MDR strains, 94% for pre-XDR strains, and 96% for XDR Mtbc strains. 31 (4%) of 704 Mtbc strains, belonging to a diagnostic escape outbreak strain previously described in Eswatini (group_56), had an rpoB Ile491Phe mutation which is not detected by Xpert MTB/RIF (no other rpoB mutation). Of these, 23 (74%) showed additional resistance to bedaquiline, 13 (42%) had bedaquiline and fluoroquinolone resistance, and two (6%) were bedaquiline, fluoroquinolone, and delamanid resistant. INTERPRETATION Pre-XDR resistance is highly prevalent among MDR Mtbc strains in Mozambique and so is bedaquiline resistance; and the frequency of bedaquiline resistance quadrupled over time and was found even in Mtbc strains without fluoroquinolone resistance. Importantly, strains with Ile491Phe mutation were frequent, accounting for 31% (n=10) of MDR plus bedaquiline-resistant strains and 54% (n=13) of XDR Mtbc strains. Given the current diagnostic algorithms and treatment regimens, both the emergence of rifampicin resistance due to Ile491Phe and bedaquiline resistance might jeopardise MDR tuberculosis prevention and care unless sequencing-based technology is rolled out. The potential cross border spread of diagnostic escape strains needs further investigation. FUNDING The German Ministry of Health through the Seq_MDRTB-Net project, the Deutsche Forschungsgemeinschaft under Germany's Excellence Strategy Precision Medicine in Inflammation and the Research Training Group 2501 TransEvo, the Leibniz Science Campus Evolutionary Medicine of the Lung, and the German Ministry of Education and Research via the German Center for Infection Research.
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Affiliation(s)
- Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | | | - Benedita José
- National Tuberculosis Control Program, Directorate of Public Health, Ministry of Health, Maputo, Mozambique
| | - Claudia Mutaquiha
- National Tuberculosis Control Program, Directorate of Public Health, Ministry of Health, Maputo, Mozambique
| | - Katharina Kranzer
- Biomedical Research and Training Institute, Harare, Zimbabwe; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Division of Infectious Diseases and Tropical Medicine, University Hospital, Ludwig-Maximilians-Universität, Munich, Munich, Germany
| | - Tanja Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Nalia Ismael
- Instituto Nacional de Saúde, Marracuene, Mozambique
| | - Leonardo de Araujo
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thierry Wirth
- Ecole Pratique des Hautes Etudes, Paris Sciences et Lettres University, Paris, France; Institut de Systématique, Evolution, Biodiversite, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Paris, France; Ecole Pratique des Hautes Etudes, Université des Antilles, Paris, France
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany; Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia.
| | - Sofia Viegas
- Instituto Nacional de Saúde, Marracuene, Mozambique
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Danchuk SN, Solomon OE, Kohl TA, Dreyer V, Barilar I, Utpatel C, Niemann S, Soolingen DV, Anthony R, van Ingen J, Michael JS, Behr MA. Challenging the gold standard: the limitations of molecular assays for detection of Mycobacterium tuberculosis heteroresistance. Thorax 2024:thorax-2023-220202. [PMID: 38286614 DOI: 10.1136/thorax-2023-220202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/08/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVES Heteroresistant infections are defined as infections in which a mixture of drug-resistant and drug-susceptible populations are present. In Mycobacterium tuberculosis (M. tb), heteroresistance poses a challenge in diagnosis and has been linked with poor treatment outcomes. We compared the analytical sensitivity of molecular methods, such as GeneXpert and whole genome sequencing (WGS) in detecting heteroresistance when compared with the 'gold standard' phenotypic assay: the agar proportion method (APM). METHODS Using two rounds of proficiency surveys with defined monoresistant BCG strains and mixtures of susceptible/resistant M. tb, we determined the limit of detection (LOD) of known resistance associated mutations. RESULTS The LOD for rifampin-R (RIF-R) detection was 1% using APM, 60% using GeneXpert MTB/RIF, 10% using GeneXpert MTB/RIF Ultra and 10% using WGS. While WGS could detect mutations beyond those associated with RIF resistance, the LOD for these other mutations was also 10%. Additionally, we observed instances where laboratories did not report resistance in the majority population, yet the mutations were present in the raw sequence data. CONCLUSION The gold standard APM detects minority resistant populations at a lower proportion than molecular tests. Mycobacterium bovis BCG strains with defined resistance and extracted DNA from M. tb provided concordant results and can serve in quality control of laboratories offering molecular testing for resistance. Further research is required to determine whether the higher LOD of molecular tests is associated with negative treatment outcomes.
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Affiliation(s)
- Sarah N Danchuk
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Ori E Solomon
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Ivan Barilar
- German Centre for Infection Research, Research Centre Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | - Stefan Niemann
- Research Center Borstel Leibniz Lung Center, Borstel, Schleswig-Holstein, Germany
| | | | | | | | - Joy S Michael
- Microbiology, Christian Medical College and Hospital Vellore, Vellore, Tamil Nadu, India
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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Barilar I, Battaglia S, Borroni E, Brandao AP, Brankin A, Cabibbe AM, Carter J, Chetty D, Cirillo DM, Claxton P, Clifton DA, Cohen T, Coronel J, Crook DW, Dreyer V, Earle SG, Escuyer V, Ferrazoli L, Fowler PW, Gao GF, Gardy J, Gharbia S, Ghisi KT, Ghodousi A, Gibertoni Cruz AL, Grandjean L, Grazian C, Groenheit R, Guthrie JL, He W, Hoffmann H, Hoosdally SJ, Hunt M, Iqbal Z, Ismail NA, Jarrett L, Joseph L, Jou R, Kambli P, Khot R, Knaggs J, Koch A, Kohlerschmidt D, Kouchaki S, Lachapelle AS, Lalvani A, Lapierre SG, Laurenson IF, Letcher B, Lin WH, Liu C, Liu D, Malone KM, Mandal A, Mansjö M, Calisto Matias DVL, Meintjes G, de Freitas Mendes F, Merker M, Mihalic M, Millard J, Miotto P, Mistry N, Moore D, Musser KA, Ngcamu D, Nhung HN, Niemann S, Nilgiriwala KS, Nimmo C, O’Donnell M, Okozi N, Oliveira RS, Omar SV, Paton N, Peto TEA, Pinhata JMW, Plesnik S, Puyen ZM, Rabodoarivelo MS, Rakotosamimanana N, Rancoita PMV, Rathod P, Robinson ER, Rodger G, Rodrigues C, Rodwell TC, Roohi A, Santos-Lazaro D, Shah S, Smith G, Kohl TA, Solano W, Spitaleri A, Steyn AJC, Supply P, Surve U, Tahseen S, Thuong NTT, Thwaites G, Todt K, Trovato A, Utpatel C, Van Rie A, Vijay S, Walker AS, Walker TM, Warren R, Werngren J, Wijkander M, Wilkinson RJ, Wilson DJ, Wintringer P, Xiao YX, Yang Y, Yanlin Z, Yao SY, Zhu B. Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach. Nat Commun 2024; 15:488. [PMID: 38216576 PMCID: PMC10786857 DOI: 10.1038/s41467-023-44325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024] Open
Abstract
The World Health Organization has a goal of universal drug susceptibility testing for patients with tuberculosis. However, molecular diagnostics to date have focused largely on first-line drugs and predicting susceptibilities in a binary manner (classifying strains as either susceptible or resistant). Here, we used a multivariable linear mixed model alongside whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration (MIC) in 15,211 Mycobacterium tuberculosis clinical isolates from 23 countries across five continents. We identified 492 unique MIC-elevating variants across 13 drugs, as well as 91 mutations likely linked to hypersensitivity. Our results advance genetics-based diagnostics for tuberculosis and serve as a curated training/testing dataset for development of drug resistance prediction algorithms.
