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Bonsa Z, Tadesse M, Balay G, Kebede W, Abebe G. Discordance between genotypic and phenotypic methods for the detection of rifampicin and isoniazid resistant Mycobacterium tuberculosis and the correlation with patient treatment outcomes. J Clin Tuberc Other Mycobact Dis 2024; 34:100410. [PMID: 38225941 PMCID: PMC10788488 DOI: 10.1016/j.jctube.2023.100410] [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] [Indexed: 01/17/2024] Open
Abstract
Background Accurate drug susceptibility testing (DST) of Mycobacterium tuberculosis (MTB) is essential for proper patient management. We investigated discordance between genotypic (Xpert MTB/RIF and MTBDRplus) and phenotypic (MGIT 960) methods for the detection of rifampicin (RIF) and isoniazid (INH) resistant MTB and its correlation with patient treatment outcomes in Jimma, Southwest Oromia, Ethiopia. Methods A retrospective study was conducted on 57 stored MTB isolates with known Xpert RIF resistance status (45 RIF resistant and 12 RIF susceptible) at Jimma University Mycobacteriology Research Center from November 2, 2021, to December 28, 2022. We did MTBDRplus and phenotypic DST (using the Mycobacterial Growth Indicator Tube (MGIT) system). The Xpert and MTBDRplus results were compared using phenotypic DST as a reference standard method. The treatment outcome was determined as per national guideline. The discordance between the genotypic and phenotypic DST was calculated using GraphPad software. Results Among the 57 MTB isolates, six (10.5 %) had discordant results between the two DST methods. Xpert yielded five discordant results for RIF when compared with phenotypic DST (kappa coefficient (κ) = 0.76, 95 % confidence interval 0.56-0.96). The MTBDRplus compared with phenotypic DST gave three discordant results for RIF (κ = 0.86, 95 % confidence interval 0.71-1.00) and three for INH (κ = 0.86, 95 % confidence interval 0.70-1.00). Compared with Xpert, MTBDRplus yielded lower discordance with phenotypic DST for RIF. Out of six patients with discordant results, three had unfavorable outcomes while the other three were cured. Of the three patients with unfavorable outcomes, only one patient has received an inappropriate treatment regimen. There was no correlation between unfavorable outcomes and incorrect treatment regimens due to discordant results (Χ2 = 0.404; P = 0.525). Conclusions Discordance between genotypic and phenotypic DST for RIF or INH occurred in 10.5 % of isolates. Only one patient with discordant results has received an inappropriate treatment regimen, resulting in an unfavorable outcome. The impact of parallel use of rapid molecular assay with phenotypic DST on patient treatment outcomes requires further study.
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Affiliation(s)
- Zegeye Bonsa
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
| | - Mulualem Tadesse
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Oromia, Ethiopia
| | - Getu Balay
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
| | - Wakjira Kebede
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Oromia, Ethiopia
| | - Gemeda Abebe
- Mycobacteriology Research Center, Jimma University, Jimma, Oromia, Ethiopia
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Oromia, Ethiopia
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2
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Qadir M, Faryal R, Khan MT, Khan SA, Zhang S, Li W, Wei DQ, Tahseen S, McHugh TD. Phenotype versus genotype discordant rifampicin susceptibility testing in tuberculosis: implications for a diagnostic accuracy. Microbiol Spectr 2024; 12:e0163123. [PMID: 37982632 PMCID: PMC10783056 DOI: 10.1128/spectrum.01631-23] [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: 04/18/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE An accurate diagnosis of drug resistance in clinical isolates is an important step for better treatment outcomes. The current study observed a higher discordance rate of rifampicin resistance on Mycobacteria Growth Indicator Tube (MGIT) drug susceptibility testing (DST) than Lowenstein-Jenson (LJ) DST when compared with the rpoB sequencing. We detected a few novel mutations and their combination in rifampicin resistance isolates that were missed by MGIT DST and may be useful for the better management of tuberculosis (TB) treatment outcomes. Few novel deletions in clinical isolates necessitate the importance of rpoB sequencing in large data sets in geographic-specific locations, especially high-burden countries. We explored the discordance rate on MGIT and LJ, which is important for the clinical management of rifampicin resistance to avoid the mistreatment of drug-resistant TB. Furthermore, MGIT-sensitive isolates may be subjected to molecular methods of diagnosis for further confirmation and treatment options.
