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Deng MZ, Liu Q, Cui SJ, Wang YX, Zhu G, Fu H, Gan M, Xu YY, Cai X, Wang S, Sha W, Zhao GP, Fortune SM, Lyu LD. An additional proofreader contributes to DNA replication fidelity in mycobacteria. Proc Natl Acad Sci U S A 2024; 121:e2322938121. [PMID: 39141351 DOI: 10.1073/pnas.2322938121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
Abstract
The removal of mis-incorporated nucleotides by proofreading activity ensures DNA replication fidelity. Whereas the ε-exonuclease DnaQ is a well-established proofreader in the model organism Escherichia coli, it has been shown that proofreading in a majority of bacteria relies on the polymerase and histidinol phosphatase (PHP) domain of replicative polymerase, despite the presence of a DnaQ homolog that is structurally and functionally distinct from E. coli DnaQ. However, the biological functions of this type of noncanonical DnaQ remain unclear. Here, we provide independent evidence that noncanonical DnaQ functions as an additional proofreader for mycobacteria. Using the mutation accumulation assay in combination with whole-genome sequencing, we showed that depletion of DnaQ in Mycolicibacterium smegmatis leads to an increased mutation rate, resulting in AT-biased mutagenesis and increased insertions/deletions in the homopolymer tract. Our results showed that mycobacterial DnaQ binds to the β clamp and functions synergistically with the PHP domain proofreader to correct replication errors. Furthermore, the loss of dnaQ results in replication fork dysfunction, leading to attenuated growth and increased mutagenesis on subinhibitory fluoroquinolones potentially due to increased vulnerability to fork collapse. By analyzing the sequence polymorphism of dnaQ in clinical isolates of Mycobacterium tuberculosis (Mtb), we demonstrated that a naturally evolved DnaQ variant prevalent in Mtb lineage 4.3 may enable hypermutability and is associated with drug resistance. These results establish a coproofreading model and suggest a division of labor between DnaQ and PHP domain proofreader. This study also provides real-world evidence that a mutator-driven evolutionary pathway may exist during the adaptation of Mtb.
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Affiliation(s)
- Ming-Zhi Deng
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Shu-Jun Cui
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yi-Xin Wang
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Guoliang Zhu
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Chinese Academy of Sciences Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyu Gan
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yuan-Yuan Xu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xia Cai
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Wei Sha
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, China
| | - Guo-Ping Zhao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
- Chinese Academy of Sciences Key Laboratory of Synthetic Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, China
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Dekhil N, Mardassi H. Delineating the evolutionary pathway to multidrug-resistant outbreaks of a Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage. Int J Infect Dis 2024; 144:107077. [PMID: 38697608 DOI: 10.1016/j.ijid.2024.107077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/23/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024] Open
Abstract
OBJECTIVES We sought to capture the evolutionary itinerary of the Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, where it caused a major multidrug-resistant (MDR) tuberculosis outbreak in a context strictly negative for HIV infection. METHODS We combined whole genome sequencing and Bayesian approaches using a representative collection of drug-susceptible and drug-resistant L4.1.2.1/Haarlem clinical strains (n = 121) recovered from the outbreak region over 16 years. RESULTS In the absence of drug resistance, the L4.1.2.1/Haarlem sublineage showed a propensity for rapid transmission as witnessed by the high clustering (44.6%) and recent transmission rates (25%), as well as the reduced mean distance between genome pairs. The entire pool of L4.1.2.1/Haarlem MDR strains was found to be linked to either the aforementioned major outbreak (68 individuals, 2001-2016) or to a minor, newly uncovered outbreak (six cases, 2001-2011). Strikingly, the two outbreaks descended independently from a common ancestor that can be dated back to 1886. CONCLUSIONS Our data point to the intrinsic propensity for rapid transmission of the M. tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, linking the overall MDR tuberculosis epidemic to a single ancestor. These findings bring out the important role of the bacillus' genetic background in the emergence of successful MDR M. tuberculosis clones.
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Affiliation(s)
- Naira Dekhil
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia.
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Catana-Botello N, Becerril-Montes P, Castro-Garza J, González-Salazar F, Almanza-Reyes H, Del Bosque-Moncayo MDLÁ, Morales-Vargas A, Velázquez-Moreno VM. Mycobacterium tuberculosis Beijing in the State of Nuevo Leon, Mexico. Rev Argent Microbiol 2024:S0325-7541(24)00046-4. [PMID: 38942679 DOI: 10.1016/j.ram.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/16/2023] [Accepted: 12/31/2023] [Indexed: 06/30/2024] Open
Abstract
Tuberculosis remains a serious threat to human health as an infectious disease in Mexico. Data about the genotypes of circulating Mycobacterium tuberculosis isolates (MTB) in the State of Nuevo Leon, Mexico are scarce. We aimed to determine the genotypes of circulating MTB belonging to the Beijing lineage recovered from patients in the State of Nuevo Leon, Mexico. A total of 406 MTB isolates from this state were genotyped using the spoligotyping method and 18-locus MIRU-VNTR. Lineage classification and MTB transmission analysis were performed. Based on the spoligotyping analysis, we found 24 strains belonging to the Beijing genotype that were characterized phylogenetically. The MIRUs showed greater discriminatory power than the standard RFLP-IS6110 method; therefore, the greatest allelic diversity among the Beijing strains was observed with MIRU10, MIRU31, MIRU39, MRU40, and MIRU 26. MVLA analysis showed a profile variation between Beijing and non-Beijing strains. The minimum spanning tree (MST) showed that 79% (19) of the strains are related. All Beijing strains exhibited the deletion of region TbD1, which is a characteristic of modern strains. The application of spoligotyping and MIRU-VNTR-18 methods together proved to be more sensitive, discriminatory, and rapid than the standard method for the epidemiological analysis of Mycobacterium Beijing isolates. This study is one of the first to describe the genomic diversity of M. Beijing in the State of Nuevo Leon, Mexico.
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Affiliation(s)
- Nohemí Catana-Botello
- Faculty of Biological Sciences, Autonomous University of Nuevo León, Ave. Pedro de Alba S/N, Niños Héroes, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León 64260, Mexico
| | - Pola Becerril-Montes
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico.
| | - Jorge Castro-Garza
- Secretary of Health of the State of Nuevo León, C. Mariano Matamoros 520, Nuevo León 64000, Mexico
| | - Francisco González-Salazar
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico; Health Sciences, University of Monterrey, Av. Ignacio Morones Prieto 4500 poniente, Col. Jesús M. Garza, San Pedro Garza García, Nuevo León 66238, Mexico.
| | - Horacio Almanza-Reyes
- Faculty of Medicine and Psychology, Autonomous University of Baja California, Universidad 14418, UABC, Parque Internacional Industrial Tijuana, Tijuana Baja California 22390, Mexico.
| | | | - Alejandro Morales-Vargas
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
| | - Víctor Manuel Velázquez-Moreno
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
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Esteves LS, Gomes LL, Brites D, Fandinho FCO, Bhering M, Pereira MADS, Conceição EC, Salvato R, da Costa BP, Medeiros RFDM, Caldas PCDS, Redner P, Dalcolmo MP, Eldholm V, Gagneux S, Rossetti ML, Kritski AL, Suffys PN. Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing. Antibiotics (Basel) 2024; 13:496. [PMID: 38927163 PMCID: PMC11200758 DOI: 10.3390/antibiotics13060496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.
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Affiliation(s)
- Leonardo Souza Esteves
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Lia Lima Gomes
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Daniela Brites
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Fátima Cristina Onofre Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Marcela Bhering
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Márcia Aparecida da Silva Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation 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 7505, South Africa;
| | - Richard Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
| | - Bianca Porphirio da Costa
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Reginalda Ferreira de Melo Medeiros
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Redner
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Margareth Pretti Dalcolmo
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Vegard Eldholm
- Norwegian Institute of Public Health, 0213 Oslo, Norway;
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Maria Lucia Rossetti
- Laboratório de Biologia Molecular, Universidade Luterana do Brasil (ULBRA), Canoas 92425-020, RS, Brazil;
| | - Afrânio Lineu Kritski
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
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Datta D, Jamwal S, Jyoti N, Patnaik S, Kumar D. Actionable mechanisms of drug tolerance and resistance in Mycobacterium tuberculosis. FEBS J 2024. [PMID: 38676952 DOI: 10.1111/febs.17142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/23/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
The emergence of antimicrobial resistance (AMR) across bacterial pathogens presents a serious threat to global health. This threat is further exacerbated in tuberculosis (TB), mainly due to a protracted treatment regimen involving a combination of drugs. A diversity of factors contributes to the emergence of drug resistance in TB, which is caused by the pathogen Mycobacterium tuberculosis (Mtb). While the traditional genetic mutation-driven drug resistance mechanisms operate in Mtb, there are also several additional unique features of drug resistance in this pathogen. Research in the past decade has enriched our understanding of such unconventional factors as efflux pumps, bacterial heterogeneity, metabolic states, and host microenvironment. Given that the discovery of new antibiotics is outpaced by the emergence of drug resistance patterns displayed by the pathogen, newer strategies for combating drug resistance are desperately needed. In the context of TB, such approaches include targeting the efflux capability of the pathogen, modulating the host environment to prevent bacterial drug tolerance, and activating the host anti-mycobacterial pathways. In this review, we discuss the traditional mechanisms of drug resistance in Mtb, newer understandings and the shaping of a set of unconventional approaches to target both the emergence and treatment of drug resistance in TB.
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Affiliation(s)
- Dipanwita Datta
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Shaina Jamwal
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nishant Jyoti
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Chitwood MH, Colijn C, Yang C, Crudu V, Ciobanu N, Codreanu A, Kim J, Rancu I, Rhee K, Cohen T, Sobkowiak B. The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova. Nat Commun 2024; 15:2962. [PMID: 38580642 PMCID: PMC10997638 DOI: 10.1038/s41467-024-47282-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
The projected trajectory of multidrug resistant tuberculosis (MDR-TB) epidemics depends on the reproductive fitness of circulating strains of MDR M. tuberculosis (Mtb). Previous efforts to characterize the fitness of MDR Mtb have found that Mtb strains of the Beijing sublineage (Lineage 2.2.1) may be more prone to develop resistance and retain fitness in the presence of resistance-conferring mutations than other lineages. Using Mtb genome sequences from all culture-positive cases collected over two years in Moldova, we estimate the fitness of Ural (Lineage 4.2) and Beijing strains, the two lineages in which MDR is concentrated in the country. We estimate that the fitness of MDR Ural strains substantially exceeds that of other susceptible and MDR strains, and we identify several mutations specific to these MDR Ural strains. Our findings suggest that MDR Ural Mtb has been transmitting efficiently in Moldova and poses a substantial risk of spreading further in the region.
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Affiliation(s)
- Melanie H Chitwood
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, 8888 University Drive West, Burnaby, BC, Canada
| | - Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 132 Outer Ring East Road, Guangzhou University Town Guangdong, Guangdong, PR China
| | - Valeriu Crudu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Alexandru Codreanu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Jaehee Kim
- Department of Computational Biology, Cornell University, 237 Tower Road, Ithaca, NY, USA
| | - Isabel Rancu
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA
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7
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Castro-Rodriguez B, Franco-Sotomayor G, Benitez-Medina JM, Cardenas-Franco G, Jiménez-Pizarro N, Cardenas-Franco C, Aguirre-Martinez JL, Orlando SA, Hermoso de Mendoza J, Garcia-Bereguiain MA. Prevalence, drug resistance, and genotypic diversity of the RD Rio subfamily of Mycobacterium tuberculosis in Ecuador: a retrospective analysis for years 2012-2016. Front Public Health 2024; 12:1337357. [PMID: 38689770 PMCID: PMC11060180 DOI: 10.3389/fpubh.2024.1337357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Introduction A major sublineage within the Mycobacterium tuberculosis (MTB) LAM family characterized by a new in-frame fusion gene Rv3346c/55c was discovered in Rio de Janeiro (Brazil) in 2007, called RDRio, associated to drug resistance. The few studies about prevalence of MTB RDRio strains in Latin America reported values ranging from 3% in Chile to 69.8% in Venezuela, although no information is available for countries like Ecuador. Methods A total of 814 MTB isolates from years 2012 to 2016 were screened by multiplex PCR for RDRio identification, followed by 24-loci MIRU-VNTR and spoligotyping. Results A total number of 17 MTB RDRio strains were identified, representing an overall prevalence of 2.09% among MTB strains in Ecuador. While 10.9% of the MTB isolates included in the study were multidrug resistance (MDR), 29.4% (5/17) of the RDRio strains were MDR. Discussion This is the first report of the prevalence of MTB RDRio in Ecuador, where a strong association with MDR was found, but also a very low prevalence compared to other countries in Latin America. It is important to improve molecular epidemiology tools as a part of MTB surveillance programs in Latin America to track the transmission of potentially dangerous MTB stains associated to MDR TB like MTB RDRio.