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Modongo C, Barilar I, Wang Q, Molefi T, Makhondo T, Niemann S, Shin SS. Tuberculosis Variant with Rifampin Resistance Undetectable by Xpert MTB/RIF, Botswana. Emerg Infect Dis 2023; 29:2403-2406. [PMID: 37877680 PMCID: PMC10617350 DOI: 10.3201/eid2911.230987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
GeneXpert MTB/RIF, a tool widely used for diagnosing tuberculosis, has limitations for detecting rifampin resistance in certain variants. We report transmission of a pre-extensively drug-resistant variant in Botswana that went undetected by GeneXpert. The public health impact of misdiagnosis emphasizes the need for comprehensive molecular testing to identify resistance and guide treatment.
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Economou Lundeberg E, Andersson V, Wijkander M, Groenheit R, Mansjö M, Werngren J, Cortes T, Barilar I, Niemann S, Merker M, Köser CU, Davies Forsman L. In vitro activity of new combinations of β-lactam and β-lactamase inhibitors against the Mycobacterium tuberculosis complex. Microbiol Spectr 2023; 11:e0178123. [PMID: 37737628 PMCID: PMC10580993 DOI: 10.1128/spectrum.01781-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/24/2023] [Indexed: 09/23/2023] Open
Abstract
As meropenem-clavulanic acid is recommended for the treatment of drug-resistant tuberculosis, the repurposing of new carbapenem combinations may provide new treatment options, including oral alternatives. Therefore, we studied the in vitro activities of meropenem-vaborbactam, meropenem-clavulanic acid, and tebipenem-clavulanic acid. One hundred nine Mycobacterium tuberculosis complex (MTBC) clinical isolates were tested, of which 69 were pan-susceptible and the remaining pyrazinamide- or multidrug-resistant. Broth microdilution MICs were determined using the EUCAST reference method. Meropenem and tebipenem were tested individually and in combination with vaborbactam 8 mg/L and clavulanic-acid 2 and 4 mg/L, respectively. Whole-genome sequencing was performed to explore resistance mechanisms. Clavulanic acid lowered the modal tebipenem MIC approximately 16-fold (from 16 to 1 mg/L). The modal meropenem MIC was reduced twofold by vaborbactam compared with an approximately eightfold decrease by clavulanic acid. The only previously described high-confidence carbapenem resistance mutation, crfA T62A, was shared by a subgroup of lineage 4.3.4.1 isolates and did not correlate with elevated MICs. The presence of a β-lactamase inhibitor reduced the MTBC MICs of tebipenem and meropenem. The resulting MIC distribution was lowest for the orally available drugs tebipenem-clavulanic acid. Whether this in vitro activity translates to similar or greater clinical efficacy of tebipenem-clavulanic acid compared with the currently WHO-endorsed meropenem-clavulanic acid requires clinical studies. IMPORTANCE Repurposing of already approved antibiotics, such as β-lactams in combination with β-lactamase inhibitors, may provide new treatment alternatives for drug-resistant tuberculosis. Meropenem-clavulanic acid was more active in vitro compared to meropenem-vaborbactam. Notably, tebipenem-clavulanic acid showed even better activity, raising the potential of an all-oral treatment option. Clinical data are needed to investigate whether the better in vitro activity of tebipenem-clavulanic acid correlates with greater clinical efficacy compared with the currently WHO-endorsed meropenem-clavulanic acid.
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Affiliation(s)
| | - Viktoria Andersson
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Wijkander
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Ramona Groenheit
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Mikael Mansjö
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Jim Werngren
- Department of Microbiology, Public Health Agency of Sweden, Stockholm, Sweden
| | - Teresa Cortes
- Pathogen Gene Regulation Unit, Biomedicine Institute of Valencia (IBV), CSIC, Valencia, Spain
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Matthias Merker
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Claudio U. Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lina Davies Forsman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medicine, Division of Infectious Diseases, Karolinska Institutet, Solna, Sweden
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Pérez-Llanos FJ, Dreyer V, Barilar I, Utpatel C, Kohl TA, Murcia MI, Homolka S, Merker M, Niemann S. Transmission Dynamics of a Mycobacterium tuberculosis Complex Outbreak in an Indigenous Population in the Colombian Amazon Region. Microbiol Spectr 2023; 11:e0501322. [PMID: 37222610 PMCID: PMC10269451 DOI: 10.1128/spectrum.05013-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/04/2023] [Indexed: 05/25/2023] Open
Abstract
Whole genome sequencing (WGS) has become the main tool for studying the transmission of Mycobacterium tuberculosis complex (MTBC) strains; however, the clonal expansion of one strain often limits its application in local MTBC outbreaks. The use of an alternative reference genome and the inclusion of repetitive regions in the analysis could potentially increase the resolution, but the added value has not yet been defined. Here, we leveraged short and long WGS read data of a previously reported MTBC outbreak in the Colombian Amazon Region to analyze possible transmission chains among 74 patients in the indigenous setting of Puerto Nariño (March to October 2016). In total, 90.5% (67/74) of the patients were infected with one distinct MTBC strain belonging to lineage 4.3.3. Employing a reference genome from an outbreak strain and highly confident single nucleotide polymorphisms (SNPs) in repetitive genomic regions, e.g., the proline-glutamic acid/proline-proline-glutamic-acid (PE/PPE) gene family, increased the phylogenetic resolution compared to a classical H37Rv reference mapping approach. Specifically, the number of differentiating SNPs increased from 890 to 1,094, which resulted in a more granular transmission network as judged by an increasing number of individual nodes in a maximum parsimony tree, i.e., 5 versus 9 nodes. We also found in 29.9% (20/67) of the outbreak isolates, heterogenous alleles at phylogenetically informative sites, suggesting that these patients are infected with more than one clone. In conclusion, customized SNP calling thresholds and employment of a local reference genome for a mapping approach can improve the phylogenetic resolution in highly clonal MTBC populations and help elucidate within-host MTBC diversity. IMPORTANCE The Colombian Amazon around Puerto Nariño has a high tuberculosis burden with a prevalence of 1,267/100,000 people in 2016. Recently, an outbreak of Mycobacterium tuberculosis complex (MTBC) bacteria among the indigenous populations was identified with classical MTBC genotyping methods. Here, we employed a whole-genome sequencing-based outbreak investigation in order to improve the phylogenetic resolution and gain new insights into the transmission dynamics in this remote Colombian Amazon Region. The inclusion of well-supported single nucleotide polymorphisms in repetitive regions and a de novo-assembled local reference genome provided a more granular picture of the circulating outbreak strain and revealed new transmission chains. Multiple patients from different settlements were possibly infected with at least two different clones in this high-incidence setting. Thus, our results have the potential to improve molecular surveillance studies in other high-burden settings, especially regions with few clonal multidrug-resistant (MDR) MTBC lineages/clades.
