1
|
Rupasinghe P, Reenaers R, Vereecken J, Mulders W, Cogneau S, Merker M, Niemann S, Vally Omar S, Rigouts L, Köser CU, Decroo T, de Jong BC. Refined understanding of the impact of the Mycobacterium tuberculosis complex diversity on the intrinsic susceptibility to pretomanid. Microbiol Spectr 2024; 12:e0007024. [PMID: 38334384 PMCID: PMC10913522 DOI: 10.1128/spectrum.00070-24] [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: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
Previous work reported unprecedented differences in the intrinsic in vitro susceptibility of the Mycobacterium tuberculosis complex (MTBC) to pretomanid (Pa) using the Mycobacteria Growth Indicator Tube (MGIT) system. We tested 125 phylogenetically diverse strains from all known MTBC lineages (1-9) without known Pa resistance mutations and four strains with known resistance mutations as controls. This confirmed that MTBC, unlike most bacteria-antimicrobial combinations, displayed substantial differences in the intrinsic susceptibility relative to the technical variation of Pa MIC testing. This was also the case for the Middlebrook 7H11 (7H11) medium, demonstrating that these differences were not specific to MGIT. Notably, lineage 1 was confirmed to have intrinsically elevated MICs compared with lineages 2, 3, 4, and 7 (L2-4/7), underlining the urgent need for WHO to publish its decision of whether lineage 1 should be deemed treatable by BPaL(M), the now preferred all-oral regimen for treating rifampin-resistant tuberculosis. Lineages 5 and 6, which are most frequent in West Africa, responded differently to Pa, with lineage 5 being more similar to L2-4/7 and lineage 6 being more susceptible. More data are needed to determine whether 7H11 MICs are systematically lower than those in MGIT. IMPORTANCE This study confirmed that the Mycobacterium tuberculosis complex lineage 1, responsible for 28% of global tuberculosis cases, is less susceptible to pretomanid (Pa). It also refined the understanding of the intrinsic susceptibilities of lineages 5 and 6, most frequent in West Africa, and lineages 8 and 9. Regulators must review whether these in vitro differences affect the clinical efficacy of the WHO-recommended BPaL(M) regimen and set breakpoints for antimicrobial susceptibility testing accordingly. Notably, regulators should provide detailed justifications for their decisions to facilitate public scrutiny.
Collapse
Affiliation(s)
- Praharshinie Rupasinghe
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Rabab Reenaers
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jens Vereecken
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wim Mulders
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sari Cogneau
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Parkallee, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Parkallee, Borstel, Germany
| | - Shaheed Vally Omar
- Center for Tuberculosis, National Institute of Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Leen Rigouts
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Claudio U. Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Tom Decroo
- Unit of HIV and TB, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bouke C. de Jong
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| |
Collapse
|
2
|
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.
Collapse
|
3
|
Schlanderer J, Hoffmann H, Lüddecke J, Golubov A, Grasse W, Kindler EV, Kohl TA, Merker M, Metzger C, Mohr V, Niemann S, Pilloni C, Plesnik S, Raya B, Shresta B, Utpatel C, Zengerle R, Beutler M, Paust N. Two-stage tuberculosis diagnostics: combining centrifugal microfluidics to detect TB infection and Inh and Rif resistance at the point of care with subsequent antibiotic resistance profiling by targeted NGS. Lab Chip 2023; 24:74-84. [PMID: 37999937 DOI: 10.1039/d3lc00783a] [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] [Indexed: 11/25/2023]
Abstract
Globally, tuberculosis (TB) remains the deadliest bacterial infectious disease, and spreading antibiotic resistances is the biggest challenge for combatting the disease. Rapid and comprehensive diagnostics including drug susceptibility testing (DST) would assure early treatment, reduction of morbidity and the interruption of transmission chains. To date, rapid genetic resistance testing addresses only one to four drug groups while complete DST is done phenotypically and takes several weeks. To overcome these limitations, we developed a two-stage workflow for rapid TB diagnostics including DST from a single sputum sample that can be completed within three days. The first stage is qPCR detection of M. tuberculosis complex (MTBC) including antibiotic resistance testing against the first-line antibiotics, isoniazid (Inh) and rifampicin (Rif). The test is automated by centrifugal microfluidics and designed for point of care (PoC). Furthermore, enriched MTBC DNA is provided in a detachable sample tube to enable the second stage: if the PCR detects MTBC and resistance to either Inh or Rif, the MTBC DNA is shipped to specialized facilities and analyzed by targeted next generation sequencing (tNGS) to assess the complete resistance profile. Proof-of-concept testing of the PoC test revealed an analytical sensitivity of 44.2 CFU ml-1, a diagnostic sensitivity of 96%, and a diagnostic specificity of 100% for MTBC detection. Coupled tNGS successfully provided resistance profiles, demonstrated for samples from 17 patients. To the best of our knowledge, the presented combination of PoC qPCR with tNGS allows for the fastest comprehensive TB diagnostics comprising decentralized pathogen detection with subsequent resistance profiling in a facility specialized in tNGS.
Collapse
Affiliation(s)
| | - Harald Hoffmann
- SYNLAB Gauting SYNLAB Human Genetics Munich, 82131 Gauting, Germany
| | - Jan Lüddecke
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
| | - Andrey Golubov
- WHO supranational Tuberculosis Reference Laboratory, IML red, 82131 Gauting, Germany
| | | | | | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | | | - Vanessa Mohr
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | - Claudia Pilloni
- WHO supranational Tuberculosis Reference Laboratory, IML red, 82131 Gauting, Germany
| | - Sara Plesnik
- WHO supranational Tuberculosis Reference Laboratory, IML red, 82131 Gauting, Germany
| | - Bijendra Raya
- German Nepal Tuberculosis Project (GENETUP), Nepal Anti-Tuberculosis Association (NATA), Kalimati, Nepal
| | - Bhawana Shresta
- German Nepal Tuberculosis Project (GENETUP), Nepal Anti-Tuberculosis Association (NATA), Kalimati, Nepal
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, 23845 Borstel, Germany
| | - Roland Zengerle
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
| | - Markus Beutler
- WHO supranational Tuberculosis Reference Laboratory, IML red, 82131 Gauting, Germany
| | - Nils Paust
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
| |
Collapse
|
4
|
Chesov E, Chesov D, Reimann M, Dreyer V, Utpatel C, Gröschel MI, Ciobanu N, Crudu V, Lange C, Heyckendorf J, Merker M. Impact of Mycobacterium tuberculosis strain type on multidrug-resistant tuberculosis severity, Republic of Moldova. J Infect 2023; 87:588-591. [PMID: 37827458 DOI: 10.1016/j.jinf.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Affiliation(s)
- Elena Chesov
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova; Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany
| | - Dumitru Chesov
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova; Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany
| | - Maja Reimann
- Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Germany
| | - Viola Dreyer
- German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Matthias I Gröschel
- Department of Infectious Diseases and Respiratory Medicine, Charite ́ - Universitaetsmedizin Berlin, Berlin, Germany
| | - Nelly Ciobanu
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- Nicolae Testemitanu State University of Medicine and Pharmacy, Chisinau, Republic of Moldova; Chiril Draganiuc Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Christoph Lange
- Division of Clinical Infectious Disease, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-Riems-Borstel, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Germany; Baylor College of Medicine and Texas Children´s Hospital, Houston, TX, USA
| | - Jan Heyckendorf
- Clinic for Internal Medicine I, University Clinic Schleswig-Holstein Campus Kiel, Germany
| | - Matthias Merker
- Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Sonnenkalb L, Carter JJ, Spitaleri A, Iqbal Z, Hunt M, Malone KM, Utpatel C, Cirillo DM, Rodrigues C, Nilgiriwala KS, Fowler PW, Merker M, Niemann S. Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis. Lancet Microbe 2023; 4:e358-e368. [PMID: 37003285 PMCID: PMC10156607 DOI: 10.1016/s2666-5247(23)00002-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/21/2022] [Accepted: 12/21/2022] [Indexed: 03/30/2023]
Abstract
BACKGROUND Bedaquiline is a core drug for the treatment of multidrug-resistant tuberculosis; however, the understanding of resistance mechanisms is poor, which is hampering rapid molecular diagnostics. Some bedaquiline-resistant mutants are also cross-resistant to clofazimine. To decipher bedaquiline and clofazimine resistance determinants, we combined experimental evolution, protein modelling, genome sequencing, and phenotypic data. METHODS For this in-vitro and in-silico data analysis, we used a novel in-vitro evolutionary model using subinhibitory drug concentrations to select bedaquiline-resistant and clofazimine-resistant mutants. We determined bedaquiline and clofazimine minimum inhibitory concentrations and did Illumina and PacBio sequencing to characterise selected mutants and establish a mutation catalogue. This catalogue also includes phenotypic and genotypic data of a global collection of more than 14 000 clinical Mycobacterium tuberculosis complex isolates, and publicly available data. We investigated variants implicated in bedaquiline resistance by protein modelling and dynamic simulations. FINDINGS We discerned 265 genomic variants implicated in bedaquiline resistance, with 250 (94%) variants affecting the transcriptional repressor (Rv0678) of the MmpS5-MmpL5 efflux system. We identified 40 new variants in vitro, and a new bedaquiline resistance mechanism caused by a large-scale genomic rearrangement. Additionally, we identified in vitro 15 (7%) of 208 mutations found in clinical bedaquiline-resistant isolates. From our in-vitro work, we detected 14 (16%) of 88 mutations so far identified as being associated with clofazimine resistance and also seen in clinically resistant strains, and catalogued 35 new mutations. Structural modelling of Rv0678 showed four major mechanisms of bedaquiline resistance: impaired DNA binding, reduction in protein stability, disruption of protein dimerisation, and alteration in affinity for its fatty acid ligand. INTERPRETATION Our findings advance the understanding of drug resistance mechanisms in M tuberculosis complex strains. We have established an extended mutation catalogue, comprising variants implicated in resistance and susceptibility to bedaquiline and clofazimine. Our data emphasise that genotypic testing can delineate clinical isolates with borderline phenotypes, which is essential for the design of effective treatments. FUNDING Leibniz ScienceCampus Evolutionary Medicine of the Lung, Deutsche Forschungsgemeinschaft, Research Training Group 2501 TransEvo, Rhodes Trust, Stanford University Medical Scientist Training Program, National Institute for Health and Care Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Bill & Melinda Gates Foundation, Wellcome Trust, and Marie Skłodowska-Curie Actions.