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Affiliation(s)
- Mehmood Qadir
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rani Faryal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Tahir Khan
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Sajjad Ahmed Khan
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Shulin Zhang
- School of Medicine, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Weimin Li
- National Tuberculosis Clinical Lab of China, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Dong Qing Wei
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| | - Sabira Tahseen
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London, United Kingdom
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3
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Patel Y, Soni V, Rhee KY, Helmann JD. Mutations in rpoB That Confer Rifampicin Resistance Can Alter Levels of Peptidoglycan Precursors and Affect β-Lactam Susceptibility. mBio 2023; 14:e0316822. [PMID: 36779708 PMCID: PMC10128067 DOI: 10.1128/mbio.03168-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/23/2023] [Indexed: 02/14/2023] Open
Abstract
Bacteria can adapt to stressful conditions through mutations affecting the RNA polymerase core subunits that lead to beneficial changes in transcription. In response to selection with rifampicin (RIF), mutations arise in the RIF resistance-determining region (RRDR) of rpoB that reduce antibiotic binding. These changes can also alter transcription and thereby have pleiotropic effects on bacterial fitness. Here, we studied the evolution of resistance in Bacillus subtilis to the synergistic combination of RIF and the β-lactam cefuroxime (CEF). Two independent evolution experiments led to the recovery of a single rpoB allele (S487L) that was able to confer resistance to RIF and CEF through a single mutation. Two other common RRDR mutations made the cells 32 times more sensitive to CEF (H482Y) or led to only modest CEF resistance (Q469R). The diverse effects of these three mutations on CEF resistance are correlated with differences in the expression of peptidoglycan (PG) synthesis genes and in the levels of two metabolites crucial in regulating PG synthesis, glucosamine-6-phosphate (GlcN-6-P) and UDP-N-acetylglucosamine (UDP-GlcNAc). We conclude that RRDR mutations can have widely varying effects on pathways important for cell wall biosynthesis, and this may restrict the spectrum of mutations that arise during combination therapy. IMPORTANCE Rifampicin (RIF) is one of the most valued drugs in the treatment of tuberculosis. TB treatment relies on a combination therapy and for multidrug-resistant strains may include β-lactams. Mutations in rpoB present a common route for emergence of resistance to RIF. In this study, using B. subtilis as a model, we evaluate the emergence of resistance for the synergistic combination of RIF and the β-lactam cefuroxime (CEF). One clinically relevant rpoB mutation conferred resistance to both RIF and CEF, whereas one other increased CEF sensitivity. We were able to link these CEF sensitivity phenotypes to accumulation of UDP-N-acetylglucosamine (UDP-GlcNAc), which feedback regulates GlmS activity and thereby peptidoglycan synthesis. Further, we found that higher CEF concentrations precluded the emergence of high RIF resistance. Collectively, these results suggest that multidrug treatment regimens may limit the available pathways for the evolution of antibiotic resistance.
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Affiliation(s)
- Yesha Patel
- Department of Microbiology, Cornell University, Ithaca, New York, USA
| | - Vijay Soni
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Kyu Y. Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, New York, USA
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4
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Feng S, Liang L, Shen C, Lin D, Li J, Lyu L, Liang W, Zhong LL, Cook GM, Doi Y, Chen C, Tian GB. A CRISPR-guided mutagenic DNA polymerase strategy for the detection of antibiotic-resistant mutations in M. tuberculosis. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:354-367. [PMID: 35950213 PMCID: PMC9358013 DOI: 10.1016/j.omtn.2022.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/08/2022] [Indexed: 11/26/2022]
Abstract
A sharp increase in multidrug-resistant tuberculosis (MDR-TB) threatens human health. Spontaneous mutation in essential gene confers an ability of Mycobacterium tuberculosis resistance to anti-TB drugs. However, conventional laboratory strategies for identification and prediction of the mutations in this slowly growing species remain challenging. Here, by combining XCas9 nickase and the error-prone DNA polymerase A from M. tuberculosis, we constructed a CRISPR-guided DNA polymerase system, CAMPER, for effective site-directed mutagenesis of drug-target genes in mycobacteria. CAMPER was able to generate mutagenesis of all nucleotides at user-defined loci, and its bidirectional mutagenesis at nick sites allowed editing windows with lengths up to 80 nucleotides. Mutagenesis of drug-targeted genes in Mycobacterium smegmatis and M. tuberculosis with this system significantly increased the fraction of the antibiotic-resistant bacterial population to a level approximately 60- to 120-fold higher than that in unedited cells. Moreover, this strategy could facilitate the discovery of the mutation conferring antibiotic resistance and enable a rapid verification of the growth phenotype-mutation genotype association. Our data demonstrate that CAMPER facilitates targeted mutagenesis of genomic loci and thus may be useful for broad functions such as resistance prediction and development of novel TB therapies.