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Affiliation(s)
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
| | - Martha Isabel Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Germany
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Noroc E, Chesov D, Merker M, Gröschel MI, Barilar I, Dreyer V, Ciobanu N, Reimann M, Crudu V, Lange C. Limited Nosocomial Transmission of Drug-Resistant Tuberculosis, Moldova. Emerg Infect Dis 2023; 29:1046-1050. [PMID: 37081601 PMCID: PMC10124655 DOI: 10.3201/eid2905.230035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Applying whole-genome-sequencing, we aimed to detect transmission events of multidrug-resistant/rifampin-resistant strains of Mycobacterium tuberculosis complex at a tuberculosis hospital in Chisinau, Moldova. We recorded ward, room, and bed information for each patient and monitored in-hospital transfers over 1 year. Detailed molecular and patient surveillance revealed only 2 nosocomial transmission events.
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Baker CR, Barilar I, de Araujo LS, Rimoin AW, Parker DM, Boyd R, Tobias JL, Moonan PK, Click ES, Finlay A, Oeltmann JE, Minin VN, Modongo C, Zetola NM, Niemann S, Shin SS. Use of High-Resolution Geospatial and Genomic Data to Characterize Recent Tuberculosis Transmission, Botswana. Emerg Infect Dis 2023; 29:977-987. [PMID: 37081530 PMCID: PMC10124643 DOI: 10.3201/eid2905.220796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
Combining genomic and geospatial data can be useful for understanding Mycobacterium tuberculosis transmission in high-burden tuberculosis (TB) settings. We performed whole-genome sequencing on M. tuberculosis DNA extracted from sputum cultures from a population-based TB study conducted in Gaborone, Botswana, during 2012-2016. We determined spatial distribution of cases on the basis of shared genotypes among isolates. We considered clusters of isolates with ≤5 single-nucleotide polymorphisms identified by whole-genome sequencing to indicate recent transmission and clusters of ≥10 persons to be outbreaks. We obtained both molecular and geospatial data for 946/1,449 (65%) participants with culture-confirmed TB; 62 persons belonged to 5 outbreaks of 10-19 persons each. We detected geospatial clustering in just 2 of those 5 outbreaks, suggesting heterogeneous spatial patterns. Our findings indicate that targeted interventions applied in smaller geographic areas of high-burden TB identified using integrated genomic and geospatial data might help interrupt TB transmission during outbreaks.
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Smith JP, Modongo C, Oeltmann JE, Dima M, Matsiri O, Fane O, Molefi T, Shin SS, Barilar I, Niemann S, Zetola NM, Moonan PK. HIGH-RESOLUTION CHARACTERIZATION OF NOSOCOMIAL MYCOBACTERIUM TUBERCULOSIS TRANSMISSION EVENTS IN BOTSWANA. Am J Epidemiol 2023; 192:503-506. [PMID: 36549903 PMCID: PMC10372855 DOI: 10.1093/aje/kwac214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/08/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
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Goldstein IH, Bayer D, Barilar I, Kizito B, Matsiri O, Modongo C, Zetola NM, Niemann S, Minin VM, Shin SS. Using genetic data to identify transmission risk factors: Statistical assessment and application to tuberculosis transmission. PLoS Comput Biol 2022; 18:e1010696. [PMID: 36469509 DOI: 10.1371/journal.pcbi.1010696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 12/15/2022] [Accepted: 10/31/2022] [Indexed: 12/12/2022] Open
Abstract
Identifying host factors that influence infectious disease transmission is an important step toward developing interventions to reduce disease incidence. Recent advances in methods for reconstructing infectious disease transmission events using pathogen genomic and epidemiological data open the door for investigation of host factors that affect onward transmission. While most transmission reconstruction methods are designed to work with densely sampled outbreaks, these methods are making their way into surveillance studies, where the fraction of sampled cases with sequenced pathogens could be relatively low. Surveillance studies that use transmission event reconstruction then use the reconstructed events as response variables (i.e., infection source status of each sampled case) and use host characteristics as predictors (e.g., presence of HIV infection) in regression models. We use simulations to study estimation of the effect of a host factor on probability of being an infection source via this multi-step inferential procedure. Using TransPhylo-a widely-used method for Bayesian estimation of infectious disease transmission events-and logistic regression, we find that low sensitivity of identifying infection sources leads to dilution of the signal, biasing logistic regression coefficients toward zero. We show that increasing the proportion of sampled cases improves sensitivity and some, but not all properties of the logistic regression inference. Application of these approaches to real world data from a population-based TB study in Botswana fails to detect an association between HIV infection and probability of being a TB infection source. We conclude that application of a pipeline, where one first uses TransPhylo and sparsely sampled surveillance data to infer transmission events and then estimates effects of host characteristics on probabilities of these events, should be accompanied by a realistic simulation study to better understand biases stemming from imprecise transmission event inference.
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Affiliation(s)
- Isaac H Goldstein
- Department of Statistics, University of California, Irvine, California, United States of America
| | - Damon Bayer
- Department of Statistics, University of California, Irvine, California, United States of America
| | - Ivan Barilar
- German Center for Infection Research, Research Center Borstel, Borstel, Germany
| | | | | | | | - Nicola M Zetola
- Augusta University, Augusta, Georgia, United States of America
| | - Stefan Niemann
- German Center for Infection Research, Research Center Borstel, Borstel, Germany
| | - Volodymyr M Minin
- Department of Statistics, University of California, Irvine, California, United States of America
| | - Sanghyuk S Shin
- Sue & Bill Gross School of Nursing, University of California, Irvine, California, United States of America
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12
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Finci I, Albertini A, Merker M, Andres S, Bablishvili N, Barilar I, Cáceres T, Crudu V, Gotuzzo E, Hapeela N, Hoffmann H, Hoogland C, Kohl TA, Kranzer K, Mantsoki A, Maurer FP, Nicol MP, Noroc E, Plesnik S, Rodwell T, Ruhwald M, Savidge T, Salfinger M, Streicher E, Tukvadze N, Warren R, Zemanay W, Zurek A, Niemann S, Denkinger CM. Investigating resistance in clinical Mycobacterium tuberculosis complex isolates with genomic and phenotypic antimicrobial susceptibility testing: a multicentre observational study. Lancet Microbe 2022; 3:e672-e682. [PMID: 35907429 PMCID: PMC9436784 DOI: 10.1016/s2666-5247(22)00116-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/10/2022] [Accepted: 04/14/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) of Mycobacterium tuberculosis complex has become an important tool in diagnosis and management of drug-resistant tuberculosis. However, data correlating resistance genotype with quantitative phenotypic antimicrobial susceptibility testing (AST) are scarce. METHODS In a prospective multicentre observational study, 900 clinical M tuberculosis complex isolates were collected from adults with drug-resistant tuberculosis in five high-endemic tuberculosis settings around the world (Georgia, Moldova, Peru, South Africa, and Viet Nam) between Dec 5, 2014, and Dec 12, 2017. Minimum inhibitory concentrations (MICs) and resulting binary phenotypic AST results for up to nine antituberculosis drugs were determined and correlated with resistance-conferring mutations identified by WGS. FINDINGS Considering WHO-endorsed critical concentrations as reference, WGS had high accuracy for prediction of resistance to isoniazid (sensitivity 98·8% [95% CI 98·5-99·0]; specificity 96·6% [95% CI 95·2-97·9]), levofloxacin (sensitivity 94·8% [93·3-97·6]; specificity 97·1% [96·7-97·6]), kanamycin (sensitivity 96·1% [95·4-96·8]; specificity 95·0% [94·4-95·7]), amikacin (sensitivity 97·2% [96·4-98·1]; specificity 98·6% [98·3-98·9]), and capreomycin (sensitivity 93·1% [90·0-96·3]; specificity 98·3% [98·0-98·7]). For rifampicin, pyrazinamide, and ethambutol, the specificity of resistance prediction was suboptimal (64·0% [61·0-67·1], 83·8% [81·0-86·5], and 40·1% [37·4-42·9], respectively). Specificity for rifampicin increased to 83·9% when borderline mutations with MICs overlapping with the critical concentration were excluded. Consequently, we highlighted mutations in M tuberculosis complex isolates that are often falsely identified as susceptible by phenotypic AST, and we identified potential novel resistance-conferring mutations. INTERPRETATION The combined analysis of mutations and quantitative phenotypes shows the potential of WGS to produce a refined interpretation of resistance, which is needed for individualised therapy, and eventually could allow differential drug dosing. However, variability of MIC data for some M tuberculosis complex isolates carrying identical mutations also reveals limitations of our understanding of the genotype and phenotype relationships (eg, including epistasis and strain genetic background). FUNDING Bill & Melinda Gates Foundation, German Centre for Infection Research, German Research Foundation, Excellence Cluster Precision Medicine of Inflammation (EXC 2167), and Leibniz ScienceCampus EvoLUNG.