Collapse
Affiliation(s)
- Lindsay Sonnenkalb
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Joshua James Carter
- Medical Scientist Training Program, Stanford University, Stanford, CA, USA; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy; Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University, Milan, Italy
| | - Zamin Iqbal
- European Bioinformatics Institute, Cambridge, UK
| | - Martin Hunt
- European Bioinformatics Institute, Cambridge, UK; Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Rodrigues
- Department of Microbiology, P D Hinduja National Hospital and Medical Research Centre, Mumbai, India
| | | | - Philip William Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Matthias Merker
- Evolution of the Resistome, Research Center Borstel Leibniz Lung Center, Borstel, Germany; National Reference Center, Research Center Borstel Leibniz Lung Center, Borstel, Germany; German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel Leibniz Lung Center, Borstel, Germany; National Reference Center, Research Center Borstel Leibniz Lung Center, Borstel, Germany; German Centre for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| |
Collapse
|
9
|
Domínguez J, Boeree MJ, Cambau E, Chesov D, Conradie F, Cox V, Dheda K, Dudnyk A, Farhat MR, Gagneux S, Grobusch MP, Gröschel MI, Guglielmetti L, Kontsevaya I, Lange B, van Leth F, Lienhardt C, Mandalakas AM, Maurer FP, Merker M, Miotto P, Molina-Moya B, Morel F, Niemann S, Veziris N, Whitelaw A, Horsburgh CR, Lange C. Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement. Lancet Infect Dis 2023; 23:e122-e137. [PMID: 36868253 DOI: 10.1016/s1473-3099(22)00875-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 03/05/2023]
Abstract
Drug-resistant tuberculosis is a substantial health-care concern worldwide. Despite culture-based methods being considered the gold standard for drug susceptibility testing, molecular methods provide rapid information about the Mycobacterium tuberculosis mutations associated with resistance to anti-tuberculosis drugs. This consensus document was developed on the basis of a comprehensive literature search, by the TBnet and RESIST-TB networks, about reporting standards for the clinical use of molecular drug susceptibility testing. Review and the search for evidence included hand-searching journals and searching electronic databases. The panel identified studies that linked mutations in genomic regions of M tuberculosis with treatment outcome data. Implementation of molecular testing for the prediction of drug resistance in M tuberculosis is key. Detection of mutations in clinical isolates has implications for the clinical management of patients with multidrug-resistant or rifampicin-resistant tuberculosis, especially in situations when phenotypic drug susceptibility testing is not available. A multidisciplinary team including clinicians, microbiologists, and laboratory scientists reached a consensus on key questions relevant to molecular prediction of drug susceptibility or resistance to M tuberculosis, and their implications for clinical practice. This consensus document should help clinicians in the management of patients with tuberculosis, providing guidance for the design of treatment regimens and optimising outcomes.
Collapse
Affiliation(s)
- José Domínguez
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain.
| | - Martin J Boeree
- Department of Lung Diseases, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Emmanuelle Cambau
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France, APHP-Hôpital Bichat, Mycobacteriology Laboratory, INSERM, University Paris Cite, IAME UMR1137, Paris, France
| | - Dumitru Chesov
- Department of Pneumology and Allergology, Nicolae Testemițanu State University of Medicine and Pharmacy, Chisinau, Moldova; Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Francesca Conradie
- Department of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Vivian Cox
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrii Dudnyk
- Department of Tuberculosis, Clinical Immunology and Allergy, National Pirogov Memorial Medical University, Vinnytsia, Ukraine; Public Health Center, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Martin P Grobusch
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection & Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, Netherlands
| | - Matthias I Gröschel
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lorenzo Guglielmetti
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Berit Lange
- Department for Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research, TI BBD, Braunschweig, Germany
| | - Frank van Leth
- Department of Health Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands; Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Christian Lienhardt
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; UMI 233 IRD-U1175 INSERM - Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Anna M Mandalakas
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Merker
- Division of Evolution of the Resistome, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Molina-Moya
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain
| | - Florence Morel
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Stefan Niemann
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia
| | - Nicolas Veziris
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charles R Horsburgh
- Departments of Epidemiology, Biostatistics, Global Health and Medicine, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | | |
Collapse
|
10
|
Koehler N, Andres S, Merker M, Dreyer V, John A, Kuhns M, Krieger D, Choong E, Verougstraete N, Zur Wiesch PA, Wicha SG, König C, Kalsdorf B, Sanchez Carballo PM, Schaub D, Werngren J, Schön T, Peloquin CA, Schönfeld N, Verstraete AG, Decosterd LA, Aarnoutse R, Niemann S, Maurer FP, Lange C. Pretomanid-resistant tuberculosis. J Infect 2023; 86:520-524. [PMID: 36738862 DOI: 10.1016/j.jinf.2023.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Affiliation(s)
- Niklas Koehler
- Department of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Sönke Andres
- National and World Health Organization Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Parkallee 18, 23845 Borstel, Germany
| | - Matthias Merker
- German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; Evolution of the Resistome, Research Center Borstel, Parkallee 1, 23845 Borstel, Germany
| | - Viola Dreyer
- German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Parkallee 1, 23845 Borstel, Germany
| | - Agnieszka John
- Department of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany
| | - Martin Kuhns
- National and World Health Organization Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Parkallee 18, 23845 Borstel, Germany
| | - David Krieger
- Department of Pulmonology, Lungenklinik Heckeshorn, HELIOS Klinikum Emil von Behring, Walterhöferstraße 11, 14165 Berlin, Germany
| | - Eva Choong
- Laboratory of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Nick Verougstraete
- Department of Laboratory Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Pia Abel Zur Wiesch
- Department of Pharmacy, Faculty of Health Sciences, UiT - The Arctic University of Norway, Hansine Hansens veg 18, 9019 Tromsø, Norway; Centre for Molecular Medicine Norway, Nordic EMBL Partnership, Forskningsparken, Gaustadalléen 21, 0349 Oslo, Norway; Department of Biology, The Pennsylvania State University, University Park Pennsylvania, Mueller Laboratory, 208 Curtin Rd, State College, PA 16801, USA; Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park Pennsylvania, 101 Huck Life Sciences Building, University Park, PA 16802, USA
| | - Sebastian G Wicha
- Institute of Pharmacy, University of Hamburg, Bundesstraße 45, 20146 Hamburg, Germany
| | - Christina König
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Martinstraße 52, 20246 Hamburg, Germany; Department of Pharmacy, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Barbara Kalsdorf
- Department of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Patricia M Sanchez Carballo
- Department of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Dagmar Schaub
- Department of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Jim Werngren
- Department of Microbiology, Unit for Laboratory Surveillance of Bacterial Pathogens, Public Health Agency of Sweden, Nobels väg 18, 171 65 Solna, Sweden
| | - Thomas Schön
- Department of Infectious Diseases, Linköping University Hospital, Universitetssjukhuset, 581 85 Linköping, Sweden; Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Universitetssjukhuset, 581 85 Linköping, Sweden
| | - Charles A Peloquin
- Infectious Disease Pharmacokinetics Laboratory, Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, Gainesville, FL 32610, USA; Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, 1225 Center Dr, Gainesville, FL 32610, USA
| | - Nicolas Schönfeld
- Department of Pulmonology, Lungenklinik Heckeshorn, HELIOS Klinikum Emil von Behring, Walterhöferstraße 11, 14165 Berlin, Germany
| | - Alain G Verstraete
- Department of Laboratory Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium; Department of Diagnostic Sciences, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Laurent A Decosterd
- Laboratory of Clinical Pharmacology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, 1011 Lausanne, Switzerland
| | - Rob Aarnoutse
- Department of Pharmacy, Radboud University Medical Center, Radboud Institute for Health Sciences, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; National and World Health Organization Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Parkallee 18, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, National Reference Center for Mycobacteria, Research Center Borstel, Parkallee 1, 23845 Borstel, Germany
| | - Florian P Maurer
- National and World Health Organization Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Parkallee 18, 23845 Borstel, Germany; Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinstraße 52, 20246 Hamburg, Germany
| | - Christoph Lange
- Department of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Parkallee 35, 23845 Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Parkallee 1-40, 23845 Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Baylor College of Medicine and Texas Childrens' Hospital, 1 Baylor Plaza, Houston, TX 77030, USA.
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
Merker M, Rasigade JP, Barbier M, Cox H, Feuerriegel S, Kohl TA, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P, Niemann S, Wirth T. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun 2022; 13:5105. [PMID: 36042200 PMCID: PMC9426364 DOI: 10.1038/s41467-022-32455-1] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/01/2022] [Indexed: 11/09/2022] Open
Abstract
Transmission-driven multi-/extensively drug resistant (M/XDR) tuberculosis (TB) is the largest single contributor to human mortality due to antimicrobial resistance. A few major clades of the Mycobacterium tuberculosis complex belonging to lineage 2, responsible for high prevalence of MDR-TB in Eurasia, show outstanding transnational distributions. Here, we determined factors underlying the emergence and epidemic spread of the W148 clade by genome sequencing and Bayesian demogenetic analyses of 720 isolates from 23 countries. We dated a common ancestor around 1963 and identified two successive epidemic expansions in the late 1980s and late 1990s, coinciding with major socio-economic changes in the post-Soviet Era. These population expansions favored accumulation of resistance mutations to up to 11 anti-TB drugs, with MDR evolving toward additional resistances to fluoroquinolones and second-line injectable drugs within 20 years on average. Timescaled haplotypic density analysis revealed that widespread acquisition of compensatory mutations was associated with transmission success of XDR strains. Virtually all W148 strains harbored a hypervirulence-associated ppe38 gene locus, and incipient recurrent emergence of prpR mutation-mediated drug tolerance was detected. The outstanding genetic arsenal of this geographically widespread M/XDR strain clade represents a “perfect storm” that jeopardizes the successful introduction of new anti-M/XDR-TB antibiotic regimens. An outbreak of the multidrug-resistant Mycobacterium tuberculosis lineage W148 has spread widely across Russia, Central Asia and Europe. Here, the authors use whole genome sequences of ~700 isolates of this lineage collected over ~20 years to analyze its spread, evolution of drug resistance, and impact of compensatory mutations.
Collapse
Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Jean-Philippe Rasigade
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Maxime Barbier
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Helen Cox
- Division of Medical Microbiology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Kadri Klaos
- SA TUH United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany.,Lung Clinic Grosshansdorf, German Center for Lung Research (DZL), Airway Research Center North (ARCN), 22927, Großhansdorf, Germany
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Valeriu Crudu
- National TB Reference Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, 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.
| | - Thierry Wirth
- EPHE, PSL University, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Mesfin EA, Merker M, Beyene D, Tesfaye A, Shuaib YA, Addise D, Tessema B, Niemann S. Prediction of drug resistance by Sanger sequencing of Mycobacterium tuberculosis complex strains isolated from multidrug resistant tuberculosis suspect patients in Ethiopia. PLoS One 2022; 17:e0271508. [PMID: 35930613 PMCID: PMC9355188 DOI: 10.1371/journal.pone.0271508] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Background Ethiopia is one of the high multidrug-resistant tuberculosis (MDR-TB) burden countries. However, phenotypic drug susceptibility testing can take several weeks due to the slow growth of Mycobacterium tuberculosis complex (MTBC) strains. In this study, we assessed the performance of a Sanger sequencing approach to predict resistance against five anti-tuberculosis drugs and the pattern of resistance mediating mutations. Methods We enrolled 226 MTBC culture-positive MDR-TB suspects and collected sputum specimens and socio-demographic and TB related data from each suspect between June 2015 and December 2016 in Addis Ababa, Ethiopia. Phenotypic drug susceptibility testing (pDST) for rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin using BACTEC MGIT 960 was compared with the results of a Sanger sequencing analysis of seven resistance determining regions in the genes rpoB, katG, fabG-inhA, pncA, embB, rpsL, and rrs. Result DNA isolation for Sanger sequencing was successfully extracted from 92.5% (209/226) of the MTBC positive cultures, and the remaining 7.5% (17/226) strains were excluded from the final analysis. Based on pDST results, drug resistance proportions were as follows: isoniazid: 109/209 (52.2%), streptomycin: 93/209 (44.5%), rifampicin: 88/209 (42.1%), ethambutol: 74/209 (35.4%), and pyrazinamide: 69/209 (33.0%). Resistance against isoniazid was mainly mediated by the mutation katG S315T (97/209, 46.4%) and resistance against rifampicin by rpoB S531L (58/209, 27.8%). The dominating resistance-conferring mutations for ethambutol, streptomycin, and pyrazinamide affected codon 306 in embB (48/209, 21.1%), codon 88 in rpsL (43/209, 20.6%), and codon 65 in pncA (19/209, 9.1%), respectively. We observed a high agreement between phenotypic and genotypic DST, such as 89.9% (at 95% confidence interval [CI], 84.2%–95.8%) for isoniazid, 95.5% (95% CI, 91.2%–99.8%) for rifampicin, 98.6% (95% CI, 95.9–100%) for ethambutol, 91.3% (95% CI, 84.6–98.1%) for pyrazinamide and 57.0% (95% CI, 46.9%–67.1%) for streptomycin. Conclusion We detected canonical mutations implicated in resistance to rifampicin, isoniazid, pyrazinamide, ethambutol, and streptomycin. High agreement with phenotypic DST results for all drugs renders Sanger sequencing promising to be performed as a complementary measure to routine phenotypic DST in Ethiopia. Sanger sequencing directly from sputum may accelerate accurate clinical decision-making in the future.