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Affiliation(s)
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | | | - Natalia Jiménez-Pizarro
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | | | | | - Solon Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Guayaquil, Ecuador
- Universidad Espiritu Santo, Guayaquil, Ecuador
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8
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Fuller NM, McQuaid CF, Harker MJ, Weerasuriya CK, McHugh TD, Knight GM. Mathematical models of drug-resistant tuberculosis lack bacterial heterogeneity: A systematic review. PLoS Pathog 2024; 20:e1011574. [PMID: 38598556 PMCID: PMC11060536 DOI: 10.1371/journal.ppat.1011574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 04/30/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Drug-resistant tuberculosis (DR-TB) threatens progress in the control of TB. Mathematical models are increasingly being used to guide public health decisions on managing both antimicrobial resistance (AMR) and TB. It is important to consider bacterial heterogeneity in models as it can have consequences for predictions of resistance prevalence, which may affect decision-making. We conducted a systematic review of published mathematical models to determine the modelling landscape and to explore methods for including bacterial heterogeneity. Our first objective was to identify and analyse the general characteristics of mathematical models of DR-mycobacteria, including M. tuberculosis. The second objective was to analyse methods of including bacterial heterogeneity in these models. We had different definitions of heterogeneity depending on the model level. For between-host models of mycobacterium, heterogeneity was defined as any model where bacteria of the same resistance level were further differentiated. For bacterial population models, heterogeneity was defined as having multiple distinct resistant populations. The search was conducted following PRISMA guidelines in five databases, with studies included if they were mechanistic or simulation models of DR-mycobacteria. We identified 195 studies modelling DR-mycobacteria, with most being dynamic transmission models of non-treatment intervention impact in M. tuberculosis (n = 58). Studies were set in a limited number of specific countries, and 44% of models (n = 85) included only a single level of "multidrug-resistance (MDR)". Only 23 models (8 between-host) included any bacterial heterogeneity. Most of these also captured multiple antibiotic-resistant classes (n = 17), but six models included heterogeneity in bacterial populations resistant to a single antibiotic. Heterogeneity was usually represented by different fitness values for bacteria resistant to the same antibiotic (61%, n = 14). A large and growing body of mathematical models of DR-mycobacterium is being used to explore intervention impact to support policy as well as theoretical explorations of resistance dynamics. However, the majority lack bacterial heterogeneity, suggesting that important evolutionary effects may be missed.
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Affiliation(s)
- Naomi M. Fuller
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher F. McQuaid
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin J. Harker
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chathika K. Weerasuriya
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Timothy D. McHugh
- UCL Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, University College London, London, United Kingdom
| | - Gwenan M. Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
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9
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Bobba S, Chauhan KS, Akter S, Das S, Mittal E, Mathema B, Philips JA, Khader SA. A protective role for type I interferon signaling following infection with Mycobacterium tuberculosis carrying the rifampicin drug resistance-conferring RpoB mutation H445Y. PLoS Pathog 2024; 20:e1012137. [PMID: 38603763 PMCID: PMC11037539 DOI: 10.1371/journal.ppat.1012137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 04/23/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Interleukin-1 (IL-1) signaling is essential for controlling virulent Mycobacterium tuberculosis (Mtb) infection since antagonism of this pathway leads to exacerbated pathology and increased susceptibility. In contrast, the triggering of type I interferon (IFN) signaling is associated with the progression of tuberculosis (TB) disease and linked with negative regulation of IL-1 signaling. However, mice lacking IL-1 signaling can control Mtb infection if infected with an Mtb strain carrying the rifampin-resistance conferring mutation H445Y in its RNA polymerase β subunit (rpoB-H445Y Mtb). The mechanisms that govern protection in the absence of IL-1 signaling during rpoB-H445Y Mtb infection are unknown. In this study, we show that in the absence of IL-1 signaling, type I IFN signaling controls rpoB-H445Y Mtb replication, lung pathology, and excessive myeloid cell infiltration. Additionally, type I IFN is produced predominantly by monocytes and recruited macrophages and acts on LysM-expressing cells to drive protection through nitric oxide (NO) production to restrict intracellular rpoB-H445Y Mtb. These findings reveal an unexpected protective role for type I IFN signaling in compensating for deficiencies in IL-1 pathways during rpoB-H445Y Mtb infection.
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Affiliation(s)
- Suhas Bobba
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kuldeep S. Chauhan
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Sadia Akter
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
| | - Shibali Das
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ekansh Mittal
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, United States of America
| | - Jennifer A. Philips
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Shabaana A. Khader
- Department of Microbiology, University of Chicago, Chicago, Illinois, United States of America
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10
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Liu Z, Jing C, Hooblal YM, Yang H, Chen Z, Kong F. Construction and validation of log odds of positive lymph nodes (LODDS)-based nomograms for predicting overall survival and cancer-specific survival in ovarian clear cell carcinoma patients. Front Oncol 2024; 14:1370272. [PMID: 38577328 PMCID: PMC10991783 DOI: 10.3389/fonc.2024.1370272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Background Ovarian clear cell carcinoma (OCCC) is one of the special histologic subtypes of ovarian cancer. This study aimed to construct and validate log odds of positive lymph nodes (LODDS)-based nomograms for predicting the overall survival (OS) and cancer-specific survival (CSS) in patients with OCCC. Methods Patients who underwent surgical treatment between 2010 and 2016 were extracted from the Surveillance Epidemiology and End Results (SEER) database and the data of OCCC patients from the First Affiliated Hospital of Dalian Medical University were used as the external validation group to test the validity of the prognostic model. The best-fitting models were selected by stepwise Cox regression analysis. Survival probability was calculated by the Kaplan-Meier method, and the differences in survival time between subgroups were compared using the log-rank test. Each nomogram's performance was assessed by the calibration plots, decision curve analysis (DCA), and receiver operating characteristics (ROC) curves. Results T stage, distant metastasis, marital status, and LODDS were identified as significant risk factors for OS. A model with four risk factors (age, T stage, stage, and LODDS value) was obtained for CSS. Nomograms were constructed by incorporating the prognostic factors to predict 1-, 3- and 5-year OS and CSS for OCCC patients, respectively. The area under the curve (AUC) range of our nomogram model for OS and CSS prediction ranged from 0.738-0.771 and 0.769-0.794, respectively, in the training cohort. The performance of this model was verified in the internal and external validation cohorts. Calibration plots illustrated nomograms have good prognostic reliability. Conclusion Predictive nomograms were constructed and validated to evaluate the OS and CSS of OCCC patients. These nomograms may provide valuable prognostic information and guide postoperative personalized care in OCCC.
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Affiliation(s)
- Zesi Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Chunli Jing
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Yashi Manisha Hooblal
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Hongxia Yang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Ziyu Chen
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Fandou Kong
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
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11
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Brunner VM, Fowler PW. Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis. Microb Genom 2024; 10:001187. [PMID: 38315172 PMCID: PMC10926696 DOI: 10.1099/mgen.0.001187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of M. tuberculosis populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase of M. tuberculosis, using over 70 000 M. tuberculosis genomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests more power to investigate the association of putative CMs with resistance-conferring mutations. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higher in vitro growth densities, and hence presumably with higher fitness, in resistant samples in the more virulent M. tuberculosis lineage 2. Our results suggest the association of CM presence with significantly higher in vitro growth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasize the integral role of CMs and lineage affiliation in resistance spread and increases the urgency of antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics for M. tuberculosis infections to not only improve patient outcomes but also prevent the spread of resistant strains.
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Affiliation(s)
| | - Philip W. Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
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12
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Suman SK, Chandrasekaran N, Priya Doss CG. Micro-nanoemulsion and nanoparticle-assisted drug delivery against drug-resistant tuberculosis: recent developments. Clin Microbiol Rev 2023; 36:e0008823. [PMID: 38032192 PMCID: PMC10732062 DOI: 10.1128/cmr.00088-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Tuberculosis (TB) is a major global health problem and the second most prevalent infectious killer after COVID-19. It is caused by Mycobacterium tuberculosis (Mtb) and has become increasingly challenging to treat due to drug resistance. The World Health Organization declared TB a global health emergency in 1993. Drug resistance in TB is driven by mutations in the bacterial genome that can be influenced by prolonged drug exposure and poor patient adherence. The development of drug-resistant forms of TB, such as multidrug resistant, extensively drug resistant, and totally drug resistant, poses significant therapeutic challenges. Researchers are exploring new drugs and novel drug delivery systems, such as nanotechnology-based therapies, to combat drug resistance. Nanodrug delivery offers targeted and precise drug delivery, improves treatment efficacy, and reduces adverse effects. Along with nanoscale drug delivery, a new generation of antibiotics with potent therapeutic efficacy, drug repurposing, and new treatment regimens (combinations) that can tackle the problem of drug resistance in a shorter duration could be promising therapies in clinical settings. However, the clinical translation of nanomedicines faces challenges such as safety, large-scale production, regulatory frameworks, and intellectual property issues. In this review, we present the current status, most recent findings, challenges, and limiting barriers to the use of emulsions and nanoparticles against drug-resistant TB.
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Affiliation(s)
- Simpal Kumar Suman
- School of Bio Sciences & Technology (SBST), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Natarajan Chandrasekaran
- Centre for Nano Biotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C. George Priya Doss
- Laboratory for Integrative Genomics, Department of Integrative Biology, School of Bio Sciences & Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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13
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Wang X, Su H, Wallach JB, Wagner JC, Braunecker B, Gardner M, Guinn KM, Klevorn T, Lin K, Liu YJ, Liu Y, Mugahid D, Rodgers M, Sixsmith J, Wakabayashi S, Zhu J, Zimmerman M, Dartois V, Flynn JL, Lin PL, Ehrt S, Fortune SM, Rubin EJ, Schnappinger D. Development of an Engineered Mycobacterium tuberculosis Strain for a Safe and Effective Tuberculosis Human Challenge Model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567569. [PMID: 38014062 PMCID: PMC10680849 DOI: 10.1101/2023.11.19.567569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Human challenge experiments could greatly accelerate the development of a tuberculosis (TB) vaccine. Human challenge for tuberculosis requires a strain that can both replicate in the host and be reliably cleared. To accomplish this, we designed Mycobacterium tuberculosis (Mtb) strains featuring up to three orthogonal kill switches, tightly regulated by exogenous tetracyclines and trimethoprim. The resultant strains displayed immunogenicity and antibiotic susceptibility similar to wild-type Mtb under permissive conditions. In the absence of supplementary exogenous compounds, the strains were rapidly killed in axenic culture, mice and nonhuman primates. Notably, the strain that contained three kill switches had an escape rate of less than 10 -10 per genome per generation and displayed no relapse in a SCID mouse model. Collectively, these findings suggest that this engineered Mtb strain could be a safe and effective candidate for a human challenge model.