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Affiliation(s)
- Iris Finci
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | | | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; Evolution of the Resistome, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Nino Bablishvili
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Tatiana Cáceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Valeriu Crudu
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Nchimunya Hapeela
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Harald Hoffmann
- SYNLAB Gauting, SYNLAB MVZ Dachau, Gauting, Germany; Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | | | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Katharina Kranzer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Biomedical Research and Training Institute, Harare, Zimbabwe
| | | | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark P Nicol
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Ecaterina Noroc
- Phthisiopneumology Institute Chiril Draganiuc, Chisinau, Moldova
| | - Sara Plesnik
- Institute of Microbiology and Laboratory Medicine (IML Red), WHO Supranational TB Reference Laboratory, Gauting, Germany
| | - Timothy Rodwell
- FIND, Geneva, Switzerland; Division of Pulmonary, Critical Care and Sleep Medicine, University of California San Diego, La Jolla, CA, USA
| | | | - Theresa Savidge
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA; Alaska State Public Health Laboratories, Anchorage, AK, USA
| | - Max Salfinger
- College of Public Health, University of South Florida, Tampa, FL, USA; Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Elizabeth Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Nestani Tukvadze
- National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Robin Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Widaad Zemanay
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anna Zurek
- Advanced Diagnostic Laboratories, National Jewish Health, Denver, CO, USA
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany; Hamburg-Borstel-Lübeck-Riems, Germany
| | - Claudia M Denkinger
- FIND, Geneva, Switzerland; German Center for Infection Research, Heidelberg, Germany; Division of Clinical Tropical Medicine and German Centre for Infection Research, Heidelberg University Hospital, Heidelberg, Germany.
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13
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Dreyer V, Mandal A, Dev P, Merker M, Barilar I, Utpatel C, Nilgiriwala K, Rodrigues C, Crook DW, Crook DW, Peto TEA, Walker AS, Hoosdally SJ, Gibertoni Cruz AL, Carter J, Earle S, Kouchaki S, Yang Y, Walker TM, Fowler PW, Wilson D, Clifton DA, Iqbal Z, Hunt M, Knaggs J, Cirillo DM, Borroni E, Battaglia S, Ghodousi A, Spitaleri A, Cabibbe A, Tahseen S, Nilgiriwala K, Shah S, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Kohl T, Merker M, Hoffmann H, Todt K, Plesnik S, Ismail N, Omar SV, Ngcamu LJD, Okozi N, Yao SY, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Moore D, Coronel J, Solano W, Gao GF, He G, Zhao Y, Ma A, Liu C, Zhu B, Laurenson I, Claxton P, Wilkinson RJ, Koch A, Lalvani A, Posey J, Gardy J, Werngren J, Paton N, Jou R, Wu MH, Xiao YX, Ferrazoli L, de Oliveira RS, Millard J, Warren R, Van Rie A, Lapierre SG, Rabodoarivelo MS, Rakotosamimanana N, Nimmo C, Musser K, Escuyer V, Cohen T, Rasigade JP, Wirth T, Mistry N, Niemann S. High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region. Genome Med 2022; 14:95. [PMID: 35989319 PMCID: PMC9394022 DOI: 10.1186/s13073-022-01076-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined.
Methods
In a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively.
Results
In total, 1016 MTBC strains were MDR, out of which 703 (69.2%) were pre-XDR and 45 (4.4%) were XDR. Cluster rates were high among MDR (57.8%) and pre-XDR/XDR (79%) strains with three dominant L2 (Beijing) strain clusters (Cl 1–3) representing half of the pre-XDR and 40% of the XDR-TB cases. L2 strains were associated with pre-XDR/XDR-TB (P < 0.001) and, particularly Cl 1–3 strains, had high first-line and FQ resistance rates (81.6–90.6%). Epidemic success analysis using THD showed that L2 strains outperformed L1, L3, and L4 strains in short- and long-term time scales. More importantly, L2 MDR and MDR + strains had higher THD success indices than their not-MDR counterparts. Overall, compensatory mutation rates were highest in L2 strains and positive selection was detected in genes of L2 strains associated with drug tolerance (prpB and ppsA) and virulence (Rv2828c). Compensatory mutations in L2 strains were associated with a threefold increase of THD indices, suggesting improved transmissibility.
Conclusions
Our data indicate a drastic increase of FQ resistance, as well as emerging bedaquiline resistance which endangers the success of newly endorsed MDR-TB treatment regimens. Rapid changes in treatment and control strategies are required to contain transmission of highly successful pre-XDR L2 strains in the Mumbai Metropolitan region but presumably also India-wide.
