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Che Y, Lu Y, Zhu Y, He T, Li X, Gao J, Gao J, Wang X, Liu Z, Tong F. Surveillance of fluoroquinolones resistance in rifampicin-susceptible tuberculosis in eastern China with whole-genome sequencing-based approach. Front Microbiol 2024; 15:1413618. [PMID: 39050625 PMCID: PMC11266052 DOI: 10.3389/fmicb.2024.1413618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Background Leveraging well-established DNA-level drug resistance mechanisms, whole-genome sequencing (WGS) has emerged as a valuable methodology for predicting drug resistance. As the most effective second-line anti-tuberculosis (anti-TB) drugs, fluoroquinoloness (FQs) are generally used to treat multidrug-resistant tuberculosis (MDR-TB, defined as being resistant to resistant to rifampicin and isoniazid) or rifampicin-resistant tuberculosis (RR-TB). However, FQs are also commonly used in the management of other bacterial infections. There are few published data on the rates of FQs resistance among rifampicin-susceptible TB. The prevalence of FQs resistance among TB patients who are rifampicin-susceptible has not been studied in Zhejiang Province, China. The goal of this study was to provide a baseline characterization of the prevalence of FQs resistance, particularly among rifampicin-susceptible TB in Zhejiang Province, China. Methods Based on WGS, we have investigated the prevalence of FQs resistance among rifampicin-susceptible TB in Zhejiang Province. All pulmonary TB patients with positive cultures who were identified in Zhejiang area during TB drug resistance surveillance from 2018 to 2019 have enrolled in this population-based retrospective study. Results The rate of FQs resistance was 4.6% (32/698) among TB, 4.0% (27/676) among rifampicin-susceptible TB, and 22.7% (5/22) among RR-TB. According to WGS, strains that differ within 12 single-nucleotide polymorphisms (SNPs) were considered to be transmission of FQ-resistant strains. Specifically, 3.7% (1/27) of FQs resistance was caused by the transmission of FQs-resistant strains among the rifampicin-susceptible TB and 40.7% (11/27) of FQs resistance was identified as hetero-resistance. Conclusion The prevalence of FQs resistance among TB patients who were rifampicin-susceptible was severe in Zhejiang. The emergence of FQs resistance in TB isolates that are rifampicin-susceptible was mainly caused by the selection of drug-resistant strains. In order to prevent the emergence of FQs resistance, the WGS-based surveillance system for TB should be urgently established, and clinical awareness of the responsible use of FQs for respiratory infections should be enhanced.
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Affiliation(s)
- Yang Che
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Yewei Lu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Yelei Zhu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Tianfeng He
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Junli Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Junshun Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, China
| | - Xiaomeng Wang
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhengwei Liu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Feng Tong
- Institute of Tuberculosis Prevention and Control, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
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Shen Z, Lin L, Zhai Z, Liang J, Chen L, Hao Y, Zhao L. bglG Regulates the Heterogeneity Driven by the Acid Tolerance Response in Lacticaseibacillus paracasei L9. Foods 2023; 12:3971. [PMID: 37959089 PMCID: PMC10650579 DOI: 10.3390/foods12213971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/24/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
The acid tolerance of lactic acid bacteria is crucial for their fermentation and probiotic functions. Acid adaption significantly enhances the acid tolerance of strains, and the phenotypic heterogeneity driven by the acid tolerance response (ATR) contributes to this process by providing a selective advantage in harsh environments. The mechanism of heterogeneity under the ATR is not yet clear, but individual gene expression differences are recognized as the cause. In this study, we observed four heterogeneous subpopulations (viable, injured, dead, and unstained) of Lacticaseibacillus paracasei L9 (L9) induced by acid adaption (pH 5.0, 40 min) using flow cytometry. The viable subpopulation represented a significantly superior acid tolerance to the injured subpopulation or total population. Different subpopulations were sorted and transcriptomic analysis was performed. Five genes were found to be upregulated in the viable subpopulation and downregulated in the injured subpopulation, and bglG (LPL9_RS14735) was identified as having a key role in this process. Using salicin (glucoside)-inducing gene expression and gene insertion mutagenesis, we verified that bglG regulated the heterogeneity of the acid stress response and that the relevant mechanisms might be related to activating hsp20. This study provides new evidence for the mechanism of the ATR and may contribute to the theoretical basis of improving the acid tolerance of Lacticaseibacillus paracasei L9.
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Affiliation(s)
- Zhichao Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China;
| | - Li Lin
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Zhengyuan Zhai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Jingjing Liang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Long Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
| | - Yanling Hao
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China;
| | - Liang Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (Z.S.); (L.L.); (Z.Z.); (J.L.); (L.C.)
- Key Laboratory of Functional Dairy, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China;
- Research Center for Probiotics, China Agricultural University, Sanhe 065200, China
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Zhang S, Chen X, Lin Z, Tan Y, Liang B, Pan Y, Huang M, Su B, Hu X, Xu Y, Li Q. Quantification of Isoniazid-Heteroresistant Mycobacterium tuberculosis Using Droplet Digital PCR. J Clin Microbiol 2023; 61:e0188422. [PMID: 37195177 PMCID: PMC10281145 DOI: 10.1128/jcm.01884-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The quantitative detection of drug-resistance mutations in Mycobacterium tuberculosis (MTB) is critical for determining the drug resistance status of a sample. We developed a drop-off droplet digital PCR (ddPCR) assay targeting all major isoniazid (INH)-resistant mutations. The ddPCR assay consisted of three reactions: reaction A detects mutations at katG S315; reaction B detects inhA promoter mutations; and reaction C detects ahpC promoter mutations. All reactions could quantify 1%-50% of mutants in the presence of the wild-type, ranging from 100 to 50,000 copies/reaction. Clinical evaluation with 338 clinical isolates yielded clinical sensitivity of 94.5% (95% confidence interval [CI] = 89.1%-97.3%) and clinical specificity of 97.6% (95% CI = 94.6%-99.0%) compared with the traditional drug susceptibility testing (DST). Further clinical evaluation using 194 nucleic acid-positive MTB sputum samples revealed clinical sensitivity of 87.8% (95% CI = 75.8%-94.3%) and clinical specificity of 96.5% (95% CI = 92.2%-98.5%) in comparison with DST. All the mutant and heteroresistant samples detected by the ddPCR assay but susceptible by DST were confirmed by combined molecular assays, including Sanger sequencing, mutant-enriched Sanger sequencing and a commercial melting curve analysis-based assay. Finally, the ddPCR assay was used to monitor longitudinally the INH-resistance status and the bacterial load in nine patients undergoing treatment. Overall, the developed ddPCR assay could be an indispensable tool for quantification of INH-resistant mutations in MTB and bacterial loads in patients.
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Affiliation(s)
- Siqi Zhang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaohong Chen
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Zhonghui Lin
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Bin Liang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuying Pan
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingxiang Huang
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Xiaoman Hu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
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Hu Y, Chi Y, Feng X, Yu F, Li H, Shang Y, Pan J, Pang Y. Comparison of the Diagnostic Performance of MeltPro and Next-Generation Sequencing in Determining Fluoroquinolone Resistance in Multidrug-Resistant Tuberculosis Isolates. J Mol Diagn 2023; 25:342-351. [PMID: 37208048 DOI: 10.1016/j.jmoldx.2023.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/20/2022] [Accepted: 02/09/2023] [Indexed: 05/21/2023] Open
Abstract
This study systematically investigated the performance of MeltPro and next-generation sequencing in the diagnosis of fluoroquinolone (FQ) resistance among multidrug-resistant tuberculosis patients and explored the relationship between nucleotide alteration and the level of phenotypic susceptibility to FQs. From March 2019 to June 2020, a feasibility and validation study with both MeltPro and next-generation sequencing was performed in 126 patients with multidrug-resistant tuberculosis. Using phenotypic drug susceptibility testing as the gold standard, 95.3% (82 of 86) of ofloxacin-resistant isolates were identified correctly by MeltPro. In addition, whole-genome sequencing was able to detect 83 phenotypically ofloxacin-resistant isolates. The isolates with an individual gyrB mutation outside the quinolone resistance-determining region (QRDR) had minimum inhibitory concentrations (MICs) of ≤2 μg/mL. Despite showing low MICs close to the breakpoint for isolates carrying only gyrA_Ala90Val, the combined mutation gyrB_Asp461Asn caused the ofloxacin MIC to be eight higher than that obtained in Mycobacterium tuberculosis (MTB) isolates with the Ala90Val mutation alone (median, 32 μg/mL; P = 0.038). Heteroresistance was observed in 12 of 88 isolates harboring mutations in the QRDRs. In conclusion, our data show that MeltPro and the whole-genome sequencing assay correctly can identify FQ resistance caused by mutations in the gyrA QRDR. The combined gyrB_Asp461Asn mutation may significantly decrease in vitro FQ susceptibility of MTB isolates with low-level-resistance-associated gyrA mutations.
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Yuqing Chi
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xin Feng
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Fengping Yu
- Tuberculosis Reference Laboratory, Chongqing Municipal Institute of Tuberculosis, Chongqing, China
| | - Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Junhua Pan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
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Wu SH, Xiao YX, Hsiao HC, Jou R. Development and Assessment of a Novel Whole-Gene-Based Targeted Next-Generation Sequencing Assay for Detecting the Susceptibility of Mycobacterium tuberculosis to 14 Drugs. Microbiol Spectr 2022; 10:e0260522. [PMID: 36255328 PMCID: PMC9769975 DOI: 10.1128/spectrum.02605-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as an alternative method for detecting drug-resistant tuberculosis (DR-TB). To provide comprehensive drug susceptibility information and to address mutations missed by available commercial molecular diagnostics, we developed and evaluated a tNGS panel with 22 whole-gene targets using the Ion Torrent platform to predict drug resistance to 14 drugs, namely, rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide (PZA), moxifloxacin (MFX), levofloxacin (LFX), amikacin (AMK), capreomycin (CM), kanamycin (KM), streptomycin (SM), bedaquiline (BDQ), clofazimine (CFZ), linezolid (LZD), and delamanid (DLM). We selected 50 and 35 Mycobacterium tuberculosis isolates with various DR profiles as the training set and the challenge set, respectively. Comparative variant analyses of the DR genes were performed using Sanger sequencing and whole-genome sequencing (WGS). Phenotypic drug susceptibility testing (pDST) results were used as gold standards. Regarding the limit of detection, the tNGS assay detected 2.9 to 3.8% minority variants in 4% mutant mixtures. The sensitivity and specificity of tNGS were 97.0% (95% confidence interval [CI] = 93.1 to 98.7%) and 99.1% (95% CI = 97.7 to 99.7%), respectively. The concordance of tNGS with pDST was 98.5% (95% CI = 97.2 to 99.2%), which was comparable to that of WGS (98.7%, 95% CI = 97.4 to 99.3%) and better than that of Sanger sequencing (96.9%, 95% CI = 95.3 to 98.0%). The agreement between tNGS and pDST was almost perfect for RIF, INH, EMB, MFX, LFX, AMK, CM, KM, SM, BDQ, and LZD (kappa value = 0.807 to 1.000) and substantial for PZA (kappa value = 0.791). Our customized novel whole-gene-based tNGS panel is highly consistent with pDST and WGS for comprehensive and accurate prediction of drug resistance in a strengthened and streamlined DR-TB laboratory program. IMPORTANCE We developed and validated a tNGS assay that was the first to target 22 whole genes instead of regions of drug resistance genes and comprehensively detected susceptibility to 14 anti-TB drugs, with great flexibility to include new or repurposed drugs. Notably, we demonstrated that our custom-designed Ion AmpliSeq TB research panel platform had high concordance with pDST and could significantly reduce turnaround time (by approximately 70%) to meet a clinically actionable time frame. Our tNGS assay is a promising DST solution for providing needed clinical information for precision medicine-guided therapies for DR-TB and allows the rollout of active pharmacovigilance.