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5
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Yokobori N, López B, Ritacco V. The host-pathogen-environment triad: Lessons learned through the study of the multidrug-resistant Mycobacterium tuberculosis M strain. Tuberculosis (Edinb) 2022; 134:102200. [PMID: 35339874 DOI: 10.1016/j.tube.2022.102200] [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: 12/30/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
Abstract
Multidrug-resistant tuberculosis is one of the major obstacles that face the tuberculosis eradication efforts. Drug-resistant Mycobacterium tuberculosis clones were initially disregarded as a public health threat, because they were assumed to have paid a high fitness cost in exchange of resistance acquisition. However, some genotypes manage to overcome the impact of drug-resistance conferring mutations, retain transmissibility and cause large outbreaks. In Argentina, the HIV-AIDS epidemics fuelled the expansion of the so-called M strain in the early 1990s, which is responsible for the largest recorded multidrug-resistant tuberculosis cluster of Latin America. The aim of this work is to review the knowledge gathered after nearly three decades of multidisciplinary research on epidemiological, microbiological and immunological aspects of this highly successful strain. Collectively, our results indicate that the successful transmission of the M strain could be ascribed to its unaltered virulence, low Th1/Th17 response, a low fitness cost imposed by the resistance conferring mutations and a high resistance to host-related stress. In the early 2000s, the incident cases due to the M strain steadily declined and stabilized in the latest years. Improvements in the management, diagnosis and treatment of multidrug-resistant tuberculosis along with societal factors such as the low domestic and international mobility of the patients affected by this strain probably contributed to the outbreak containment. This stresses the importance of sustaining the public health interventions to avoid the resurgence of this conspicuous multidrug-resistant strain.
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Affiliation(s)
- Noemí Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
| | - Beatriz López
- Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina.
| | - Viviana Ritacco
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
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Environmental dependence of competitive fitness in rifampin-resistant
rpoB
mutants of
Bacillus subtilis. Appl Environ Microbiol 2022; 88:e0242221. [DOI: 10.1128/aem.02422-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RNA polymerase (RNAP) is a highly conserved macromolecular machine that contributes to the flow of genetic information from genotype to phenotype. In
Bacillus subtilis
, mutations in the
rpoB
gene encoding the β-subunit of RNAP have been shown to alter a number of global phenotypes including growth, utilization of unusual nutrient sources, sporulation, germination, and production of secondary metabolites. In addition, the spectrum of mutations in
rpoB
leading to rifampin resistance (Rif
R
) can change dramatically depending upon the environment to which
B. subtilis
cells or spores are exposed. Rif
R
rpoB
mutations have historically been associated with slower growth and reduced fitness; however, these assessments of fitness were conducted on limited collections of mutants in rich laboratory media that poorly reflect natural environments typically inhabited by
B. subtilis
. Using a novel, deep-sequencing approach in addition to traditional measurements of growth rate, lag time, and pairwise competitions, we demonstrated the competitive advantage of specific
rpoB
alleles differs depending on the growth environment in which they are determined.
IMPORTANCE
Microbial resistance to antibiotics is a growing threat to public health across the world. Historically, resistance to antibiotics has been associated with reduced fitness. A growing body of evidence indicates that resistance to rifampin, a frontline antibiotic used to treat mycobacterial and biofilm-associated infections, may increase fitness given an appropriate environment even in the absence of the selective antibiotic. Here we experimentally confirm this phenomenon by directly comparing the fitness of multiple rifampin-resistant mutants of
Bacillus subtilis
in rich LB medium and an asparagine minimal medium. Our research demonstrates that the fitness cost of rifampin resistance can vary greatly depending upon the environment. This has important implications for understanding how microbes develop antimicrobial resistance in the absence of antibiotic selection.
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Rodríguez-Beltrán É, López GD, Anzola JM, Rodríguez-Castillo JG, Carazzone C, Murcia MI. Heterogeneous fitness landscape cues, pknG low expression, and phthiocerol dimycocerosate low production of Mycobacterium tuberculosis ATCC25618 rpoB S450L in enriched broth. Tuberculosis (Edinb) 2021; 132:102156. [PMID: 34891037 DOI: 10.1016/j.tube.2021.102156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
Multidrug-resistant tuberculosis (isoniazid/rifampin[RIF]-resistant TB) ravages developing countries. Fitness is critical in clinical outcomes. Previous studies on RIF-resistant TB (RR-TB) showed competitive fitness gains and losses, with rpoB-S450L as the most isolated/fit mutation. This study measured virulence/resistance genes, phthiocerol dimycocerosate (PDIM) levels and their relationship with rpoB S450L ATCC25618 RR-TB strain fitness. After obtaining 10 different RR-TB GenoType MTBDRplus 2.0-genotyped isolates (with nontyped, S441, H445 and S450 positions), only one S450L isolate (R9, rpoB-S450L ATCC 25618, RR 1 μg/mL) was observed, with H445Y being the most common. A competitive fitness in vitro assay with wild-type (wt) ATCC 25618: R9 1:1 in 50 mL Middlebrook 7H9/OADC was performed, and generation time (G) in vitro and relative fitness were obtained. mRNA and PDIM were extracted on log and stationary phases. Fitness decreased in rpoB S450L and H445Y strains, with heterogeneous fitness cues in three biological replicas of rpoB-S450L: one high and two low fitness replicas. S450L strain had significant pknG increase. Compared with S450L, wt-rpoB showed increased polyketide synthase ppsA expression and high PDIM peak measured by HPLC-MS in log phase compared to S450L. This contrasts with previously increased PDIM in other RR-TB isolates.
