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Wu Z, Li H, Wu J, Lai X, Huang S, Yu M, Liao Q, Zhang C, Zhou L, Chen X, Guo H, Chen L. The profile of genome-wide DNA methylation, transcriptome, and proteome in streptomycin-resistant Mycobacterium tuberculosis. PLoS One 2024; 19:e0297477. [PMID: 38285653 PMCID: PMC10824437 DOI: 10.1371/journal.pone.0297477] [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: 03/23/2023] [Accepted: 01/06/2024] [Indexed: 01/31/2024] Open
Abstract
Streptomycin-resistant (SM-resistant) Mycobacterium tuberculosis (M. tuberculosis) is a major concern in tuberculosis (TB) treatment. However, the mechanisms underlying streptomycin resistance remain unclear. This study primarily aimed to perform preliminary screening of genes associated with streptomycin resistance through conjoint analysis of multiple genomics. Genome-wide methylation, transcriptome, and proteome analyses were used to elucidate the associations between specific genes and streptomycin resistance in M. tuberculosis H37Rv. Methylation analysis revealed that 188 genes were differentially methylated between the SM-resistant and normal groups, with 89 and 99 genes being hypermethylated and hypomethylated, respectively. Furthermore, functional analysis revealed that these 188 differentially methylated genes were enriched in 74 pathways, with most of them being enriched in metabolic pathways. Transcriptome analysis revealed that 516 genes were differentially expressed between the drug-resistant and normal groups, with 263 and 253 genes being significantly upregulated and downregulated, respectively. KEGG analysis indicated that these 516 genes were enriched in 79 pathways, with most of them being enriched in histidine metabolism. The methylation level was negatively related to mRNA abundance. Proteome analysis revealed 56 differentially expressed proteins, including 14 upregulated and 42 downregulated proteins. Moreover, three hub genes (coaE, fadE5, and mprA) were obtained using synthetic analysis. The findings of this study suggest that an integrated DNA methylation, transcriptome, and proteome analysis can provide important resources for epigenetic studies in SM-resistant M. tuberculosis H37Rv.
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Affiliation(s)
- Zhuhua Wu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Haicheng Li
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiawen Wu
- Institute for tuberculosis control of Zhaoqing, Zhaoqing, China
| | - Xiaoyu Lai
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Shanshan Huang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Meiling Yu
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Qinghua Liao
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Chenchen Zhang
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Lin Zhou
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Xunxun Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Huixin Guo
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
| | - Liang Chen
- Center for Tuberculosis Control of Guangdong Province, Guangzhou, China
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2
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [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: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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3
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Whole-Genome Sequencing of Streptomycin-Resistant Mycobacterium tuberculosis Strain SBH145 from Sabah, Malaysia. Microbiol Resour Announc 2022; 11:e0104021. [PMID: 34989616 PMCID: PMC8759369 DOI: 10.1128/mra.01040-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
This paper reports on the whole-genome sequencing of a streptomycin-resistant Mycobacterium tuberculosis strain that was isolated from a patient with pulmonary tuberculosis in Sabah state of Malaysian Borneo. The strain belongs to the EAI2-Manila family of lineage 1 and is clustered with M. tuberculosis strains from the Philippines, India, and Taiwan.
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4
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Abstract
Whole-genome sequencing (WGS) has shown tremendous potential in rapid diagnosis of drug-resistant tuberculosis (TB). In the current study, we performed WGS on drug-resistant Mycobacterium tuberculosis isolates obtained from Shanghai (n = 137) and Russia (n = 78). We aimed to characterise the underlying and high-frequency novel drug-resistance-conferring mutations, and also create valuable combinations of resistance mutations with high predictive sensitivity to predict multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB) phenotype using a bootstrap method. Most strains belonged to L2.2, L4.2, L4.4, L4.5 and L4.8 lineages. We found that WGS could predict 82.07% of phenotypically drug-resistant domestic strains. The prediction sensitivity for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STR), ofloxacin (OFL), amikacin (AMK) and capreomycin (CAP) was 79.71%, 86.30%, 76.47%, 88.37%, 83.33%, 70.00% and 70.00%, respectively. The mutation combination with the highest sensitivity for MDR prediction was rpoB S450L + rpoB H445A/P + katG S315T + inhA I21T + inhA S94A, with a sensitivity of 92.17% (0.8615, 0.9646), and the mutation combination with highest sensitivity for XDR prediction was rpoB S450L + katG S315T + gyrA D94G + rrs A1401G, with a sensitivity of 92.86% (0.8158, 0.9796). The molecular information presented here will be of particular value for the rapid clinical detection of MDR- and XDR-TB isolates through laboratory diagnosis.