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14
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Rubinstein M, Makhon A, Losev Y, Valenci GZ, Gatt YE, Margalit H, Fass E, Kutikov I, Murik O, Zeevi DA, Savyon M, Tau L, Kaidar Shwartz H, Dveyrin Z, Rorman E, Nissan I. Prolonged survival of a patient with active MDR-TB HIV co-morbidity: insights from a Mycobacterium tuberculosis strain with a unique genomic deletion. Front Med (Lausanne) 2023; 10:1292665. [PMID: 38020140 PMCID: PMC10657812 DOI: 10.3389/fmed.2023.1292665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Coinfection of HIV and multidrug-resistant tuberculosis (MDR-TB) presents significant challenges in terms of the treatment and prognosis of tuberculosis, leading to complexities in managing the disease and impacting the overall outcome for TB patients. This study presents a remarkable case of a patient with MDR-TB and HIV coinfection who survived for over 8 years, despite poor treatment adherence and comorbidities. Whole genome sequencing (WGS) of the infecting Mycobacterium tuberculosis (Mtb) strain revealed a unique genomic deletion, spanning 18 genes, including key genes involved in hypoxia response, intracellular survival, immunodominant antigens, and dormancy. This deletion, that we have called "Del-X," potentially exerts a profound influence on the bacterial physiology and its virulence. Only few similar deletions were detected in other non-related Mtb genomes worldwide. In vivo evolution analysis identified drug resistance and metabolic adaptation mutations and their temporal dynamics during the patient's treatment course.
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Affiliation(s)
- Mor Rubinstein
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Andrei Makhon
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yelena Losev
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Gal Zizelski Valenci
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Yair E. Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ephraim Fass
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Ina Kutikov
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Omer Murik
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - David A. Zeevi
- Translational Genomics Laboratory, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Michal Savyon
- Tel Aviv District Health Office, Ministry of Health, Tel Aviv, Israel
| | - Luba Tau
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hasia Kaidar Shwartz
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Zeev Dveyrin
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Efrat Rorman
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
| | - Israel Nissan
- National Public Health Laboratory, Public Health Directorate, Ministry of Health, Tel Aviv, Israel
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15
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Bobba S, Howard NC, Das S, Ahmed M, Tang L, Thirunavukkarasu S, Larsen MH, Mathema B, Divangahi M, Khader SA. Mycobacterium tuberculosis carrying the rifampicin drug-resistance-conferring rpoB mutation H445Y is associated with suppressed immunity through type I interferons. mBio 2023; 14:e0094623. [PMID: 37682004 PMCID: PMC10653897 DOI: 10.1128/mbio.00946-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/22/2023] [Indexed: 09/09/2023] Open
Abstract
IMPORTANCE This study highlights the impact of specific rifampicin-resistance-conferring mutations on the host immune response to Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB). Clinical reports have previously suggested that multi-drug-resistant) TB patients exhibit altered peripheral immune responses as compared with their drug-sensitive TB counterparts. The murine model of infection with Mtb strains carrying drug-resistance-conferring mutations recapitulated these findings and allowed us to mechanistically interrogate the pathways responsible for driving the divergent immune responses. Our findings underscore the need for greater investigation into bacterial heterogeneity to better appreciate the diversity in host-pathogen interactions during TB disease.
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Affiliation(s)
- Suhas Bobba
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicole C. Howard
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shibali Das
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mushtaq Ahmed
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Linrui Tang
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Shyamala Thirunavukkarasu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michelle H. Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill International TB Centre, Montreal, Quebec, Canada
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Shabaana A. Khader
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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16
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Deng MZ, Liu Q, Cui SJ, Fu H, Gan M, Xu YY, Cai X, Sha W, Zhao GP, Fortune SM, Lyu LD. Mycobacterial DnaQ is an Alternative Proofreader Ensuring DNA Replication Fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563508. [PMID: 37961690 PMCID: PMC10634781 DOI: 10.1101/2023.10.24.563508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Remove of mis-incorporated nucleotides ensures replicative fidelity. Although the ε-exonuclease DnaQ is a well-established proofreader in the model organism Escherichia coli, proofreading in mycobacteria relies on the polymerase and histidinol phosphatase (PHP) domain of replicative polymerase despite the presence of an alternative DnaQ homolog. Here, we show that depletion of DnaQ in Mycolicibacterium smegmatis results in increased mutation rate, leading to AT-biased mutagenesis and elevated insertions/deletions in homopolymer tract. We demonstrated that mycobacterial DnaQ binds to the b-clamp and functions synergistically with the PHP domain to correct replication errors. Further, we found that the mycobacterial DnaQ sustains replicative fidelity upon chromosome topological stress. Intriguingly, we showed that a naturally evolved DnaQ variant prevalent in clinical Mycobacterium tuberculosis isolates enables hypermutability and is associated with extensive drug resistance. These results collectively establish that the alternative DnaQ functions in proofreading, and thus reveal that mycobacteria deploy two proofreaders to maintain replicative fidelity.
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Affiliation(s)
- Ming-Zhi Deng
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- These authors contributed equally
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
- These authors contributed equally
| | - Shu-Jun Cui
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
| | - Han Fu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Mingyu Gan
- Center for Molecular Medicine, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, 201102, P.R.China
| | - Yuan-Yuan Xu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Xia Cai
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
| | - Wei Sha
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
| | - Guo-Ping Zhao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, P.R.China
- CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 200032, P.R.China
- University of Chinese Academy of Sciences, Beijing 100049, P.R.China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115
| | - Liang-Dong Lyu
- Key Laboratory of Medical Molecular Virology of the Ministry of Education/Ministry of Health (MOE/NHC), School of Basic Medical Sciences, Fudan University, Shanghai 200032, P.R.China
- Shanghai Clinical Research Center for Tuberculosis, Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai 200433, P.R.China
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17
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Bobba S, Howard NC, Das S, Ahmed M, Khan N, Marchante I, Barreiro LB, Sanz J, Divangahi M, Khader SA. Mycobacterium tuberculosis infection drives differential responses in the bone marrow hematopoietic stem and progenitor cells. Infect Immun 2023; 91:e0020123. [PMID: 37754680 PMCID: PMC10580947 DOI: 10.1128/iai.00201-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) play a vital role in the host response to infection through the rapid and robust production of mature immune cells. These HSPC responses can be influenced, directly and indirectly, by pathogens as well. Infection with Mycobacterium tuberculosis (Mtb) can drive lymphopoiesis through modulation of type I interferon (IFN) signaling. We have previously found that the presence of a drug resistance (DR)-conferring mutation in Mtb drives altered host-pathogen interactions and heightened type I IFN production in vitro. But the impacts of this DR mutation on in vivo host responses to Mtb infection, particularly the hematopoietic compartment, remain unexplored. Using a mouse model, we show that, while drug-sensitive Mtb infection induces expansion of HSPC subsets and a skew toward lymphopoiesis, DR Mtb infection fails to induce an expansion of these subsets and an accumulation of mature granulocytes in the bone marrow. Using single-cell RNA sequencing, we show that the HSCs from DR Mtb-infected mice fail to upregulate pathways related to cytokine signaling across all profiled HSC subsets. Collectively, our studies report a novel finding of a chronic infection that fails to induce a potent hematopoietic response that can be further investigated to understand pathogen-host interaction at the level of hematopoiesis.
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Affiliation(s)
- Suhas Bobba
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicole C. Howard
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Shibali Das
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Mushtaq Ahmed
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Nargis Khan
- Meakins-Christie Laboratories, Department of Medicine, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Department of Pathology, McGill University, Montreal, Quebec, Canada
| | - Ignacio Marchante
- Department of Theoretical Physics, University of Zaragoza, Institute for Biocomputation and Physics of Complex Systems (BIFI), Zaragoza, Spain
| | - Luis B. Barreiro
- Department of Medicine, Genetic Section, University of Chicago, Chicago, Illinois, USA
| | - Joaquin Sanz
- Department of Theoretical Physics, University of Zaragoza, Institute for Biocomputation and Physics of Complex Systems (BIFI), Zaragoza, Spain
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
- Meakins-Christie Laboratories, Department of Pathology, McGill University, Montreal, Quebec, Canada
| | - Shabaana A. Khader
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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Wang L, Campino S, Phelan J, Clark TG. Mixed infections in genotypic drug-resistant Mycobacterium tuberculosis. Sci Rep 2023; 13:17100. [PMID: 37816829 PMCID: PMC10564873 DOI: 10.1038/s41598-023-44341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/06/2023] [Indexed: 10/12/2023] Open
Abstract
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major global public health problem, resulting in more than 1 million deaths each year. Drug resistance (DR), including multi-drug (MDR-TB), is making TB control difficult and accounts for 16% of new and 48% of previously treated cases. To further complicate treatment decision-making, many clinical studies have reported patients harbouring multiple distinct strains of M. tuberculosis across the main lineages (L1 to L4). The extent to which drug-resistant strains can be deconvoluted within mixed strain infection samples is understudied. Here, we analysed M. tuberculosis isolates with whole genome sequencing data (n = 50,723), which covered the main lineages (L1 9.1%, L2 27.6%, L3 11.8%, L4 48.3%), with genotypic resistance to isoniazid (HR-TB; n = 9546 (29.2%)), rifampicin (RR-TB; n = 7974 (24.4%)), and at least MDR-TB (n = 5385 (16.5%)). TB-Profiler software revealed 531 (1.0%) isolates with potential mixed sub-lineage infections, including some with DR mutations (RR-TB 21/531; HR-TB 59/531; at least MDR-TB 173/531). To assist with the deconvolution of such mixtures, we adopted and evaluated a statistical Gaussian Mixture model (GMM) approach. By simulating 240 artificial mixtures of different ratios from empirical data across L1 to L4, a GMM approach was able to accurately estimate the DR profile of each lineage, with a low error rate for the estimated mixing proportions (mean squared error 0.012) and high accuracy for the DR predictions (93.5%). Application of the GMM model to the clinical mixtures (n = 531), found that 33.3% (188/531) of samples consisted of DR and sensitive lineages, 20.2% (114/531) consisted of lineages with only DR mutations, and 40.6% (229/531) consisted of lineages with genotypic pan-susceptibility. Overall, our work demonstrates the utility of combined whole genome sequencing data and GMM statistical analysis approaches for providing insights into mono and mixed M. tuberculosis infections, thereby potentially assisting diagnosis, treatment decision-making, drug resistance and transmission mapping for infection control.
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Affiliation(s)
- Linfeng Wang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, UK.
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Koleske BN, Jacobs WR, Bishai WR. The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions. J Clin Invest 2023; 133:e173156. [PMID: 37781921 PMCID: PMC10541200 DOI: 10.1172/jci173156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
First achieved in 1998 by Cole et al., the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. Likewise, we discuss several recent efforts to extract further discoveries from this powerful resource.
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Affiliation(s)
- Benjamin N. Koleske
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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20
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Song Z, Liu C, He W, Pei S, Liu D, Cao X, Wang Y, He P, Zhao B, Ou X, Xia H, Wang S, Zhao Y. Insight into the drug-resistant characteristics and genetic diversity of multidrug-resistant Mycobacterium tuberculosis in China. Microbiol Spectr 2023; 11:e0132423. [PMID: 37732780 PMCID: PMC10581218 DOI: 10.1128/spectrum.01324-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/16/2023] [Indexed: 09/22/2023] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) has a severe impact on public health. To investigate the drug-resistant profile, compensatory mutations and genetic variations among MDR-TB isolates, a total of 546 MDR-TB isolates from China underwent drug-susceptibility testing and whole genome sequencing for further analysis. The results showed that our isolates have a high rate of fluoroquinolone resistance (45.60%, 249/546) and a low proportion of conferring resistance to bedaquiline, clofazimine, linezolid, and delamanid. The majority of MDR-TB isolates (77.66%, 424/546) belong to Lineage 2.2.1, followed by Lineage 4.5 (6.41%, 35/546), and the Lineage 2 isolates have a strong association with pre-XDR/XDR-TB (P < 0.05) in our study. Epidemic success analysis using time-scaled haplotypic density (THD) showed that clustered isolates outperformed non-clustered isolates. Compensatory mutations happened in rpoA, rpoC, and non-RRDR of rpoB genes, which were found more frequently in clusters and were associated with the increase of THD index, suggesting that increased bacterial fitness was associated with MDR-TB transmission. In addition, the variants in resistance associated genes in MDR isolates are mainly focused on single nucleotide polymorphism mutations, and only a few genes have indel variants, such as katG, ethA. We also found some genes underwent indel variation correlated with the lineage and sub-lineage of isolates, suggesting the selective evolution of different lineage isolates. Thus, this analysis of the characterization and genetic diversity of MDR isolates would be helpful in developing effective strategies for treatment regimens and tailoring public interventions. IMPORTANCE Multidrug-resistant tuberculosis (MDR-TB) is a serious obstacle to tuberculosis prevention and control in China. This study provides insight into the drug-resistant characteristics of MDR combined with phenotypic drug-susceptibility testing and whole genome sequencing. The compensatory mutations and epidemic success analysis were analyzed by time-scaled haplotypic density (THD) method, suggesting clustered isolates and compensatory mutations are associated with MDR-TB transmission. In addition, the insertion and deletion variants happened in some genes, which are associated with the lineage and sub-lineage of isolates, such as the mpt64 gene. This study offered a valuable reference and increased understanding of MDR-TB in China, which could be crucial for achieving the objective of precision medicine in the prevention and treatment of MDR-TB.