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Affiliation(s)
- Édgar Rodríguez-Beltrán
- MicobacUN Group, Microbiology Department, The National University of Colombia (NUC) School of Medicine, AV CR 30 45-03, Bogotá, D.C, 111321, Colombia
| | - Gerson-Dirceu López
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, CR 1 18A-12, Bogotá, D.C, 111711, Colombia
| | - Juan Manuel Anzola
- Corpogen, CR 4 20-41, Bogotá, D.C, 110311, Colombia; Universidad Central, CR 5 21-38, Bogotá, D.C, 110311, Colombia
| | - Juan Germán Rodríguez-Castillo
- MicobacUN Group, Microbiology Department, The National University of Colombia (NUC) School of Medicine, AV CR 30 45-03, Bogotá, D.C, 111321, Colombia
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, CR 1 18A-12, Bogotá, D.C, 111711, Colombia
| | - Martha I Murcia
- MicobacUN Group, Microbiology Department, The National University of Colombia (NUC) School of Medicine, AV CR 30 45-03, Bogotá, D.C, 111321, Colombia.
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Singh P, Jamal S, Ahmed F, Saqib N, Mehra S, Ali W, Roy D, Ehtesham NZ, Hasnain SE. Computational modeling and bioinformatic analyses of functional mutations in drug target genes in Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:2423-2446. [PMID: 34025934 PMCID: PMC8113780 DOI: 10.1016/j.csbj.2021.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022] Open
Abstract
MycoTRAP-DB, a database of mutations and their impact on normal functionality of protein in M.tb genes. Several secondary mutations were identified with significant impact on protein structure and function. Comprehensive information gives insight for screening of suspected hotspots in advance to combat drug resistant TB.
Tuberculosis (TB) continues to be the leading cause of deaths due to its persistent drug resistance and the consequent ineffectiveness of anti-TB treatment. Recent years witnessed huge amount of sequencing data, revealing mutations responsible for drug resistance. However, the lack of an up-to-date repository remains a barrier towards utilization of these data and identifying major mutations-associated with resistance. Amongst all mutations, non-synonymous mutations alter the amino acid sequence of a protein and have a much greater effect on pathogenicity. Hence, this type of gene mutation is of prime interest of the present study. The purpose of this study is to develop an updated database comprising almost all reported substitutions within the Mycobacterium tuberculosis (M.tb) drug target genes rpoB, inhA, katG, pncA, gyrA and gyrB. Various bioinformatics prediction tools were used to assess the structural and biophysical impacts of the resistance causing non-synonymous single nucleotide polymorphisms (nsSNPs) at the molecular level. This was followed by evaluating the impact of these mutations on binding affinity of the drugs to target proteins. We have developed a comprehensive online resource named MycoTRAP-DB (Mycobacterium tuberculosis Resistance Associated Polymorphisms Database) that connects mutations in genes with their structural, functional and pathogenic implications on protein. This database is accessible at http://139.59.12.92. This integrated platform would enable comprehensive analysis and prioritization of SNPs for the development of improved diagnostics and antimycobacterial medications. Moreover, our study puts forward secondary mutations that can be important for prognostic assessments of drug-resistance mechanism and actionable anti-TB drugs.
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Affiliation(s)
- Pooja Singh
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Salma Jamal
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Faraz Ahmed
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Najumu Saqib
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Seema Mehra
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Waseem Ali
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Deodutta Roy
- Department of Environmental and Occupational Health, Florida International University, Miami 33029, USA
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201301, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110016, India
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9
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le Roux SP, Upton C, Vanker N, Dooley KE. Resistance-Conferring Mycobacterial Mutations and Quantification of Early Bactericidal Activity. Am J Respir Crit Care Med 2021; 203:635-637. [PMID: 33080154 PMCID: PMC7924570 DOI: 10.1164/rccm.202007-2740le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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10
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Hu M, Fu L, Wang B, Xu J, Guo S, Zhao J, Li Y, Chen X, Lu Y. Genetic and Virulence Characteristics of Linezolid and Pretomanid Dual Drug-Resistant Strains Induced from Mycobacterium tuberculosis in vitro. Infect Drug Resist 2020; 13:1751-1761. [PMID: 32606825 PMCID: PMC7297343 DOI: 10.2147/idr.s257145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/16/2020] [Indexed: 01/01/2023] Open
Abstract
Purpose Linezolid (LZD) and pretomanid (PA-824) are promising candidates in regimens for the treatment of drug-resistant tuberculosis. However, research on LZD and PA-824 dual drug-resistant (LPDR) strains is rarely reported. This study aimed to investigate the genotypic and virulence characteristics of LPDR strains. Methods To obtain the LPDR strains (marked as LP or PL strains), we used a two-way induction method, namely, we first induced LZD- or PA-824-resistant mutants from the parental Mycobacterium tuberculosis (MTB) strain H37Rv in vitro, then we obtained the LPDR strains from induction of LZD- or PA-824-resistant mutants. Mutations in rplC, rrl, or ddn and fgd1 were identified in all mutants. To investigate the virulence of these strains, six strains were selected as representative strains, including LZD-resistant strains, PA-824-resistant strains and LPDR strains. We performed the animal survival study as virulence of MTB can be measured as survival time of an animal after being infected. Results We induced 38 mutant strains of LZD and PA-824 mono or dual drug resistance from H37Rv in vitro. The mutation frequency of rplC (C154R) gene in LPDR strains was 100% and 86%, respectively. In the animal survival study, animals infected with different drug-resistant strains survived significantly longer than those infected with H37Rv; animals infected with LPDR strains and PA-824-resistant strains survived similarly and both of which survived significantly shorter than those infected with LZD-resistant strains. Conclusion Our study showed that rplC gene had a high mutation frequency in LPDR strains. The virulence of LPDR strains was similar to PA-824-resistant strains, and the virulence of the LZD-resistant strains was weaker than PA-824-resistant strains.