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Affiliation(s)
- Sheng-Han Wu
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Xin Xiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hseuh-Chien Hsiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
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Narang A, Marras SAE, Kurepina N, Chauhan V, Shashkina E, Kreiswirth B, Varma-Basil M, Vinnard C, Subbian S. Ultrasensitive Detection of Multidrug-Resistant Mycobacterium tuberculosis Using SuperSelective Primer-Based Real-Time PCR Assays. Int J Mol Sci 2022; 23:ijms232415752. [PMID: 36555395 PMCID: PMC9779475 DOI: 10.3390/ijms232415752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of drug-resistant tuberculosis is a significant global health issue. The presence of heteroresistant Mycobacterium tuberculosis is critical to developing fully drug-resistant tuberculosis cases. The currently available molecular techniques may detect one copy of mutant bacterial genomic DNA in the presence of about 1-1000 copies of wild-type M. tuberculosis DNA. To improve the limit of heteroresistance detection, we developed SuperSelective primer-based real-time PCR assays, which, by their unique assay design, enable selective and exponential amplification of selected point mutations in the presence of abundant wild-type DNA. We designed SuperSelective primers to detect genetic mutations associated with M. tuberculosis resistance to the anti-tuberculosis drugs isoniazid and rifampin. We evaluated the efficiency of our assay in detecting heteroresistant M. tuberculosis strains using genomic DNA isolated from laboratory strains and clinical isolates from the sputum of tuberculosis patients. Results show that our assays detected heteroresistant mutations with a specificity of 100% in a background of up to 104 copies of wild-type M. tuberculosis genomic DNA, corresponding to a detection limit of 0.01%. Therefore, the SuperSelective primer-based RT-PCR assay is an ultrasensitive tool that can efficiently diagnose heteroresistant tuberculosis in clinical specimens and contributes to understanding the drug resistance mechanisms. This approach can improve the management of antimicrobial resistance in tuberculosis and other infectious diseases.
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Affiliation(s)
- Anshika Narang
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Salvatore A. E. Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Correspondence: (S.A.E.M.); (S.S.)
| | | | - Varsha Chauhan
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110021, India
| | | | | | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110021, India
| | | | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Correspondence: (S.A.E.M.); (S.S.)
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Zheng Y, Xia H, Bao X, Zhao B, He P, Zhao Y. Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium Tuberculosis by Droplet Digital PCR. Infect Drug Resist 2022; 15:6245-6254. [PMID: 36329987 PMCID: PMC9624153 DOI: 10.2147/idr.s381097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022] Open
Abstract
Purpose The drug resistance of Mycobacterium tuberculosis constitutes a major public health threat. Existing approaches make it challenging to detect low levels of drug-resistant TB, also known as heteroresistance (HR), in a population. The recently found droplet digital PCR (ddPCR) is a sensitive method for determining the precise amount of nucleic acid in a sample. We used ddPCR to test the Mycobacterium tuberculosis heteroresistance because it delivers more exact quantitative data without the need for a reference curve. Patients and Methods A TaqMan-MGB probe mutation detection assay was developed in order to determine the mutant and wild-type sequences of the isoniazid resistance katG (315) gene. We produced heteroresistant MTB combinations, which were subsequently identified by ddPCR, qPCR, and MeltPro/INH. In addition, 21 clinical sputum samples with positive smears were used to validate each method’s capacity to determine HR in sputum. Results We discovered that ddPCR can detect mutant sequences in as few as 0.01% of a combination. DeepMelt TB/INH, which is less sensitive in comparison, cannot detect HR with high resolution and requires a mutation rate of 50% to identify. qPCR likewise has a high resolution of 0.02%, but unlike ddPCR, it cannot determine the exact number of mutations. Our assay is applicable to sputum as well. ddPCR found a katG 315 substitution in two sputums with extremely low values of HR (0.26% and 0.14%). In 21 samples of clinical sputum, the HR prevalence of INH was 9.5%. Conclusion This work demonstrates that a well-designed ddPCR HR detection test can detect low levels of HR with high accuracy and consistency and gives new information for the clinical diagnosis of drug resistance.
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Affiliation(s)
- Yang Zheng
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xia
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xundi Bao
- Laboratory Department, Anhui Chest Hospital, Anhui, People’s Republic of China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Ping He
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China,Correspondence: Yanlin Zhao, National Center for TB Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District,Beijing, 102206, People’s Republic of China, Tel +86-10-58900517, Fax +86-10-58900556, Email
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Singh A, Zhao X, Drlica K. Fluoroquinolone heteroresistance, antimicrobial tolerance, and lethality enhancement. Front Cell Infect Microbiol 2022; 12:938032. [PMID: 36250047 PMCID: PMC9559723 DOI: 10.3389/fcimb.2022.938032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
With tuberculosis, the emergence of fluoroquinolone resistance erodes the ability of treatment to interrupt the progression of MDR-TB to XDR-TB. One way to reduce the emergence of resistance is to identify heteroresistant infections in which subpopulations of resistant mutants are likely to expand and make the infections fully resistant: treatment modification can be instituted to suppress mutant enrichment. Rapid DNA-based detection methods exploit the finding that fluoroquinolone-resistant substitutions occur largely in a few codons of DNA gyrase. A second approach for restricting the emergence of resistance involves understanding fluoroquinolone lethality through studies of antimicrobial tolerance, a condition in which bacteria fail to be killed even though their growth is blocked by lethal agents. Studies with Escherichia coli guide work with Mycobacterium tuberculosis. Lethal action, which is mechanistically distinct from blocking growth, is associated with a surge in respiration and reactive oxygen species (ROS). Mutations in carbohydrate metabolism that attenuate ROS accumulation create pan-tolerance to antimicrobials, disinfectants, and environmental stressors. These observations indicate the existence of a general death pathway with respect to stressors. M. tuberculosis displays a variation on the death pathway idea, as stress-induced ROS is generated by NADH-mediated reductive stress rather than by respiration. A third approach, which emerges from lethality studies, uses a small molecule, N-acetyl cysteine, to artificially increase respiration and additional ROS accumulation. That enhances moxifloxacin lethality with M. tuberculosis in culture, during infection of cultured macrophages, and with infection of mice. Addition of ROS stimulators to fluoroquinolone treatment of tuberculosis constitutes a new direction for suppressing the transition of MDR-TB to XDR-TB.
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Affiliation(s)
- Amit Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- *Correspondence: Amit Singh, ; Karl Drlica,
| | - Xilin Zhao
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China
| | - Karl Drlica
- Public Health Research Institute and Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers University, Newark, NJ, United States
- *Correspondence: Amit Singh, ; Karl Drlica,
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Zhang Y, Jiang Y, Yu C, Li J, Shen X, Pan Q, Shen X. Whole-genome sequencing for surveillance of fluoroquinolone resistance in rifampicin-susceptible tuberculosis in a rural district of Shanghai: A 10-year retrospective study. Front Public Health 2022; 10:990894. [PMID: 36187694 PMCID: PMC9521709 DOI: 10.3389/fpubh.2022.990894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 08/19/2022] [Indexed: 01/26/2023] Open
Abstract
Background Fluoroquinolones (FQs) are the most important second-line anti-tuberculosis (anti-TB) drugs, primarily used for the treatment of multidrug- or rifampicin-resistant TB (MDR/RR-TB). However, FQs are also commonly used to treat other bacterial infections. There are few published data on the rates of FQ resistance among rifampicin-susceptible TB. Methods We used whole-genome sequencing (WGS) to determine the prevalence of FQ resistance among rifampicin-susceptible TB in a rural district of Shanghai. This was a population-based retrospective study of all culture-positive pulmonary TB patients diagnosed in the Chongming district of Shanghai, China during 2009-2018. Results The rate of FQ resistance was 8.4% (29/345) among TB, 6.2% (20/324) among rifampicin-susceptible TB, and 42.9% (9/21) among MDR/RR-TB. Transmission of FQ-resistant strains was defined as strains differing within 12 single-nucleotide polymorphisms (SNPs) based on WGS. Among the rifampicin-susceptible TB, 20% (4/20) of FQ resistance was caused by the transmission of FQ-resistant strains and 45% (9/20) of FQ resistance was identified as hetero-resistance. Conclusions The prevalence of FQ resistance in rifampicin-susceptible TB was higher than expected in Shanghai. Both the transmission and the selection of drug-resistant strains drive the emergence of FQ resistance in rifampicin-susceptible TB isolates. Therefore, the WGS-based surveillance system for TB should be urgently established and the clinical awareness of the rational use of FQs for respiratory infections should be enhanced to prevent the premature occurrence of FQ resistance.
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Affiliation(s)
- Yangyi Zhang
- Division of Tuberculosis and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China,Shanghai Institutes of Preventive Medicine, Shanghai, China,Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - Yuan Jiang
- Division of Tuberculosis and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China,Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Chenlei Yu
- Division of Tuberculosis and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China,Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Jing Li
- Division of Tuberculosis and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China,Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Xuhui Shen
- Division of Tuberculosis and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China,Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Qichao Pan
- Division of Tuberculosis and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China,Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Xin Shen
- Division of Tuberculosis and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China,Shanghai Institutes of Preventive Medicine, Shanghai, China,*Correspondence: Xin Shen
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10
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Ye M, Yuan W, Molaeipour L, Azizian K, Ahmadi A, Kouhsari E. Antibiotic heteroresistance in Mycobacterium tuberculosis isolates: a systematic review and meta-analysis. Ann Clin Microbiol Antimicrob 2021; 20:73. [PMID: 34645463 PMCID: PMC8513340 DOI: 10.1186/s12941-021-00478-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) is responsible for tuberculosis; that continues to be a public health threat across the globe. Furthermore, increasing heteroresistance (HR)-the presence of resistant and susceptible isolates among MTB strains- has been reported from around the world. This phenomenon can lead to full resistance development and treatment failure. METHODS We systematically searched the relevant studies in PubMed, Scopus, and Embase (Until October 21, 2020). The study outcomes revealed the weighted pooled prevalence of antibiotic HR in MTB isolates with subgroup analysis by year, quality of study, and heteroresistance detection method. RESULTS A total of 38 studies which had investigated MTB isolates were included in the meta-analysis. Geographically, the highest number of studies were reported from Asia (n = 24), followed by Africa (n = 5). Nineteen studies reported HR to isoniazid, with a weighted pooled prevalence of 5% (95% CI 0-12) among 11,761 MTB isolates. Also, there is no important trend for the subgroup analysis by the study period (2001-2014 vs 2015-2017 vs 2018-2020). HR to rifampin was reported in 17 studies, with a weighted pooled prevalence of 7% (95% CI 2-14) among 3782 MTB isolates. HR to fluoroquinolone and ethambutol were reported in 12 and 4 studies, respectively, with weighted pooled prevalence of 10% and 1% among 2153 and 1509 MTB isolates, correspondingly. CONCLUSION Based on our analysis, HR in MTB isolates with different frequency rate is present worldwide. Thus, the selection of appropriate and reliable methods for HR detection is crucial for TB eradication.