Collapse
Affiliation(s)
- Eyob Abera Mesfin
- Ethiopian Public Health Institute, National Laboratory Capacity Building Directorate, Addis Ababa, Ethiopia
- * E-mail:
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- Evolution of the Resistome, Research Center Borstel, Sülfeld, Germany
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abreham Tesfaye
- Addis Ababa City Administration Health Bureau Health Research and Laboratory Services, Addis Ababa, Ethiopia
| | - Yassir Adam Shuaib
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- College of Veterinary Medicine, Sudan University of Science and Technology, Khartoum North, Sudan
| | - Desalegn Addise
- Ethiopian Public Health Institute, National Laboratory Capacity Building Directorate, Addis Ababa, Ethiopia
| | - Belay Tessema
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Sülfeld, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck- Borstel-Riems, Hamburg, Germany
| |
Collapse
|
15
|
Heim C, Moser LM, Merker M, Wels WS, Ivics Z, Bönig H, Ullrich E, Klusmann JH, Bader P, Rettinger E. ErbB2-CAR mediated immunotherapy for the treatment of high-risk
rhabdomyosarcoma. KLINISCHE PADIATRIE 2022. [DOI: 10.1055/s-0042-1748747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- C Heim
- Division for Stem Cell Transplantation, Immunology, and Intensive Care
Medicine, Department for Children and Adolescents, University Hospital
Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - LM Moser
- Division for Stem Cell Transplantation, Immunology, and Intensive Care
Medicine, Department for Children and Adolescents, University Hospital
Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - M Merker
- Division for Stem Cell Transplantation, Immunology, and Intensive Care
Medicine, Department for Children and Adolescents, University Hospital
Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - WS Wels
- Mental Therapy, Frankfurt, Germany
| | - Z Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen,
Germany
| | - H Bönig
- Department of Cellular Therapeutics/Cell Processing (Good
Manufacturing Practice, GMP), Institute for Transfusion Medicine and
Immunotherapy, Goethe University, Frankfurt, Germany
| | - E Ullrich
- Experimental Immunology, Department for Children and Adolescents,
University Hospital Frankfurt, Goethe University, Frankfurt,
Germany
| | - J-H Klusmann
- Division for Stem Cell Transplantation, Immunology, and Intensive Care
Medicine, Department for Children and Adolescents, University Hospital
Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - P Bader
- Division for Stem Cell Transplantation, Immunology, and Intensive Care
Medicine, Department for Children and Adolescents, University Hospital
Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - E Rettinger
- Division for Stem Cell Transplantation, Immunology, and Intensive Care
Medicine, Department for Children and Adolescents, University Hospital
Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| |
Collapse
|
16
|
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
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Diricks M, Kohl TA, Käding N, Leshchinskiy V, Hauswaldt S, Vázquez OJ, Utpatel C, Niemann S, Rupp J, Merker M. Correction to: Whole genome sequencing-based classifcation of human-related Haemophilus species and detection of antimicrobial resistance genes. Genome Med 2022; 14:22. [PMID: 35209955 PMCID: PMC8867676 DOI: 10.1186/s13073-022-01028-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, 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, Hamburg, Germany
| | - Nadja Käding
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Vladislav Leshchinskiy
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susanne Hauswaldt
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Omar Jiménez Vázquez
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany. .,Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
| |
Collapse
|
19
|
Diricks M, Kohl TA, Käding N, Leshchinskiy V, Hauswaldt S, Jiménez Vázquez O, Utpatel C, Niemann S, Rupp J, Merker M. Whole genome sequencing-based classification of human-related Haemophilus species and detection of antimicrobial resistance genes. Genome Med 2022; 14:13. [PMID: 35139905 PMCID: PMC8830169 DOI: 10.1186/s13073-022-01017-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/31/2021] [Accepted: 01/24/2022] [Indexed: 12/31/2022] Open
Abstract
Background Bacteria belonging to the genus Haemophilus cause a wide range of diseases in humans. Recently, H. influenzae was classified by the WHO as priority pathogen due to the wide spread of ampicillin resistant strains. However, other Haemophilus spp. are often misclassified as H. influenzae. Therefore, we established an accurate and rapid whole genome sequencing (WGS) based classification and serotyping algorithm and combined it with the detection of resistance genes. Methods A gene presence/absence-based classification algorithm was developed, which employs the open-source gene-detection tool SRST2 and a new classification database comprising 36 genes, including capsule loci for serotyping. These genes were identified using a comparative genome analysis of 215 strains belonging to ten human-related Haemophilus (sub)species (training dataset). The algorithm was evaluated on 1329 public short read datasets (evaluation dataset) and used to reclassify 262 clinical Haemophilus spp. isolates from 250 patients (German cohort). In addition, the presence of antibiotic resistance genes within the German dataset was evaluated with SRST2 and correlated with results of traditional phenotyping assays. Results The newly developed algorithm can differentiate between clinically relevant Haemophilus species including, but not limited to, H. influenzae, H. haemolyticus, and H. parainfluenzae. It can also identify putative haemin-independent H. haemolyticus strains and determine the serotype of typeable Haemophilus strains. The algorithm performed excellently in the evaluation dataset (99.6% concordance with reported species classification and 99.5% with reported serotype) and revealed several misclassifications. Additionally, 83 out of 262 (31.7%) suspected H. influenzae strains from the German cohort were in fact H. haemolyticus strains, some of which associated with mouth abscesses and lower respiratory tract infections. Resistance genes were detected in 16 out of 262 datasets from the German cohort. Prediction of ampicillin resistance, associated with blaTEM-1D, and tetracycline resistance, associated with tetB, correlated well with available phenotypic data. Conclusions Our new classification database and algorithm have the potential to improve diagnosis and surveillance of Haemophilus spp. and can easily be coupled with other public genotyping and antimicrobial resistance databases. Our data also point towards a possible pathogenic role of H. haemolyticus strains, which needs to be further investigated. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01017-x.
Collapse
Affiliation(s)
- Margo Diricks
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, 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, Hamburg, Germany
| | - Nadja Käding
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Vladislav Leshchinskiy
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Susanne Hauswaldt
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Omar Jiménez Vázquez
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University Hospital Schleswig-Holstein, Lübeck, Germany.,German Center for Infection Research (DZIF), TTU HAARBI, Lübeck, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany. .,Evolution of the Resistome, Research Center Borstel, Borstel, Germany.
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Bateson A, Ortiz Canseco J, McHugh TD, Witney AA, Feuerriegel S, Merker M, Kohl TA, Utpatel C, Niemann S, Andres S, Kranzer K, Maurer FP, Ghodousi A, Borroni E, Cirillo DM, Wijkander M, Toro JC, Groenheit R, Werngren J, Machado D, Viveiros M, Warren RM, Sirgel F, Dippenaar A, Köser CU, Sun E, Timm J. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1685-1693. [PMID: 35260883 PMCID: PMC9155602 DOI: 10.1093/jac/dkac070] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 10/14/2021] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives To develop a robust phenotypic antimicrobial susceptibility testing (AST) method with a correctly set breakpoint for pretomanid (Pa), the most recently approved anti-tuberculosis drug. Methods The Becton Dickinson Mycobacterial Growth Indicator Tube™ (MGIT) system was used at six laboratories to determine the MICs of a phylogenetically diverse collection of 356 Mycobacterium tuberculosis complex (MTBC) strains to establish the epidemiological cut-off value for pretomanid. MICs were correlated with WGS data to study the genetic basis of differences in the susceptibility to pretomanid. Results We observed ancient differences in the susceptibility to pretomanid among various members of MTBC. Most notably, lineage 1 of M. tuberculosis, which is estimated to account for 28% of tuberculosis cases globally, was less susceptible than lineages 2, 3, 4 and 7 of M. tuberculosis, resulting in a 99th percentile of 2 mg/L for lineage 1 compared with 0.5 mg/L for the remaining M. tuberculosis lineages. Moreover, we observed that higher MICs (≥8 mg/L), which probably confer resistance, had recently evolved independently in six different M. tuberculosis strains. Unlike the aforementioned ancient differences in susceptibility, these recent differences were likely caused by mutations in the known pretomanid resistance genes. Conclusions In light of these findings, the provisional critical concentration of 1 mg/L for MGIT set by EMA must be re-evaluated. More broadly, these findings underline the importance of considering the global diversity of MTBC during clinical development of drugs and when defining breakpoints for AST.