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5
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Rocha DMGC, Magalhães C, Cá B, Ramos A, Carvalho T, Comas I, Guimarães JT, Bastos HN, Saraiva M, Osório NS. Heterogeneous Streptomycin Resistance Level Among Mycobacterium tuberculosis Strains From the Same Transmission Cluster. Front Microbiol 2021; 12:659545. [PMID: 34177837 PMCID: PMC8226182 DOI: 10.3389/fmicb.2021.659545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
Widespread and frequent resistance to the second-line tuberculosis (TB) medicine streptomycin, suggests ongoing transmission of low fitness cost streptomycin resistance mutations. To investigate this hypothesis, we studied a cohort of 681 individuals from a TB epidemic in Portugal. Whole-genome sequencing (WGS) analyses were combined with phenotypic growth studies in culture media and in mouse bone marrow derived macrophages. Streptomycin resistance was the most frequent resistance in the cohort accounting for 82.7% (n = 67) of the resistant Mycobacterium tuberculosis isolates. WGS of 149 clinical isolates identified 13 transmission clusters, including three clusters containing only streptomycin resistant isolates. The biggest cluster was formed by eight streptomycin resistant isolates with a maximum of five pairwise single nucleotide polymorphisms of difference. Interestingly, despite their genetic similarity, these isolates displayed different resistance levels to streptomycin, as measured both in culture media and in infected mouse bone marrow derived macrophages. The genetic bases underlying this phenotype are a combination of mutations in gid and other genes. This study suggests that specific streptomycin resistance mutations were transmitted in the cohort, with the resistant isolates evolving at the cluster level to allow low-to-high streptomycin resistance levels without a significative fitness cost. This is relevant not only to better understand transmission of streptomycin resistance in a clinical setting dominated by Lineage 4 M. tuberculosis infections, but mainly because it opens new prospects for the investigation of selection and spread of drug resistance in general.
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Affiliation(s)
- Deisy M G C Rocha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal.,i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
| | - Carlos Magalhães
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
| | - Baltazar Cá
- i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
| | - Angelica Ramos
- Department of Clinical Pathology, Centro Hospitalar São João, Porto, Portugal
| | - Teresa Carvalho
- Department of Clinical Pathology, Centro Hospitalar São João, Porto, Portugal
| | - Iñaki Comas
- Biomedicine Institute of Valencia IBV-CSIC, Valencia, Spain.,CIBER in Epidemiology and Public Health, Valencia, Spain
| | - João Tiago Guimarães
- Department of Clinical Pathology, Centro Hospitalar São João, Porto, Portugal.,Institute of Public Health, University of Porto, Porto, Portugal.,Department of Biochemistry, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Helder Novais Bastos
- i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal.,Serviço de Pneumologia, Centro Hospitalar Universitário de São João EPE, Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigacão e Inovação em Saúde, University of Porto, Porto, Portugal.,Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
| | - Nuno S Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Portugal
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6
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Chauhan A, Kumar M, Kumar A, Kanchan K. Comprehensive review on mechanism of action, resistance and evolution of antimycobacterial drugs. Life Sci 2021; 274:119301. [PMID: 33675895 DOI: 10.1016/j.lfs.2021.119301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023]
Abstract
Tuberculosis is one of the deadliest infectious diseases existing in the world since ancient times and still possesses serious threat across the globe. Each year the number of cases increases due to high drug resistance shown by Mycobacterium tuberculosis (Mtb). Available antimycobacterial drugs have been classified as First line, Second line and Third line antibiotics depending on the time of their discoveries and their effectiveness in the treatment. These antibiotics have a broad range of targets ranging from cell wall to metabolic processes and their non-judicious and uncontrolled usage in the treatment for years has created a significant problem called multi-drug resistant (MDR) tuberculosis. In this review, we have summarized the mechanism of action of all the classified antibiotics currently in use along with the resistance mechanisms acquired by Mtb. We have focused on the new drug candidates/repurposed drugs, and drug in combinations, which are in clinical trials for either treating the MDR tuberculosis more effectively or involved in reducing the time required for the chemotherapy of drug sensitive TB. This information is not discussed very adequately on a single platform. Additionally, we have discussed the recent technologies that are being used to discover novel resistance mechanisms acquired by Mtb and for exploring novel drugs. The story of intrinsic resistance mechanisms and evolution in Mtb is far from complete. Therefore, we have also discussed intrinsic resistance mechanisms of Mtb and their evolution with time, emphasizing the hope for the development of novel antimycobacterial drugs for effective therapy of tuberculosis.