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Affiliation(s)
- Mao Ye
- Department of Pharmacy, Clinical Pharmaceutics Room, Sichuan Science City Hospital, Mianyang, 621000, China
| | - Wen Yuan
- Sichuan College of Traditional Chinese Medicine, Mianyang, 621000, China
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Khalil Azizian
- Department of Clinical Microbiology, Sirjan School of Medical Sciences, P.O. Box 78169-16338, Sirjan, Iran.
| | - Alireza Ahmadi
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran.
- Laboratory Sciences Research Center, Faculty of Paramedical Sciences, Golestan University of Medical Sciences, Negative Floor 1, Gorgan-Sari Road, P.O. Box: 4918936316, Gorgan, Golestan Province, Iran.
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11
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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12
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Detection of Pyrazinamide Heteroresistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:e0072021. [PMID: 34181476 PMCID: PMC8370246 DOI: 10.1128/aac.00720-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Heteroresistance is defined as the coexistence of both susceptible and resistant bacteria in a bacterial population. Previously published data show that it may occur in 9 to 57% of Mycobacterium tuberculosis isolates for various drugs. Pyrazinamide (PZA) is an important first-line drug used for treatment of both drug-susceptible and PZA-susceptible multidrug-resistant TB. Clinical PZA resistance is defined as a proportion of resistant bacteria in the isolate exceeding 10%, when the drug is no longer considered clinically effective. The ability of traditional drug susceptibility testing techniques to detect PZA heteroresistance has not yet been evaluated. The aim of this study was to compare the capacity of Bactec MGIT 960, Wayne's test, and whole-genome sequencing (WGS) to detect PZA-resistant subpopulations in bacterial suspensions prepared with different proportions of mutant strains. Both Bactec MGIT 960 and WGS were able to detect the critical level of 10% PZA heteroresistance, whereas Wayne's test failed to do so, with the latter falsely reporting highly resistant samples as PZA susceptible. Failure to detect drug-resistant subpopulations may lead to inadvertently weak treatment regimens if ineffective drugs are included, with the risk of treatment failure with the selective growth of resistant subpopulations. We need clinical awareness of heteroresistance as well as evaluation of new diagnostic tools for their capacity to detect heteroresistance in TB.
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13
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Alame Emane AK, Guo X, Takiff HE, Liu S. Highly transmitted M. tuberculosis strains are more likely to evolve MDR/XDR and cause outbreaks, but what makes them highly transmitted? Tuberculosis (Edinb) 2021; 129:102092. [PMID: 34102584 DOI: 10.1016/j.tube.2021.102092] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022]
Abstract
Multi-Drug-Resistant strains of Mycobacterium tuberculosis (MDR-TB) are a serious obstacle to global TB eradication. While most MDR-TB strains are infrequently transmitted, a few cause large transmission clusters that contribute substantially to local MDR-TB burdens. Here we examine whether the known mutations in these strains can explain their success. Drug resistance mutations differ in fitness costs and strains can also acquire compensatory mutations (CM) to restore fitness, but some highly transmitted MDR strains have no CM. The acquisition of resistance mutations that maintain high transmissibility seems to occur by chance and are more likely in strains that are intrinsically highly transmitted and cause many cases. Modern Beijing lineage strains have caused several large outbreaks, but MDR outbreaks are also caused by ancient Beijing and lineage 4 strains, suggesting the lineage is less important than the characteristics of the individual strain. The development of fluoroquinolone resistance appears to represent another level of selection, in which strains must surmount unknown fitness costs of gyrA mutations. The genetic determinants of high transmission are poorly defined but may involve genes encoding proteins involved in molybdenum acquisition and the Esx systems. In addition, strains eliciting lower cytokine responses and producing more caseating granulomas may have advantages for transmission. Successful MDR/XDR strains generally evolve from highly transmitted drug sensitive parent strains due to selection pressures from deficiencies in local TB control programs. Until TB incidence is considerably reduced, there will likely be highly transmitted strains that develop resistance to any new antibiotic.
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Affiliation(s)
- Amel Kevin Alame Emane
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Xujun Guo
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Howard E Takiff
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China; Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, 28 Rue du Dr Roux, Paris, 75015, France; Laboratorio de Genética Molecular, CMBC, IVIC, Km. 11 Carr. Panamericana, Caracas, Venezuela.
| | - Shengyuan Liu
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
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14
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Maruri F, Guo Y, Blackman A, van der Heijden YF, Rebeiro PF, Sterling TR. Resistance-Conferring Mutations on Whole-Genome Sequencing of Fluoroquinolone-resistant and -Susceptible Mycobacterium tuberculosis Isolates: A Proposed Threshold for Identifying Resistance. Clin Infect Dis 2021; 72:1910-1918. [PMID: 32348473 PMCID: PMC8315129 DOI: 10.1093/cid/ciaa496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Fluoroquinolone resistance in Mycobacterium tuberculosis (Mtb) is conferred by DNA gyrase mutations, but not all fluoroquinolone-resistant Mtb isolates have mutations detected. The optimal allele frequency threshold to identify resistance-conferring mutations by whole-genome sequencing is unknown. METHODS Phenotypically ofloxacin-resistant and lineage-matched ofloxacin-susceptible Mtb isolates underwent whole-genome sequencing at an average coverage depth of 868 reads. Polymorphisms within the quinolone-resistance-determining region (QRDR) of gyrA and gyrB were identified. The allele frequency threshold using the Genome Analysis Toolkit pipeline was ~8%; allele-level data identified the predominant variant allele frequency and mutational burden (ie, sum of all variant allele frequencies in the QRDR) in gyrA, gyrB, and gyrA + gyrB for each isolate. Receiver operating characteristic (ROC) curves assessed the optimal measure of allele frequency and potential thresholds for identifying phenotypically resistant isolates. RESULTS Of 42 ofloxacin-resistant Mtb isolates, area under the ROC curve (AUC) was highest for predominant variant allele frequency, so that measure was used to evaluate optimal mutation detection thresholds. AUCs for 8%, 2.5%, and 0.8% thresholds were 0.8452, 0.9286, and 0.9069, respectively. Sensitivity and specificity were 69% and 100% for 8%, 86% and 100% for 2.5%, 91% and 91% for 0.8%. The sensitivity of the 2.5% and 0.8% thresholds were significantly higher than the 8% threshold (P = .016 and .004, respectively) but not significantly different between one another (P = .5). CONCLUSIONS A predominant mutation allele frequency threshold of 2.5% had the highest AUC for detecting DNA gyrase mutations that confer ofloxacin resistance, and was therefore the optimal threshold.
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Affiliation(s)
- Fernanda Maruri
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yan Guo
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Amondrea Blackman
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yuri F van der Heijden
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- The Aurum Institute, Johannesburg, South Africa
| | - Peter F Rebeiro
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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15
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Cao Y, Parmar H, Gaur RL, Lieu D, Raghunath S, Via N, Battaglia S, Cirillo DM, Denkinger C, Georghiou S, Kwiatkowski R, Persing D, Alland D, Chakravorty S. Xpert MTB/XDR: a 10-Color Reflex Assay Suitable for Point-of-Care Settings To Detect Isoniazid, Fluoroquinolone, and Second-Line-Injectable-Drug Resistance Directly from Mycobacterium tuberculosis-Positive Sputum. J Clin Microbiol 2021; 59:e02314-20. [PMID: 33298611 PMCID: PMC8106700 DOI: 10.1128/jcm.02314-20] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/22/2020] [Indexed: 11/20/2022] Open
Abstract
We describe the design, development, analytical performance, and a limited clinical evaluation of the 10-color Xpert MTB/XDR assay (CE-IVD only, not for sale in the United States). This assay is intended as a reflex test to detect resistance to isoniazid (INH), fluoroquinolones (FLQ), ethionamide (ETH), and second-line injectable drugs (SLIDs) in unprocessed sputum samples and concentrated sputum sediments which are positive for Mycobacterium tuberculosis The Xpert MTB/XDR assay simultaneously amplifies eight genes and promoter regions in M. tuberculosis and analyzes melting temperatures (Tm s) using sloppy molecular beacon (SMB) probes to identify mutations associated with INH, FLQ, ETH, and SLID resistance. Results can be obtained in under 90 min using 10-color GeneXpert modules. The assay can differentiate low- versus high-level resistance to INH and FLQ as well as cross-resistance versus individual resistance to SLIDs by identifying mutation-specific Tm s or Tm patterns generated by the SMB probes. The assay has a limit of detection comparable to that of the Xpert MTB/RIF assay and successfully detected 16 clinically significant mutations in a challenge set of clinical isolate DNA. In a clinical study performed at two sites with 100 sputum and 214 clinical isolates, the assay showed a sensitivity of 94% to 100% and a specificity of 100% for all drugs except for ETH compared to that of sequencing. The sensitivity and specificity were in the same ranges as those of phenotypic drug-susceptibility testing. Used in combination with a primary tuberculosis diagnostic test, this assay should expand the capacity for detection of drug-resistant tuberculosis near the point of care.
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Affiliation(s)
- Yuan Cao
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Heta Parmar
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | | | | | | | - Nova Via
- Cepheid Inc., Sunnyvale, California, USA
| | | | | | | | | | | | | | - David Alland
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Soumitesh Chakravorty
- New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
- Cepheid Inc., Sunnyvale, California, USA
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16
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Molecular Evaluation of Fluoroquinolone Resistance in Serial Mycobacterium tuberculosis Isolates from Individuals Diagnosed with Multidrug-Resistant Tuberculosis. Antimicrob Agents Chemother 2020; 65:AAC.01663-20. [PMID: 33106264 DOI: 10.1128/aac.01663-20] [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: 07/31/2020] [Accepted: 10/20/2020] [Indexed: 11/20/2022] Open
Abstract
Fluoroquinolones (FQ) are crucial components of multidrug-resistant tuberculosis (MDR TB) treatment. Differing levels of resistance are associated with specific mutations within the quinolone-resistance-determining region (QRDR) of gyrA We sequenced the QRDR from serial isolates of MDR TB patients in the Preserving Effective TB Treatment Study (PETTS) with baseline FQ resistance (FQR) or acquired FQ resistance (FQACQR) using an Ion Torrent Personal Genome Machine (PGM) to a depth of 10,000× and reported single nucleotide polymorphisms in ≥1% of reads. FQR isolates harbored 15 distinct alleles with 1.3 (maximum = 6) on average per isolate. Eighteen alleles were identified in FQACQR isolates with an average of 1.6 (maximum = 9) per isolate. Isolates from 78% of FQACQR individuals had mutant alleles identified within 6 months of treatment initiation. Asp94Gly was the predominant allele in the initial FQ-resistant isolates followed by Ala90Val. Seventy-seven percent (36/47) of FQACQR group patients had isolates with FQ resistance alleles prior to changes to the FQ component of their treatment. Unlike the individuals treated initially with other FQs, none of the 21 individuals treated initially with levofloxacin developed genotypic or phenotypic FQ resistance, although country of residence was likely a contributing factor since 69% of these individuals were from a single country. Initial detection of phenotypic resistance and genotypic resistance occurred simultaneously for most; however, phenotypic resistance occurred earlier in isolates harboring mixtures of alleles of very low abundance (<1% of reads), whereas genotypic resistance often occurred earlier for alleles associated with low-level resistance. Understanding factors influencing acquisition and evolution of FQ resistance could reveal strategies for improved treatment success.