Collapse
Affiliation(s)
- Anna Bateson
- Centre for Clinical Microbiology, University College London, Royal Free Campus, London, UK
| | - Julio Ortiz Canseco
- Centre for Clinical Microbiology, University College London, Royal Free Campus, London, UK
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, Royal Free Campus, London, UK
| | - Adam A. Witney
- Institute of Infection and Immunity, St George’s, University of London, London, UK
| | - Silke Feuerriegel
- 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
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Laboratory for Tuberculosis, Research Center Borstel, Borstel, Germany
| | - Katharina Kranzer
- Department of Clinical Research, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Biomedical Research & Training Institute, Harare, Zimbabwe
- Division of Infectious & Tropical Medicine, Medical Centre of the University of Munich, Munich, Germany
| | - Florian P Maurer
- German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
- 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
| | - Arash Ghodousi
- IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | | | - Daniela Maria Cirillo
- IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Maria Wijkander
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Juan C. Toro
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Ramona Groenheit
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Jim Werngren
- Supranational Reference Laboratory for Tuberculosis, Public Health Agency of Sweden, Solna, Sweden
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Robin M. Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/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
| | - Frederick Sirgel
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/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
| | - Anzaan Dippenaar
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/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
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Juliano Timm
- TB Alliance, New York City, NY, USA
- Corresponding author. E-mail:
| |
Collapse
|
22
|
Peker N, Schuele L, Kok N, Terrazos M, Neuenschwander SM, de Beer J, Akkerman O, Peter S, Ramette A, Merker M, Niemann S, Couto N, Sinha B, Rossen JWA. Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis. Microb Genom 2021; 7:000695. [PMID: 34825880 PMCID: PMC8743536 DOI: 10.1099/mgen.0.000695] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022] Open
Abstract
Whole-genome sequencing (WGS) of Mycobacterium tuberculosis (MTB) isolates can be used to get an accurate diagnosis, to guide clinical decision making, to control tuberculosis (TB) and for outbreak investigations. We evaluated the performance of long-read (LR) and/or short-read (SR) sequencing for anti-TB drug-resistance prediction using the TBProfiler and Mykrobe tools, the fraction of genome recovery, assembly accuracies and the robustness of two typing approaches based on core-genome SNP (cgSNP) typing and core-genome multi-locus sequence typing (cgMLST). Most of the discrepancies between phenotypic drug-susceptibility testing (DST) and drug-resistance prediction were observed for the first-line drugs rifampicin, isoniazid, pyrazinamide and ethambutol, mainly with LR sequence data. Resistance prediction to second-line drugs made by both TBProfiler and Mykrobe tools with SR- and LR-sequence data were in complete agreement with phenotypic DST except for one isolate. The SR assemblies were more accurate than the LR assemblies, having significantly (P <0.05) fewer indels and mismatches per 100 kbp. However, the hybrid and LR assemblies had slightly higher genome fractions. For LR assemblies, Canu followed by Racon, and Medaka polishing was the most accurate approach. The cgSNP approach, based on either reads or assemblies, was more robust than the cgMLST approach, especially for LR sequence data. In conclusion, anti-TB drug-resistance prediction, particularly with only LR sequence data, remains challenging, especially for first-line drugs. In addition, SR assemblies appear more accurate than LR ones, and reproducible phylogeny can be achieved using cgSNP approaches.
Collapse
Affiliation(s)
- Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Nienke Kok
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Miguel Terrazos
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | | | - Jessica de Beer
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Onno Akkerman
- University of Groningen, University Medical Center Groningen, Department of Pulmonary diseases and Tuberculosis, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, TB Center Beatrixoord, Haren, The Netherlands
| | - Silke Peter
- University of Tübingen, Institute of Medical Microbiology and Hygiene, Tübingen, Germany
| | - Alban Ramette
- University of Bern, Institute for Infectious Diseases, Bern, Switzerland
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Bhanu Sinha
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - John WA Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
- IDbyDNA Inc., San Carlos, CA, USA
| |
Collapse
|
23
|
Merker M, Egbe NF, Ngangue YR, Vuchas C, Kohl TA, Dreyer V, Kuaban C, Noeske J, Niemann S, Sander MS. Transmission patterns of rifampicin resistant Mycobacterium tuberculosis complex strains in Cameroon: a genomic epidemiological study. BMC Infect Dis 2021; 21:891. [PMID: 34465301 PMCID: PMC8406724 DOI: 10.1186/s12879-021-06593-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 06/14/2021] [Accepted: 08/17/2021] [Indexed: 11/29/2022] Open
Abstract
Background Determining factors affecting the transmission of rifampicin (RR) and multidrug-resistant (MDR) Mycobacterium tuberculosis complex strains under standardized tuberculosis (TB) treatment is key to control TB and prevent the evolution of drug resistance. Methods We combined bacterial whole genome sequencing (WGS) and epidemiological investigations for 37% (n = 195) of all RR/MDR-TB patients in Cameroon (2012–2015) to identify factors associated with recent transmission. Results Patients infected with a strain resistant to high-dose isoniazid, and ethambutol had 7.4 (95% CI 2.6–21.4), and 2.4 (95% CI 1.2–4.8) times increased odds of being in a WGS-cluster, a surrogate for recent transmission. Furthermore, age between 30 and 50 was positively correlated with recent transmission (adjusted OR 3.8, 95% CI 1.3–11.4). We found high drug-resistance proportions against three drugs used in the short standardized MDR-TB regimen in Cameroon, i.e. high-dose isoniazid (77.4%), ethambutol (56.9%), and pyrazinamide (43.1%). Virtually all strains were susceptible to fluoroquinolones, kanamycin, and clofazimine, and treatment outcomes were mostly favourable (87.5%). Conclusion Pre-existing resistance to high-dose isoniazid, and ethambutol is associated with recent transmission of RR/MDR strains in our study. A possible contributing factor for this observation is the absence of universal drug susceptibility testing in Cameroon, likely resulting in prolonged exposure of new RR/MDR-TB patients to sub-optimal or failing first-line drug regimens. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06593-8.
Collapse
Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,Evolution of the Resistome, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| | - Nkongho F Egbe
- Tuberculosis Reference Laboratory Bamenda, Center for Health Promotion and Research, Bamenda, Cameroon.,School of Life Sciences, College of Science, University of Lincoln, Lincoln, England, UK
| | - Yannick R Ngangue
- Tuberculosis Reference Laboratory Bamenda, Center for Health Promotion and Research, Bamenda, Cameroon
| | - Comfort Vuchas
- Tuberculosis Reference Laboratory Bamenda, Center for Health Promotion and Research, Bamenda, Cameroon
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Center Borstel, 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
| | - Melissa S Sander
- Tuberculosis Reference Laboratory Bamenda, Center for Health Promotion and Research, Bamenda, Cameroon
| |
Collapse
|
24
|
Thiel U, Schober SJ, Ranft A, Gassmann H, Jabar S, Gall K, von Lüttichau I, Wawer A, Koscielniak E, Diaz MA, Ussowicz M, Kazantsev I, Afanasyev B, Merker M, Klingebiel T, Prete A, Gruhn B, Bader P, Jürgens H, Dirksen U, Handgretinger R, Burdach S, Lang P. Correction to: No difference in survival after HLA mismatched versus HLA matched allogeneic stem cell transplantation in Ewing sarcoma patients with advanced disease. Bone Marrow Transplant 2021; 56:2320. [PMID: 34373590 PMCID: PMC8410592 DOI: 10.1038/s41409-021-01421-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- U Thiel
- Department of Pediatrics and Children's Cancer Research Center, School of Medicine, Kinderklinik München Schwabing, Technical University of Munich, Munich, Germany.
| | - S J Schober
- Department of Pediatrics and Children's Cancer Research Center, School of Medicine, Kinderklinik München Schwabing, Technical University of Munich, Munich, Germany
| | - A Ranft
- Pediatrics III, West German Cancer Centre Essen, University Hospital Essen, Essen, Germany
| | - H Gassmann
- Department of Pediatrics and Children's Cancer Research Center, School of Medicine, Kinderklinik München Schwabing, Technical University of Munich, Munich, Germany
| | - S Jabar
- Pediatrics III, West German Cancer Centre Essen, University Hospital Essen, Essen, Germany
| | - K Gall
- Department of Pediatrics and Children's Cancer Research Center, School of Medicine, Kinderklinik München Schwabing, Technical University of Munich, Munich, Germany
| | - I von Lüttichau
- Department of Pediatrics and Children's Cancer Research Center, School of Medicine, Kinderklinik München Schwabing, Technical University of Munich, Munich, Germany
| | - A Wawer
- Department of Pediatrics and Children's Cancer Research Center, School of Medicine, Kinderklinik München Schwabing, Technical University of Munich, Munich, Germany
| | - E Koscielniak
- Department of Pediatric Oncology, Hematology and Immunology, Olgahospital, Stuttgart, Germany
| | - M A Diaz
- Department of Pediatric Hematology-Oncology and Hematopoietic Stem Cell Transplantation, Hospital Infantil Universitario Niño Jesus, Madrid, Spain
| | - M Ussowicz
- Department of Pediatric Hematology, Oncology and Bone Marrow Transplantation, Wroclaw Medical University, Wroclaw, Poland
| | - I Kazantsev
- Raisa Gorbacheva Memorial Institute for Pediatric Oncology, Hematology and Transplantat, Pavlov First St. Petersburg State Universityion, St. Petersburg, Russia
| | - B Afanasyev
- Raisa Gorbacheva Memorial Institute for Pediatric Oncology, Hematology and Transplantat, Pavlov First St. Petersburg State Universityion, St. Petersburg, Russia
| | - M Merker
- Department of Pediatric Hematology and Oncology, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - T Klingebiel
- Department of Pediatric Hematology and Oncology, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - A Prete
- Department of Pediatric Hematology and Oncology, Ospedale S Orsola Malpighi, Bologna, Italy
| | - B Gruhn
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - P Bader
- Department of Pediatric Hematology and Oncology, Universitätsklinikum Frankfurt, Frankfurt, Germany
| | - H Jürgens
- Department of Pediatric Hematology and Oncology, Universitätsklinikum Münster, Münster, Germany
| | - U Dirksen
- Pediatrics III, West German Cancer Centre Essen, University Hospital Essen, Essen, Germany
| | - R Handgretinger
- Department of Pediatric Hematology and Oncology, Universitätsklinikum Tübingen, Tübingen, Germany
| | - S Burdach
- Department of Pediatrics and Children's Cancer Research Center, School of Medicine, Kinderklinik München Schwabing, Technical University of Munich, Munich, Germany
| | - P Lang
- Department of Pediatric Hematology and Oncology, Universitätsklinikum Tübingen, Tübingen, Germany
| |
Collapse
|
25
|
Sonnenkalb L, Strohe G, Dreyer V, Andres S, Hillemann D, Maurer FP, Niemann S, Merker M. Microevolution of Mycobacterium tuberculosis Subpopulations and Heteroresistance in a Patient Receiving 27 Years of Tuberculosis Treatment in Germany. Antimicrob Agents Chemother 2021; 65:e0252020. [PMID: 33903103 PMCID: PMC8218629 DOI: 10.1128/aac.02520-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/03/2020] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
Preexisting and newly emerging resistant pathogen subpopulations (heteroresistance) are potential risk factors for treatment failure of multi/extensively drug resistant (MDR/XDR) tuberculosis (TB). Intrapatient evolutionary dynamics of Mycobacterium tuberculosis complex (Mtbc) strains and their implications on treatment outcomes are still not completely understood. To elucidate how Mtbc strains escape therapy, we analyzed 13 serial isolates from a German patient by whole-genome sequencing. Sequencing data were compared with phenotypic drug susceptibility profiles and the patient's collective 27-year treatment history to further elucidate factors fostering intrapatient resistance evolution. The patient endured five distinct TB episodes, ending in resistance to 16 drugs and a nearly untreatable XDR-TB infection. The first isolate obtained, during the patient's 5th TB episode, presented fixed resistance mutations to 7 anti-TB drugs, including isoniazid, rifampin, streptomycin, pyrazinamide, prothionamide, para-aminosalicylic acid, and cycloserine-terizidone. Over the next 13 years, a dynamic evolution with coexisting, heterogeneous subpopulations was observed in 6 out of 13 sequential bacterial isolates. The emergence of drug-resistant subpopulations coincided with frequent changes in treatment regimens, which often included two or fewer active compounds. This evolutionary arms race between competing subpopulations ultimately resulted in the fixation of a single XDR variant. Our data demonstrate the complex intrapatient microevolution of Mtbc subpopulations during failing MDR/XDR-TB treatment. Designing effective treatment regimens based on rapid detection of (hetero) resistance is key to avoid resistance development and treatment failure.