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14
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Georghiou SB, Rodwell TC, Korobitsyn A, Abbadi SH, Ajbani K, Alffenaar JW, Alland D, Alvarez N, Andres S, Ardizzoni E, Aubry A, Baldan R, Ballif M, Barilar I, Böttger EC, Chakravorty S, Claxton PM, Cirillo DM, Comas I, Coulter C, Denkinger CM, Derendinger B, Desmond EP, de Steenwinkel JE, Dheda K, Diacon AH, Dolinger DL, Dooley KE, Egger M, Ehsani S, Farhat MR, Fattorini L, Finci I, Le Ray LF, Furió V, Groenheit R, Gumbo T, Heysell SK, Hillemann D, Hoffmann H, Hsueh PR, Hu Y, Huang H, Hussain A, Ismail F, Izumi K, Jagielski T, Johnson JL, Kambli P, Kaniga K, Eranga Karunaratne G, Sharma MK, Keller PM, Kelly EC, Kholina M, Kohli M, Kranzer K, Laurenson IF, Limberis J, Grace Lin SY, Liu Y, López-Gavín A, Lyander A, Machado D, Martinez E, Masood F, Mitarai S, Mvelase NR, Niemann S, Nikolayevskyy V, Maurer FP, Merker M, Miotto P, Omar SV, Otto-Knapp R, Palaci M, Palacios Gutiérrez JJ, Peacock SJ, Peloquin CA, Perera J, Pierre-Audigier C, Pholwat S, Posey JE, Prammananan T, Rigouts L, Robledo J, Rockwood N, Rodrigues C, Salfinger M, Schechter MC, Seifert M, Sengstake S, Shinnick T, Shubladze N, Sintchenko V, Sirgel F, Somasundaram S, Sterling TR, Spitaleri A, Streicher E, Supply P, Svensson E, Tagliani E, Tahseen S, Takaki A, Theron G, Torrea G, Van Deun A, van Ingen J, Van Rie A, van Soolingen D, Vargas Jr R, Venter A, Veziris N, Villellas C, Viveiros M, Warren R, Wen S, Werngren J, Wilkinson RJ, Yang C, Yılmaz FF, Zhang T, Zimenkov D, Ismail N, Köser CU, Schön T. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment. Eur Respir J 2022; 59:2200166. [PMID: 35422426 PMCID: PMC9059840 DOI: 10.1183/13993003.00166-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/05/2022] [Indexed: 11/07/2022]
Abstract
Approximately 85 000 deaths globally in 2019 were due to drug-resistant tuberculosis (TB), which corresponds to 7% of global deaths attributable to bacterial antimicrobial resistance [1]. Yet concerns have been mounting that drug-resistant TB was being underestimated because the approaches to define susceptibility and resistance to anti-TB agents had not kept up with those used for other major bacterial pathogens [2–9]. Here, we outline the recent, evidence-based initiatives spearheaded by the World Health Organization (WHO) and others to update breakpoints (traditionally referred to as critical concentrations (CCs)) that are used for phenotypic antimicrobial susceptibility testing (AST), also called drug susceptibility testing in the TB literature. Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6
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15
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Chesov E, Chesov D, Maurer FP, Andres S, Utpatel C, Barilar I, Donica A, Reimann M, Niemann S, Lange C, Crudu V, Heyckendorf J, Merker M. Emergence of bedaquiline resistance in a high tuberculosis burden country. Eur Respir J 2022; 59:2100621. [PMID: 34503982 PMCID: PMC8943268 DOI: 10.1183/13993003.00621-2021] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/18/2021] [Indexed: 11/05/2022]
Abstract
RATIONALE Bedaquiline has been classified as a group A drug for the treatment of multidrug-resistant tuberculosis (MDR-TB) by the World Health Organization; however, globally emerging resistance threatens the effectivity of novel MDR-TB treatment regimens. OBJECTIVES We analysed pre-existing and emerging bedaquiline resistance in bedaquiline-based MDR-TB therapies, and risk factors associated with treatment failure and death. METHODS In a cross-sectional cohort study, we employed patient data, whole-genome sequencing (WGS) and phenotyping of Mycobacterium tuberculosis complex (MTBC) isolates. We could retrieve baseline isolates from 30.5% (62 out of 203) of all MDR-TB patients who received bedaquiline between 2016 and 2018 in the Republic of Moldova. This includes 26 patients for whom we could also retrieve a follow-up isolate. MEASUREMENTS AND MAIN RESULTS At baseline, all MTBC isolates were susceptible to bedaquiline. Among 26 patients with available baseline and follow-up isolates, four (15.3%) patients harboured strains which acquired bedaquiline resistance under therapy, while one (3.8%) patient was re-infected with a second bedaquiline-resistant strain. Treatment failure and death were associated with cavitary disease (p=0.011), and any additional drug prescribed in the bedaquiline-containing regimen with WGS-predicted resistance at baseline (OR 1.92 per unit increase, 95% CI 1.15-3.21; p=0.012). CONCLUSIONS MDR-TB treatments based on bedaquiline require a functional background regimen to achieve high cure rates and to prevent the evolution of bedaquiline resistance. Novel MDR-TB therapies with bedaquiline require timely and comprehensive drug resistance monitoring.
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Affiliation(s)
- Elena Chesov
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova
- Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- These authors contributed equally
| | - Dumitru Chesov
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- These authors contributed equally
| | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Ana Donica
- Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Maja Reimann
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Stefan Niemann
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christoph Lange
- Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
- Department of Medicine, Umeå University, Umeå, Sweden
- Global TB Program, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Valeriu Crudu
- Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Jan Heyckendorf
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
- These authors contributed equally
| | - Matthias Merker
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
- These authors contributed equally
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16
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Mbelele PM, Utpatel C, Sauli E, Mpolya EA, Mutayoba BK, Barilar I, Dreyer V, Merker M, Sariko ML, Swema BM, Mmbaga BT, Gratz J, Addo KK, Pletschette M, Niemann S, Houpt ER, Mpagama SG, Heysell SK. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac042. [PMID: 35465240 PMCID: PMC9021016 DOI: 10.1093/jacamr/dlac042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background Rifampicin- or multidrug-resistant (RR/MDR) Mycobacterium tuberculosis complex (MTBC) strains account for considerable morbidity and mortality globally. WGS-based prediction of drug resistance may guide clinical decisions, especially for the design of RR/MDR-TB therapies. Methods We compared WGS-based drug resistance-predictive mutations for 42 MTBC isolates from MDR-TB patients in Tanzania with the MICs of 14 antibiotics measured in the Sensititre™ MycoTB assay. An isolate was phenotypically categorized as resistant if it had an MIC above the epidemiological-cut-off (ECOFF) value, or as susceptible if it had an MIC below or equal to the ECOFF. Results Overall, genotypically non-wild-type MTBC isolates with high-level resistance mutations (gNWT-R) correlated with isolates with MIC values above the ECOFF. For instance, the median MIC value (mg/L) for rifampicin-gNWT-R strains was >4.0 (IQR 4.0–4.0) compared with 0.5 (IQR 0.38–0.50) in genotypically wild-type (gWT-S, P < 0.001); isoniazid-gNWT-R >4.0 (IQR 2.0–4.0) compared with 0.25 (IQR 0.12–1.00) among gWT-S (P = 0.001); ethionamide-gNWT-R 15.0 (IQR 10.0–20.0) compared with 2.50 (IQR; 2.50–5.00) among gWT-S (P < 0.001). WGS correctly predicted resistance in 95% (36/38) and 100% (38/38) of the rifampicin-resistant isolates with ECOFFs >0.5 and >0.125 mg/L, respectively. No known resistance-conferring mutations were present in genes associated with resistance to fluoroquinolones, aminoglycosides, capreomycin, bedaquiline, delamanid, linezolid, clofazimine, cycloserine, or p-amino salicylic acid. Conclusions WGS-based drug resistance prediction worked well to rule-in phenotypic drug resistance and the absence of second-line drug resistance-mediating mutations has the potential to guide the design of RR/MDR-TB regimens in the future.