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17
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Herricks T, Donczew M, Mast FD, Rustad T, Morrison R, Sterling TR, Sherman DR, Aitchison JD. ODELAM, rapid sequence-independent detection of drug resistance in isolates of Mycobacterium tuberculosis. eLife 2020; 9:56613. [PMID: 32401195 PMCID: PMC7263823 DOI: 10.7554/elife.56613] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/12/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial-resistant Mycobacterium tuberculosis (Mtb) causes over 200,000 deaths each year. Current assays of antimicrobial resistance need knowledge of mutations that confer drug resistance, or long periods of culture time to test growth under drug pressure. We present ODELAM (One-cell Doubling Evaluation of Living Arrays of Mycobacterium), a time-lapse microscopy-based method that observes individual cells growing into microcolonies. ODELAM enables rapid quantitative measures of growth kinetics in as little as 30 hrs under a wide variety of environmental conditions. We demonstrate ODELAM’s utility by identifying ofloxacin resistance in cultured clinical isolates of Mtb and benchmark its performance with standard minimum inhibitory concentration (MIC) assays. ODELAM identified ofloxacin heteroresistance and the presence of drug resistant colony forming units (CFUs) at 1 per 1000 CFUs in as little as 48 hrs. ODELAM is a powerful new tool that can rapidly evaluate Mtb drug resistance in a laboratory setting.
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Affiliation(s)
- Thurston Herricks
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Magdalena Donczew
- Department of Microbiology, University of Washington, Seattle, United States
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Tige Rustad
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Robert Morrison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States
| | - Timothy R Sterling
- Division of Infectious Disease, Department of Medicine, Vanderbilt University Medical Center, Nashville, United States
| | - David R Sherman
- Department of Microbiology, University of Washington, Seattle, United States
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, United States.,Department of Pediatrics, University of Washington, Seattle, United States
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18
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How Well Do Routine Molecular Diagnostics Detect Rifampin Heteroresistance in Mycobacterium tuberculosis? J Clin Microbiol 2019; 57:JCM.00717-19. [PMID: 31413081 PMCID: PMC6812990 DOI: 10.1128/jcm.00717-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/09/2019] [Indexed: 11/20/2022] Open
Abstract
Rifampin heteroresistance—where rifampin-resistant and -susceptible tuberculosis (TB) bacilli coexist—may result in failed standard TB treatment and potential spread of rifampin-resistant strains. The detection of rifampin heteroresistance in routine rapid diagnostic tests (RDTs) allows for patients to receive prompt and effective multidrug-resistant-TB treatment and may improve rifampin-resistant TB control. Rifampin heteroresistance—where rifampin-resistant and -susceptible tuberculosis (TB) bacilli coexist—may result in failed standard TB treatment and potential spread of rifampin-resistant strains. The detection of rifampin heteroresistance in routine rapid diagnostic tests (RDTs) allows for patients to receive prompt and effective multidrug-resistant-TB treatment and may improve rifampin-resistant TB control. The limit of detection (LOD) of rifampin heteroresistance for phenotypic drug susceptibility testing by the proportion method is 1% and, yet, is insufficiently documented for RDTs. We, therefore, aimed to determine, for the four RDTs (XpertMTB/RIF, XpertMTB/RIF Ultra, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII), the LOD per probe and mutation, validated by CFU counting and targeted deep sequencing (Deeplex-MycTB). We selected one rifampin-susceptible and four rifampin-resistant strains, with mutations D435V, H445D, H445Y, and S450L, respectively, mixed them in various proportions in triplicate, tested them with each RDT, and determined the LODs per mutation type. Deeplex-MycTB revealed concordant proportions of the minority resistant variants in the mixtures. The Deeplex-MycTB-validated LODs ranged from 20% to 80% for XpertMTB/RIF, 20% to 70% for Xpert Ultra, 5% to 10% for GenoTypeMTBDRplusv2.0, and 1% to 10% for GenoscholarNTM+MDRTBII for the different mutations. Deeplex-MycTB, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII provide explicit information on rifampin heteroresistance for the most frequently detected mutations. Classic Xpert and Ultra report rifampin heteroresistance as rifampin resistance, while Ultra may denote rifampin heteroresistance through “mixed patterns” of wild-type and mutant melt probe, melt peak temperatures. Overall, our findings inform end users that the threshold for reporting resistance in the case of rifampin heteroresistance is the highest for Classic Xpert and Ultra to resolve phenotypic and genotypic discordant rifampin-resistant TB results.
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19
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Rigouts L, Miotto P, Schats M, Lempens P, Cabibbe AM, Galbiati S, Lampasona V, de Rijk P, Cirillo DM, de Jong BC. Fluoroquinolone heteroresistance in Mycobacterium tuberculosis: detection by genotypic and phenotypic assays in experimentally mixed populations. Sci Rep 2019; 9:11760. [PMID: 31409849 PMCID: PMC6692311 DOI: 10.1038/s41598-019-48289-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 08/01/2019] [Indexed: 12/19/2022] Open
Abstract
Heteroresistance - the simultaneous presence of drug-susceptible and -resistant organisms - is common in Mycobacterium tuberculosis. In this study, we aimed to determine the limit of detection (LOD) of genotypic assays to detect gatifloxacin-resistant mutants in experimentally mixed populations. A fluoroquinolone-susceptible M. tuberculosis mother strain (S) and its in vitro selected resistant daughter strain harbouring the D94G mutation in gyrA (R) were mixed at different ratio’s. Minimum inhibitory concentrations (MICs) against gatifloxacin were determined, while PCR-based techniques included: line probe assays (Genotype MTBDRsl and GenoScholar-FQ + KM TB II), Sanger sequencing and targeted deep sequencing. Droplet digital PCR was used as molecular reference method. A breakpoint concentration of 0.25 mg/L allows the phenotypic detection of ≥1% resistant bacilli, whereas at 0.5 mg/L ≥ 5% resistant bacilli are detected. Line probe assays detected ≥5% mutants. Sanger sequencing required the presence of around 15% mutant bacilli to be detected as (hetero) resistant, while targeted deep sequencing detected ≤1% mutants. Deep sequencing and phenotypic testing are the most sensitive methods for detection of fluoroquinolone-resistant minority populations, followed by line probe assays (provided that the mutation is confirmed by a mutation band), while Sanger sequencing proved to be the least sensitive method.
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Affiliation(s)
- L Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. .,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - P Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - M Schats
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - P Lempens
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - A M Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - S Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - V Lampasona
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - P de Rijk
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - B C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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20
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Park YJ, Hong DJ, Yoon EJ, Kim D, Choi MH, Hong JS, Lee H, Yong D, Jeong SH. Differences in Colistin-resistant Acinetobacter baumannii Clinical Isolates Between Patients With and Without Prior Colistin Treatment. Ann Lab Med 2018; 38:545-554. [PMID: 30027698 PMCID: PMC6056399 DOI: 10.3343/alm.2018.38.6.545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/26/2018] [Accepted: 06/08/2018] [Indexed: 11/30/2022] Open
Abstract
Background The increasing morbidity and mortality rates associated with Acinetobacter baumannii are due to the emergence of drug resistance and the limited treatment options. We compared characteristics of colistin-resistant Acinetobacter baumannii (CR-AB) clinical isolates recovered from patients with and without prior colistin treatment. We assessed whether prior colistin treatment affects the resistance mechanism of CR-AB isolates, mortality rates, and clinical characteristics. Additionally, a proper method for identifying CR-AB was determined. Methods We collected 36 non-duplicate CR-AB clinical isolates resistant to colistin. Antimicrobial susceptibility testing, Sanger sequencing analysis, molecular typing, lipid A structure analysis, and in vitro synergy testing were performed. Eleven colistin-susceptible AB isolates were used as controls. Results Despite no differences in clinical characteristics between patients with and without prior colistin treatment, resistance-causing genetic mutations were more frequent in isolates from colistin-treated patients. Distinct mutations were overlooked via the Sanger sequencing method, perhaps because of a masking effect by the colistin-susceptible AB subpopulation of CR-AB isolates lacking genetic mutations. However, modified lipid A analysis revealed colistin resistance peaks, despite the population heterogeneity, and peak levels were significantly different between the groups. Conclusions Although prior colistin use did not induce clinical or susceptibility differences, we demonstrated that identification of CR-AB by sequencing is insufficient. We propose that population heterogeneity has a masking effect, especially in colistin non-treated patients; therefore, accurate testing methods reflecting physiological alterations of the bacteria, such as phosphoethanolamine-modified lipid A identification by matrix-assisted laser desorption ionization-time of flight, should be employed.
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Affiliation(s)
- Yu Jin Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Duck Jin Hong
- Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, UAE
| | - Eun Jeong Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, Seoul, Korea
| | - Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, Seoul, Korea
| | - Min Hyuk Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jun Sung Hong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, Seoul, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, Seoul, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, Seoul, Korea.
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21
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Guérillot R, Li L, Baines S, Howden B, Schultz MB, Seemann T, Monk I, Pidot SJ, Gao W, Giulieri S, Gonçalves da Silva A, D’Agata A, Tomita T, Peleg AY, Stinear TP, Howden BP. Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq). Genome Med 2018; 10:63. [PMID: 30165908 PMCID: PMC6117896 DOI: 10.1186/s13073-018-0572-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/24/2018] [Indexed: 12/15/2022] Open
Abstract
Mutation acquisition is a major mechanism of bacterial antibiotic resistance that remains insufficiently characterised. Here we present RM-seq, a new amplicon-based deep sequencing workflow based on a molecular barcoding technique adapted from Low Error Amplicon sequencing (LEA-seq). RM-seq allows detection and functional assessment of mutational resistance at high throughput from mixed bacterial populations. The sensitive detection of very low-frequency resistant sub-populations permits characterisation of antibiotic-linked mutational repertoires in vitro and detection of rare resistant populations during infections. Accurate quantification of resistance mutations enables phenotypic screening of mutations conferring pleiotropic phenotypes such as in vivo persistence, collateral sensitivity or cross-resistance. RM-seq will facilitate comprehensive detection, characterisation and surveillance of resistant bacterial populations ( https://github.com/rguerillot/RM-seq ).