Collapse
Affiliation(s)
- Lindsay Sonnenkalb
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Gerald Strohe
- Landratsamt Karlsruhe, Gesundheitsamt, Karlsruhe, Germany
| | - Viola Dreyer
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| | - Sönke Andres
- National and Supranational Reference Centre for Mycobacteria, Research Centre Borstel, Borstel, Germany
| | - Doris Hillemann
- National and Supranational Reference Centre for Mycobacteria, Research Centre Borstel, Borstel, Germany
| | - Florian P. Maurer
- National and Supranational Reference Centre for Mycobacteria, Research Centre Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
- German Centre for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Centre Borstel, Borstel, Germany
| |
Collapse
|
26
|
Kontsevaya I, Lange C, Comella-Del-Barrio P, Coarfa C, DiNardo AR, Gillespie SH, Hauptmann M, Leschczyk C, Mandalakas AM, Martinecz A, Merker M, Niemann S, Reimann M, Rzhepishevska O, Schaible UE, Scheu KM, Schurr E, Abel Zur Wiesch P, Heyckendorf J. Perspectives for systems biology in the management of tuberculosis. Eur Respir Rev 2021; 30:30/160/200377. [PMID: 34039674 DOI: 10.1183/16000617.0377-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/28/2021] [Indexed: 12/18/2022] Open
Abstract
Standardised management of tuberculosis may soon be replaced by individualised, precision medicine-guided therapies informed with knowledge provided by the field of systems biology. Systems biology is a rapidly expanding field of computational and mathematical analysis and modelling of complex biological systems that can provide insights into mechanisms underlying tuberculosis, identify novel biomarkers, and help to optimise prevention, diagnosis and treatment of disease. These advances are critically important in the context of the evolving epidemic of drug-resistant tuberculosis. Here, we review the available evidence on the role of systems biology approaches - human and mycobacterial genomics and transcriptomics, proteomics, lipidomics/metabolomics, immunophenotyping, systems pharmacology and gut microbiomes - in the management of tuberculosis including prediction of risk for disease progression, severity of mycobacterial virulence and drug resistance, adverse events, comorbidities, response to therapy and treatment outcomes. Application of the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach demonstrated that at present most of the studies provide "very low" certainty of evidence for answering clinically relevant questions. Further studies in large prospective cohorts of patients, including randomised clinical trials, are necessary to assess the applicability of the findings in tuberculosis prevention and more efficient clinical management of patients.
Collapse
Affiliation(s)
- Irina Kontsevaya
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Christoph Lange
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Patricia Comella-Del-Barrio
- Research Institute Germans Trias i Pujol, CIBER Respiratory Diseases, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Cristian Coarfa
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.,Molecular and Cellular Biology, Center for Precision Environmental health, Baylor College of Medicine, Houston, TX, USA
| | - Andrew R DiNardo
- The Global Tuberculosis Program, Texas Children's Hospital, Dept of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Matthias Hauptmann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Christoph Leschczyk
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Anna M Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Dept of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Antal Martinecz
- Dept of Biology, Pennsylvania State University, University Park, PA, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.,Dept of Pharmacy, Faculty of Health Sciences, UiT, Arctic University of Norway, Tromsø, Norway
| | - Matthias Merker
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Stefan Niemann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Maja Reimann
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Olena Rzhepishevska
- Dept of Chemistry, Umeå University, Umeå, Sweden.,Dept of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Ulrich E Schaible
- Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Erwin Schurr
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Canada
| | - Pia Abel Zur Wiesch
- Dept of Biology, Pennsylvania State University, University Park, PA, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Jan Heyckendorf
- Research Center Borstel, Borstel, Germany .,German Center for Infection Research, Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| |
Collapse
|
27
|
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
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Nadarajan D, Hillemann D, Kamara R, Foray L, Conteh OS, Merker M, Niemann S, Lau J, Njoya M, Kranzer K, Somoskovi A, Maurer FP. Evaluation of the Roche cobas MTB and MTB-RIF/INH Assays in Samples from Germany and Sierra Leone. J Clin Microbiol 2021; 59:e02983-20. [PMID: 33658264 PMCID: PMC8091830 DOI: 10.1128/jcm.02983-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/24/2020] [Accepted: 02/23/2021] [Indexed: 12/03/2022] Open
Abstract
The Roche cobas MTB and MTB-RIF/INH assays allow for detection of Mycobacterium tuberculosis complex (MTBC) nucleic acid and rifampicin (RIF) and isoniazid (INH) resistance-associated mutations in an automated, high-throughput workflow. In this study, we evaluated the performance of these assays, employing samples from settings of low and high tuberculosis (TB) burdens. A total of 325 frozen, leftover respiratory samples collected from treatment-naive patients with presumptive TB in Germany (n = 280) and presumptive RIF-resistant TB in Sierra Leone (n = 45) were used in this study. cobas MTB results for detection of MTBC DNA from N-acetyl-l-cysteine-sodium hydroxide (NALC-NaOH)-treated samples were compared to culture results. Predictions of RIF and INH resistance by the cobas MTB-RIF/INH assay were compared to a composite reference standard (phenotypic drug susceptibility testing and line probe assay). Whole-genome sequencing was used to resolve discordances. The overall sensitivity of cobas MTB for detection of MTBC DNA in culture-positive samples (n = 102) was 89.2% (95% confidence interval [CI], 81.7 to 93.9%). The specificity of cobas MTB was 98.6% (95% CI, 96.1 to 99.5%). Sensitivity and specificity for detection of RIF and INH resistance were 88.4% (95% CI, 75.5 to 94.9%) and 97.6% (95% CI, 87.4 to 99.6%) and 76.6% (95% CI, 62.8 to 86.4%) and 100.0% (95% CI, 90.8 to 100.0%), respectively. Discordant results for RIF and INH resistance were mainly due to uncommon mutations in samples from Sierra Leone that were not covered by the cobas MTB-RIF/INH assay. In conclusion, cobas MTB and MTB-RIF/INH assays provide accurate detection of MTBC DNA and resistance-associated mutations in respiratory samples. The influence of regional variations in the prevalence of resistance-conferring mutations requires further investigation.
Collapse
Affiliation(s)
- Darshaalini Nadarajan
- National and Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Doris Hillemann
- National and Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Rashidatu Kamara
- National Leprosy and Tuberculosis Control Programme (NLTCP), Ministry of Health and Sanitation (MOHS), Freetown, Sierra Leone
| | - Lynda Foray
- National Leprosy and Tuberculosis Control Programme (NLTCP), Ministry of Health and Sanitation (MOHS), Freetown, Sierra Leone
| | - Ousman S Conteh
- National Leprosy and Tuberculosis Control Programme (NLTCP), Ministry of Health and Sanitation (MOHS), Freetown, Sierra Leone
| | - Matthias Merker
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Jasmine Lau
- Roche Molecular Systems, Pleasanton, California, USA
| | - Merlin Njoya
- Roche Molecular Systems, Pleasanton, California, USA
| | - Katharina Kranzer
- London School of Hygiene and Tropical Medicine, Clinical Research Department, London, United Kingdom
| | | | - Florian P Maurer
- National and Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
30
|
Shuaib YA, Khalil EA, Wieler LH, Schaible UE, Bakheit MA, Mohamed-Noor SE, Abdalla MA, Kerubo G, Andres S, Hillemann D, Richter E, Kranzer K, Niemann S, Merker M. Mycobacterium tuberculosis Complex Lineage 3 as Causative Agent of Pulmonary Tuberculosis, Eastern Sudan 1. Emerg Infect Dis 2021; 26:427-436. [PMID: 32091355 PMCID: PMC7045825 DOI: 10.3201/eid2603.191145] [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: 12/11/2022] Open
Abstract
Pathogen-based factors associated with tuberculosis (TB) in eastern Sudan are not well defined. We investigated genetic diversity, drug resistance, and possible transmission clusters of Mycobacterium tuberculosis complex (MTBC) strains by using a genomic epidemiology approach. We collected 383 sputum specimens at 3 hospitals in 2014 and 2016 from patients with symptoms suggestive of TB; of these, 171 grew MTBC strains. Whole-genome sequencing could be performed on 166 MTBC strains; phylogenetic classification revealed that most (73.4%; n = 122) belonged to lineage 3 (L3). Genome-based cluster analysis showed that 76 strains (45.9%) were grouped into 29 molecular clusters, comprising 2–8 strains/patients. Of the strains investigated, 9.0% (15/166) were multidrug resistant (MDR); 10 MDR MTBC strains were linked to 1 large MDR transmission network. Our findings indicate that L3 strains are the main causative agent of TB in eastern Sudan; MDR TB is caused mainly by transmission of MDR L3 strains.
Collapse
|
31
|
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.
Collapse
|
32
|
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.
Collapse
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.
| |
Collapse
|
33
|
Lange C, Aarnoutse R, Chesov D, van Crevel R, Gillespie SH, Grobbel HP, Kalsdorf B, Kontsevaya I, van Laarhoven A, Nishiguchi T, Mandalakas A, Merker M, Niemann S, Köhler N, Heyckendorf J, Reimann M, Ruhwald M, Sanchez-Carballo P, Schwudke D, Waldow F, DiNardo AR. Perspective for Precision Medicine for Tuberculosis. Front Immunol 2020; 11:566608. [PMID: 33117351 PMCID: PMC7578248 DOI: 10.3389/fimmu.2020.566608] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/02/2020] [Indexed: 12/28/2022] Open
Abstract
Tuberculosis is a bacterial infectious disease that is mainly transmitted from human to human via infectious aerosols. Currently, tuberculosis is the leading cause of death by an infectious disease world-wide. In the past decade, the number of patients affected by tuberculosis has increased by ~20 percent and the emergence of drug-resistant strains of Mycobacterium tuberculosis challenges the goal of elimination of tuberculosis in the near future. For the last 50 years, management of patients with tuberculosis has followed a standardized management approach. This standardization neglects the variation in human susceptibility to infection, immune response, the pharmacokinetics of drugs, and the individual duration of treatment needed to achieve relapse-free cure. Here we propose a package of precision medicine-guided therapies that has the prospect to drive clinical management decisions, based on both host immunity and M. tuberculosis strains genetics. Recently, important scientific discoveries and technological advances have been achieved that provide a perspective for individualized rather than standardized management of patients with tuberculosis. For the individual selection of best medicines and host-directed therapies, personalized drug dosing, and treatment durations, physicians treating patients with tuberculosis will be able to rely on these advances in systems biology and to apply them at the bedside.