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Affiliation(s)
- Peter M. Mbelele
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Corresponding author. E-mail:
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Elingarami Sauli
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Emmanuel A. Mpolya
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
| | - Beatrice K. Mutayoba
- Ministry of Health, National AIDS Control Program, Department of Preventive Services, Dodoma, Tanzania
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | | | | | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Kennedy K. Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Michel Pletschette
- CIHLMU Center for International Health, University Hospital, LMU Munich, Germany
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Munich, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Stellah G. Mpagama
- Kibong’oto Infectious Diseases Hospital (KIDH), Siha, Kilimanjaro, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology (NM-AIST), Arusha, Tanzania
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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17
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Vargas R, Freschi L, Spitaleri A, Tahseen S, Barilar I, Niemann S, Miotto P, Cirillo DM, Köser CU, Farhat MR. Role of Epistasis in Amikacin, Kanamycin, Bedaquiline, and Clofazimine Resistance in Mycobacterium tuberculosis Complex. Antimicrob Agents Chemother 2021; 65:e0116421. [PMID: 34460306 PMCID: PMC8522733 DOI: 10.1128/aac.01164-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic resistance among bacterial pathogens poses a major global health threat. Mycobacterium tuberculosis complex (MTBC) is estimated to have the highest resistance rates of any pathogen globally. Given the low growth rate and the need for a biosafety level 3 laboratory, the only realistic avenue to scale up drug susceptibility testing (DST) for this pathogen is to rely on genotypic techniques. This raises the fundamental question of whether a mutation is a reliable surrogate for phenotypic resistance or whether the presence of a second mutation can completely counteract its effect, resulting in major diagnostic errors (i.e., systematic false resistance results). To date, such epistatic interactions have only been reported for streptomycin that is now rarely used. By analyzing more than 31,000 MTBC genomes, we demonstrated that the eis C-14T promoter mutation, which is interrogated by several genotypic DST assays endorsed by the World Health Organization, cannot confer resistance to amikacin and kanamycin if it coincides with loss-of-function (LoF) mutations in the coding region of eis. To our knowledge, this represents the first definitive example of antibiotic reversion in MTBC. Moreover, we raise the possibility that mmpR (Rv0678) mutations are not valid markers of resistance to bedaquiline and clofazimine if these coincide with an LoF mutation in the efflux pump encoded by mmpS5 (Rv0677c) and mmpL5 (Rv0676c).
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Affiliation(s)
- Roger Vargas
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sabira Tahseen
- National TB Reference Laboratory, National TB Control Program, Islamabad, Pakistan
| | - Ivan Barilar
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Maha R. Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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18
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Omar SV, Hillemann D, Pandey S, Merker M, Witt AK, Nadarajan D, Barilar I, Bainomugisa A, Kelly EC, Diel R, Vidanagama DS, Samarasinghe AIP, Cader MR, Götsch U, Lavu E, Alabi A, Schön T, Coulter C, Niemann S, Maurer FP, Ismail NA, Köser CU, Ismail F. Systematic rifampicin resistance errors with Xpert ® MTB/RIF Ultra: implications for regulation of genotypic assays. Int J Tuberc Lung Dis 2021; 24:1307-1311. [PMID: 33317678 DOI: 10.5588/ijtld.20.0396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- S V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa, Department of Molecular Medicine & Haematology, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - D Hillemann
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - S Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, QLD, Australia
| | - M Merker
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany, German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - A-K Witt
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - D Nadarajan
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - I Barilar
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, QLD, Australia, Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany
| | - A Bainomugisa
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, QLD, Australia
| | - E C Kelly
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - R Diel
- Institute for Epidemiology, University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | - D S Vidanagama
- National Tuberculosis Reference Laboratory, Welisara, Sri Lanka
| | - A I P Samarasinghe
- National Programme for Tuberculosis Control & Chest Diseases, Colombo, Sri Lanka
| | - M R Cader
- National Programme for Tuberculosis Control & Chest Diseases, Colombo, Sri Lanka
| | - U Götsch
- Department of Infectious Diseases, Public Health Authority, City of Frankfurt am Main, Germany
| | - E Lavu
- Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - A Alabi
- TB Laboratory, Centre de Recherches Medicales de Lambarene, Lambarene, Gabon
| | - T Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden, Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - C Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, QLD, Australia
| | - S Niemann
- Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, Borstel, Germany, German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - F P Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany, Department of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - N A Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa, Department of Internal Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - C U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - F Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa, Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
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19
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Grobbel HP, Merker M, Köhler N, Andres S, Hoffmann H, Heyckendorf J, Reimann M, Barilar I, Dreyer V, Hillemann D, Kalsdorf B, Kohl TA, Sanchez-Carballo P, Schaub D, Todt K, Utpatel C, Maurer FP, Lange C, Niemann S. Design of multidrug-resistant tuberculosis treatment regimens based on DNA sequencing. Clin Infect Dis 2021; 73:1194-1202. [PMID: 33900387 DOI: 10.1093/cid/ciab359] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Comprehensive and reliable drug susceptibility testing (DST) is urgently needed to provide adequate treatment regimens for patients with multidrug-resistant/rifampicin-resistant tuberculosis (MDR/RR-TB). We investigated if next generation sequencing (NGS) analysis of Mycobacterium tuberculosis complex isolates and genes implicated in drug resistance can guide the design of effective MDR/RR-TB treatment regimens. METHODS NGS-based genomic DST predictions of M. tuberculosis complex isolates from MDR/RR-TB patients admitted to a TB reference center in Germany between 01/01/2015 and 04/30/2019 were compared with phenotypic DST results of Mycobacteria growth indicator tubes (MGIT). Standardized treatment algorithms were applied to design individualized therapies based on either genomic or phenotypic DST results, and discrepancies were further evaluated by determination of minimum inhibitory drug concentrations (MIC) using Sensititre MYCOTBI and UKMYC microtiter plates. RESULTS In 70 patients with MDR/RR-TB, agreement among 1048 pairwise comparisons of genomic and phenotypic DST was 86.3%; 76 (7.2%) results were discordant, and 68 (6.5%) could not be evaluated due to presence of polymorphisms with yet unknown implications for drug resistance. Importantly, 549/561 (97.9%) predictions of drug susceptibility were phenotypically confirmed in MGIT, and 27/64 (42.2%) false positive results were linked to previously described mutations mediating a low or moderate MIC increase. Virtually all drugs (99.0%) used in combination therapies that were inferred from genomic DST, were confirmed to be susceptible by pDST. CONCLUSIONS NGS-based genomic DST can reliably guide the design of effective MDR/RR-TB treatment regimens.