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Affiliation(s)
- Aditi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Manoj Kumar
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida 201313, India
| | - Awanish Kumar
- Department of Bio Technology, National Institute of Technology, Raipur, India
| | - Kajal Kanchan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India.
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7
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Verma H, Nagar S, Vohra S, Pandey S, Lal D, Negi RK, Lal R, Rawat CD. Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets. Microb Genom 2021; 7:mgen000542. [PMID: 33750515 PMCID: PMC8190606 DOI: 10.1099/mgen.0.000542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis is a known human pathogen that causes the airborne infectious disease tuberculosis (TB). Every year TB infects millions of people worldwide. The emergence of multi-drug resistant (MDR), extensively drug resistant (XDR) and totally drug resistant (TDR) M. tuberculosis strains against the first- and second-line anti-TB drugs has created an urgent need for the development and implementation of new drug strategies. In this study, the complete genomes of 174 strains of M. tuberculosis are analysed to understand the evolution of molecular drug target (MDT) genes. Phylogenomic placements of M. tuberculosis strains depicted close association and temporal clustering. Selection pressure analysis by deducing the ratio of non-synonymous to synonymous substitution rates (dN/dS) in 51 MDT genes of the 174 M. tuberculosis strains led to categorizing these genes into diversifying (D, dN/dS>0.70), moderately diversifying (MD, dN/dS=0.35-0.70) and stabilized (S, dN/dS<0.35) genes. The genes rpsL, gidB, pncA and ahpC were identified as diversifying, and Rv0488, kasA, ndh, ethR, ethA, embR and ddn were identified as stabilized genes. Furthermore, sequence similarity networks were drawn that supported these divisions. In the multiple sequence alignments of diversifying and stabilized proteins, previously reported resistance mutations were checked to predict sensitive and resistant strains of M. tuberculosis. Finally, to delineate the potential of stabilized or least diversified genes/proteins as anti-TB drug targets, protein-protein interactions of MDT proteins with human proteins were analysed. We predict that kasA (dN/dS=0.29), a stabilized gene that encodes the most host-interacting protein, KasA, should serve as a potential drug target for the treatment of TB.
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Affiliation(s)
- Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | - Shekhar Nagar
- Department of Zoology, University of Delhi, Delhi 110007, India
| | - Shivani Vohra
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
- Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi 110021, India
| | - Shubhanshu Pandey
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
- Department of Biotechnology, Jamia Millia Islamia, Okhla, New Delhi 110025, India
| | - Devi Lal
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | | | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
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8
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Molecular analysis of streptomycin-resistance associating genes in Mycobacterium tuberculosis isolates from Nepal. Tuberculosis (Edinb) 2020; 125:101985. [PMID: 32829153 DOI: 10.1016/j.tube.2020.101985] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 11/24/2022]
Abstract
Mutation in rpsL (encoding ribosomal protein S12), rrs (encoding 16S ribosomal RNA) and gidB (encoding 7-methylguanosine methyltransferase) are associated with resistance to streptomycin (STR), which is used for the treatment of multi-drug resistant tuberculosis (MDR-TB) in Nepal. The aim of our study is to analyze the correlation between mutations in the target genes and STR-resistance in 197 Mycobacterium tuberculosis (MTB) isolates from Nepal. Mutations in rpsL was harbored by 65.9% of isolates, in which the most common mutation in rpsL is caused by K43R (58.8%) and were significantly associated with Beijing genotype (P < 0.001). About 13.2% of isolates harbored mutations in two highly mutable regions of rrs, the 530 loop and the 912 region. About 13.2% of gidB mutants do not show any mutation in rpsL and rrs, which might suggest the role of gidB mutations in STR-resistance in MTB. In addition, 5.6% of isolates do not show any mutations in three genes examined, suggesting the involvement of other mechanism in STR-resistance in MTB. Our findings can be implemented for the establishment of molecular STR-susceptibility testing, in which tuberculosis can be treated with appropriate drugs and can improve control strategies for DR-TB.