Collapse
Affiliation(s)
- Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Rob Aarnoutse
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Dumitru Chesov
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Department of Pulmonology and Allergology, Nicolae Testemitanu University of Medicine and Pharmacy, Chisinau, Moldova
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Hans-Peter Grobbel
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Barbara Kalsdorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Arjan van Laarhoven
- Department of Internal Medicine, Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, Netherlands
| | - Tomoki Nishiguchi
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Anna Mandalakas
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Matthias Merker
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Niklas Köhler
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Morten Ruhwald
- Foundation of Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Patricia Sanchez-Carballo
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Respiratory Medicine and International Health, University of Lübeck, Lübeck, Germany
| | - Dominik Schwudke
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Airway Research Center North, German Center for Lung Research (DZL), Borstel, Germany
| | - Franziska Waldow
- German Center for Infection Research (DZIF) Partner Site Borstel-Hamburg-Lübeck-Riems, Borstel, Germany
- Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrew R. DiNardo
- The Global Tuberculosis Program, Texas Children's Hospital, Immigrant and Global Health, Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| |
Collapse
|
34
|
Godfroid M, Dagan T, Merker M, Kohl TA, Diel R, Maurer FP, Niemann S, Kupczok A. Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak. PLoS Pathog 2020; 16:e1008357. [PMID: 32997707 PMCID: PMC7549793 DOI: 10.1371/journal.ppat.1008357] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 10/12/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
In genome evolution, genetic variants are the source of diversity, which natural selection acts upon. Treatment of human tuberculosis (TB) induces a strong selection pressure for the emergence of antibiotic resistance-conferring variants in the infecting Mycobacterium tuberculosis (MTB) strains. MTB evolution in response to treatment has been intensively studied and mainly attributed to point substitutions. However, the frequency and contribution of insertions and deletions (indels) to MTB genome evolution remains poorly understood. Here, we analyzed a multi-drug resistant MTB outbreak for the presence of high-quality indels and substitutions. We find that indels are significantly enriched in genes conferring antibiotic resistance. Furthermore, we show that indels are inherited during the outbreak and follow a molecular clock with an evolutionary rate of 5.37e-9 indels/site/year, which is 23 times lower than the substitution rate. Inherited indels may co-occur with substitutions in genes along related biological pathways; examples are iron storage and resistance to second-line antibiotics. This suggests that epistatic interactions between indels and substitutions affect antibiotic resistance and compensatory evolution in MTB.
Collapse
Affiliation(s)
- Maxime Godfroid
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas A. Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Roland Diel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany
- Lungenclinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany
| | - Florian P. Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, 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
| | - Anne Kupczok
- Institute of General Microbiology, Kiel University, Kiel, Germany
| |
Collapse
|
35
|
Andres S, Merker M, Heyckendorf J, Kalsdorf B, Rumetshofer R, Indra A, Hofmann-Thiel S, Hoffmann H, Lange C, Niemann S, Maurer FP. Bedaquiline-Resistant Tuberculosis: Dark Clouds on the Horizon. Am J Respir Crit Care Med 2020; 201:1564-1568. [PMID: 32053752 DOI: 10.1164/rccm.201909-1819le] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Matthias Merker
- Research Center BorstelBorstel, Germany.,German Center for Infection ResearchBorstel, Germany
| | - Jan Heyckendorf
- Research Center BorstelBorstel, Germany.,German Center for Infection ResearchBorstel, Germany
| | - Barbara Kalsdorf
- Research Center BorstelBorstel, Germany.,German Center for Infection ResearchBorstel, Germany
| | | | - Alexander Indra
- Austrian Agency for Health and Food Safety (AGES)Vienna, Austria
| | - Sabine Hofmann-Thiel
- World Health Organization Supranational Reference Laboratory of TB MunichGauting, Germany.,SYNLABGauting, Germany.,SYNLAB Human Genetics MunichMunich, Germany
| | - Harald Hoffmann
- World Health Organization Supranational Reference Laboratory of TB MunichGauting, Germany.,SYNLABGauting, Germany.,SYNLAB Human Genetics MunichMunich, Germany
| | - Christoph Lange
- Research Center BorstelBorstel, Germany.,German Center for Infection ResearchBorstel, Germany.,University of LübeckLübeck, Germany.,Karolinska InstituteStockholm, Swedenand
| | - Stefan Niemann
- Research Center BorstelBorstel, Germany.,German Center for Infection ResearchBorstel, Germany
| | - Florian P Maurer
- Research Center BorstelBorstel, Germany.,University Medical Center Hamburg-EppendorfHamburg, Germany
| |
Collapse
|
36
|
Merker M, Tueffers L, Vallier M, Groth EE, Sonnenkalb L, Unterweger D, Baines JF, Niemann S, Schulenburg H. Evolutionary Approaches to Combat Antibiotic Resistance: Opportunities and Challenges for Precision Medicine. Front Immunol 2020; 11:1938. [PMID: 32983122 PMCID: PMC7481325 DOI: 10.3389/fimmu.2020.01938] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 06/01/2020] [Accepted: 07/17/2020] [Indexed: 12/18/2022] Open
Abstract
The rise of antimicrobial resistance (AMR) in bacterial pathogens is acknowledged by the WHO as a major global health crisis. It is estimated that in 2050 annually up to 10 million people will die from infections with drug resistant pathogens if no efficient countermeasures are implemented. Evolution of pathogens lies at the core of this crisis, which enables rapid adaptation to the selective pressures imposed by antimicrobial usage in both medical treatment and agriculture, consequently promoting the spread of resistance genes or alleles in bacterial populations. Approaches developed in the field of Evolutionary Medicine attempt to exploit evolutionary insight into these adaptive processes, with the aim to improve diagnostics and the sustainability of antimicrobial therapy. Here, we review the concept of evolutionary trade-offs in the development of AMR as well as new therapeutic approaches and their impact on host-microbiome-pathogen interactions. We further discuss the possible translation of evolution-informed treatments into clinical practice, considering both the rapid cure of the individual patients and the prevention of AMR.
Collapse
Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Hamburg, Germany.,Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
| | - Leif Tueffers
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany.,Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany
| | - Marie Vallier
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University and Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Espen E Groth
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany.,Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany.,Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Lindsay Sonnenkalb
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Daniel Unterweger
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University and Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - John F Baines
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University and Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Borstel-Hamburg-Lübeck-Riems, Hamburg, Germany.,Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany
| | - Hinrich Schulenburg
- Cluster of Excellence Precision Medicine in Chronic Inflammation, Kiel, Germany.,Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität, Kiel, Germany
| |
Collapse
|
37
|
Kranzer K, Kalsdorf B, Heyckendorf J, Andres S, Merker M, Hofmann-Thiel S, Bloemberg GV, Hoffmann H, Niemann S, Lange C, Maurer FP. New World Health Organization Treatment Recommendations for Multidrug-Resistant Tuberculosis: Are We Well Enough Prepared? Am J Respir Crit Care Med 2020; 200:514-515. [PMID: 31026398 DOI: 10.1164/rccm.201902-0260le] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Katharina Kranzer
- 1Research Center BorstelBorstel, Germany.,2London School of Hygiene and Tropical MedicineLondon, United Kingdom
| | - Barbara Kalsdorf
- 1Research Center BorstelBorstel, Germany.,3German Center for Infection Research-DZIFBorstel, Germany.,4University of LübeckLübeck, Germany
| | - Jan Heyckendorf
- 1Research Center BorstelBorstel, Germany.,3German Center for Infection Research-DZIFBorstel, Germany.,4University of LübeckLübeck, Germany
| | - Sönke Andres
- 1Research Center BorstelBorstel, Germany.,9National and WHO Supranational Reference Laboratory for MycobacteriaBorstel, Germany
| | - Matthias Merker
- 1Research Center BorstelBorstel, Germany.,3German Center for Infection Research-DZIFBorstel, Germany
| | - Sabine Hofmann-Thiel
- 5SYNLAB GautingGauting, Germany.,6WHO Supranational Reference Laboratory for TuberculosisGauting, Germany
| | | | - Harald Hoffmann
- 5SYNLAB GautingGauting, Germany.,6WHO Supranational Reference Laboratory for TuberculosisGauting, Germany
| | - Stefan Niemann
- 1Research Center BorstelBorstel, Germany.,3German Center for Infection Research-DZIFBorstel, Germany
| | - Christoph Lange
- 1Research Center BorstelBorstel, Germany.,3German Center for Infection Research-DZIFBorstel, Germany.,4University of LübeckLübeck, Germany.,8Karolinska InstituteStockholm, Sweden
| | - Florian P Maurer
- 1Research Center BorstelBorstel, Germany.,10University of HamburgHamburg, Germanyand.,11National and WHO Supranational Reference Laboratory for Mycobacteria Borstel, Germany
| |
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Klopper M, Heupink TH, Hill-Cawthorne G, Streicher EM, Dippenaar A, de Vos M, Abdallah AM, Limberis J, Merker M, Burns S, Niemann S, Dheda K, Posey J, Pain A, Warren RM. A landscape of genomic alterations at the root of a near-untreatable tuberculosis epidemic. BMC Med 2020; 18:24. [PMID: 32014024 PMCID: PMC6998097 DOI: 10.1186/s12916-019-1487-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/24/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Atypical Beijing genotype Mycobacterium tuberculosis strains are widespread in South Africa and have acquired resistance to up to 13 drugs on multiple occasions. It is puzzling that these strains have retained fitness and transmissibility despite the potential fitness cost associated with drug resistance mutations. METHODS We conducted Illumina sequencing of 211 Beijing genotype M. tuberculosis isolates to facilitate the detection of genomic features that may promote acquisition of drug resistance and restore fitness in highly resistant atypical Beijing forms. Phylogenetic and comparative genomic analysis was done to determine changes that are unique to the resistant strains that also transmit well. Minimum inhibitory concentration (MIC) determination for streptomycin and bedaquiline was done for a limited number of isolates to demonstrate a difference in MIC between isolates with and without certain variants. RESULTS Phylogenetic analysis confirmed that two clades of atypical Beijing strains have independently developed resistance to virtually all the potent drugs included in standard (pre-bedaquiline) drug-resistant TB treatment regimens. We show that undetected drug resistance in a progenitor strain was likely instrumental in this resistance acquisition. In this cohort, ethionamide (ethA A381P) resistance would be missed in first-line drug-susceptible isolates, and streptomycin (gidB L79S) resistance may be missed due to an MIC close to the critical concentration. Subsequent inadequate treatment historically led to amplification of resistance and facilitated spread of the strains. Bedaquiline resistance was found in a small number of isolates, despite lack of exposure to the drug. The highly resistant clades also carry inhA promoter mutations, which arose after ethA and katG mutations. In these isolates, inhA promoter mutations do not alter drug resistance, suggesting a possible alternative role. CONCLUSION The presence of the ethA mutation in otherwise susceptible isolates from ethionamide-naïve patients demonstrates that known exposure is not an adequate indicator of drug susceptibility. Similarly, it is demonstrated that bedaquiline resistance can occur without exposure to the drug. Inappropriate treatment regimens, due to missed resistance, leads to amplification of resistance, and transmission. We put these results into the context of current WHO treatment regimens, underscoring the risks of treatment without knowledge of the full drug resistance profile.