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Affiliation(s)
- Minghao Hu
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
| | - Lei Fu
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
| | - Bin Wang
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
| | - Jian Xu
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
| | - Shaochen Guo
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
| | - Jiaojie Zhao
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
| | - Yuanyuan Li
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
| | - Xiaoyou Chen
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Yu Lu
- Department of Pharmacology, Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, People's Republic of China
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11
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Olsen RJ, Zhu L, Musser JM. A Single Amino Acid Replacement in Penicillin-Binding Protein 2X in Streptococcus pyogenes Significantly Increases Fitness on Subtherapeutic Benzylpenicillin Treatment in a Mouse Model of Necrotizing Myositis. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1625-1631. [PMID: 32407732 DOI: 10.1016/j.ajpath.2020.04.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/14/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022]
Abstract
Invasive strains of Streptococcus pyogenes with significantly reduced susceptibility to β-lactam antibiotics have been recently described. These reports have caused considerable concern in the international infectious disease, medical microbiology, and public health communities because S. pyogenes has remained universally susceptible to β-lactam antibiotics for 70 years. Virtually all analyzed strains had single amino acid replacements in penicillin-binding protein 2X (PBP2X), a major target of β-lactam antibiotics in pathogenic bacteria. We used isogenic strains to test the hypothesis that a single amino acid replacement in PBP2X conferred a fitness advantage in a mouse model of necrotizing myositis. We determined that when mice were administered intermittent subtherapeutic dosing of benzylpenicillin, the strain with a Pro601Leu amino acid replacement in PBP2X that confers reduced β-lactam susceptibility in vitro was more fit, as assessed by the magnitude of colony-forming units recovered from disease tissue. These data provide important pathogenesis information that bears on this emerging global infectious disease problem.
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Affiliation(s)
- Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Clinical Microbiology Laboratory, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Luchang Zhu
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, Texas; Clinical Microbiology Laboratory, Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
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12
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Nieto Ramirez LM, Quintero Vargas K, Diaz G. Whole Genome Sequencing for the Analysis of Drug Resistant Strains of Mycobacterium tuberculosis: A Systematic Review for Bedaquiline and Delamanid. Antibiotics (Basel) 2020; 9:antibiotics9030133. [PMID: 32209979 PMCID: PMC7148535 DOI: 10.3390/antibiotics9030133] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 11/24/2022] Open
Abstract
Tuberculosis (TB) remains the deadliest Infectious disease worldwide, partially due to the increasing dissemination of multidrug and extensively drug-resistant (MDR/XDR) strains. Drug regimens containing the new anti-TB drugs bedaquiline (BDQ) and delamanid (DLM) appear as a last resort for the treatment of MDR or XDR-TB. Unfortunately, resistant cases to these drugs emerged just one year after their introduction in clinical practice. Early detection of resistant strains to BDQ and DLM is crucial to preserving the effectiveness of these drugs. Here, we present a systematic review aiming to define all available genotypic variants linked to different levels of resistance to BDQ and DLM that have been described through whole genomic sequencing (WGS) and the available drug susceptibility testing methods. During the review, we performed a thorough analysis of 18 articles. BDQ resistance was associated with genetic variants in Rv0678 and atpE, while mutations in pepQ were linked to a low-level of resistance for BDQ. For DLM, mutations in the genes ddn, fgd1, fbiA, and fbiC were found in phenotypically resistant cases, while all the mutations in fbiB were reported only in DLM-susceptible strains. Additionally, WGS analysis allowed the detection of heteroresistance to both drugs. In conclusion, we present a comprehensive panel of gene mutations linked to different levels of drug resistance to BDQ and DLM.