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9
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Sorokin VV, Pshenichnikova AB, Kalenov SV, Suyasov NA, Skladnev DA. Comparison of the Wild-Type Obligate Methylotrophic Bacterium Methylophilus quaylei and its Isogenic Streptomycin-Resistant Mutant via Metal Nanoparticle Generation. Biol Trace Elem Res 2020; 193:564-573. [PMID: 31073700 PMCID: PMC6944653 DOI: 10.1007/s12011-019-01740-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/22/2019] [Indexed: 11/16/2022]
Abstract
Metal nanoparticles synthesized by green methods with the use of microorganisms are currently one of the most closely studied types of nanomaterials. It has accurately been shown that the characteristics of metal nanoparticles generated in the presence of different bacteria vary. For the two isogenic strains of obligate methylotrophic bacteria of the wild type (M. quaylei MTT) and its streptomycin-resistant mutant (M. quaylei SMR), the pleiotropic character of streptomycin resistance mutation in the SMR cells has been revealed. It has been shown that both cultures can generate silver nanoparticles. There is a dramatic difference in the formation of palladium nanoparticles, which are formed only in the presence of cells of the streptomycin-resistant mutant M. quaylei SMR. This study shows that closely related isogenic strains of obligate methylotrophic bacteria can be distinguished by the spectra of biogenic nanoparticles of two noble metals. While palladium nanoparticles are only generated by the cells of the streptomycin-resistant mutant M. quaylei SMR, biogenic silver nanoparticles can be generated from both cultures. Thus, the assessment of the ability of microorganisms to form biogenic nanoparticles of different metals allows the revelation of subtle metabolic differences of even close cultures.
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Affiliation(s)
- Vladimir V Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, Bld. 2 Leninsky Ave., Moscow, Russia
| | - Anna B Pshenichnikova
- Department of Biotechnology and Industrial Pharmacy, MIREA - Russian Technological University, 86 Vernadsky Avenue, Moscow, Russia
| | - Sergei V Kalenov
- Department of Biotechnology, Faculty of Biotechnology and Industrial Ecology, D.I. Mendeleyev University of Chemical Technology of Russia, 9 Miusskaya Square, Moscow, Russia.
| | - Nikolay A Suyasov
- Department of Biotechnology, Faculty of Biotechnology and Industrial Ecology, D.I. Mendeleyev University of Chemical Technology of Russia, 9 Miusskaya Square, Moscow, Russia
| | - Dmitry A Skladnev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 33, Bld. 2 Leninsky Ave., Moscow, Russia
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10
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Islam MM, Tan Y, Hameed HMA, Chhotaray C, Liu Z, Liu Y, Lu Z, Wang S, Cai X, Gao Y, Cai X, Guo L, Li X, Tan S, Yew WW, Zhong N, Liu J, Zhang T. Phenotypic and Genotypic Characterization of Streptomycin-Resistant Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolates in Southern China. Microb Drug Resist 2020; 26:766-775. [PMID: 31976809 DOI: 10.1089/mdr.2019.0245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Streptomycin (STR) is the first antibiotic used in the treatment of tuberculosis (TB) and the earliest antituberculosis drug with acquired resistance developed by Mycobacterium tuberculosis. The high prevalence of such resistance in many parts of the world limits its use for treating multidrug-resistant (MDR) TB. The aims of this study are to characterize of mutations in rpsL, rrs, and gidB genes in MDR M. tuberculosis isolates originating from southern China and to investigate possible relationship between mutations and strain genotypes for precise diagnosis and treatment. Sequences of rpsL, rrs, and gidB genes and the resistance profiles were analyzed for 218 MDR M. tuberculosis isolates. Our study showed that 68.35% of MDR M. tuberculosis isolates were resistant to STR and 89.91% of STR-resistant (STRR) isolates were Beijing lineage strains. Mutations were observed in STRR MDR M. tuberculosis isolates at the following rates: 72.48% in rpsL, 36.91% in rrs, and 15.44% in gidB. Compared with the phenotypic data, the combination of mutations in rpsL, rrs, and gidB has sensitivity and specificity of 96.64% and 100.00%, respectively. The most common mutations in STRR isolates were rpsL128,263 and rrs514,1401, of which rpsL128 showed association with Beijing lineage (p < 0.001). It is noteworthy that a1401g mutation was present in rrs, while MDR M. tuberculosis isolates were resistant to both STR and amikacin. Twenty two novel mutations were found in STRR isolates. These findings could be helpful to develop rapid molecular diagnostic methods and understand STR resistance in China for developing TB precision medicine and disturbance of drug-resistant TB transmission.