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Affiliation(s)
- Zexuan Song
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chunfa Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wencong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, China
| | - Dongxin Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaolong Cao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xia
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
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He CJ, Wan JL, Luo SF, Guo RJ, Paerhati P, Cheng X, Duan CH, Xu AM. Comparative Study on Tuberculosis Drug Resistance and Molecular Detection Methods Among Different Mycobacterium Tuberculosis Lineages. Infect Drug Resist 2023; 16:5941-5951. [PMID: 37700800 PMCID: PMC10494918 DOI: 10.2147/idr.s423390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/24/2023] [Indexed: 09/14/2023] Open
Abstract
Purpose This study aims to compare drug resistance and detection efficacy across different Mycobacterium tuberculosis lineages, offering insights for precise treatment and molecular diagnosis. Methods 161 strains of Mycobacterium tuberculosis (M.tb) were tested for drug resistance using Phenotypic Drug Susceptibility Testing (pDST), High-Resolution Melting analysis (HRM), and Whole Genome Sequencing (WGS) methods. The main focus was on evaluating the accuracy of different methods for detecting resistance to rifampicin (RIF), isoniazid (INH), and streptomycin (SM). Results Among the 161 strains of M.tb, 83.85% (135/161) were fully sensitive to RIF, INH, and SM according to pDST, and the rate of multidrug resistance was 4.35% (7/161). The drug resistance rates of lineage 2 M.tb to the three drugs (26/219, 11.87%) were significantly higher than those of non-lineage 2 M.tb (12/264, 4.45%) (P<0.05). Compared with pDST, WGS had a sensitivity of 100%, 94.12%, and 92.31% and a specificity of 100%, 99.31%, and 98.65% for RIF, INH, and SM, respectively, with no significant difference. The sensitivity of HRM for RIF, INH, and SM was 87.50%, 52.94%, and 76.92%, respectively, while the specificity was 96.08%, 99.31%, and 99.32%, respectively. The sensitivity of HRM for detecting INH resistance was significantly lower than that of pDST (P=0.039). Compared with HRM, WGS increased the sensitivity of RIF, INH, and SM by 12.50%, 41.18%, and 15.38%, respectively. Conclusion There are significant differences in drug resistance rates among different lineages of M.tb, with lineage 2 having higher rates of RIF, INH, and SM resistance than lineages 3 and 4. The sensitivity of HRM is far lower than that of pDST, and currently, the accuracy of HRM is not sufficient to replace pDST. WGS has no significant difference in detecting drug resistance compared with pDST but can identify new anti-tuberculosis drug-resistant mutations, providing effective guidance for clinical decision-making.
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Affiliation(s)
- Chuan-Jiang He
- Department of Laboratory Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, People’s Republic of China
- Department of Laboratory Medicine, The First People’s Hospital of Kashgar, Kashgar, 844000, People’s Republic of China
| | - Jiang-Li Wan
- Department of Laboratory Medicine, The First People’s Hospital of Kashgar, Kashgar, 844000, People’s Republic of China
| | - Sheng-Fang Luo
- Department of Laboratory Medicine, The First People’s Hospital of Kashgar, Kashgar, 844000, People’s Republic of China
| | - Rui-Jie Guo
- Department of Laboratory Medicine, The First People’s Hospital of Kashgar, Kashgar, 844000, People’s Republic of China
| | - Pawuziye Paerhati
- Department of Laboratory Medicine, The First People’s Hospital of Kashgar, Kashgar, 844000, People’s Republic of China
| | - Xiang Cheng
- Department of Laboratory Medicine, The First People’s Hospital of Kashgar, Kashgar, 844000, People’s Republic of China
| | - Chao-Hui Duan
- Department of Laboratory Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, People’s Republic of China
| | - Ai-Min Xu
- Department of Laboratory Medicine, The First People’s Hospital of Kashgar, Kashgar, 844000, People’s Republic of China
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22
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Lempens P, Van Deun A, Aung KJM, Hossain MA, Behruznia M, Decroo T, Rigouts L, de Jong BC, Meehan CJ. Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh. Microb Genom 2023; 9:001109. [PMID: 37750750 PMCID: PMC10569737 DOI: 10.1099/mgen.0.001109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
The spread of multidrug-resistant tuberculosis (MDR-TB) is a growing problem in many countries worldwide. Resistance to one of the primary first-line drugs, rifampicin, is caused by mutations in the Mycobacterium tuberculosis rpoB gene. So-called borderline rpoB mutations confer low-level resistance, in contrast to more common rpoB mutations which confer high-level resistance. While some borderline mutations show lower fitness in vitro than common mutations, their in vivo fitness is currently unknown. We used a dataset of 394 whole genome sequenced MDR-TB isolates from Bangladesh, representing around 44 % of notified MDR-TB cases over 6 years, to look at differences in transmission clustering between isolates with borderline rpoB mutations and those with common rpoB mutations. We found a relatively low percentage of transmission clustering in the dataset (34.8 %) but no difference in clustering between different types of rpoB mutations. Compensatory mutations in rpoA, rpoB, and rpoC were associated with higher levels of transmission clustering as were lineages two, three, and four relative to lineage one. Young people as well as patients with high sputum smear positive TB were more likely to be in a transmission cluster. Our findings show that although borderline rpoB mutations have lower in vitro growth potential this does not translate into lower transmission potential or in vivo fitness. Proper detection of these mutations is crucial to ensure they do not go unnoticed and spread MDR-TB within communities.
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Affiliation(s)
- Pauline Lempens
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | | | | | | | - Tom Decroo
- Unit of HIV and TB, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Bouke C. de Jong
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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23
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Sobkowiak B, Haghmaram P, Prystajecky N, Zlosnik JEA, Tyson J, Hoang LMN, Colijn C. The utility of SARS-CoV-2 genomic data for informative clustering under different epidemiological scenarios and sampling. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105484. [PMID: 37531976 DOI: 10.1016/j.meegid.2023.105484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/25/2023] [Accepted: 07/30/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES Clustering pathogen sequence data is a common practice in epidemiology to gain insights into the genetic diversity and evolutionary relationships among pathogens. We can find groups of cases with a shared transmission history and common origin, as well as identifying transmission hotspots. Motivated by the experience of clustering SARS-CoV-2 cases using whole genome sequence data during the COVID-19 pandemic to aid with public health investigation, we investigated how differences in epidemiology and sampling can influence the composition of clusters that are identified. METHODS We performed genomic clustering on simulated SARS-CoV-2 outbreaks produced with different transmission rates and levels of genomic diversity, along with varying the proportion of cases sampled. RESULTS In single outbreaks with a low transmission rate, decreasing the sampling fraction resulted in multiple, separate clusters being identified where intermediate cases in transmission chains are missed. Outbreaks simulated with a high transmission rate were more robust to changes in the sampling fraction and largely resulted in a single cluster that included all sampled outbreak cases. When considering multiple outbreaks in a sampled jurisdiction seeded by different introductions, low genomic diversity between introduced cases caused outbreaks to be merged into large clusters. If the transmission and sampling fraction, and diversity between introductions was low, a combination of the spurious break-up of outbreaks and the linking of closely related cases in different outbreaks resulted in clusters that may appear informative, but these did not reflect the true underlying population structure. Conversely, genomic clusters matched the true population structure when there was relatively high diversity between introductions and a high transmission rate. CONCLUSION Differences in epidemiology and sampling can impact our ability to identify genomic clusters that describe the underlying population structure. These findings can help to guide recommendations for the use of pathogen clustering in public health investigations.
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Affiliation(s)
| | - Pouya Haghmaram
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
| | - Natalie Prystajecky
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Canada
| | - James E A Zlosnik
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada
| | - John Tyson
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada
| | - Linda M N Hoang
- BC Centre for Disease Control Public Health Laboratory, BC Centre for Disease Control, Vancouver, Canada; Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, Burnaby, Canada
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24
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Berry SB, Espich S, Thuong NTT, Chang X, Dorajoo R, Khor CC, Heng CK, Yuan JM, Fox D, Anaya-Sanchez A, Tenney L, Chang CJ, Kotov DI, Vance RE, Dunstan SJ, Darwin KH, Stanley SA. Disruption of Aldehyde Dehydrogenase 2 protects against bacterial infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554661. [PMID: 37662190 PMCID: PMC10473740 DOI: 10.1101/2023.08.24.554661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The ALDH2*2 (rs671) allele is one of the most common genetic mutations in humans, yet the positive evolutionary selective pressure to maintain this mutation is unknown, despite its association with adverse health outcomes. ALDH2 is responsible for the detoxification of metabolically produced aldehydes, including lipid-peroxidation end products derived from inflammation. Here, we demonstrate that host-derived aldehydes 4-hydroxynonenal (4HNE), malondialdehyde (MDA), and formaldehyde (FA), all of which are metabolized by ALDH2, are directly toxic to the bacterial pathogens Mycobacterium tuberculosis and Francisella tularensis at physiological levels. We find that Aldh2 expression in macrophages is decreased upon immune stimulation, and that bone marrow-derived macrophages from Aldh2 -/- mice contain elevated aldehydes relative to wild-type mice. Macrophages deficient for Aldh2 exhibited enhanced control of Francisella infection. Finally , mice lacking Aldh2 demonstrated increased resistance to pulmonary infection by M. tuberculosis , including in a hypersusceptible model of tuberculosis, and were also resistant to Francisella infection. We hypothesize that the absence of ALDH2 contributes to the host's ability to control infection by pathogens such as M. tuberculosis and F. tularensis , and that host-derived aldehydes act as antimicrobial factors during intracellular bacterial infections. One sentence summary Aldehydes produced by host cells contribute to the control of bacterial infections.
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25
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Shibabaw A, Gelaw B, Ghanem M, Legall N, Schooley AM, Soehnlen MK, Salvador LCM, Gebreyes W, Wang SH, Tessema B. Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia. BMC Genomics 2023; 24:400. [PMID: 37460951 DOI: 10.1186/s12864-023-09502-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA.