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Affiliation(s)
- Romain Guérillot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Lucy Li
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Sarah Baines
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Brian Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Mark B. Schultz
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria Australia
| | - Ian Monk
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Sacha J. Pidot
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Wei Gao
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Stefano Giulieri
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Anders Gonçalves da Silva
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Anthony D’Agata
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Takehiro Tomita
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Anton Y. Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria Australia
- Infection and Immunity Theme, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria Australia
- Infectious Diseases Department, Austin Health, Heidelberg, Victoria Australia
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22
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Klotoe BJ, Molina-Moya B, Gomes HM, Gomgnimbou MK, Oliveira Suzarte L, Féres Saad MH, Ali S, Dominguez J, Pimkina E, Zholdybayeva E, Sola C, Refrégier G. TB-EFI, a novel 18-Plex microbead-based method for prediction of second-line drugs and ethambutol resistance in Mycobacterium tuberculosis complex. J Microbiol Methods 2018; 152:10-17. [PMID: 29913189 DOI: 10.1016/j.mimet.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
Abstract
Several diagnostic tests are being developed to detect drug resistance in tuberculosis. In line with previous developments detecting rifampicin and isoniazid resistance using microbead-based systems (spoligoriftyping and TB-SPRINT), we present here an assay called TB-EFI detecting mutations involved in resistance to ethambutol, fluoroquinolones and the three classical injectable drugs (kanamycin, amikacin and capreomycin) in Mycobacterium tuberculosis. The proposed test includes both wild-type and mutant probes for each targeted locus. Basic analysis can be performed manually. An upgraded interpretation is made available in Excel 2016®. Using a reference set of 61 DNA extracts, we show that TB-EFI provides perfect concordance with pyrosequencing. Concordance between genotypic resistance and phenotypic DST was relatively good (72 to 98% concordance), with lower efficiency for fluoroquinolones and ethambutol due to some untargeted mutations. When compared to phenotypical resistance, performances were similar to those obtained with Hain MTBDRsl assay, possibly thanks to the use of automatized processing of data although some mutations involved in fluoroquinolone resistance could not be included. When applied on three uncharacterized sets, phenotype could be predicted for 51% to 98% depending on the setting and the drug investigated, detecting one extensively drug-resistant isolate in each of a Pakistan and a Brazilian set of 91 samples, and 9 XDR among 43 multi-resistant Kazakhstan samples. By allowing high-throughput detection of second-line drugs resistance and of resistance to ethambutol that is often combined to second-line treatments, TB-EFI is a cost-effective assay for large-scale worldwide surveillance of resistant tuberculosis and XDR-TB control.
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Affiliation(s)
- Bernice J Klotoe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Barbara Molina-Moya
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Harrison Magdinier Gomes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France; Laboratório de Biologia Molecular Aplicada à Micobactérias, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Michel K Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France; Centre Muraz, Bobo-Dioulasso, Burkina Faso; Univ. Polytech, Bobo-Dioulasso, Burkina Faso
| | - Lorenna Oliveira Suzarte
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Maria H Féres Saad
- Laboratório de Microbiologia Celular, Instituto Oswaldo Cruz, Av. Brasil, 4365 - 20245, Rio de Janeiro, Brazil
| | - Sajid Ali
- Microbiology Department, Quaid-i-Azam University, Islamabad, Pakistan
| | - José Dominguez
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Institut d'Investigació Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
| | - Edita Pimkina
- Infectious Diseases and Tuberculosis Hospital, Affiliate of Vilnius University Hospital Santariskiu klinikos, Vilnius, Lithuania
| | - Elena Zholdybayeva
- National Center for Biotechnology, Astana, Kazakhstan; Universitat Autònoma de Barcelona. CIBER Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Spain
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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23
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McNerney R, Zignol M, Clark TG. Use of whole genome sequencing in surveillance of drug resistant tuberculosis. Expert Rev Anti Infect Ther 2018; 16:433-442. [PMID: 29718745 DOI: 10.1080/14787210.2018.1472577] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The threat of resistance to anti-tuberculosis drugs is of global concern. Current efforts to monitor resistance rely on phenotypic testing where cultured bacteria are exposed to critical concentrations of the drugs. Capacity for such testing is low in TB endemic countries. Drug resistance is caused by mutations in the Mycobacterium tuberculosis genome and whole genome sequencing to detect these mutations offers an alternative means of assessing resistance. Areas covered: The challenges of assessing TB drug resistance are discussed. Progress in elucidating the M. tuberculosis resistome and evidence of the accuracy of next generation sequencing for detecting resistance is reviewed. Expert Commentary: There are considerable advantages to using next generation sequencing for TB drug resistance surveillance. Accuracy is high for detecting resistance to the major first-line drugs but is currently lower for the second-line drugs due to our incomplete knowledge regarding resistance causing mutations. With the advances in sequencing technology and the opportunity to replace phenotypic drug susceptibility testing with safer and more cost effective methods it would appear that the question is when to implement. Current bottlenecks are sample extraction to allow whole genome sequencing directly from sputum and the lack of bioinformatics expertise in some TB endemic countries.
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Affiliation(s)
- Ruth McNerney
- a Division of Pulmonary Medicine, Department of Medicine , University of Cape Town , Cape Town , South Africa
| | - Matteo Zignol
- b Global Tuberculosis Programme , World Health Organization , Geneva , Switzerland
| | - Taane G Clark
- c Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health , London School of Hygiene & Tropical Medicine , London , United Kingdom
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24
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Zimenkov DV, Nosova EY, Kulagina EV, Antonova OV, Arslanbaeva LR, Isakova AI, Krylova LY, Peretokina IV, Makarova MV, Safonova SG, Borisov SE, Gryadunov DA. Examination of bedaquiline- and linezolid-resistant Mycobacterium tuberculosis isolates from the Moscow region. J Antimicrob Chemother 2018; 72:1901-1906. [PMID: 28387862 DOI: 10.1093/jac/dkx094] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/28/2017] [Indexed: 12/17/2022] Open
Abstract
Objectives To study the isolates with acquired resistance to bedaquiline and linezolid that were obtained from patients enrolled in a clinical study of a novel therapy regimen for drug-resistant TB in Moscow, Russia. Methods Linezolid resistance was detected using MGIT 960 with a critical concentration of 1 mg/L. The MIC of bedaquiline was determined using the proportion method. To identify genetic determinants of resistance, sequencing of the mmpR ( Rv0678 ), atpE , atpC , pepQ , Rv1979c , rrl , rplC and rplD loci was performed. Results A total of 85 isolates from 27 patients with acquired resistance to linezolid and reduced susceptibility to bedaquiline (MIC ≥0.06 mg/L) were tested. Most mutations associated with a high MIC of bedaquiline were found in the mmpR gene. We identified for the first time two patients whose clinical isolates had substitutions D28N and A63V in AtpE, which had previously been found only in in vitro -selected strains. Several patients had isolates with elevated MICs of bedaquiline prior to treatment; four of them also bore mutations in mmpR , indicating the presence of some hidden factors in bedaquiline resistance acquisition. The C154R substitution in ribosomal protein L3 was the most frequent in the linezolid-resistant strains. Mutations in the 23S rRNA gene (g2294a and g2814t) associated with linezolid resistance were also found in two isolates. Heteroresistance was identified in ∼40% of samples, which reflects the complex nature of resistance acquisition. Conclusions The introduction of novel drugs into treatment must be accompanied by continuous phenotypic susceptibility testing and the analysis of genetic determinants of resistance.
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Affiliation(s)
- Danila V Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elena Yu Nosova
- Moscow Research and Clinical Centre for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russian Federation
| | - Elena V Kulagina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Antonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Liaisan R Arslanbaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexandra I Isakova
- Moscow Research and Clinical Centre for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russian Federation
| | - Ludmila Yu Krylova
- Moscow Research and Clinical Centre for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russian Federation
| | - Irina V Peretokina
- Moscow Research and Clinical Centre for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russian Federation
| | - Marina V Makarova
- Moscow Research and Clinical Centre for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russian Federation
| | - Svetlana G Safonova
- Moscow Research and Clinical Centre for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russian Federation
| | - Sergey E Borisov
- Moscow Research and Clinical Centre for Tuberculosis Control of the Moscow Government Health Department, Moscow, Russian Federation
| | - Dmitry A Gryadunov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
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25
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Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium tuberculosis by DeepMelt Assay. J Clin Microbiol 2018; 56:JCM.01239-17. [PMID: 29118176 DOI: 10.1128/jcm.01239-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/02/2017] [Indexed: 12/18/2022] Open
Abstract
Detection of heteroresistance of Mycobacterium tuberculosis remains challenging using current genotypic drug susceptibility testing methods. Here, we described a melting curve analysis-based approach, termed DeepMelt, that can detect less-abundant mutants through selective clamping of the wild type in mixed populations. The singleplex DeepMelt assay detected 0.01% katG S315T in 105M. tuberculosis genomes/μl. The multiplex DeepMelt TB/INH detected 1% of mutant species in the four loci associated with isoniazid resistance in 104M. tuberculosis genomes/μl. The DeepMelt TB/INH assay was tested on a panel of DNA extracted from 602 precharacterized clinical isolates. Using the 1% proportion method as the gold standard, the sensitivity was found to be increased from 93.6% (176/188, 95% confidence interval [CI] = 89.2 to 96.3%) to 95.7% (180/188, 95% CI = 91.8 to 97.8%) compared to the MeltPro TB/INH assay. Further evaluation of 109 smear-positive sputum specimens increased the sensitivity from 83.3% (20/24, 95% CI = 64.2 to 93.3%) to 91.7% (22/24, 95% CI = 74.2 to 97.7%). In both cases, the specificity remained nearly unchanged. All heteroresistant samples newly identified by the DeepMelt TB/INH assay were confirmed by DNA sequencing and even partially by digital PCR. The DeepMelt assay may fill the gap between current genotypic and phenotypic drug susceptibility testing for detecting drug-resistant tuberculosis patients.
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26
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Mortimer TD, Weber AM, Pepperell CS. Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis. mSystems 2018; 3:e00108-17. [PMID: 29404424 PMCID: PMC5790871 DOI: 10.1128/msystems.00108-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis. Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis, we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution. We found resistant subpopulations to be less diverse than susceptible subpopulations, consistent with ongoing transmission of resistant M. tuberculosis. A subset of resistance genes ("sloppy targets") were characterized by high diversity and multiple rare variants; we posit that a large genetic target for resistance and relaxation of purifying selection contribute to high diversity at these loci. For "tight targets" of selection, the path to resistance appeared narrower, evidenced by single favored mutations that arose numerous times in the phylogeny and segregated at markedly different frequencies in resistant and susceptible subpopulations. These results suggest that diverse genetic architectures underlie drug resistance in M. tuberculosis and that combined approaches are needed to identify causal mutations. Extrapolating from patterns observed for well-characterized genes, we identified novel candidate variants involved in resistance. The approach outlined here can be extended to identify resistance variants for new drugs, to investigate the genetic architecture of resistance, and when phenotypic data are available, to find candidate genetic loci underlying other positively selected traits in clonal bacteria. IMPORTANCEMycobacterium tuberculosis, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on M. tuberculosis populations. Identifying the mutations that cause drug resistance in M. tuberculosis is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of M. tuberculosis isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant M. tuberculosis to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in M. tuberculosis and other clonal pathogens.