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Affiliation(s)
- Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Xiaoyin Cai
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Xingshan Cai
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Lingmin Guo
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Wing Wai Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China.,University of Chinese Academy of Sciences (UCAS), Beijing, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, China.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Tuberculosis risk factors and Mycobacterium tuberculosis transmission among HIV-infected patients in Vietnam. Tuberculosis (Edinb) 2019; 115:67-75. [PMID: 30948179 DOI: 10.1016/j.tube.2019.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/18/2018] [Accepted: 02/03/2019] [Indexed: 01/28/2023]
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Thida Oo NA, San LL, Thapa J, Aye KS, Aung WW, Nakajima C, Suzuki Y. Characterization of mutations conferring streptomycin resistance to multidrug-resistant Mycobacterium tuberculosis isolates from Myanmar. Tuberculosis (Edinb) 2018; 111:8-13. [DOI: 10.1016/j.tube.2018.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 04/15/2018] [Accepted: 05/06/2018] [Indexed: 10/17/2022]
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Pang H, Wan K, Wei L. Single-nucleotide polymorphisms related to fluoroquinolone and aminoglycoside resistance in Mycobacterium avium isolates. Infect Drug Resist 2018; 11:515-521. [PMID: 29674849 PMCID: PMC5898888 DOI: 10.2147/idr.s160899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Objective The relationships between fluoroquinolone and aminoglycoside resistance and single-nucleotide polymorphisms (SNPs) in gyrA, gyrB, and rpsL genes were investigated in 95 clinical isolates of Mycobacterium avium from China. Methods Fluoroquinolone and aminoglycoside resistance were determined by the broth microdilution method. GyrA, gyrB, and rpsL were sequenced, SNPs were identified, and the corresponding amino acid mutations were recorded. Results The M. avium isolates displayed high levels of ofloxacin (93.68%), ciprofloxacin (92.63%), and streptomycin (65.26%) resistance. Moxifloxacin (18.95%) and amikacin (2.11%) were highly active against the strains. Fluoroquinolone resistance involving gyrA and gyrB gene mutations was identified. For gyrA, the most frequent SNPs were T→C (71/95, 74.74%), followed by A→G (64/95, 67.37%) and T→C (62/95, 65.26%). The amino acid mutations occurred mainly at Gly2444Asp (GGT→GAT) (20/95, 21.05%), Ala2445Ser (GCC→TCC) (20/95, 21.05%), Ala2447Val (GCC→GTC) (20/95, 21.05%), Val2449Ile (GTC→ATC) (20/95, 21.05%), and Glu2450Gln (GAA→CAA) (20/95, 21.05%). Prominent SNPs in gyrB included A→C (69/95, 72.63%), C→T (51/95, 53.68%), and T→G (29/95, 30.53%), and their amino acid substitutions were Ile2160Val (ATT→GTT) (21/95, 22.11%), Ile2160Met (ATT→ATG) (20/95, 21.05%), and Ile2273Leu (ATC→CTC) (11/95, 11.58%). Among the strains with aminoglycoside resistance, SNPs in rpsL were identified mostly at position G→A (73/95, 76.84%). G→C (21/95, 22.11%) was commonly seen. The amino acid mutations primarily involved Ala1539985Thr (GCC→ACC) (19/95, 20.00%), His1539992Asp (CAC→GAC) (19/95, 20.00%), and Gln-1539983Glu (CAG→GAG) (18/95, 18.95%). Conclusion Our study provides valuable information that could be used for the future diagnosis and treatment of M. avium disease.
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Affiliation(s)
- Hui Pang
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China.,Department of Immunology, Changzhi Medical College, Changzhi, Shanxi, China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lin Wei
- Department of Immunology, Hebei Medical University, Shijiazhuang, Hebei, China
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