Collapse
Affiliation(s)
- Marisa Klopper
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Tim Hermanus Heupink
- Global Health Institute, Epidemiology and Social Medicine, University of Antwerp, Antwerp, Belgium
| | - Grant Hill-Cawthorne
- Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Elizabeth Maria Streicher
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anzaan Dippenaar
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Margaretha de Vos
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Abdallah Musa Abdallah
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Basic Medical Sciences, College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Jason Limberis
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Scott Burns
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.,Faculty of Infectious and Tropical Diseases, Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Center for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Robin Mark Warren
- South African Medical Research Council Centre for Tuberculosis Research, DST NRF Centre of Excellence for Biomedical Tuberculosis research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
40
|
Hunt M, Bradley P, Lapierre SG, Heys S, Thomsit M, Hall MB, Malone KM, Wintringer P, Walker TM, Cirillo DM, Comas I, Farhat MR, Fowler P, Gardy J, Ismail N, Kohl TA, Mathys V, Merker M, Niemann S, Omar SV, Sintchenko V, Smith G, van Soolingen D, Supply P, Tahseen S, Wilcox M, Arandjelovic I, Peto TEA, Crook DW, Iqbal Z. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe. Wellcome Open Res 2019; 4:191. [PMID: 32055708 PMCID: PMC7004237 DOI: 10.12688/wellcomeopenres.15603.1] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2019] [Indexed: 01/08/2023] Open
Abstract
Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the use of WGS as an alternative to conventional phenotype-based DST, due to mutation catalogue limitations. Here we present a new tool, Mykrobe, which provides the same functionality based on a new software implementation. Improvements include i) an updated mutation catalogue giving greater sensitivity to detect pyrazinamide resistance, ii) support for user-defined resistance catalogues, iii) improved identification of non-tuberculous mycobacterial species, and iv) an updated statistical model for Oxford Nanopore Technologies sequencing data. Mykrobe is released under MIT license at https://github.com/mykrobe-tools/mykrobe. We incorporate mutation catalogues from the CRyPTIC consortium et al. (2018) and from Walker et al. (2015), and make improvements based on performance on an initial set of 3206 and an independent set of 5845 M. tuberculosis Illumina sequences. To give estimates of error rates, we use a prospectively collected dataset of 4362 M. tuberculosis isolates. Using culture based DST as the reference, we estimate Mykrobe to be 100%, 95%, 82%, 99% sensitive and 99%, 100%, 99%, 99% specific for rifampicin, isoniazid, pyrazinamide and ethambutol resistance prediction respectively. We benchmark against four other tools on 10207 (=5845+4362) samples, and also show that Mykrobe gives concordant results with nanopore data. We measure the ability of Mykrobe-based DST to guide personalized therapeutic regimen design in the context of complex drug susceptibility profiles, showing 94% concordance of implied regimen with that driven by phenotypic DST, higher than all other benchmarked tools.
Collapse
Affiliation(s)
- Martin Hunt
- European Bioinformatics Institute, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Simon Grandjean Lapierre
- Centre de Recherche du Centre Hospitalier de l'Universite de Montreal, Montreal, Canada
- Infectiology & immunology department, Universite de Montreal Microbiology, Montreal, Canada
| | - Simon Heys
- European Bioinformatics Institute, Cambridge, UK
| | - Mark Thomsit
- European Bioinformatics Institute, Cambridge, UK
| | | | | | | | - Timothy M. Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Daniela M. Cirillo
- Emerging Bacterial Pathogens Unit, WHO collaborating Centre and TB Supranational Reference laboratory, IRCCS San Raffaele Scientific institute, Milan, Italy
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- FISABIO Public Health, Valencia, Spain
- CIBER in Epidemiology and Public Health, Madrid, Spain
| | | | - Phillip Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Gardy
- British Columbia Centre for Disease Control, Vancouver, Canada
- Bill and Melinda Gates Foundation, Seattle, USA
| | - Nazir Ismail
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Thomas A. Kohl
- Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Matthias Merker
- Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
| | - Stefan Niemann
- Forschungszentrum Borstel, Leibniz Lungenzentrum, Borstel, Germany
- German Center for Infection Research, Borstel Site, Borstel, Germany
| | - Shaheed Vally Omar
- National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology - Public Health, University of Sydney, Sydney, Australia
| | - Grace Smith
- National Mycobacterial Reference Service, Public Health England Public Health Laboratory, Birmingham, UK
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunite de Lille, Lille, France
| | - Sabira Tahseen
- National TB Reference Laboratory, National TB control Program, Islamabad, Pakistan
| | - Mark Wilcox
- Leeds Teaching Hospital NHS Trust, Leeds, UK
- University of Leeds, Leeds, UK
| | - Irena Arandjelovic
- Faculty of Medicine, Institute of Microbiology and Immunology, Belgrade, Serbia
| | - Tim E. A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Infection Service, Public Health England, UK
| | - Zamin Iqbal
- European Bioinformatics Institute, Cambridge, UK
| |
Collapse
|
41
|
Diel R, Kohl TA, Maurer FP, Merker M, Meywald Walter K, Hannemann J, Nienhaus A, Supply P, Niemann S. Accuracy of whole-genome sequencing to determine recent tuberculosis transmission: an 11-year population-based study in Hamburg, Germany. Eur Respir J 2019; 54:13993003.01154-2019. [PMID: 31467121 PMCID: PMC6881715 DOI: 10.1183/13993003.01154-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/10/2019] [Indexed: 01/29/2023]
Abstract
Controlling human-to-human tuberculosis (TB) transmission is key for achieving the targets of the End TB Strategy set by the World Health Organization (WHO) [1, 2]. Stopping TB transmission, in large cities especially, is a challenging top priority worldwide [3]. Metropolitan areas have higher TB case notification rates than the rest of a country, as they concentrate high-risk groups, such as homeless people, drug users and migrants often from (other) high TB incidence settings. Opportunities for transmission are amplified by population density and complex social interactions, regularly leading to large, temporally extended transmission networks [3]. Targeted interventions to interrupt transmission require the combination of effective genotyping of TB strains with enhanced epidemiological investigation. While classic IS6110 DNA fingerprinting and 24-locus MIRU–VNTR (mycobacterial interspersed repetitive units–variable number of tandem repeats) typing provide standardised and easily computable typing results with an online nomenclature system, several studies have now demonstrated that whole-genome sequencing (WGS) has a superior discriminatory power, allowing for an unparalleled resolution of outbreak strains [4–10]. However, predictivity of WGS for detecting transmission in metropolitan areas has not yet been quantified versus most deterministic references, i.e. tangible epidemiological links identified by ad hoc investigation, at extended time and population scales. WGS typing with a five-SNP c:d:ut-off delineates recent transmission chains with highest accuracy and also provides high-resolution resistance patterns, thus enabling direct clinical benefitshttp://bit.ly/2Pk37Wo
Collapse
Affiliation(s)
- Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany .,Institution for Statutory Accident Insurance and Prevention in the Health and Welfare Services (BGW), Hamburg, Germany.,Both authors contributed equally
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Both authors contributed equally
| | - Florian P Maurer
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | | | - Jörg Hannemann
- Public Health Department Hamburg-Central, Hamburg, Germany
| | - Albert Nienhaus
- Institution for Statutory Accident Insurance and Prevention in the Health and Welfare Services (BGW), Hamburg, Germany.,Institute for Health Services Research in Dermatology and Nursing, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, Lille, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8204, Center for Infection and Immunity of Lille, Lille, France.,Université Lille Nord de France, Center for Infection and Immunity of Lille, Lille, France.,Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, 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
| |
Collapse
|
42
|
Engström A, Antonenka U, Kadyrov A, Kalmambetova G, Kranzer K, Merker M, Kabirov O, Parpieva N, Rajabov A, Sahalchyk E, Sayfudtinov Z, Niemann S, Hoffmann H. Population structure of drug-resistant Mycobacterium tuberculosis in Central Asia. BMC Infect Dis 2019; 19:908. [PMID: 31664926 PMCID: PMC6819405 DOI: 10.1186/s12879-019-4480-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 02/24/2019] [Accepted: 09/13/2019] [Indexed: 05/13/2023] Open
Abstract
Background Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan. Methods The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed. Results The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94–32 (n = 145) and 100–32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes. Conclusions Beijing clusters 94–32 and 100–32 are the dominant MTB genotypes in Central Asia. The relative size of 100–32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.
Collapse
Affiliation(s)
- Anna Engström
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany. .,Department of Medical Biochemistry and Microbiology, Uppsala University, IMBIM, Box 582, 751 23, Uppsala, Uppsala, Sweden. .,Present address: Clinical Genomics, Science for Life Laboratory, Tomtebodavägen 23 A, 17165, Solna, Sweden. .,Present address: School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden. .,Postal address: Science for Life Laboratory, Tomtebodavägen 23 A, 17165, Solna, Sweden.
| | - Uladzimir Antonenka
- WHO Supranational Reference Laboratory of Tuberculosis, IML red GmbH, Institute of Microbiology and Laboratory Medicine, Robert Koch-Allee 2, D-82131, Gauting, Germany
| | - Abdylat Kadyrov
- National Tuberculosis Institute, 90a Ahuunbaen Street, 720075, Bishkek, Kyrgyzstan
| | - Gulmira Kalmambetova
- National Reference Laboratory of Tuberculosis, 90a Ahuunbaen Street, 720075, Bishkek, Kyrgyzstan
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Olim Kabirov
- National Reference Laboratory of Tuberculosis, Vakhdat District, Dushanbe, Tajikistan
| | - Nargiza Parpieva
- Republican Specialized Scientific and Practical Medical Center of Tuberculosis and Pulmonology, Alimov Str.1, Tashkent, Uzbekistan, 100086
| | - Asliddin Rajabov
- National TB Center, National Tuberculosis Program, Dushanbe, Tajikistan
| | - Evgeni Sahalchyk
- WHO Supranational Reference Laboratory of Tuberculosis, IML red GmbH, Institute of Microbiology and Laboratory Medicine, Robert Koch-Allee 2, D-82131, Gauting, Germany
| | - Zayniddin Sayfudtinov
- National Reference Laboratory of Tuberculosis, Alimov Str.1, Tashkent, Uzbekistan, 100086
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Harald Hoffmann
- WHO Supranational Reference Laboratory of Tuberculosis, IML red GmbH, Institute of Microbiology and Laboratory Medicine, Robert Koch-Allee 2, D-82131, Gauting, Germany.,SYNLAB Gauting, SYNLAB Human Genetics Munich, Robert Koch-Allee 2, 82131, Gauting, Germany.,Kuratorium Tuberculosis in the World e.V, Robert Koch-Allee 2, 82131, Gauting, Germany
| |
Collapse
|
43
|
Arandjelović I, Merker M, Richter E, Kohl TA, Savić B, Soldatović I, Wirth T, Vuković D, Niemann S. Longitudinal Outbreak of Multidrug-Resistant Tuberculosis in a Hospital Setting, Serbia. Emerg Infect Dis 2019; 25:555-558. [PMID: 30789133 PMCID: PMC6390760 DOI: 10.3201/eid2503.181220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 12/01/2022] Open
Abstract
A retrospective population-based molecular epidemiologic study of multidrug-resistant Mycobacterium tuberculosis complex strains in Serbia (2008–2014) revealed an outbreak of TUR genotype strains in a psychiatric hospital starting around 1990. Drug unavailability, poor infection control, and schizophrenia likely fueled acquisition of additional resistance and bacterial fitness–related mutations over 2 decades.