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Affiliation(s)
- Tatum D. Mortimer
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Alexandra M. Weber
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Caitlin S. Pepperell
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, Wisconsin, USA
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27
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Metcalfe JZ, Streicher E, Theron G, Colman RE, Allender C, Lemmer D, Warren R, Engelthaler DM. Cryptic Microheteroresistance Explains Mycobacterium tuberculosis Phenotypic Resistance. Am J Respir Crit Care Med 2017; 196:1191-1201. [PMID: 28614668 DOI: 10.1164/rccm.201703-0556oc] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RATIONALE Minority drug-resistant Mycobacterium tuberculosis subpopulations can be associated with phenotypic resistance but are poorly detected by Sanger sequencing or commercial molecular diagnostic assays. OBJECTIVES To determine the role of targeted next-generation sequencing in resolving these minor variant subpopulations. METHODS We used single molecule overlapping reads (SMOR), a targeted next-generation sequencing approach that dramatically reduces sequencing error, to analyze primary cultured isolates phenotypically resistant to rifampin, fluoroquinolones, or aminoglycosides, but for which Sanger sequencing found no resistance-associated variants (RAVs) within respective resistance-determining regions (study group). Isolates also underwent single-colony selection on antibiotic-containing agar, blinded to sequencing results. As a positive control, isolates with multiple colocalizing chromatogram peaks were also analyzed (control group). MEASUREMENTS AND MAIN RESULTS Among 61 primary culture isolates (25 study group and 36 control group), SMOR described 66 (49%) and 45 (33%) of 135 total heteroresistant RAVs at frequencies less than 5% and less than 1% of the total mycobacterial population, respectively. In the study group, SMOR detected minor resistant variant subpopulations in 80% (n = 20/25) of isolates with no Sanger-identified RAVs (median subpopulation size, 1.0%; interquartile range, 0.2-3.9%). Single-colony selection on drug-containing media corroborated SMOR results for 90% (n = 18/20) of RAV-containing specimens, and the absence of RAVs in 60% (n = 3/5) of isolates. Overall, Sanger sequencing was concordant with SMOR for 77% (n = 53/69) of macroheteroresistant (5-95% total population), but only 5% of microheteroresistant (<5%) subpopulations (n = 3/66) across both groups. CONCLUSIONS Cryptic minor variant mycobacterial subpopulations exist below the resolving capability of current drug susceptibility testing methodologies, and may explain an important proportion of false-negative resistance determinations.
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Affiliation(s)
- John Z Metcalfe
- 1 Division of Pulmonary and Critical Care Medicine, San Francisco General Hospital, University of California, San Francisco, San Francisco, California
| | - Elizabeth Streicher
- 2 DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Grant Theron
- 2 DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Rebecca E Colman
- 3 Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, San Diego, California; and
| | | | - Darrin Lemmer
- 4 Translational Genomics Research Institute, Flagstaff, Arizona
| | - Rob Warren
- 2 DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, and SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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28
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Nimmo C, Doyle R, Burgess C, Williams R, Gorton R, McHugh TD, Brown M, Morris-Jones S, Booth H, Breuer J. Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum. Int J Infect Dis 2017; 62:44-46. [PMID: 28716462 DOI: 10.1016/j.ijid.2017.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/07/2017] [Indexed: 10/19/2022] Open
Abstract
INTRODUCTION Resistance to second-line tuberculosis drugs is common, but slow to diagnose with phenotypic drug sensitivity testing. Rapid molecular tests speed up diagnosis, but can only detect limited mutations. Whole genome sequencing (WGS) of culture isolates can generate a complete genetic drug resistance profile, but is delayed by the initial culture step. In the case presented here, successful WGS directly from sputum was achieved using targeted enrichment. CASE REPORT A 29-year-old Nigerian woman was diagnosed with tuberculosis. Xpert MTB/RIF and Hain line probe assays identified rpoB and inhA mutations consistent with rifampicin and intermediate isoniazid resistance, and a further possible mutation conferring fluoroquinolone resistance. WGS directly from sputum identified a further inhA mutation consistent with high-level isoniazid resistance and confirmed the absence of fluoroquinolone resistance. Isoniazid was stopped, and the patient has completed 18 months of a fluoroquinolone-based regimen without relapse. DISCUSSION Compared to rapid molecular tests (which can only examine a limited number of mutations) and WGS of culture isolates (which requires a culture step), WGS directly from sputum can quickly generate a complete genetic drug resistance profile. In this case, WGS altered the clinical management of drug-resistant tuberculosis and demonstrated potential for guiding individualized drug treatment where second-line drug resistance is common.
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, UK.
| | - Ronan Doyle
- Division of Infection and Immunity, University College London, London, UK
| | - Carrie Burgess
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, UK
| | - Rebecca Gorton
- Division of Infection and Immunity, University College London, London, UK
| | - Timothy D McHugh
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Brown
- University College Hospitals NHS Foundation Trust and North Central London TB Service - South Hub at Whittington Health NHS Trust, London, UK
| | - Stephen Morris-Jones
- University College Hospitals NHS Foundation Trust and North Central London TB Service - South Hub at Whittington Health NHS Trust, London, UK
| | - Helen Booth
- University College Hospitals NHS Foundation Trust and North Central London TB Service - South Hub at Whittington Health NHS Trust, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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Shea J, Halse TA, Lapierre P, Shudt M, Kohlerschmidt D, Van Roey P, Limberger R, Taylor J, Escuyer V, Musser KA. Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol 2017; 55:1871-1882. [PMID: 28381603 PMCID: PMC5442544 DOI: 10.1128/jcm.00298-17] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/28/2017] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterize Mycobacterium tuberculosis and other M. tuberculosis complex (MTBC) strains, composed of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics pipeline. This new assay was assessed using 608 MTBC isolates, with 146 isolates during the validation portion of this study and 462 samples received prospectively. In February 2016, this assay was implemented to test all clinical cases of MTBC in New York State, including isolates and early positive Bactec mycobacterial growth indicator tube (MGIT) 960 cultures from primary specimens. Since the inception of the assay, we have assessed the accuracy of identification of MTBC strains to the species level, concordance with culture-based drug susceptibility testing (DST), and turnaround time. Species identification by WGS was determined to be 99% accurate. Concordance between drug resistance profiles generated by WGS and culture-based DST methods was 96% for eight drugs, with an average resistance-predictive value of 93% and susceptible-predictive value of 96%. This single comprehensive WGS assay has replaced seven molecular assays and has resulted in resistance profiles being reported to physicians an average of 9 days sooner than with culture-based DST for first-line drugs and 32 days sooner for second-line drugs.
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Affiliation(s)
- Joseph Shea
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Tanya A Halse
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Donna Kohlerschmidt
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Patrick Van Roey
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Ronald Limberger
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vincent Escuyer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kimberlee A Musser
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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30
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Operario DJ, Koeppel AF, Turner SD, Bao Y, Pholwat S, Banu S, Foongladda S, Mpagama S, Gratz J, Ogarkov O, Zhadova S, Heysell SK, Houpt ER. Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis. PLoS One 2017; 12:e0176522. [PMID: 28545050 PMCID: PMC5436647 DOI: 10.1371/journal.pone.0176522] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/12/2017] [Indexed: 12/31/2022] Open
Abstract
Amplicon-based Next Generation Sequencing (NGS) is an emerging method for Mycobacterium tuberculosis drug susceptibility testing (DST) but has not been well described. We examined 158 clinical multidrug-resistant M. tuberculosis isolates via NGS of 11 resistance-associated gene regions covering 3519 nucleotides. Across these gene regions, complete resistance or heteroresistance (defined as 1%-99% mutation) was present in at least one isolate in 6.3% of loci. The number of isolates with heteroresistance was highest for gyrA codon 94, rpoB codons 526 and 531, and embB codons 306, 372 and 406 (range 11-26% of isolates exhibited heteroresistance). 57% of MDR strains had heteroresistance of one or more recognized resistance-associated mutation. Heteroresistant loci generally exhibited high or low degrees of mutation (>90% or <10%). The deep sensitivity of NGS for detecting low level pncA heteroresistance appeared to improve genotypic-phenotypic PZA susceptibility correlations over that of Sanger. NGS demonstrates that heteroresistance in TB in the regions of key genes is common and will need to be bioinformatically managed. The clinical significance of such heteroresistance is unclear, and further study of pncA should be pursued.
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Affiliation(s)
- Darwin J. Operario
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Alexander F. Koeppel
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States of America
| | - Stephen D. Turner
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States of America
| | - Yongde Bao
- Department of Microbiology, University of Virginia, Charlottesville, VA, United States of America
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Sayera Banu
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Stellah Mpagama
- Kibong’oto Infectious Diseases Hospital, Kilimanjaro, Tanzania
| | - Jean Gratz
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Oleg Ogarkov
- Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Siberia, Russian Federation
| | - Svetlana Zhadova
- Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Siberia, Russian Federation
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
- * E-mail:
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31
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Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDR sl Assays. Antimicrob Agents Chemother 2017; 61:AAC.02169-16. [PMID: 28137812 PMCID: PMC5365657 DOI: 10.1128/aac.02169-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/16/2017] [Indexed: 11/20/2022] Open
Abstract
In this study, using the Hain GenoType MTBDRsl assays (versions 1 and 2), we found that some nonsynonymous and synonymous mutations in gyrA in Mycobacterium tuberculosis result in systematic false-resistance results to fluoroquinolones by preventing the binding of wild-type probes. Moreover, such mutations can prevent the binding of mutant probes designed for the identification of specific resistance mutations. Although these mutations are likely rare globally, they occur in approximately 7% of multidrug-resistant tuberculosis strains in some settings.
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32
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Direct Detection of Rifampin and Isoniazid Resistance in Sputum Samples from Tuberculosis Patients by High-Resolution Melt Curve Analysis. J Clin Microbiol 2017; 55:1755-1766. [PMID: 28330890 DOI: 10.1128/jcm.02104-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/17/2017] [Indexed: 01/22/2023] Open
Abstract
Drug-resistant tuberculosis (TB) is a major threat to TB control worldwide. Globally, only 40% of the 340,000 notified TB patients estimated to have multidrug-resistant-TB (MDR-TB) were detected in 2015. This study was carried out to evaluate the utility of high-resolution melt curve analysis (HRM) for the rapid and direct detection of MDR-TB in Mycobacterium tuberculosis in sputum samples. A reference plasmid library was first generated of the most frequently observed mutations in the resistance-determining regions of rpoB, katG, and an inhA promoter and used as positive controls in HRM. The assay was first validated in 25 MDR M. tuberculosis clinical isolates. The assay was evaluated on DNA isolated from 99 M. tuberculosis culture-positive sputum samples that included 84 smear-negative sputum samples, using DNA sequencing as gold standard. Mutants were discriminated from the wild type by comparing melting-curve patterns with those of control plasmids using HRM software. Rifampin (RIF) and isoniazid (INH) monoresistance were detected in 11 and 21 specimens, respectively, by HRM. Six samples were classified as MDR-TB by sequencing, one of which was missed by HRM. The HRM-RIF, INH-katG, and INH-inhA assays had 89% (95% confidence interval [CI], 52, 100%), 85% (95% CI, 62, 97%), and 100% (95% CI, 74, 100%) sensitivity, respectively, in smear-negative samples, while all assays had 100% sensitivity in smear-positive samples. All assays had 100% specificity. Concordance of 97% to 100% (κ value, 0.9 to 1) was noted between sequencing and HRM. Heteroresistance was observed in 5 of 99 samples by sequencing. In conclusion, the HRM assay was a cost-effective (Indian rupee [INR]400/US$6), rapid, and closed-tube method for the direct detection of MDR-TB in sputum, especially for direct smear-negative cases.