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Affiliation(s)
| | - Karina Quintero Vargas
- Facultad de Ciencias para la Salud, Departamento de Ciencias Básicas, Universidad de Caldas, Manizales 170002, Colombia;
| | - Gustavo Diaz
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali 760031, Colombia;
- Facultad de Ciencias Naturales, Universidad Icesi, Calle 18 No. 122-135, Cali 760031, Colombia
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13
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Zhan L, Wang J, Wang L, Qin C. The correlation of drug resistance and virulence in Mycobacterium tuberculosis. BIOSAFETY AND HEALTH 2020. [DOI: 10.1016/j.bsheal.2020.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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14
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AlMatar M, Var I, Kayar B, Köksal F. Differential Expression of Resistant and Efflux Pump Genes in MDR-TB Isolates. Endocr Metab Immune Disord Drug Targets 2020; 20:271-287. [DOI: 10.2174/1871530319666191009153834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/21/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022]
Abstract
Background:Numerous investigations demonstrate efflux as a worldwide bacterial mode of action which contributes to the resistance of drugs. The activity of antibiotics, which subjects to efflux, can be improved by the combined usage of efflux inhibitors. However, the efflux role to the overall levels of antibiotic resistance of clinical M. tuberculosis isolates is inadequately comprehended and is still disregarded by many.Method:Here, we assessed the contribution of resistant genes associated with isoniazid (INH) and rifampin (R) resistance to the levels of drug resistance in the (27) clinical isolates of MDR-TB. Additionally, the role of the resistance for six putative drug efflux pump genes to the antibiotics was investigated. The level of katG expression was down-regulated in 24/27 (88.88%) of MDR-TB isolates. Of the 27 MDR-TB isolates, inhA, oxyR-ahpC, and rpoB showed either overexpression or up-regulation in 8 (29.62%), 4 (14.81 %), and 24 (88.88%), respectively. Moreover, the efflux pump genes drrA, drrB, efpA, Rv2459, Rv1634, and Rv1250 were overexpressed under INH/RIF plus fresh pomegranate juice (FPJ) stress signifying the efflux pumps contribution to the overall levels of the resistance of MDR-TB isolates.Conclusion:These results displayed that the levels of drug resistance of MDR-TB clinical isolates are due to combination among drug efflux pump and the presence of mutations in target genes, a truth which is often ignored by the specialists of tuberculosis in favour of the almost undoubted significance of drug target- gene mutations for the resistance in M. tuberculosis.
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Affiliation(s)
- Manaf AlMatar
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitusu), Cukurova University, Adana, Turkey
| | - Işıl Var
- Department of Food Engineering, Agricultural Faculty, Cukurova University, Adana, Turkey
| | - Begüm Kayar
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
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15
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Tang Y, Davies R, Petrovska L. Identification of Genetic Features for Attenuation of Two Salmonella Enteritidis Vaccine Strains and Differentiation of These From Wildtype Isolates Using Whole Genome Sequencing. Front Vet Sci 2019; 6:447. [PMID: 31921908 PMCID: PMC6930191 DOI: 10.3389/fvets.2019.00447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/26/2019] [Indexed: 01/10/2023] Open
Abstract
Salmonella Enteritidis is a major cause of salmonellosis worldwide and more than 80% of outbreaks investigated in Europe have been associated with the consumption of poorly cooked eggs or foods containing raw eggs. Vaccination has been proven to be one of the most important measures to control Salmonella Enteritidis infections in poultry farms as it can decrease colonization of the reproductive organs and intestinal tract of laying hens, thereby reducing egg contamination. Differentiation of live vaccine from field or wild type S. Enteritidis isolates in poultry is essential for monitoring of veterinary isolates and targetting control actions. Due to decreasing costs, whole genome sequencing (WGS) is becoming a key tool for characterization of Salmonella isolates, including vaccine strains. Using WGS we described the genetic changes in the live attenuated Salmovac 440 and AviPro SALMONELLA VAC E vaccine strains and developed a method for differentiation from the wildtype S. Enteritidis strains. SNP analysis confirmed that streptomycin resistance was associated with a Lys43Arg missense mutation in the rpsL gene whilst 3 missense mutations in acrB and 1 missense mutation in acrA confer erythromycin sensitivity in AviPro SALMONELLA VAC E. Further mutations Arg242His in purK and Gly236Arg in the hisB gene were related to adenine and histidine dependencies in Salmovac 440. Unique SNPs were used to construct a database of variants for differentiation of vaccine from the wildtype isolates. Two fragments from each vaccine were represented in the database to ensure high accuracy. Each of the two selected Salmovac 440 fragments differed by 6 SNPs from the wildtype and the AviPro SALMONELLA VAC E fragments differed by 4 and 6 SNPs, respectively. CD-hit software was applied to cluster similar fragments that produced the best fit output when searched with SRST2. The developed vaccine differentiation method was tested with 1,253 genome samples including field isolates of Salmovac 440 (n = 51), field isolates of AviPro SALMONELLA VAC E (n = 13), S. Gallinarum (n = 19), S. Pullorum (n = 116), S. Enteritidis (n = 244), S. Typhimurium (n = 810) and achieved 100% sensitivity and specificity.