Collapse
|
44
|
Shitikov E, Guliaev A, Bespyatykh J, Malakhova M, Kolchenko S, Smirnov G, Merker M, Niemann S, Mokrousov I, Ilina E, Govorun V. The role of IS6110 in micro- and macroevolution of Mycobacterium tuberculosis lineage 2. Mol Phylogenet Evol 2019; 139:106559. [PMID: 31302224 DOI: 10.1016/j.ympev.2019.106559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 01/31/2019] [Revised: 05/16/2019] [Accepted: 07/10/2019] [Indexed: 11/29/2022]
Abstract
The insertion sequence 6110 (IS6110) is the most studied transposable element in the Mycobacterium tuberculosis complex species. The element plays a significant role in genome plasticity of this important human pathogen, but still many causes and consequences of its transposition have not been fully studied. Here, we analyzed insertion sites for 902 Mycobacterium tuberculosis lineage 2 strains using whole-genome sequencing data. In total, 17,972 insertions were found, corresponding to 827 independent positions in the genome of the reference strain H37Rv. To trace the history of IS6110 expansion since proto-Beijing strains up to modern sublineages, we looked at the distribution of IS6110 across the genome-wide SNP-based phylogenetic tree. This analysis demonstrated a stepwise transposition of IS6110 that occurs by «copy-and-paste» mechanism. Additionally, we detected evolutionary-scale and sublineage-specific integration sites, which can be used for typing and for understanding the reasons for the success of the lineage. A significant part of such insertions affected the genes that are essential for the pathogen. Finally, we identified and confirmed deletions that occurred between differently oriented elements, which is uncommon for this family of insertion elements and appears to be another mechanism of genome variability.
Collapse
Affiliation(s)
- Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation.
| | - Andrei Guliaev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maja Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Sergey Kolchenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Georgy Smirnov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, 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-Riems, Germany
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| |
Collapse
|
45
|
Polsfuss S, Hofmann-Thiel S, Merker M, Krieger D, Niemann S, Rüssmann H, Schönfeld N, Hoffmann H, Kranzer K. Emergence of Low-level Delamanid and Bedaquiline Resistance During Extremely Drug-resistant Tuberculosis Treatment. Clin Infect Dis 2019; 69:1229-1231. [DOI: 10.1093/cid/ciz074] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/21/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
Two new drugs, delamanid and bedaquiline, have recently been approved for treatment of multidrug-resistant and extensively drug-resistant (XDR) tuberculosis. Here, we report a case of clofazimine, bedaquiline, and low-level delamanid resistances acquired during treatment of a patient with XDR tuberculosis.
Collapse
Affiliation(s)
- Silke Polsfuss
- Institute for Microbiology, Immunology and Laboratory Medicine, Helios Klinikum Emil von Behring, Berlin
| | - Sabine Hofmann-Thiel
- Synlab Gauting, synlab MVZ Humane Genetik
- IML red GmbH, Tuberculosis Supranational Reference Laboratory, Gauting
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel
| | - David Krieger
- Department of Pneumology, Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel
| | - Holger Rüssmann
- Institute for Microbiology, Immunology and Laboratory Medicine, Helios Klinikum Emil von Behring, Berlin
| | - Nicolas Schönfeld
- Department of Pneumology, Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, Berlin
| | - Harald Hoffmann
- Synlab Gauting, synlab MVZ Humane Genetik
- IML red GmbH, Tuberculosis Supranational Reference Laboratory, Gauting
| | - Katharina Kranzer
- National Reference Laboratory for Mycobacteria, Research Center Borstel, Borstel, Germany
- Clinical Research Unit, London School of Hygiene and Tropical Medicine, London, United Kingdom
| |
Collapse
|
46
|
Havlicek J, Dachsel B, Slickers P, Andres S, Beckert P, Feuerriegel S, Niemann S, Merker M, Labugger I. Rapid microarray-based assay for detection of pyrazinamide resistant Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2018; 94:147-154. [PMID: 30733004 PMCID: PMC6531379 DOI: 10.1016/j.diagmicrobio.2018.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 08/01/2018] [Revised: 12/17/2018] [Accepted: 12/24/2018] [Indexed: 01/25/2023]
Abstract
Pyrazinamide (PZA) is a key antibiotic for the treatment of drug susceptible tuberculosis. PZA-resistance is mainly mediated by mutations in the pncA gene; however the current gold standard is a phenotypic drug susceptibility test requiring a well-adjusted pH-value for reliable results. Our melting curve assay detects a non-wild type genotype in selected pncA regions in at least 3750 gene copies/mL within 2.5 hours. The prototype assay was further evaluated by analyzing 271 Mycobacterium tuberculosis complex isolates from Swaziland originating from a previously published drug resistance survey and including 118 isolates with pncA mutations. Sensitivity was 83% (95% CI 75-89%) and specificity was 100% (95% CI 98-100%). Under consideration of further improvements with regard to the target range our melting curve assay has the potential as a rapid rule-in test for PZA susceptibility (wild type pncA), however false resistant results (mutant pncA, but PZA susceptible) cannot be ruled out completely.
Collapse
Affiliation(s)
| | | | | | - Sönke Andres
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany.
| | | |
Collapse
|
47
|
Al-Ghafli H, Kohl TA, Merker M, Varghese B, Halees A, Niemann S, Al-Hajoj S. Drug-resistance profiling and transmission dynamics of multidrug-resistant Mycobacterium tuberculosis in Saudi Arabia revealed by whole genome sequencing. Infect Drug Resist 2018; 11:2219-2229. [PMID: 30519060 PMCID: PMC6237142 DOI: 10.2147/idr.s181124] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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] [Indexed: 11/23/2022] Open
Abstract
Background In Saudi Arabia, cross-border transmission of multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains might be particularly fostered by high immigration rates. Herein, we aimed to elucidate the transmission dynamics of MDR-MTBC strains and reveal a detailed prediction of all resistance-conferring mutations for the first- and second-line drugs. Methods We investigated all MDR-MTBC strains collected between 2015 and 2017 from provincial mycobacteria referral laboratories and compared demographic and clinical parameters to a cohort of non-MDR-TB patients using a whole genome sequencing approach. Clusters were defined based on a maximum strain-to-strain genetic distance of five single-nucleotide polymorphisms (SNPs) as surrogate marker for recent transmission, and then investigated molecular drug-resistance markers (37 genes). Results Forty-eight (67.6%) MDR-MTBC strains were grouped in 14 different clusters, ranging in size from two to six strains; 22.5% (16/71) of all MDR-MTBC isolates were predicted to be fully resistant to all five first-line drugs, and five strains (7.0%) exhibited fluoroquinolone resistance. Moreover, we revealed the presence of 12 compensatory mutations as well as 26 non-synonymous SNPs in the rpoC gene and non-hotspot region in rpoB, respectively. Conclusion Optimized TB molecular surveillance, diagnosis, and patient management are urgently needed to contain MDR-MTBC transmission and prevent the development of additional drug resistance.
Collapse
Affiliation(s)
- Hawra Al-Ghafli
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Bright Varghese
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| | - Anason Halees
- Data and Information Office, Anfas Medical Centre, Hittin District, Riyadh, Saudi Arabia
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel 23845, Germany.,German Centre for Infection Research (DZIF), Partner site Borstel, Borstel 38124, Germany
| | - Sahal Al-Hajoj
- Mycobacteriology Research Section, Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia,
| |
Collapse
|
48
|
Meehan CJ, Moris P, Kohl TA, Pečerska J, Akter S, Merker M, Utpatel C, Beckert P, Gehre F, Lempens P, Stadler T, Kaswa MK, Kühnert D, Niemann S, de Jong BC. The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine 2018; 37:410-416. [PMID: 30341041 PMCID: PMC6284411 DOI: 10.1016/j.ebiom.2018.10.013] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/17/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult. METHODS This study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated. FINDINGS Our results suggest that clusters based on Spoligotyping could encompass transmission events that occurred almost 200 years prior to sampling while 24-loci-MIRU-VNTR often represented three decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events, e.g. in timespans of up to 10 years for a 5 SNP/allele cut-off. INTERPRETATION With the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.
Collapse
Affiliation(s)
- Conor J Meehan
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium.
| | - Pieter Moris
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Adrem Data Lab (Adrem), Department of Mathematics and Computer Science, University of Antwerp, Antwerp 2020, Belgium; Biomedical Informatics Research Network Antwerp (biomina), University of Antwerp, Antwerp 2020, Belgium
| | - Thomas A Kohl
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Jūlija Pečerska
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Suriya Akter
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Matthias Merker
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Patrick Beckert
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Florian Gehre
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Serekunda, Gambia; Department Infectious Diseases Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg 20359, Germany
| | - Pauline Lempens
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| | - Tanja Stadler
- Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Michel K Kaswa
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium; National Tuberculosis Program, Kinshasa, DR Congo
| | - Denise Kühnert
- Max Planck Institute for the Science of Human History, 07745 JENA, Germany
| | - Stefan Niemann
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, D-23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Priority Area Infections, Research Center Borstel, D-23845 Borstel, Germany
| | - Bouke C de Jong
- Unit of Mycobacteriology, Biomedical Sciences, Institute of Tropical Medicine, Antwerp 2000, Belgium
| |
Collapse
|
49
|
Merker M, Barbier M, Cox H, Rasigade JP, Feuerriegel S, Kohl TA, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Nübel U, Supply P, Wirth T, Niemann S. Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. eLife 2018; 7:38200. [PMID: 30373719 PMCID: PMC6207422 DOI: 10.7554/elife.38200] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [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: 05/08/2018] [Accepted: 10/02/2018] [Indexed: 12/21/2022] Open
Abstract
Bacterial factors favoring the unprecedented multidrug-resistant tuberculosis (MDR-TB) epidemic in the former Soviet Union remain unclear. We utilized whole genome sequencing and Bayesian statistics to analyze the evolutionary history, temporal emergence of resistance and transmission networks of MDR Mycobacterium tuberculosis complex isolates from Karakalpakstan, Uzbekistan (2001-2006). One clade (termed Central Asian outbreak, CAO) dating back to 1974 (95% HPD 1969-1982) subsequently acquired resistance mediating mutations to eight anti-TB drugs. Introduction of standardized WHO-endorsed directly observed treatment, short-course in Karakalpakstan in 1998 likely selected for CAO-strains, comprising 75% of sampled MDR-TB isolates in 2005/2006. CAO-isolates were also identified in a published cohort from Russia (2008-2010). Similarly, the presence of mutations supposed to compensate bacterial fitness deficits was associated with transmission success and higher drug resistance rates. The genetic make-up of these MDR-strains threatens the success of both empirical and standardized MDR-TB therapies, including the newly WHO-endorsed short MDR-TB regimen in Uzbekistan.
Collapse
Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Maxime Barbier
- Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Helen Cox
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jean-Philippe Rasigade
- Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France.,CIRI INSERM U1111, University of Lyon, Lyon, France
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Vladyslav Nikolayevskyy
- Imperial College London, London, United Kingdom.,Public Health England, London, United Kingdom
| | - Sönke Andres
- Division of Mycobacteriology, National Tuberculosis Reference Laboratory, Research Center Borstel, Borstel, Germany
| | - Ulrich Nübel
- Microbial Genome Research, Leibniz-Institut DSMZ- Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Philip Supply
- Université de Lille, CNRS UMR 8204, Inserm U1019, CHU de Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche, Center for Infection and Immunity of Lille, Lille, France.,Center for Infection and Immunity of Lille, Université de Lille Nord de France, Lille, France.,Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Thierry Wirth
- Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| |
Collapse
|
50
|
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
- * E-mail:
| | - Timothy M. Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tjip S. van der Werf
- Department of Pulmonary Diseases & Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christoph Lange
- Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- International Health / Infectious Diseases, University of Lübeck, Lübeck, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
- German Center for Infection Research (DZIF) Tuberculosis Unit, Borstel, Germany
| | - Stefan Niemann
- 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
| |
Collapse
|