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Satta G, Atzeni A, McHugh T. Mycobacterium tuberculosis and whole genome sequencing: a practical guide and online tools available for the clinical microbiologist. Clin Microbiol Infect 2017; 23:69-72. [DOI: 10.1016/j.cmi.2016.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/02/2016] [Accepted: 09/03/2016] [Indexed: 11/15/2022]
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Shakoor S, Tahseen S, Jabeen K, Fatima R, Malik F, Rizvi A, Hasan R. Fluoroquinolone consumption and -resistance trends in Mycobacterium tuberculosis and other respiratory pathogens: Ecological antibiotic pressure and consequences in Pakistan, 2009–2015. Int J Mycobacteriol 2016; 5:412-416. [DOI: 10.1016/j.ijmyco.2016.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022] Open
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35
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Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus. J Clin Microbiol 2016; 55:457-469. [PMID: 27903602 PMCID: PMC5277515 DOI: 10.1128/jcm.02116-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/18/2016] [Indexed: 01/01/2023] Open
Abstract
The emergence and spread of drug-resistant Mycobacterium tuberculosis (DR-TB) are critical global health issues. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB. Using a phylogenomic approach, we estimated that the majority of MDR-TB was due to the recent transmission of already-resistant M. tuberculosis strains rather than repeated de novo evolution of resistance within patients, while XDR-TB was acquired through both routes. Longitudinal sampling of M. tuberculosis from 34 patients with treatment failure showed that most strains persisted genetically unchanged during treatment or acquired resistance to fluoroquinolones. HIV+ patients were significantly more likely to have multiple infections over time than HIV− patients, highlighting a specific need for careful infection control in these patients. These data provide a better understanding of the genomic composition, transmission, and evolution of MDR- and XDR-TB in Belarus and will enable improved diagnostics, treatment protocols, and prognostic decision-making.
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36
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Ellington MJ, Ekelund O, Aarestrup FM, Canton R, Doumith M, Giske C, Grundman H, Hasman H, Holden MTG, Hopkins KL, Iredell J, Kahlmeter G, Köser CU, MacGowan A, Mevius D, Mulvey M, Naas T, Peto T, Rolain JM, Samuelsen Ø, Woodford N. The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. Clin Microbiol Infect 2016; 23:2-22. [PMID: 27890457 DOI: 10.1016/j.cmi.2016.11.012] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/11/2022]
Abstract
Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST). The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values in order to improve differentiation of wild-type from non-wild-type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretive criteria for WGS-based predictive AST. Only data sets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. To facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical laboratories remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on previous culture because analysis directly on specimens remains challenging. For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.
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Affiliation(s)
- M J Ellington
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - O Ekelund
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - F M Aarestrup
- National Food Institute, Research Group for Genomic Epidemiology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - R Canton
- Servicio de Microbiología, Hospital Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - M Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - C Giske
- Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - H Grundman
- University Medical Centre Freiburg, Infection Prevention and Hospital Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Hasman
- Statens Serum Institute, Department of Microbiology and Infection Control, Copenhagen, Denmark
| | - M T G Holden
- School of Medicine, Medical & Biological Sciences, North Haugh, University of St Andrews, UK
| | - K L Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK
| | - J Iredell
- Westmead Institute for Medical Research, University of Sydney and Marie Bashir Institute, Sydney, NSW, Australia
| | - G Kahlmeter
- Department of Clinical Microbiology and the EUCAST Development Laboratory, Kronoberg Region, Central Hospital, Växjö, Sweden
| | - C U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - A MacGowan
- Department of Medical Microbiology, North Bristol NHS Trust, Southmead Hospital, Bristol, UK
| | - D Mevius
- Central Veterinary Institute (CVI) part of Wageningen University and Research Centre (WUR), Lelystad, The Netherlands; Department of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands
| | - M Mulvey
- National Microbiology Laboratory, Winnipeg, Manitoba, Canada
| | - T Naas
- French National Reference Centre for Antibiotic Resistance, Bacteriology-Hygiene unit, Hôpital Bicêtre, APHP, LabEx LERMIT, University Paris Sud, Le Kremlin-Bicêtre, France
| | - T Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - J-M Rolain
- PU-PH des Disciplines Pharmaceutiques, 1-URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Valorization and Transfer, Aix Marseille Université, Faculté de Médecine et de Pharmacie, Marseille, France
| | - Ø Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway, Department of Microbiology and Infection Control, Tromsø, Norway
| | - N Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, National Infection Service, Public Health England, London, UK.
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Zhang D, Gomez JE, Chien JY, Haseley N, Desjardins CA, Earl AM, Hsueh PR, Hung DT. Genomic Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis. Antimicrob Agents Chemother 2016; 60:6600-6608. [PMID: 27572408 PMCID: PMC5075065 DOI: 10.1128/aac.00664-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/07/2016] [Indexed: 02/01/2023] Open
Abstract
Fluoroquinolones (FQs) are effective second-line drugs for treating antibiotic-resistant tuberculosis (TB) and are being considered for use as first-line agents. Because FQs are used to treat a range of infections, in a setting of undiagnosed TB, there is potential to select for drug-resistant Mycobacterium tuberculosis mutants during FQ-based treatment of other infections, including pneumonia. Here we present a detailed characterization of ofloxacin-resistant M. tuberculosis samples isolated directly from patients in Taiwan, which demonstrates that selection for FQ resistance can occur within patients who have not received FQs for the treatment of TB. Several of these samples showed no mutations in gyrA or gyrB based on PCR-based molecular assays, but genome-wide next-generation sequencing (NGS) revealed minority populations of gyrA and/or gyrB mutants. In other samples with PCR-detectable gyrA mutations, NGS revealed subpopulations containing alternative resistance-associated genotypes. Isolation of individual clones from these apparently heterogeneous samples confirmed the presence of the minority drug-resistant variants suggested by the NGS data. Further NGS of these purified clones established evolutionary links between FQ-sensitive and -resistant clones derived from the same patient, suggesting de novo emergence of FQ-resistant TB. Importantly, most of these samples were isolated from patients without a history of FQ treatment for TB. Thus, selective pressure applied by FQ monotherapy in the setting of undiagnosed TB infection appears to be able to drive the full or partial emergence of FQ-resistant M. tuberculosis, which has the potential to confound diagnostic tests for antibiotic susceptibility and limit the effectiveness of FQs in TB treatment.
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Affiliation(s)
- Danfeng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - James E Gomez
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jung-Yien Chien
- Graduate Institute of Clinical Medicine, National Taiwan University Medical College, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University Medical College, Taipei, Taiwan
| | - Nathan Haseley
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Po-Ren Hsueh
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University Medical College, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, National Taiwan University Medical College, Taipei, Taiwan
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
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Schön T, Miotto P, Köser CU, Viveiros M, Böttger E, Cambau E. Mycobacterium tuberculosis drug-resistance testing: challenges, recent developments and perspectives. Clin Microbiol Infect 2016; 23:154-160. [PMID: 27810467 DOI: 10.1016/j.cmi.2016.10.022] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/21/2016] [Accepted: 10/22/2016] [Indexed: 11/16/2022]
Abstract
Drug-resistance testing, or antimicrobial susceptibility testing (AST), is mandatory for Mycobacterium tuberculosis in cases of failure on standard therapy. We reviewed the different methods and techniques of phenotypic and genotypic approaches. Although multiresistant and extensively drug-resistant (MDR/XDR) tuberculosis is present worldwide, AST for M. tuberculosis (AST-MTB) is still mainly performed according to the resources available rather than the drug-resistance rates. Phenotypic methods, i.e. culture-based AST, are commonly used in high-income countries to confirm susceptibility of new cases of tuberculosis. They are also used to detect resistance in tuberculosis cases with risk factors, in combination with genotypic tests. In low-income countries, genotypic methods screening hot-spot mutations known to confer resistance were found to be easier to perform because they avoid the culture and biosafety constraint. Given that genotypic tests can rapidly detect the prominent mechanisms of resistance, such as the rpoB mutation for rifampicin resistance, we are facing new challenges with the observation of false-resistance (mutations not conferring resistance) and false-susceptibility (mutations different from the common mechanism) results. Phenotypic and genotypic approaches are therefore complementary for obtaining a high sensitivity and specificity for detecting drug resistances and susceptibilities to accurately predict MDR/XDR cure and to gather relevant data for resistance surveillance. Although AST-MTB was established in the 1960s, there is no consensus reference method for MIC determination against which the numerous AST-MTB techniques can be compared. This information is necessary for assessing in vitro activity and setting breakpoints for future anti-tuberculosis agents.
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Affiliation(s)
- T Schön
- Department of Clinical Microbiology and Infectious Diseases, Kalmar County Hospital, Kalmar, Sweden; Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Linköping University, Sweden; European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland
| | - P Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - C U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - M Viveiros
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland; Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Lisboa, Portugal
| | - E Böttger
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland; Institut für Medizinische Mikrobiologie, Nationales Zentrum für Mykobakterien, Universität Zürich, Zürich, Switzerland
| | - E Cambau
- European Society for Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Mycobacterial Infections (ESGMYC), ESCMID, Basel, Switzerland; National Reference Center for Mycobacteria and Antimycobacterial Resistance, Paris, France; APHP, Hôpital Lariboisière, Laboratory of Bacteriology, Paris, France; University Paris Diderot, INSERM IAME UMR1137, Sorbonne Paris Cité, Paris, France.
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Bernard C, Aubry A, Chauffour A, Brossier F, Robert J, Veziris N. In vivo Mycobacterium tuberculosisfluoroquinolone resistance emergence: a complex phenomenon poorly detected by current diagnostic tests. J Antimicrob Chemother 2016; 71:3465-3472. [DOI: 10.1093/jac/dkw344] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 11/13/2022] Open
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40
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Coeck N, de Jong BC, Diels M, de Rijk P, Ardizzoni E, Van Deun A, Rigouts L. Correlation of different phenotypic drug susceptibility testing methods for four fluoroquinolones in Mycobacterium tuberculosis. J Antimicrob Chemother 2016; 71:1233-40. [PMID: 26851609 PMCID: PMC4830418 DOI: 10.1093/jac/dkv499] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/22/2015] [Indexed: 11/13/2022] Open
Abstract
Background Molecular resistance testing fails to explain all fluoroquinolone resistance, with a continued need for a suitable rapid phenotypic drug susceptibility testing method. Objective To evaluate the optimal method for phenotypic fluoroquinolone susceptibility testing. Methods Using Löwenstein–Jensen medium, Middlebrook 7H11 agar, BACTEC-MGIT 960 and the resazurin microtitre plate assay, we determined susceptibility to fluoroquinolones in Mycobacterium tuberculosis and investigated cross-resistance between ofloxacin, levofloxacin, moxifloxacin and gatifloxacin. We compared MICs of all four fluoroquinolones for 91 strains on Löwenstein–Jensen (as the gold standard) with their MICs in resazurin plates, and with ofloxacin susceptibility at a single concentration in MGIT and on 7H11 agar, in addition to sequencing of the gyrAB genes. Results and conclusions Applying a cut-off of 2 mg/L ofloxacin, 1 mg/L levofloxacin and 0.5 mg/L moxifloxacin and gatifloxacin in all methods, some discordance between solid medium and MGIT methods was observed, yet this tended to be explained by MICs around the cut-off. The high discordance between Löwenstein–Jensen (LJ) and resazurin plates suggests that the currently applied cut-offs for all fluoroquinolones in the resazurin method should decrease and minor changes in colour (from blue to purple) be considered as meaningful. High-level resistance in all assays to all drugs correlated well with the presence of gyrA mutations, in support of recent findings that fluoroquinolone resistance should be tested at different concentrations, as patients with lower levels of resistance may continue to benefit from high-dose fluoroquinolone-based therapy.