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
| | - Baye Gelaw
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Angie M Schooley
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Marty K Soehnlen
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and life sciences, University of Arizona, Tucson, AZ, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Belay Tessema
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Hassanin ESA, Mohamed Hussein AA, Abdelrheem SS, Dongol E, Mhsb AHA, Zahran AM, Zein M, G Sayed I. Frequency of rifampicin-resistant mycobacterium tuberculosis by GeneXpert MTB/RIF assay and its correlates among 2605 probable tuberculosis patients in upper Egypt. Indian J Tuberc 2023; 70:345-355. [PMID: 37562911 DOI: 10.1016/j.ijtb.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 08/12/2023]
Abstract
RATIONALE GeneXpert MTB/RIF (Mycobacterium tuberculosis/rifampicin) assay is a method for detecting rifampicin resistance (RR-MTB) in suspected samples in less than 2 hours with high sensitivity and specificity yield. This study aimed to use the GeneXpert MTB/RIF assay to determine the frequency of RR-MTB and to study the possible influencing correlates associated with positive results. SUBJECTS AND METHODS This is a retrospective cross-sectional study of patients who visited TB clinic in 5 years (2016-2021). According to the data sheet of the patients, all the collected specimens were divided into 2 parts one for diagnosis by Ziehl-Neelsen stain and the other part for GeneXpert analysis. GeneXpert was also used to look for evidence of RR. RESULTS Out of the 2605 total samples screened, 718 (27.6%) tested positive for MTB on GeneXpert assay; of them 633 (88.4%) were sensitive to Rifampicin, 83 (11.6%) were resistant to Rifampicin and 2 cases were undetermined. Factors contributing to RR-MTB were: smoker/ex-smoker, with 2.5 times more risk (p = 0.013.0, p = 0.001); recurrence cases had a 4-fold increased risk (p < 0.001); patients with very low M. tuberculosis detected on the GeneXpert MTB/RIF test were 8 times more likely to have RR-TB (P = 0.004). CONCLUSION This study disclosed a high-rate MTB in Egyptian probable TB cases. Smoking, recurrence and cases with a very low M. tuberculosis burden noticed on the GeneXpert MTB/RIF test had augmented risk of RR-TB.
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Affiliation(s)
| | | | - Shaimaa S Abdelrheem
- Department of Public Health and Community Medicine, Faculty of Medicine, Aswan University, Egypt and Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | | | | | - Asmaa M Zahran
- Clinical Pathology Department, South Egypt Cancer Institute Assiut University, Egypt
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Nicholson MD, Cheek D, Antal T. Sequential mutations in exponentially growing populations. PLoS Comput Biol 2023; 19:e1011289. [PMID: 37428805 PMCID: PMC10359018 DOI: 10.1371/journal.pcbi.1011289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 07/20/2023] [Accepted: 06/21/2023] [Indexed: 07/12/2023] Open
Abstract
Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with n alterations, and how long will it take for these cells to appear. For exponentially growing populations, these questions have been tackled only in special cases so far. Here, within a multitype branching process framework, we consider a general mutational path where mutations may be advantageous, neutral or deleterious. In the biologically relevant limiting regimes of large times and small mutation rates, we derive probability distributions for the number, and arrival time, of cells with n mutations. Surprisingly, the two quantities respectively follow Mittag-Leffler and logistic distributions regardless of n or the mutations' selective effects. Our results provide a rapid method to assess how altering the fundamental division, death, and mutation rates impacts the arrival time, and number, of mutant cells. We highlight consequences for mutation rate inference in fluctuation assays.
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Affiliation(s)
- Michael D. Nicholson
- Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - David Cheek
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tibor Antal
- School of Mathematics and Maxwell Institute for Mathematical Sciences, University of Edinburgh, Edinburgh, United Kingdom
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28
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Loiseau C, Windels EM, Gygli SM, Jugheli L, Maghradze N, Brites D, Ross A, Goig G, Reinhard M, Borrell S, Trauner A, Dötsch A, Aspindzelashvili R, Denes R, Reither K, Beisel C, Tukvadze N, Avaliani Z, Stadler T, Gagneux S. The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot. Nat Commun 2023; 14:1988. [PMID: 37031225 PMCID: PMC10082831 DOI: 10.1038/s41467-023-37719-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is among the most frequent causes of death due to antimicrobial resistance. Although only 3% of global TB cases are MDR, geographical hotspots with up to 40% of MDR-TB have been observed in countries of the former Soviet Union. While the quality of TB control and patient-related factors are known contributors to such hotspots, the role of the pathogen remains unclear. Here we show that in the country of Georgia, a known hotspot of MDR-TB, MDR Mycobacterium tuberculosis strains of lineage 4 (L4) transmit less than their drug-susceptible counterparts, whereas most MDR strains of L2 suffer no such defect. Our findings further indicate that the high transmission fitness of these L2 strains results from epistatic interactions between the rifampicin resistance-conferring mutation RpoB S450L, compensatory mutations in the RNA polymerase, and other pre-existing genetic features of L2/Beijing clones that circulate in Georgia. We conclude that the transmission fitness of MDR M. tuberculosis strains is heterogeneous, but can be as high as drug-susceptible forms, and that such highly drug-resistant and transmissible strains contribute to the emergence and maintenance of hotspots of MDR-TB. As these strains successfully overcome the metabolic burden of drug resistance, and given the ongoing rollout of new treatment regimens against MDR-TB, proper surveillance should be implemented to prevent these strains from acquiring resistance to the additional drugs.
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Affiliation(s)
- Chloé Loiseau
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Etthel M Windels
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sebastian M Gygli
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Levan Jugheli
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Nino Maghradze
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Galo Goig
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Anna Dötsch
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Rebecca Denes
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Nestani Tukvadze
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Zaza Avaliani
- National Center for Tuberculosis and Lung Diseases (NCTLD), Tbilisi, Georgia
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
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29
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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. THE LANCET. INFECTIOUS DISEASES 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] [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.
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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
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30
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Waller NJE, Cheung CY, Cook GM, McNeil MB. The evolution of antibiotic resistance is associated with collateral drug phenotypes in Mycobacterium tuberculosis. Nat Commun 2023; 14:1517. [PMID: 36934122 PMCID: PMC10024696 DOI: 10.1038/s41467-023-37184-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/06/2023] [Indexed: 03/20/2023] Open
Abstract
The increasing incidence of drug resistance in Mycobacterium tuberculosis has diminished the efficacy of almost all available antibiotics, complicating efforts to combat the spread of this global health burden. Alongside the development of new drugs, optimised drug combinations are needed to improve treatment success and prevent the further spread of antibiotic resistance. Typically, antibiotic resistance leads to reduced sensitivity, yet in some cases the evolution of drug resistance can lead to enhanced sensitivity to unrelated drugs. This phenomenon of collateral sensitivity is largely unexplored in M. tuberculosis but has the potential to identify alternative therapeutic strategies to combat drug-resistant strains that are unresponsive to current treatments. Here, by using drug susceptibility profiling, genomics and evolutionary studies we provide evidence for the existence of collateral drug sensitivities in an isogenic collection M. tuberculosis drug-resistant strains. Furthermore, in proof-of-concept studies, we demonstrate how collateral drug phenotypes can be exploited to select against and prevent the emergence of drug-resistant strains. This study highlights that the evolution of drug resistance in M. tuberculosis leads to collateral drug responses that can be exploited to design improved drug regimens.
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Affiliation(s)
- Natalie J E Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
| | - Matthew B McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
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31
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Jiang Q, Liu HC, Liu QY, Phelan JE, Tao FX, Zhao XQ, Wang J, Glynn JR, Takiff HE, Clark TG, Wan KL, Gao Q. The Evolution and Transmission Dynamics of Multidrug-Resistant Tuberculosis in an Isolated High-Plateau Population of Tibet, China. Microbiol Spectr 2023; 11:e0399122. [PMID: 36912683 PMCID: PMC10101056 DOI: 10.1128/spectrum.03991-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
On the Tibetan Plateau, most tuberculosis is caused by indigenous Mycobacterium tuberculosis strains with a monophyletic structure and high-level drug resistance. This study investigated the emergence, evolution, and transmission dynamics of multidrug-resistant tuberculosis (MDR-TB) in Tibet. The whole-genome sequences of 576 clinical strains from Tibet were analyzed with the TB-profiler tool to identify drug-resistance mutations. The evolution of the drug resistance was then inferred based on maximum-likelihood phylogeny and dated trees that traced the serial acquisition of mutations conferring resistance to different drugs. Among the 576 clinical M. tuberculosis strains, 346 (60.1%) carried at least 1 resistance-conferring mutation and 231 (40.1%) were MDR-TB. Using a pairwise distance of 50 single nucleotide polymorphisms (SNPs), most strains (89.9%, 518/576) were phylogenetically separated into 50 long-term transmission clusters. Eleven large drug-resistant clusters contained 76.1% (176/231) of the local multidrug-resistant strains. A total of 85.2% of the isoniazid-resistant strains were highly transmitted with an average of 6.6 cases per cluster, of which most shared the mutation KatG Ser315Thr. A lower proportion (71.6%) of multidrug-resistant strains were transmitted, with an average cluster size of 2.9 cases. The isoniazid-resistant clusters appear to have undergone substantial bacterial population growth in the 1970s to 1990s and then subsequently accumulated multiple rifampicin-resistance mutations and caused the current local MDR-TB burden. These findings highlight the importance of detecting and curing isoniazid-resistant strains to prevent the emergence of endemic MDR-TB. IMPORTANCE Emerging isoniazid resistance in the 1970s allowed M. tuberculosis strains to spread and form into large multidrug-resistant tuberculosis clusters in the isolated plateau of Tibet, China. The epidemic was driven by the high risk of transmission as well as the potential of acquiring further drug resistance from isoniazid-resistant strains. Eleven large drug-resistant clusters consisted of the majority of local multidrug-resistant cases. Among the clusters, isoniazid resistance overwhelmingly evolved before all the other resistance types. A large bacterial population growth of isoniazid-resistant clusters occurred between 1970s and 1990s, which subsequently accumulated rifampicin-resistance-conferring mutations in parallel and accounted for the local multidrug-resistant tuberculosis burden. The results of our study indicate that it may be possible to restrict MDR-TB evolution and dissemination by prioritizing screening for isoniazid (INH)-resistant TB strains before they become MDR-TB and by adopting measures that can limit their transmission.
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Affiliation(s)
- Qi Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, China
| | - Hai-Can Liu
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing-Yun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jody E. Phelan
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Feng-Xi Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, China
| | - Xiu-Qin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jian Wang
- Tibet Center for Disease Control and Prevention, Lhasa, Tibet Autonomous Region, China
| | - Judith R. Glynn
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Howard E. Takiff
- Laboratorio de Genética Molecular, CMBC, IVIC, Caracas, Venezuela
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kang-Lin Wan
- State Key Laboratory for Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qian Gao
- National Clinical Research Center for Infectious Diseases, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong, China
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Ejo M, Torrea G, Diro E, Abebe A, Kassa M, Girma Y, Tesfa E, Ejigu K, Uwizeye C, Gehre F, de Jong BC, Rigouts L. Strain diversity and gene mutations associated with presumptive multidrug-resistant Mycobacterium tuberculosis complex isolates in Northwest Ethiopia. J Glob Antimicrob Resist 2023; 32:167-175. [PMID: 36470362 DOI: 10.1016/j.jgar.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/25/2022] [Accepted: 11/25/2022] [Indexed: 12/07/2022] Open
Abstract
OBJECTIVES In this study, we assessed the genetic diversity and gene mutations that confer resistance to rifampicin (RIF), isoniazid (INH), fluoroquinolone (FQ), and second-line injectable (SLI) drugs in RIF-resistant (RR)/multidrug-resistant tuberculosis (MDR-TB) isolates in Northwest Ethiopia. METHODS Spoligotyping was used to assign isolates to TB lineages (Ls), and Hain line probe assays were used to detect resistance to RIF, INH, and FQs, and SLIs. RESULTS Among 130 analyzed strains, 68.5% were RR, and four major Mycobacterium tuberculosis complex lineages (L1, L3, L4, and L7) were identified with a predominance of the Euro-American L4 (72, 54.7%), while L7 genotypes were less common (3, 2.3%). Overall, the L4-T3-ETH (41, 32.0%), L3-CAS1-Delhi (29, 22.7%), and L3-CAS1-Killi (19, 14.8%) families were most common. Line probe analysis showed that among rpoB mutants, 65.2% were S450L, while 87.8% of katG mutants were S315T. Only three isolates showed mutation (c-15t) at the inhA gene, and no double mutation with katG and inhA genes was found. Six strains, two each of L1, L3, and L4, were resistant to FQs, having gyrA mutations (D94G, S91P), of which three isolates had additional resistance to SLI (rrs A1401G or C1402T mutations) including one isolate with low-level kanamycin (KAN) resistance. CONCLUSIONS This study showed a predominance of L4-T3-ETH, L3-CAS1-Delhi, and L3-CAS1-Killi families, with a high rate of rpoB_S450L and katG_S315T mutations and a low proportion of gyrA and rrs mutations. L7 was less frequently observed in this study. Further investigations are, therefore, needed to understand L7 and other lineages with undefined mutations.