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Affiliation(s)
- Yue Tang
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
| | | | - Liljana Petrovska
- Department of Bacteriology, Animal and Plant Health Agency, Addlestone, United Kingdom
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16
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Torrea G, Ng KCS, Van Deun A, André E, Kaisergruber J, Ssengooba W, Desmaretz C, Gabriels S, Driesen M, Diels M, Asnong S, Fissette K, Gumusboga M, Rigouts L, Affolabi D, Joloba M, De Jong BC. Variable ability of rapid tests to detect Mycobacterium tuberculosis rpoB mutations conferring phenotypically occult rifampicin resistance. Sci Rep 2019; 9:11826. [PMID: 31413308 PMCID: PMC6694172 DOI: 10.1038/s41598-019-48401-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 08/01/2019] [Indexed: 01/15/2023] Open
Abstract
We compared the ability of commercial and non-commercial, phenotypic and genotypic rapid drug susceptibility tests (DSTs) to detect rifampicin resistance (RR)-conferring ‘disputed’ mutations frequently missed by Mycobacterium Growth Indicator Tube (MGIT), namely L430P, D435Y, L452P, and I491F. Strains with mutation S450L served as positive control while wild-types were used as negative control. Of the 38 mutant strains, 5.7% were classified as RR by MGIT, 16.2% by Trek Sensititre MYCOTB MIC plate, 19.4% by resazurin microtiter plate assay (REMA), 50.0% by nitrate reductase assay (NRA), and 62.2% by microscopic observation direct susceptibility testing (MODS). Reducing MGIT rifampicin concentration to 0.5 µg/ml, and/or increasing incubation time, enhanced detection of disputed mutations from 5.7% to at least 65.7%, particularly for mutation I491F (from 0.0 to 75.0%). Compared with MGIT at standard pre-set time with 0.25 µg/ml ECOFF as breakpoint, we found a statistically significant increase in the ability of MGIT to resolve disputed mutants and WT strains at extended incubation period of 15 and 21 days, with 0.5 µg/ml and 1 µg/ml ECOFF respectively. MODS detected 75.0% of the I491F strains and NRA 62.5%, while it was predictably missed by all molecular assays. Xpert MTB/RIF, Xpert Ultra, and GenoscholarTB-NTM + MDRTB detected all mutations within the 81 bp RR determining region. Only GenoType MTBDRplus version 2 missed mutation L430P in 2 of 11 strains. Phenotypic and genotypic DSTs varied greatly in detecting occult rifampicin resistance. None of these methods detected all disputed mutations without misclassifying wild-type strains.
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Affiliation(s)
- Gabriela Torrea
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Kamela C S Ng
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Armand Van Deun
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Emmanuel André
- Laboratory of Clinical Bacteriology and Mycology, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | | | - Willy Ssengooba
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Christel Desmaretz
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Siemon Gabriels
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Michèle Driesen
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Maren Diels
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sylvie Asnong
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kristina Fissette
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mourad Gumusboga
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Moses Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Bouke C De Jong
- Mycobacteriology Unit, Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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17
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Survival of an epidemic MDR strain of Mycobacterium tuberculosis and its non-prosperous variant within activated macrophages. INFECTION GENETICS AND EVOLUTION 2019; 73:248-254. [PMID: 31077841 DOI: 10.1016/j.meegid.2019.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 11/20/2022]
Abstract
The fitness of a pathogen results from the interaction of multiple factors favoring either epidemiological success or failure. Herein, we studied the performance of the M strain, a highly successful multidrug resistant Mycobacterium tuberculosis genotype, and its non-prosperous variant, the 410 strain, in activated human monocyte-derived macrophages. Both strains showed comparable ability to induce necrotic cell death and to survive in apoptotic macrophages. Of the various macrophage activation conditions tested, none led to an enhanced control of the outbreak strain. The combination of 1,25(OH)2 vitaminD3 and IFN-γ favored significantly the control of the non-prosperous 410 strain. These observations indicate that the ability of the M strain to survive within the hostile intracellular milieu is conserved, and the overall fitness cost paid by this genotype would be low. Our results provide additional evidence on bacterial traits that may have contributed to the epidemiological success of the M strain.