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Affiliation(s)
- Hans-Peter Grobbel
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Matthias Merker
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Niklas Köhler
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Harald Hoffmann
- Institute of Microbiology and Laboratory Medicine, WHO Supranational Reference Laboratory of TB, IML red GmbH, Gauting, Bavaria, Germany.,SYNLAB Gauting, SYNLAB MVZ of Human Genetics Munich, Bavaria, Germany
| | - Jan Heyckendorf
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Doris Hillemann
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Barbara Kalsdorf
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Patricia Sanchez-Carballo
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Dagmar Schaub
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Katharina Todt
- Institute of Microbiology and Laboratory Medicine, WHO Supranational Reference Laboratory of TB, IML red GmbH, Gauting, Bavaria, Germany.,SYNLAB Gauting, SYNLAB MVZ of Human Genetics Munich, Bavaria, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Florian P Maurer
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany.,Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Lange
- Research Center Borstel, Clinical Infectious Diseases, Borstel, Germany.,German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany.,Global TB Program, Baylor College of Medicine, Houston, TX, USA
| | - Stefan Niemann
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany.,Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany.,National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
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20
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Merker M, Nikolaevskaya E, Kohl TA, Molina-Moya B, Pavlovska O, Brännberg P, Dudnyk A, Stokich V, Barilar I, Marynova I, Filipova T, Prat C, Sjöstedt A, Dominguez J, Rzhepishevska O, Niemann S. Multidrug- and Extensively Drug-Resistant Mycobacterium tuberculosis Beijing Clades, Ukraine, 2015. Emerg Infect Dis 2021; 26:481-490. [PMID: 32091369 PMCID: PMC7045844 DOI: 10.3201/eid2603.190525] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) is an emerging threat to TB control in Ukraine, a country with the third highest XDR TB burden globally. We used whole-genome sequencing of a convenience sample to identify bacterial genetic and patient-related factors associated with MDR/XDR TB in this country. MDR/XDR TB was associated with 3 distinct Mycobacterium tuberculosis complex lineage 2 (Beijing) clades, Europe/Russia W148 outbreak, Central Asia outbreak, and Ukraine outbreak, which comprised 68.9% of all MDR/XDR TB strains from southern Ukraine. MDR/XDR TB was also associated with previous treatment for TB and urban residence. The circulation of Beijing outbreak strains harboring broad drug resistance, coupled with constraints in drug supply and limited availability of phenotypic drug susceptibility testing, needs to be considered when new TB management strategies are implemented in Ukraine.
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21
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Beckert P, Sanchez-Padilla E, Merker M, Dreyer V, Kohl TA, Utpatel C, Köser CU, Barilar I, Ismail N, Omar SV, Klopper M, Warren RM, Hoffmann H, Maphalala G, Ardizzoni E, de Jong BC, Kerschberger B, Schramm B, Andres S, Kranzer K, Maurer FP, Bonnet M, Niemann S. MDR M. tuberculosis outbreak clone in Eswatini missed by Xpert has elevated bedaquiline resistance dated to the pre-treatment era. Genome Med 2020; 12:104. [PMID: 33239092 PMCID: PMC7687760 DOI: 10.1186/s13073-020-00793-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
Background Multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains not detected by commercial molecular drug susceptibility testing (mDST) assays due to the RpoB I491F resistance mutation are threatening the control of MDR tuberculosis (MDR-TB) in Eswatini. Methods We investigate the evolution and spread of MDR strains in Eswatini with a focus on bedaquiline (BDQ) and clofazimine (CFZ) resistance using whole-genome sequencing in two collections ((1) national drug resistance survey, 2009–2010; (2) MDR strains from the Nhlangano region, 2014–2017). Results MDR strains in collection 1 had a high cluster rate (95%, 117/123 MDR strains) with 55% grouped into the two largest clusters (gCL3, n = 28; gCL10, n = 40). All gCL10 isolates, which likely emerged around 1993 (95% highest posterior density 1987–1998), carried the mutation RpoB I491F that is missed by commercial mDST assays. In addition, 21 (53%) gCL10 isolates shared a Rv0678 M146T mutation that correlated with elevated minimum inhibitory concentrations (MICs) to BDQ and CFZ compared to wild type isolates. gCL10 isolates with the Rv0678 M146T mutation were also detected in collection 2. Conclusion The high clustering rate suggests that transmission has been driving the MDR-TB epidemic in Eswatini for three decades. The presence of MDR strains in Eswatini that are not detected by commercial mDST assays and have elevated MICs to BDQ and CFZ potentially jeopardizes the successful implementation of new MDR-TB treatment guidelines. Measures to limit the spread of these outbreak isolates need to be implemented urgently.
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Affiliation(s)
- Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Claudio U Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Nazir Ismail
- Centre for Tuberculosis, National TB Reference Laboratory, WHO TB Supranational Laboratory Network, National Institute for Communicable Diseases/National Health Laboratory Services, Johannesburg, South Africa.,Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,Department of Internal Medicine, University of Witwatersrand, Johannesburg, South Africa
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National TB Reference Laboratory, WHO TB Supranational Laboratory Network, National Institute for Communicable Diseases/National Health Laboratory Services, Johannesburg, South Africa
| | - Marisa Klopper
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Harald Hoffmann
- SYNLAB Gauting, Gauting, Germany, IML red GmbH, Institute of Microbiology and Laboratory Medicine, WHO Supranational Reference Laboratory of TB, Gauting, Germany
| | - Gugu Maphalala
- National Tuberculosis Reference Laboratory (NTRL), Ministry of Health, Mbabane, Swaziland
| | - Elisa Ardizzoni
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bouke C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Katharina Kranzer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany.,London School of Hygiene and Tropical Medicine, London, United Kingdom of Great Britain and Northern Ireland, UK
| | - Florian P Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany.,Eppendorf, Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg, Hamburg, Germany
| | - Maryline Bonnet
- Epicentre, Paris, France.,IRD UMI233/ INSERM U1175/Université de Montpellier, Montpellier, France
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany. .,National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany. .,Biochemistry & Microbiology, School of Medicine, University of Namibia, Windhoek, Namibia.
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22
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Gröschel MI, Meehan CJ, Barilar I, Diricks M, Gonzaga A, Steglich M, Conchillo-Solé O, Scherer IC, Mamat U, Luz CF, De Bruyne K, Utpatel C, Yero D, Gibert I, Daura X, Kampmeier S, Rahman NA, Kresken M, van der Werf TS, Alio I, Streit WR, Zhou K, Schwartz T, Rossen JWA, Farhat MR, Schaible UE, Nübel U, Rupp J, Steinmann J, Niemann S, Kohl TA. The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nat Commun 2020; 11:2044. [PMID: 32341346 PMCID: PMC7184733 DOI: 10.1038/s41467-020-15123-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/15/2020] [Indexed: 02/06/2023] Open
Abstract
Recent studies portend a rising global spread and adaptation of human- or healthcare-associated pathogens. Here, we analyse an international collection of the emerging, multidrug-resistant, opportunistic pathogen Stenotrophomonas maltophilia from 22 countries to infer population structure and clonality at a global level. We show that the S. maltophilia complex is divided into 23 monophyletic lineages, most of which harbour strains of all degrees of human virulence. Lineage Sm6 comprises the highest rate of human-associated strains, linked to key virulence and resistance genes. Transmission analysis identifies potential outbreak events of genetically closely related strains isolated within days or weeks in the same hospitals. Multidrug resistance of the opportunistic pathogen Stenotrophomonas maltophilia is an increasing problem. Here, analyzing strains from 22 countries, the authors show that the S. maltophilia complex is divided into 23 monophyletic lineages and find evidence for intra-hospital transmission.