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Affiliation(s)
- Mebrat Ejo
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Gondar, Gondar, Ethiopia; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Gabriela Torrea
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ermias Diro
- Department of Internal Medicine, University of Gondar, Gondar, Ethiopia; MDR-TB Treatment and Follow-up Center, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Ayenesh Abebe
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Meseret Kassa
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Yilak Girma
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Eyasu Tesfa
- MDR-TB Treatment and Follow-up Center, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Kefialew Ejigu
- TB culture laboratory, Amhara Public Health Institute, Bahir Dar, Ethiopia
| | - Cecile Uwizeye
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Florian Gehre
- Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany; East African Community Secretariat, Arusha, Tanzania
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Naz S, Paritosh K, Sanyal P, Khan S, Singh Y, Varshney U, Nandicoori VK. GWAS and functional studies suggest a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis. eLife 2023; 12:75860. [PMID: 36695572 PMCID: PMC9876569 DOI: 10.7554/elife.75860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, we identified for the first time, a strong association between mutations in DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis and Mtb. Results show that variant mutations compromised the functions of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. In an in vivo guinea pig infection model, the MutY variant outcompeted the wild-type strain. We show that novel variant mutations in the DNA repair genes collectively compromise their functions and contribute to better survival under antibiotic/host stress conditions.
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Affiliation(s)
- Saba Naz
- National Institute of ImmunologyNew DelhiIndia
- Centre for Cellular and Molecular BiologyHyderabadIndia
- Department of Zoology, University of DelhiDelhiIndia
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South CampusNew DelhiIndia
| | | | - Sidra Khan
- National Institute of ImmunologyNew DelhiIndia
| | | | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
| | - Vinay Kumar Nandicoori
- National Institute of ImmunologyNew DelhiIndia
- Centre for Cellular and Molecular BiologyHyderabadIndia
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Genetic Diversity and Primary Drug Resistance of Mycobacterium tuberculosis Beijing Genotype Strains in Northwestern Russia. Microorganisms 2023; 11:microorganisms11020255. [PMID: 36838219 PMCID: PMC9966048 DOI: 10.3390/microorganisms11020255] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/12/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
The Beijing genotype is the main family of Mycobacterium tuberculosis in Russia. We analyzed its diversity and drug resistance in provinces across Northwestern Russia to identify the epidemiologically relevant Beijing strains. The study collection included 497 isolates from newly-diagnosed tuberculosis (TB) patients. Bacterial isolates were subjected to drug-susceptibility testing and genotyping. The Beijing genotype was detected in 57.5% (286/497); 50% of the Beijing strains were multidrug-resistant (MDR). Central Asian/Russian and B0/W148 groups included 176 and 77 isolates, respectively. MDR was more frequent among B0/W148 strains compared to Central Asian/Russian strains (85.7% vs. 40.3%, p < 0.0001). Typing of 24 minisatellite loci of Beijing strains revealed 82 profiles; 230 isolates were in 23 clusters. The largest Central Asian/Russian types were 94-32 (n = 75), 1065-32 (n = 17), and 95-32 (n = 12). B0/W148 types were 100-32 (n = 59) and 4737-32 (n = 5). MDR was more frequent in types 1065-32 (88.2%), 100-32 (83.1%), and 4737-32 (100%). In contrast, type 9391-32 (n = 9) included only drug-susceptible strains. To conclude, M. tuberculosis Beijing genotype is dominant in Northwestern Russia, and an active transmission of overwhelmingly MDR B0/W148 types explains the reported increase of MDR-TB. The presence of MDR-associated minor variants (type 1071-32/ancient Beijing and Central Asia Outbreak strain) in some of the studied provinces also requires attention.
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Larkins-Ford J, Aldridge BB. Advances in the design of combination therapies for the treatment of tuberculosis. Expert Opin Drug Discov 2023; 18:83-97. [PMID: 36538813 PMCID: PMC9892364 DOI: 10.1080/17460441.2023.2157811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Tuberculosis requires lengthy multi-drug therapy. Mycobacterium tuberculosis occupies different tissue compartments during infection, making drug access and susceptibility patterns variable. Antibiotic combinations are needed to ensure each compartment of infection is reached with effective drug treatment. Despite drug combinations' role in treating tuberculosis, the design of such combinations has been tackled relatively late in the drug development process, limiting the number of drug combinations tested. In recent years, there has been significant progress using in vitro, in vivo, and computational methodologies to interrogate combination drug effects. AREAS COVERED This review discusses the advances in these methodologies and how they may be used in conjunction with new successful clinical trials of novel drug combinations to design optimized combination therapies for tuberculosis. Literature searches for approaches and experimental models used to evaluate drug combination effects were undertaken. EXPERT OPINION We are entering an era richer in combination drug effect and pharmacokinetic/pharmacodynamic data, genetic tools, and outcome measurement types. Application of computational modeling approaches that integrate these data and produce predictive models of clinical outcomes may enable the field to generate novel, effective multidrug therapies using existing and new drug combination backbones.
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Affiliation(s)
- Jonah Larkins-Ford
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Current address: MarvelBiome Inc, Woburn, MA, USA
| | - Bree B. Aldridge
- Department of Molecular Biology and Microbiology and Tufts University School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA, USA
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, USA
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Brown TS, Robinson DA, Buckee CO, Mathema B. Connecting the dots: understanding how human mobility shapes TB epidemics. Trends Microbiol 2022; 30:1036-1044. [PMID: 35597716 PMCID: PMC10068677 DOI: 10.1016/j.tim.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 01/13/2023]
Abstract
Tuberculosis (TB) remains a leading infectious cause of death worldwide. Reducing TB infections and TB-related deaths rests ultimately on stopping forward transmission from infectious to susceptible individuals. Critical to this effort is understanding how human host mobility shapes the transmission and dispersal of new or existing strains of Mycobacterium tuberculosis (Mtb). Important questions remain unanswered. What kinds of mobility, over what temporal and spatial scales, facilitate TB transmission? How do human mobility patterns influence the dispersal of novel Mtb strains, including emergent drug-resistant strains? This review summarizes the current state of knowledge on mobility and TB epidemic dynamics, using examples from three topic areas, including inference of genetic and spatial clustering of infections, delineating source-sink dynamics, and mapping the dispersal of novel TB strains, to examine scientific questions and methodological issues within this topic. We also review new data sources for measuring human mobility, including mobile phone-associated movement data, and discuss important limitations on their use in TB epidemiology.
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Affiliation(s)
- Tyler S Brown
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Infectious Diseases Division, Massachusetts General Hospital, Boston, MA, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
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Wang H, Feng Y, Lu H. Low-Level Cefepime Exposure Induces High-Level Resistance in Environmental Bacteria: Molecular Mechanism and Evolutionary Dynamics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15074-15083. [PMID: 35608924 DOI: 10.1021/acs.est.2c00793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antibiotics exert selective pressures on clinically relevant antibiotic resistance. It is critical to understand how antibiotic resistance evolves in environmental microbes exposed to subinhibitory concentrations of antibiotics and whether evolutionary dynamics and emergence of resistance are predictable. In this study, Comamonas testosteroni isolated from wastewater activated sludge were subcultured in a medium containing 10 ng/mL cefepime for 40 days (∼300 generations). Stepwise mutations were accumulated, leading to an ultimate 200-fold increase in the minimum inhibitory concentration (MIC) of cefepime. Early stage mutation in DNA polymerase-encoding gene dnaE2 played an important role in antibiotic resistance evolution. Diverse resistance mechanisms were employed and validated experimentally, including increased efflux, biofilm formation, reduced antibiotic uptake, and drug inactivation. The cefepime minimal selective concentrations (MSCs) and relative fitness of susceptible, intermediate, and resistant mutants were determined. Agent-based modeling of the modified Moran process enabled simulations of resistance evolution and predictions of the emergence time and frequency of resistant mutants. The unraveled cefepime resistance mechanisms could be employed by broader bacteria, and the newly developed model is applicable to the predictions of general resistance evolution. The improved knowledge facilitates the assessment, prediction, and mitigation of antibiotic resistance progression in antibiotic-polluted environments.
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Affiliation(s)
- Hanqing Wang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Youjun Feng
- Departments of Microbiology & General Intensive Care Unit of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Huijie Lu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- Academy of Ecological Civilization, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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Nimmo C, Millard J, Faulkner V, Monteserin J, Pugh H, Johnson EO. Evolution of Mycobacterium tuberculosis drug resistance in the genomic era. Front Cell Infect Microbiol 2022; 12:954074. [PMID: 36275027 PMCID: PMC9585206 DOI: 10.3389/fcimb.2022.954074] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/20/2022] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis has acquired drug resistance to all drugs that have been used against it, including those only recently introduced into clinical practice. Compared to other bacteria, it has a well conserved genome due to its role as an obligate human pathogen that has adapted to a niche over five to ten thousand years. These features facilitate reconstruction and dating of M. tuberculosis phylogenies, giving key insights into how resistance has been acquired and spread globally. Resistance to each new drug has occurred within five to ten years of clinical use and has occurred even more rapidly with recently introduced drugs. In most cases, resistance-conferring mutations come with a fitness cost, but this can be overcome by compensatory mutations which restore fitness to that of wild-type bacteria. It is likely that M. tuberculosis acquires drug resistance while maintaining limited genomic variability due the generation of low frequency within-host variation, combined with ongoing purifying selection causing loss of variants without a clear fitness advantage. However, variants that do confer an advantage, such as drug resistance, can increase in prevalence amongst all bacteria within a host and become the dominant clone. These resistant strains can then be transmitted leading to primary drug resistant infection in a new host. As many countries move towards genomic methods for diagnosis of M. tuberculosis infection and drug resistance, it is important to be aware of the implications for the evolution of resistance. Currently, understanding of resistance-conferring mutations is incomplete, and some targeted genetic diagnostics create their own selective pressures. We discuss an example where a rifampicin resistance-conferring mutation which was not routinely covered by standard testing became dominant. Finally, resistance to new drugs such as bedaquiline and delamanid is caused by individually rare mutations occurring across a large mutational genomic target that have been detected over a short time, and do not provide statistical power for genotype-phenotype correlation – in contrast to longer-established drugs that form the backbone of drug-sensitive antituberculosis therapy. Therefore, we need a different approach to identify resistance-conferring mutations of new drugs before their resistance becomes widespread, abrogating their usefulness.