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18
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Xu Z, Zhou A, Wu J, Zhou A, Li J, Zhang S, Wu W, Karakousis PC, Yao YF. Transcriptional Approach for Decoding the Mechanism of rpoC Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant Mycobacterium tuberculosis. Front Microbiol 2018; 9:2895. [PMID: 30555440 PMCID: PMC6283890 DOI: 10.3389/fmicb.2018.02895] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
Multidrug-resistant tuberculosis (TB), defined as TB resistant to the two first-line drugs, isoniazid and rifampin, is a serious challenge to global TB eradication efforts. Although mutations in rpoA or rpoC have been proposed to compensate for this fitness cost due to rpoB mutation in rifampicin-resistant Mycobacterium tuberculosis mutants, whether the compensatory effect exists and the underlying mechanisms of compensation remain unclear. Here, we used RNA sequencing to investigate the global transcriptional profiles of 6 rifampin-resistant clinical isolates with either single mutation in rpoB or dual mutations in rpoB/rpoC, as well as 3 rifampin-susceptible clinical isolates, trying to prove the potential compensatory effect of rpoC by transcriptomic alteration. In rifampin-free conditions, rpoC mutation was associated with M. tuberculosis upregulation of ribosomal protein-coding genes, dysregulation of growth-related essential genes and balancing the expression of arginine and glutamate synthesis-associated genes. Upon rifampin exposure of M. tuberculosis isolates, rpoC mutations were associated with the upregulation of the oxidative phosphorylation machinery, which was inhibited in the rpoB single mutants, as well as stabilization of the expression of rifampin-regulated essential genes and balancing the expression of genes involved in metabolism of sulfur-containing amino acids. Taken together, our data suggest that rpoC mutation may compensate for the fitness defect of rifampicin-resistant M. tuberculosis by altering gene expression in response to rifampin exposure.
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Affiliation(s)
- Zhihong Xu
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aiping Zhou
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiawei Wu
- Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aiwu Zhou
- Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Li
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Shulin Zhang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Petros C Karakousis
- Department of Medicine, Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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19
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Matern WM, Rifat D, Bader JS, Karakousis PC. Gene Enrichment Analysis Reveals Major Regulators of Mycobacterium tuberculosis Gene Expression in Two Models of Antibiotic Tolerance. Front Microbiol 2018; 9:610. [PMID: 29670589 PMCID: PMC5893760 DOI: 10.3389/fmicb.2018.00610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 03/15/2018] [Indexed: 01/10/2023] Open
Abstract
The development of antibiotic tolerance is believed to be a major factor in the lengthy duration of current tuberculosis therapies. In the current study, we have modeled antibiotic tolerance in vitro by exposing Mycobacterium tuberculosis to two distinct stress conditions: progressive hypoxia and nutrient starvation [phosphate-buffered saline (PBS)]. We then studied the bacterial transcriptional response using RNA-seq and employed a bioinformatics approach to identify important transcriptional regulators, which was facilitated by a novel Regulon Enrichment Test (RET). A total of 17 transcription factor (TF) regulons were enriched in the hypoxia gene set and 16 regulons were enriched in the nutrient starvation, with 12 regulons enriched in both conditions. Using the same approach to analyze previously published gene expression datasets, we found that three M. tuberculosis regulons (Rv0023, SigH, and Crp) were commonly induced in both stress conditions and were also among the regulons enriched in our data. These regulators are worthy of further study to determine their potential role in the development and maintenance of antibiotic tolerance in M. tuberculosis following stress exposure.
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Affiliation(s)
- William M Matern
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Dalin Rifat
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Joel S Bader
- Department of Biomedical Engineering and High-Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Petros C Karakousis
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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20
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Campodónico VL, Rifat D, Chuang YM, Ioerger TR, Karakousis PC. Altered Mycobacterium tuberculosis Cell Wall Metabolism and Physiology Associated With RpoB Mutation H526D. Front Microbiol 2018; 9:494. [PMID: 29616007 PMCID: PMC5867343 DOI: 10.3389/fmicb.2018.00494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 03/02/2018] [Indexed: 11/13/2022] Open
Abstract
Background:Mycobacterium tuberculosis (Mtb) rpoB mutations are associated with global metabolic remodeling. However, the net effects of rpoB mutations on Mtb physiology, metabolism and function are not completely understood. Based on previous work, we hypothesized that changes in the expression of cell wall molecules in Mtb mutant RpoB 526D lead to changes in cell wall permeability and to altered resistance to environmental stresses and drugs. Methods: The phenotypes of a fully drug-susceptible clinical strain of Mtb and its paired rifampin-monoresistant, RpoB H526D mutant progeny strain were compared. Results: The rpoB mutant showed altered colony morphology, bacillary length and cell wall thickness, which were associated with increased cell wall permeability and susceptibility to the cell wall detergent sodium dodecyl sulfate (SDS) after exposure to nutrient starvation. Relative to the isogenic rifampin-susceptible strain, the RpoB H526D mutant showed altered bacterial cellular metabolic activity and an eightfold increase in susceptibility to the cell-wall acting drug vancomycin. Conclusion: Our data suggest that RpoB mutation H526D is associated with altered cell wall physiology and resistance to cell wall-related stress. These findings are expected to contribute to an improved understanding of the pathogenesis of drug-resistant M. tuberculosis infections.
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Affiliation(s)
- Victoria L Campodónico
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Dalin Rifat
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yu-Min Chuang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, United States
| | - Petros C Karakousis
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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