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Affiliation(s)
- Nele Coeck
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Department of Medicine, Division of Infectious Diseases, New York University, New York, USA Vaccinology Department, Medical Research Council Unit, Fajara, The Gambia
| | - Maren Diels
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pim de Rijk
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Elisa Ardizzoni
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Médecins Sans Frontières, Paris, France
| | - Armand Van Deun
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
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Chen Y, Zhao B, Liu HC, Sun Q, Zhao XQ, Liu ZG, Wan KL, Zhao LL. Prevalence of mutations conferring resistance among multi- and extensively drug-resistant Mycobacterium tuberculosis isolates in China. J Antibiot (Tokyo) 2015; 69:149-52. [PMID: 26486879 DOI: 10.1038/ja.2015.106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2014] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 11/09/2022]
Abstract
To identify the mutations in multi- and extensively drug-resistant tuberculosis isolates and to evaluate the use of molecular markers of resistance, we analyzed 257 multi- and extensively drug-resistant isolates and 64 pan-sensitive isolates from 23 provinces in China. Seven loci associated with drug resistance, including rpoB for rifampin (RIF), katG, inhA and oxyR-ahpC for isoniazid (INH), gyrA and gyrB for ofloxacin (OFX), and rrs for kanmycin (KAN), were examined by DNA sequencing. Compared with the phenotypic data, the sensitivity and specificity for DNA sequencing were 91.1% and 98.4% for RIF, 80.2% and 98.4% for INH, 72.2% and 98.3% for OFX and 40% and 98.2% for KAN, respectively. The most common mutations found in RIF, INH, OFX and KAN resistance were Ser531Leu (48.2%) in rpoB, Ser315Thr (49.8%) in katG, C(-15)T (10.5%) in inhA, Asp94Gly (20.3%), Asp94Ala (12.7%) and Ala90Val (21.5%) in gyrA, and A1401G (40%) in rrs. This molecular information will be helpful to establish new molecular biology-based methods for diagnosing multi- and extensively drug-resistant tuberculosis in China.
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Affiliation(s)
- Yan Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hai-can Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qing Sun
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Pathogenic Biology Institute, University of South China, Hunan Province, China
| | - Xiu-qin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhi-guang Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kang-lin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Li-li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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42
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Willby M, Sikes RD, Malik S, Metchock B, Posey JE. Correlation between GyrA substitutions and ofloxacin, levofloxacin, and moxifloxacin cross-resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2015; 59:5427-34. [PMID: 26100699 PMCID: PMC4538465 DOI: 10.1128/aac.00662-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/15/2015] [Indexed: 11/20/2022] Open
Abstract
The newer fluoroquinolones moxifloxacin (MXF) and levofloxacin (LVX) are becoming more common components of tuberculosis (TB) treatment regimens. However, the critical concentrations for testing susceptibility of Mycobacterium tuberculosis to MXF and LVX are not yet well established. Additionally, the degree of cross-resistance between ofloxacin (OFX) and these newer fluoroquinolones has not been thoroughly investigated. In this study, the MICs for MXF and LVX and susceptibility to the critical concentration of OFX were determined using the agar proportion method for 133 isolates of M. tuberculosis. Most isolates resistant to OFX had LVX MICs of >1 μg/ml and MXF MICs of >0.5 μg/ml. The presence of mutations within the gyrA quinolone resistance-determining regions (QRDR) correlated well with increased MICs, and the level of LVX and MXF resistance was dependent on the specific gyrA mutation present. Substitutions Ala90Val, Asp94Ala, and Asp94Tyr resulted in low-level MXF resistance (MICs were >0.5 but ≤2 μg/ml), while other mutations led to MXF MICs of >2 μg/ml. Based on these results, a critical concentration of 1 μg/ml is suggested for LVX and 0.5 μg/ml for MXF drug susceptibility testing by agar proportion with reflex testing for MXF at 2 μg/ml.
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Affiliation(s)
- Melisa Willby
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - R David Sikes
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Seidu Malik
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Beverly Metchock
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - James E Posey
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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43
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Diagnostic Performance of the New Version (v2.0) of GenoType MTBDRsl Assay for Detection of Resistance to Fluoroquinolones and Second-Line Injectable Drugs: a Multicenter Study. J Clin Microbiol 2015; 53:2961-9. [PMID: 26179309 PMCID: PMC4540937 DOI: 10.1128/jcm.01257-15] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/06/2015] [Indexed: 11/20/2022] Open
Abstract
Resistance to fluoroquinolones (FLQ) and second-line injectable drugs (SLID) is steadily increasing, especially in eastern European countries, posing a serious threat to effective tuberculosis (TB) infection control and adequate patient management. The availability of rapid molecular tests for the detection of extensively drug-resistant TB (XDR-TB) is critical in areas with high rates of multidrug-resistant TB (MDR-TB) and XDR-TB and limited conventional drug susceptibility testing (DST) capacity. We conducted a multicenter study to evaluate the performance of the new version (v2.0) of the Genotype MTBDRsl assay compared to phenotypic DST and sequencing on a panel of 228 Mycobacterium tuberculosis isolates and 231 smear-positive clinical specimens. The inclusion of probes for the detection of mutations in the eis promoter region in the MTBDRsl v2.0 test resulted in a higher sensitivity for detection of kanamycin resistance for both direct and indirect testing (96% and 95.4%, respectively) than that seen with the original version of the assay, whereas the test sensitivities for detection of FLQ resistance remained unchanged (93% and 83.6% for direct and indirect testing, respectively). Moreover, MTBDRsl v2.0 showed better performance characteristics than v1.0 for the detection of XDR-TB, with high specificity and sensitivities of 81.8% and 80.4% for direct and indirect testing, respectively. MTBDRsl v2.0 thus represents a reliable test for the rapid detection of resistance to second-line drugs and a useful screening tool to guide the initiation of appropriate MDR-TB treatment.
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Abstract
"Heteroresistance" describes a phenomenon where subpopulations of seemingly isogenic bacteria exhibit a range of susceptibilities to a particular antibiotic. Unfortunately, a lack of standard methods to determine heteroresistance has led to inappropriate use of this term. Heteroresistance has been recognized since at least 1947 and occurs in Gram-positive and Gram-negative bacteria. Its clinical relevance may be considerable, since more resistant subpopulations may be selected during antimicrobial therapy. However, the use of nonstandard methods to define heteroresistance, which are costly and involve considerable labor and resources, precludes evaluating the clinical magnitude and severity of this phenomenon. We review the available literature on antibiotic heteroresistance and propose recommendations for definitions and determination criteria for heteroresistant bacteria. This will help in assessing the global clinical impact of heteroresistance and developing uniform guidelines for improved therapeutic outcomes.
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Coll F, McNerney R, Preston MD, Guerra-Assunção JA, Warry A, Hill-Cawthorne G, Mallard K, Nair M, Miranda A, Alves A, Perdigão J, Viveiros M, Portugal I, Hasan Z, Hasan R, Glynn JR, Martin N, Pain A, Clark TG. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences. Genome Med 2015; 7:51. [PMID: 26019726 PMCID: PMC4446134 DOI: 10.1186/s13073-015-0164-0] [Citation(s) in RCA: 277] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/16/2015] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.
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Affiliation(s)
- Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Mark D Preston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Andrew Warry
- Advanced Data Analysis Centre, University of Nottingham, Wollaton Road, Nottingham, NG8 1BB UK
| | - Grant Hill-Cawthorne
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia ; Sydney Emerging Infections and Biosecurity Institute and School of Public Health, University of Sydney, Sydney, Australia
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Mridul Nair
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Anabela Miranda
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - Adriana Alves
- Tuberculosis Laboratory, Instituto Nacional de Saude Dr. Ricardo Jorge, Porto, Portugal
| | - João Perdigão
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Isabel Portugal
- Centro de Patogénese Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Zahra Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology & Microbiology, Aga Khan University Hospital, Karachi, Pakistan
| | - Judith R Glynn
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK ; Karonga Prevention Study, Chilumba, Malawi
| | - Nigel Martin
- Department of Computer Science, Birkbeck College, University of London, Malet Street, London, WC1E 7HX UK
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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46
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Mixed Infections and Rifampin Heteroresistance among Mycobacterium tuberculosis Clinical Isolates. J Clin Microbiol 2015; 53:2138-47. [PMID: 25903578 DOI: 10.1128/jcm.03507-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/16/2015] [Indexed: 11/20/2022] Open
Abstract
Mixed infections and heteroresistance of Mycobacterium tuberculosis contribute to the difficulty of diagnosis, treatment, and control of tuberculosis. However, there is still no proper solution for these issues. This study aimed to investigate the potential relationship between mixed infections and heteroresistance and to determine the high-risk groups related to these factors. A total of 499 resistant and susceptible isolates were subjected to spoligotyping and 24-locus variable-number tandem repeat methods to analyze their genotypic lineages and the occurrence of mixed infections. Two hundred ninety-two randomly selected isolates were sequenced on their rpoB gene to examine mutations and heteroresistance. The results showed that 12 patients had mixed infections, and the corresponding isolates belonged to Manu2 (n = 8), Beijing (n = 2), T (n = 1), and unknown (n = 1) lineages. Manu2 was found to be significantly associated with mixed infections (odds ratio, 47.72; confidence interval, 9.68 to 235.23; P < 0.01). Four isolates (1.37%) were confirmed to be heteroresistant, which was caused by mixed infections in three (75%) isolates; these belonged to Manu2. Additionally, 3.8% of the rifampin-resistant isolates showing no mutation in the rpoB gene were significantly associated with mixed infections (χ(2), 56.78; P < 0.01). This study revealed for the first time that Manu2 was the predominant group in the cases of mixed infections, and this might be the main reason for heteroresistance and a possible mechanism for isolates without any mutation in the rpoB gene to become rifampin resistant. Further studies should focus on this lineage to clarify its relevance to mixed infections.
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Genetic determinants involved in p-aminosalicylic acid resistance in clinical isolates from tuberculosis patients in northern China from 2006 to 2012. Antimicrob Agents Chemother 2014; 59:1320-4. [PMID: 25421465 DOI: 10.1128/aac.03695-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
p-Aminosalicylic acid (PAS) is an important compound for treating multidrug-resistant tuberculosis (TB). Previous studies showed that thyA mutations are often related to PAS resistance in clinical isolates. We performed a systematic analysis of isolate genotypes and detected mutations in three folate pathway genes (folC, thyA, and ribD) in 61.1% (127/208) of PAS-resistant isolates, including 11 double mutants. This result expands our knowledge about the distribution and frequency of mutations related to PAS resistance in mycobacterial clinical isolates.
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48
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Köser CU, Ellington MJ, Peacock SJ. Whole-genome sequencing to control antimicrobial resistance. Trends Genet 2014; 30:401-7. [PMID: 25096945 PMCID: PMC4156311 DOI: 10.1016/j.tig.2014.07.003] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 07/10/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022]
Abstract
Following recent improvements in sequencing technologies, whole-genome sequencing (WGS) is positioned to become an essential tool in the control of antibiotic resistance, a major threat in modern healthcare. WGS has already found numerous applications in this area, ranging from the development of novel antibiotics and diagnostic tests through to antibiotic stewardship of currently available drugs via surveillance and the elucidation of the factors that allow the emergence and persistence of resistance. Numerous proof-of-principle studies have also highlighted the value of WGS as a tool for day-to-day infection control and, for some pathogens, as a primary diagnostic tool to detect antibiotic resistance. However, appropriate data analysis platforms will need to be developed before routine WGS can be introduced on a large scale.
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Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Matthew J Ellington
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, UK; Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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