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Affiliation(s)
- Camus Nimmo
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
- *Correspondence: Camus Nimmo,
| | - James Millard
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Valwynne Faulkner
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Johana Monteserin
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Hannah Pugh
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
| | - Eachan Oliver Johnson
- Systems Chemical Biology of Infection and Resistance Laboratory, Francis Crick Institute, London, United Kingdom
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Stanley S, Liu Q, Fortune SM. Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine. Front Cell Infect Microbiol 2022; 12:1007958. [PMID: 36262182 PMCID: PMC9574059 DOI: 10.3389/fcimb.2022.1007958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/14/2022] [Indexed: 01/27/2023] Open
Abstract
In the face of the unrelenting global burden of tuberculosis (TB), antibiotics remain our most effective tools to save lives and control the spread of Mycobacterium tuberculosis (Mtb). However, we confront a dual challenge in our use of antibiotics: simplifying and shortening the TB drug regimen while also limiting the emergence and propagation of antibiotic resistance. This task is now more feasible due to the increasing availability of bacterial genomic data at or near the point of care. These resources create an opportunity to envision how integration of bacterial genetic determinants of antibiotic response into treatment algorithms might transform TB care. Historically, Mtb drug resistance studies focused on mutations in genes encoding antibiotic targets and the resulting increases in the minimal inhibitory concentrations (MICs) above a breakpoint value. But recent progress in elucidating the effects of functional genetic diversity in Mtb has revealed various genetic loci that are associated with drug phenotypes such as low-level MIC increases and tolerance which predict the development of resistance and treatment failure. As a result, we are now poised to advance precision medicine approaches in TB treatment. By incorporating information regarding Mtb genetic characteristics into the development of drug regimens, clinical care which tailors antibiotic treatment to maximize the likelihood of success has come into reach.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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Liebenberg D, Gordhan BG, Kana BD. Drug resistant tuberculosis: Implications for transmission, diagnosis, and disease management. Front Cell Infect Microbiol 2022; 12:943545. [PMID: 36211964 PMCID: PMC9538507 DOI: 10.3389/fcimb.2022.943545] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/06/2022] [Indexed: 01/17/2023] Open
Abstract
Drug resistant tuberculosis contributes significantly to the global burden of antimicrobial resistance, often consuming a large proportion of the healthcare budget and associated resources in many endemic countries. The rapid emergence of resistance to newer tuberculosis therapies signals the need to ensure appropriate antibiotic stewardship, together with a concerted drive to develop new regimens that are active against currently circulating drug resistant strains. Herein, we highlight that the current burden of drug resistant tuberculosis is driven by a combination of ongoing transmission and the intra-patient evolution of resistance through several mechanisms. Global control of tuberculosis will require interventions that effectively address these and related aspects. Interrupting tuberculosis transmission is dependent on the availability of novel rapid diagnostics which provide accurate results, as near-patient as is possible, together with appropriate linkage to care. Contact tracing, longitudinal follow-up for symptoms and active mapping of social contacts are essential elements to curb further community-wide spread of drug resistant strains. Appropriate prophylaxis for contacts of drug resistant index cases is imperative to limit disease progression and subsequent transmission. Preventing the evolution of drug resistant strains will require the development of shorter regimens that rapidly eliminate all populations of mycobacteria, whilst concurrently limiting bacterial metabolic processes that drive drug tolerance, mutagenesis and the ultimate emergence of resistance. Drug discovery programs that specifically target bacterial genetic determinants associated with these processes will be paramount to tuberculosis eradication. In addition, the development of appropriate clinical endpoints that quantify drug tolerant organisms in sputum, such as differentially culturable/detectable tubercle bacteria is necessary to accurately assess the potential of new therapies to effectively shorten treatment duration. When combined, this holistic approach to addressing the critical problems associated with drug resistance will support delivery of quality care to patients suffering from tuberculosis and bolster efforts to eradicate this disease.
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Mave V, Chen L, Ranganathan UD, Kadam D, Vishwanathan V, Lokhande R, S SK, Kagal A, Pradhan N, Shivakumar SVBY, Paradkar MS, Deshmukh S, Tornheim JA, Kornfeld H, Farhat M, Gupta A, Padmapriyadarsini C, Gupte N, Golub JE, Mathema B, Kreiswirth BN. Whole Genome Sequencing Assessing Impact of Diabetes Mellitus on Tuberculosis Mutations and Type of Recurrence in India. Clin Infect Dis 2022; 75:768-776. [PMID: 34984435 PMCID: PMC9477453 DOI: 10.1093/cid/ciab1067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Evidence describing the impact of diabetes mellitus (DM) on the recurrence and mutation rate of Mycobacterium tuberculosis (Mtb) is limited. METHODS This study was nested in 3 cohort studies of tuberculosis (TB) patients with and without DM in India. Paired Mtb isolates recovered at baseline and treatment failure/recurrence underwent whole genome sequencing. We compared acquisition of single-nucleotide polymorphisms (SNPs), TB drug resistance mutations, and type of recurrence (endogenous reactivation [<8 SNPs] or exogenous reinfection [≥8 SNPs]) by DM status. RESULTS Of 1633 enrolled in the 3 parent cohorts, 236 (14.5%) had microbiologically confirmed TB treatment failure/recurrence; 76 Mtb isolate pairs were available for sequencing (22 in TB-DM and 54 in TB-only). The SNP acquisition rate was overall was 0.43 (95% confidence interval [CI], .25-.64) per 1 person-year (PY); 0.77 (95% CI, .40-1.35) per 1 PY, and 0.44 (95% CI, .19-.86) per 1 PY at treatment failure and recurrence, respectively. Significant difference in SNP rates by DM status was seen at recurrence (0.21 [95% CI, .04-.61]) per 1 PY for TB-only vs 1.28 (95% CI, .41-2.98) per 1 PY for TB-DM; P = .02). No significant difference in SNP rates by DM status was observed at treatment failure. Acquired TB drug resistance was seen in 4 of 18 (22%) in TB-DM vs 4 of 45 (9%) in TB-only (P = .21). Thirteen (17%) participants had exogenous reinfection; the reinfection rate at recurrence was 25% (3/12) for TB-DM vs 17% (4/24) in TB-only (P = .66). CONCLUSIONS Considerable intrahost Mtb mutation rates were present at recurrence among patients with DM in India. One-fourth of patients with DM had exogenous reinfection at recurrence.
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Affiliation(s)
- Vidya Mave
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Johns Hopkins India, Pune, India
| | - Liang Chen
- Hackensack Meridian Health, Center for Discovery and Innovation, Nutley, New Jersey, USA
| | | | - Dileep Kadam
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | | | - Rahul Lokhande
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | - Siva Kumar S
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Anju Kagal
- Byramjee-Jeejeebhoy Government Medical College, Pune, India
| | - Neeta N Pradhan
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins India, Pune, India
| | | | - Mandar S Paradkar
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins India, Pune, India
| | - Sona Deshmukh
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins India, Pune, India
| | | | | | - Maha Farhat
- Harvard Medical School, Boston, Massachusetts, USA
| | - Amita Gupta
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Nikhil Gupte
- Byramjee-Jeejeebhoy Medical College–Johns Hopkins University Clinical Research Site, Pune, India
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Johns Hopkins India, Pune, India
| | - Jonathan E Golub
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Barry N Kreiswirth
- Hackensack Meridian Health, Center for Discovery and Innovation, Nutley, New Jersey, USA
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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] [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.
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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.
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Dreyer V, Mandal A, Dev P, Merker M, Barilar I, Utpatel C, Nilgiriwala K, Rodrigues C, Crook DW, Crook DW, Peto TEA, Walker AS, Hoosdally SJ, Gibertoni Cruz AL, Carter J, Earle S, Kouchaki S, Yang Y, Walker TM, Fowler PW, Wilson D, Clifton DA, Iqbal Z, Hunt M, Knaggs J, Cirillo DM, Borroni E, Battaglia S, Ghodousi A, Spitaleri A, Cabibbe A, Tahseen S, Nilgiriwala K, Shah S, Rodrigues C, Kambli P, Surve U, Khot R, Niemann S, Kohl T, Merker M, Hoffmann H, Todt K, Plesnik S, Ismail N, Omar SV, Ngcamu LJD, Okozi N, Yao SY, Thwaites G, Thuong TNT, Ngoc NH, Srinivasan V, Moore D, Coronel J, Solano W, Gao GF, He G, Zhao Y, Ma A, Liu C, Zhu B, Laurenson I, Claxton P, Wilkinson RJ, Koch A, Lalvani A, Posey J, Gardy J, Werngren J, Paton N, Jou R, Wu MH, Xiao YX, Ferrazoli L, de Oliveira RS, Millard J, Warren R, Van Rie A, Lapierre SG, Rabodoarivelo MS, Rakotosamimanana N, Nimmo C, Musser K, Escuyer V, Cohen T, Rasigade JP, Wirth T, Mistry N, Niemann S. High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region. Genome Med 2022; 14:95. [PMID: 35989319 PMCID: PMC9394022 DOI: 10.1186/s13073-022-01076-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/20/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined.
Methods
In a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively.
Results
In total, 1016 MTBC strains were MDR, out of which 703 (69.2%) were pre-XDR and 45 (4.4%) were XDR. Cluster rates were high among MDR (57.8%) and pre-XDR/XDR (79%) strains with three dominant L2 (Beijing) strain clusters (Cl 1–3) representing half of the pre-XDR and 40% of the XDR-TB cases. L2 strains were associated with pre-XDR/XDR-TB (P < 0.001) and, particularly Cl 1–3 strains, had high first-line and FQ resistance rates (81.6–90.6%). Epidemic success analysis using THD showed that L2 strains outperformed L1, L3, and L4 strains in short- and long-term time scales. More importantly, L2 MDR and MDR + strains had higher THD success indices than their not-MDR counterparts. Overall, compensatory mutation rates were highest in L2 strains and positive selection was detected in genes of L2 strains associated with drug tolerance (prpB and ppsA) and virulence (Rv2828c). Compensatory mutations in L2 strains were associated with a threefold increase of THD indices, suggesting improved transmissibility.
Conclusions
Our data indicate a drastic increase of FQ resistance, as well as emerging bedaquiline resistance which endangers the success of newly endorsed MDR-TB treatment regimens. Rapid changes in treatment and control strategies are required to contain transmission of highly successful pre-XDR L2 strains in the Mumbai Metropolitan region but presumably also India-wide.
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Maddamsetti R, Grant NA. Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations. PLoS Genet 2022; 18:e1010324. [PMID: 35981004 PMCID: PMC9426924 DOI: 10.1371/journal.pgen.1010324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/30/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
A general method to infer both positive and purifying selection during the real-time evolution of hypermutator pathogens would be broadly useful. To this end, we introduce a Simple Test to Infer Mode of Selection (STIMS) from metagenomic time series of evolving microbial populations. We test STIMS on metagenomic data generated by simulations of bacterial evolution, and on metagenomic data spanning 62,750 generations of Lenski’s long-term evolution experiment with Escherichia coli (LTEE). This benchmarking shows that STIMS detects positive selection in both nonmutator and hypermutator populations, and purifying selection in hypermutator populations. Using STIMS, we find strong evidence of ongoing positive selection on key regulators of the E. coli gene regulatory network, even in some hypermutator populations. STIMS also detects positive selection on regulatory genes in hypermutator populations of Pseudomonas aeruginosa that adapted to subinhibitory concentrations of colistin–an antibiotic of last resort–for just twenty-six days of laboratory evolution. Our results show that the fine-tuning of gene regulatory networks is a general mechanism for rapid and ongoing adaptation. The simplicity of STIMS, together with its intuitive visual interpretation, make it a useful test for positive and purifying selection in metagenomic data sets that track microbial evolution in real-time. Organisms often evolve elevated mutation rates as they adapt to new environments. That said, the genomic basis of adaptation in asexual hypermutator populations has been difficult to discern, because the few mutations driving adaptation are often associated with large numbers of non-adaptive “hitchhiker” mutations elsewhere in the genome. To address this research gap, we present a Simple Test to Infer Mode of Selection (STIMS) which aggregates the overall signature of selection seen over hundreds of genes. Using STIMS, we find strong positive selection on key regulators of the E. coli gene regulatory network across nonmutator and hypermutator populations of Lenski’s long-term evolution experiment with Escherichia coli. We also find positive selection on regulatory genes in populations of Pseudomonas aeruginosa that evolved hypermutability as they evolved to resist colistin, an antibiotic of last resort. Our work shows that positive and purifying selection can be resolved in hypermutator populations, given sufficient genomic data, and show that regulatory mutations are a major driver of adaptation in experimental populations of microbes.