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Affiliation(s)
- Matthias I Gröschel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Conor J Meehan
- School of Chemistry and Bioscience, University of Bradford, Bradford, United Kingdom
| | - Ivan Barilar
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Margo Diricks
- bioMérieux, Applied Maths NV, Keistraat 120, 9830, St-Martens-Latem, Belgium
| | - Aitor Gonzaga
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matthias Steglich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Oscar Conchillo-Solé
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Isabell-Christin Scherer
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Uwe Mamat
- Cellular Microbiology, Research Center Borstel, Borstel, Germany
| | - Christian F Luz
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Katrien De Bruyne
- bioMérieux, Applied Maths NV, Keistraat 120, 9830, St-Martens-Latem, Belgium
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Daniel Yero
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Isidre Gibert
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | | | - Michael Kresken
- Antiinfectives Intelligence GmbH, Rheinbach, Germany.,Rheinische Fachhochschule Köln gGmbH, Cologne, Germany
| | - Tjip S van der Werf
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ifey Alio
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, Shenzhen, China.,Second Clinical Medical College, Jinan University, Shenzhen, China
| | - Thomas Schwartz
- Karlsruhe Institute of Technology, Institute of Functional Interfaces, Eggenstein- Leopoldshafen, Germany
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Massachusetts General Hospital, Boston, MA, USA
| | - Ulrich E Schaible
- Cellular Microbiology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany.,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany.,Germany Center for Infection Research (DZIF), partner site Hannover - Braunschweig, Cologne, Germany.,Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Medical Center Essen, Essen, Germany.,Medical Microbiology and Infection Prevention, Institute of Clinical Hygiene, Paracelsus Medical Private University, Klinikum Nürnberg, Nuremberg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany. .,Leibniz Research Alliance INFECTIONS'21, Cologne, Germany.
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), partner site Hamburg - Lübeck - Borstel - Riems, Cologne, Germany
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23
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Merker M, Kohl TA, Barilar I, Andres S, Fowler PW, Chryssanthou E, Ängeby K, Jureen P, Moradigaravand D, Parkhill J, Peacock SJ, Schön T, Maurer FP, Walker T, Köser C, Niemann S. Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex. Genome Med 2020; 12:27. [PMID: 32143680 PMCID: PMC7060619 DOI: 10.1186/s13073-020-00726-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome sequencing data for genotypic drug susceptibility testing (DST). METHODS We investigated mutations in 92 genes implicated in resistance to 21 anti-tuberculosis drugs using the genomes of 405 phylogenetically diverse MTBC strains. The role of phylogenetically informative mutations was assessed by routine phenotypic DST data for the first-line drugs isoniazid, rifampicin, ethambutol, and pyrazinamide from a separate collection of over 7000 clinical strains. Selected mutations/strains were further investigated by minimum inhibitory concentration (MIC) testing. RESULTS Out of 547 phylogenetically informative mutations identified, 138 were classified as not correlating with resistance to first-line drugs. MIC testing did not reveal a discernible impact of a Rv1979c deletion shared by M. africanum lineage 5 strains on resistance to clofazimine. Finally, we found molecular evidence that some MTBC subgroups may be hyper-susceptible to bedaquiline and clofazimine by different loss-of-function mutations affecting a drug efflux pump subunit (MmpL5). CONCLUSIONS Our findings underline that the genetic diversity in MTBC has to be studied more systematically to inform the design of clinical trials and to define sound epidemiologic cut-off values (ECOFFs) for new and repurposed anti-tuberculosis drugs. In that regard, our comprehensive variant catalogue provides a solid basis for the interpretation of mutations in genotypic as well as in phenotypic DST assays.
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Affiliation(s)
- Matthias Merker
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany.
| | - Thomas A Kohl
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Ivan Barilar
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Erja Chryssanthou
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kristian Ängeby
- Department of Clinical Science and Education, Emergency Medicine, Stockholm South General Hospital, Karolinska Institute, Stockholm, Sweden
| | | | - Danesh Moradigaravand
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Thomas Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - Florian P Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Claudio Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
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24
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Bauer E, Schmutzer T, Barilar I, Mascher M, Gundlach H, Martis MM, Twardziok SO, Hackauf B, Gordillo A, Wilde P, Schmidt M, Korzun V, Mayer KFX, Schmid K, Schön CC, Scholz U. Towards a whole-genome sequence for rye (Secale cereale L.). Plant J 2017; 89:853-869. [PMID: 27888547 DOI: 10.1111/tpj.13436] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 05/18/2023]
Abstract
We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.
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Affiliation(s)
- Eva Bauer
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Ivan Barilar
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
| | - Heidrun Gundlach
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Mihaela M Martis
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Sven O Twardziok
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Bernd Hackauf
- Julius Kühn-Institute, Institute for Breeding Research on Agricultural Crops, Rudolf-Schick-Platz 3a, 18190, Sanitz, Germany
| | - Andres Gordillo
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Peer Wilde
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Malthe Schmidt
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Viktor Korzun
- KWS LOCHOW GMBH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany
| | - Klaus F X Mayer
- Helmholtz Zentrum München, Plant Genome and Systems Biology, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Karl Schmid
- Universität Hohenheim, Crop Biodiversity and Breeding Informatics, Fruwirthstr. 21, 70599, Stuttgart, Germany
| | - Chris-Carolin Schön
- Technical University of Munich, Plant Breeding, Liesel-Beckmann-Str. 2, 85354, Freising, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466, Stadt Seeland, Germany
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25
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Günther T, Lampei C, Barilar I, Schmid KJ. Genomic and phenotypic differentiation of Arabidopsis thaliana along altitudinal gradients in the North Italian Alps. Mol Ecol 2016; 25:3574-92. [PMID: 27220345 DOI: 10.1111/mec.13705] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 04/19/2016] [Accepted: 05/02/2016] [Indexed: 12/25/2022]
Abstract
Altitudinal gradients in mountain regions are short-range clines of different environmental parameters such as temperature or radiation. We investigated genomic and phenotypic signatures of adaptation to such gradients in five Arabidopsis thaliana populations from the North Italian Alps that originated from 580 to 2350 m altitude by resequencing pools of 19-29 individuals from each population. The sample includes two pairs of low- and high-altitude populations from two different valleys. High-altitude populations showed a lower nucleotide diversity and negative Tajima's D values and were more closely related to each other than to low-altitude populations from the same valley. Despite their close geographic proximity, demographic analysis revealed that low- and high-altitude populations split between 260 000 and 15 000 years before present. Single nucleotide polymorphisms whose allele frequencies were highly differentiated between low- and high-altitude populations identified genomic regions of up to 50 kb length where patterns of genetic diversity are consistent with signatures of local selective sweeps. These regions harbour multiple genes involved in stress response. Variation among populations in two putative adaptive phenotypic traits, frost tolerance and response to light/UV stress was not correlated with altitude. Taken together, the spatial distribution of genetic diversity reflects a potentially adaptive differentiation between low- and high-altitude populations, whereas the phenotypic differentiation in the two traits investigated does not. It may resemble an interaction between adaptation to the local microhabitat and demographic history influenced by historical glaciation cycles, recent seed dispersal and genetic drift in local populations.
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Affiliation(s)
- Torsten Günther
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany.,Department of Evolutionary Biology, EBC, Uppsala University, Uppsala, Sweden
| | - Christian Lampei
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Ivan Barilar
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Karl J Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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