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Affiliation(s)
- Rohan Maddamsetti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States of America
- * E-mail: (RM); (NAG)
| | - Nkrumah A. Grant
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, United States of America
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- * E-mail: (RM); (NAG)
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Gómez-González PJ, Campino S, Phelan JE, Clark TG. Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications. Brief Bioinform 2022; 23:6650479. [PMID: 35894606 PMCID: PMC9487601 DOI: 10.1093/bib/bbac256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
With >1 million associated deaths in 2020, human tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis remains one of the deadliest infectious diseases. A plethora of genomic tools and bioinformatics pipelines have become available in recent years to assist the whole genome sequencing of M. tuberculosis. The Oxford Nanopore Technologies (ONT) portable sequencer is a promising platform for cost-effective application in clinics, including personalizing treatment through detection of drug resistance-associated mutations, or in the field, to assist epidemiological and transmission investigations. In this study, we performed a comparison of 10 clinical isolates with DNA sequenced on both long-read ONT and (gold standard) short-read Illumina HiSeq platforms. Our analysis demonstrates the robustness of the ONT variant calling for single nucleotide polymorphisms, despite the high error rate. Moreover, because of improved coverage in repetitive regions where short sequencing reads fail to align accurately, ONT data analysis can incorporate additional regions of the genome usually excluded (e.g. pe/ppe genes). The resulting extra resolution can improve the characterization of transmission clusters and dynamics based on inferring closely related isolates. High concordance in variants in loci associated with drug resistance supports its use for the rapid detection of resistant mutations. Overall, ONT sequencing is a promising tool for TB genomic investigations, particularly to inform clinical and surveillance decision-making to reduce the disease burden.
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Affiliation(s)
- Paula J Gómez-González
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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47
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Yoon SH, Goo JM, Yim JJ, Yoshiyama T, Flynn JL. CT and 18F-FDG PET abnormalities in contacts with recent tuberculosis infections but negative chest X-ray. Insights Imaging 2022; 13:112. [PMID: 35796839 PMCID: PMC9261169 DOI: 10.1186/s13244-022-01255-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/19/2022] [Indexed: 12/05/2022] Open
Abstract
Close contacts of individuals with pulmonary tuberculosis are at risk for tuberculosis infection and the development of active tuberculosis. In current contact investigations, immunologic tests (the tuberculin skin test and interferon-gamma release assay) and chest X-ray examinations are used to dichotomize contacts with Mycobacterium tuberculosis infections into those with active (X-ray abnormalities) versus latent tuberculosis (normal radiographs). This article is a critical review of computed tomographic (CT) and 18-fluorodeoxyglucose positron emission tomographic (PET) findings of incipient tuberculosis without X-ray abnormalities based on a systematic literature review of twenty-five publications. The CT and 18-fluorodeoxyglucose PET studies revealed minimal pauci-nodular infiltrations in the lung parenchyma and mediastinal lymph nodes abnormalities with metabolic uptake in approximately one-third of asymptomatic close contacts with negative chest radiographic and bacteriological/molecular results for active tuberculosis. Tuberculosis with minimal changes challenge the validity of simply dichotomizing cases of recent M. tuberculosis infections in contacts depending on the presence of X-ray abnormalities as the recent infections may spontaneously regress, remain stagnant, or progress to active tuberculosis in human and nonhuman primate studies. Whether contacts with tuberculosis with minimal changes are interpreted as having active tuberculosis or latent tuberculosis has clinical implications in terms of specific benefits and harms under the current contact management. Advanced imaging tools may help further stratify contacts intensely exposed to M. tuberculosis on a continuous spectrum from latent tuberculosis to incipient, subclinical and active tuberculosis. Identifying incipient tuberculosis would provide an opportunity for earlier and tailored treatment before active tuberculosis is established.
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Affiliation(s)
- Soon Ho Yoon
- Department of Radiology, Seoul National University College of Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Jin Mo Goo
- Department of Radiology, Seoul National University College of Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.,Institute of Radiation Medicine, Seoul National University Medical Research Center, Seoul, Republic of Korea
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Takashi Yoshiyama
- Research Institute of Tuberculosis, Japan Anti-tuberculosis Association, Kiyose, Japan, Kiyose, Japan
| | - JoAnne L Flynn
- Department of Microbiology and Molecular Genetics and the Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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48
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Shi Y, Kong W, Jiang H, Zhang W, Wang C, Wu L, Shen Y, Yao Q, Wang H. Molecular Surveillance of Antimicrobial Resistance of Mycobacterium leprae from Leprosy Patients in Zhejiang Province, China. Infect Drug Resist 2022; 15:4029-4036. [PMID: 35924023 PMCID: PMC9342246 DOI: 10.2147/idr.s368682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/06/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Reports on antimicrobial resistance (AMR) of Mycobacterium leprae (M. leprae) in Zhejiang Province are limited. Thus, this study aimed to investigate the drug resistance of new leprosy cases within several years and analyse the emergence of AMR mutations from Zhejiang Province. Methods This study enrolled 34 leprosy cases in Zhejiang Province, China, from 2018 to 2021. Gene mutation of WHO-recommended DRDRs (folP1, rpoB and gyrA) and genes of compensatory AMR-associated DRDRs, including nth, rpoA, rpoC, gyrB and 23S rRNA, were detected by amplification. Clinical data analysis was performed to investigate the epidemiological association of leprosy. Results Of the 34 samples, 2 (5.9%) strains showed drug resistance, which were mutated to dapsone and ofloxacin, separately. Two single mutations in gyrB were detected in different strains (5.9%), whereas one of the rpoC mutation was also detected in one strain each (2.9%), which were proved to be polymorphs. No correlation of drug resistance proportion was identified in male vs female, nerve vs no nerve involvement, deformity vs no deformity and reaction vs non-reaction cases. Conclusion Results showed well control of leprosy patients in Zhejiang Province. Gene mutations of WHO-recommended DRDRs folP1 and gyrA confirmed the resistance to dapsone and ofloxacin. Compensatory AMR-associated mutations confirmed to be polymorphs still require further study to determine their phenotypic outcomes in M. leprae. The results demonstrated that drug-resistant strains are not epidemic in this area. Given the few cases of leprosy, analysing the AMR of M. leprae in Zhejiang Province more comprehensively is difficult. However, regular MDT treatment and population management in the early stage may contribute to the low prevalence of leprosy.
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Affiliation(s)
- Ying Shi
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
| | - Wenming Kong
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
| | - Haiqin Jiang
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
| | - Wenyue Zhang
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
| | - Chen Wang
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Limei Wu
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
| | - Yunliang Shen
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
| | - Qiang Yao
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
- Correspondence: Qiang Yao, Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, St 61, Zhejiang, People’s Republic of China, Email
| | - Hongsheng Wang
- Department of Leprosy Control, Zhejiang Provincial Institute of Dermatology, Huzhou, People’s Republic of China
- Hospital of Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, People’s Republic of China
- National Centre for STD and Leprosy Control, China CDC, Nanjing, People’s Republic of China
- Centre for Global health, School of Public Health, Nanjing Medical University, Nanjing, People’s Republic of China
- Hongsheng Wang, Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 12 Jiangwangmiao Street, Nanjing, People’s Republic of China, Tel: +86 025 8547 8953, Email
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Zhang K, Pinto A, Cheng LY, Song P, Dai P, Wang M, Rodriguez L, Weller C, Zhang DY. Hairpin Structure Facilitates Multiplex High-Fidelity DNA Amplification in Real-Time Polymerase Chain Reaction. Anal Chem 2022; 94:9586-9594. [PMID: 35749270 DOI: 10.1021/acs.analchem.2c00575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Clinically and biologically, it is essential to detect rare DNA-sequence variants for early cancer diagnosis or drug-resistance mutation identification. Some of the common quantitative polymerase chain reaction (qPCR)-based variant detection methods are restricted in the limit of detection (LoD) because the DNA polymerases used for these methods have a high polymerase misincorporation rate; thus, the detection sensitivity is sometimes unsatisfactory. With the proofreading activity, high-fidelity (HiFi) DNA polymerases have a 50- to 250-fold higher fidelity. However, there are currently no proper probe-based designs functioning as the fluorescence indicator allowing multiplexed HiFi qPCR reactions, thus restricting the application of HiFi DNA polymerases like the variant detection. We presented the occlusion system, composed of a 5'-overhanged primer with a fluorophore modification and a probe with a short-stem hairpin and a 3' quencher modification. We demonstrated that the occlusion system allowed multiplexing HiFi qPCR reaction, and it was compatible with the current variant-enrichment method to improve the LoD up to 10-fold. Thus, the occlusion system satisfactorily functioned as an efficient fluorescence indicator in HiFi qPCR reactions and allowed the application of HiFi DNA polymerases in variant detection methods to improve detection sensitivity.
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Affiliation(s)
- Kerou Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Alessandro Pinto
- NuProbe USA, 2575 W Bellfort Street, Houston, Texas 77054, United States
| | - Lauren Yuxuan Cheng
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Peng Dai
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Michael Wang
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States
| | - Luis Rodriguez
- NuProbe USA, 2575 W Bellfort Street, Houston, Texas 77054, United States
| | - Cailin Weller
- NuProbe USA, 2575 W Bellfort Street, Houston, Texas 77054, United States
| | - David Yu Zhang
- Department of Bioengineering, Rice University, Houston, Texas 77030, United States.,Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77030, United States
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50
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Panova AE, Vinokurov AS, Shemetova AA, Burmistrova IA, Shulgina MV, Samoilova AG, Vasilyeva IA, Vakhrusheva DV, Umpeleva TV, Eremeeva NI, Lavrenchuk LS, Golubeva LA, Danilova TI, Vasilyeva TB, Ugol'kova VA, Sosova NV, Lekhlyaider MV, Gorshkova IA, Romanova TA. Molecular characteristics of Mycobacterium tuberculosis drug-resistant isolates from HIV- and HIV+ tuberculosis patients in Russia. BMC Microbiol 2022; 22:138. [PMID: 35590243 PMCID: PMC9118847 DOI: 10.1186/s12866-022-02553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background High burden of drug-resistant (DR) tuberculosis (TB) is a significant threat to national TB control programs all over the world and in the Russian Federation. Different Mycobacterium tuberculosis (MTB) genotypes are hypothesized to have specific characteristics affecting TB control programs. For example, Beijing strains are supposed to have higher mutation rates compared to strains of other genotypes and subsequently higher capability to develop drug-resistance. Results Clinical MTB isolates from HIV- and HIV+ patients from four regions of Russia were analyzed for genotypes and mutations conferring resistance to Isoniazid, Rifampicin, Ethambutol, aminoglycosides, and fluoroquinolones. Analysis of genotypes and polymorphism of genomic loci according to the HIV status of the patients – sources of MTB isolates were performed. Studied MTB isolates from HIV- TB patients belonged to 15 genotypes and from HIV + TB patients – to 6 genotypes. Beijing clinical isolates dominated in HIV- (64,7%) and HIV+ (74,4%) groups. Other isolates were of LAM (including LAM1 and LAM9), Ural, and 4 minor groups of genotypes (including 5 subclones T). The spectrum of genotypes in the HIV- group was broader than in the HIV+ group. PR of B0/W148 Beijing was significantly lower than of other Beijing genotypes in susceptible and MDR-XDR isolates. Rates of isolates belonging to non-Beijing genotypes were higher than Beijing in susceptible isolates from HIV- patients. Conclusions Beijing genotype isolates prevailed in clinical isolates of all drug susceptibility profiles both from HIV- and HIV+ patients, although B0/W148 Beijing genotype did not dominate in this study. Genome loci and mutations polymorphisms were more pronounced in clinical isolates from HIV- patients, than from HIV+.
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Affiliation(s)
- Anna E Panova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anatoliy S Vinokurov
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anastasiya A Shemetova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Burmistrova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Marina V Shulgina
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation.
| | - Anastasiya G Samoilova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Vasilyeva
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Diana V Vakhrusheva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana V Umpeleva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Nataliya I Eremeeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Leonid S Lavrenchuk
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Lyudmila A Golubeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana I Danilova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Tatiana B Vasilyeva
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Vera A Ugol'kova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Nataliya V Sosova
- Regional TB dispensary of Stavropolskiy kray, Stavropol, Russian Federation
| | - Marina V Lekhlyaider
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Irina A Gorshkova
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Tatiana A Romanova
- Regional TB dispensary of Kemerovskaya oblast, Kemerovo, Russian Federation
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