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Gupta RK, Anthwal D, Bhalla M, Tyagi JS, Choudhary S, Haldar S. Direct Detection of Fluoroquinolone Resistance in Sputum Samples from Tuberculosis Patients by High Resolution Melt Curve Analysis. Curr Microbiol 2023; 81:27. [PMID: 38041739 DOI: 10.1007/s00284-023-03519-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/07/2023] [Indexed: 12/03/2023]
Abstract
Multidrug-resistant tuberculosis (MDR-TB) requires treatment with fluoroquinolone (FLQ) drugs, however, the excessive use of FLQ has led to the rise of extensively drug-resistant TB. In 2019, ~ 20% of total MDR-TB cases were estimated to be resistant to FLQ drugs. In the present study, we developed and evaluated the utility of high-resolution melt curve analysis (HRM) for the rapid detection of FLQ-resistant Mycobacterium tuberculosis for the first time directly from sputum samples. A reference plasmid library was generated for the most frequently observed mutations of gyrA gene and was used to discriminate between mutant and wild-type samples in the FLQ-HRM assay. The developed assay was evaluated on n = 25 MDR M. tuberculosis clinical isolates followed by validation on archived sputum DNA (n = 88) using DNA sequencing as a gold standard. The FLQ-HRM assay showed a 100% sensitivity [95% Confidence Interval (CI): 71.5 to 100] and specificity (95% CI: 39.7 to 100) in smear-positive category, and a sensitivity of 88.9% (95% CI: 77.3 to 95.8) with 84.2% (95% CI: 60.4 to 96.6) specificity in smear-negative category. The assay showed a high level of concordance of ~ 90% (κ = 0.74) with DNA sequencing, however, we were limited by the absence of phenotypic drug susceptibility testing data. In conclusion, HRM is a rapid, cost-effective (INR 150/USD 1.83) and closed-tube method for direct detection of FLQ resistance in sputum samples including direct smear-negative samples.
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Affiliation(s)
- Rakesh Kumar Gupta
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, P.O. Banasthali Vidyapith, Rajasthan, 304022, India
| | - Divya Anthwal
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, P.O. Banasthali Vidyapith, Rajasthan, 304022, India
| | - Manpreet Bhalla
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Mehrauli, New Delhi, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Sangeeta Choudhary
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, P.O. Banasthali Vidyapith, Rajasthan, 304022, India
| | - Sagarika Haldar
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Sector 12, Chandigarh, India.
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3Rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, India.
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Chen S, Liu H, Li T, Lai W, Liu L, Xu Y, Qu J. Using Microfluidic Chip and Allele-Specific PCR to Rapidly Identify Drug Resistance-Associated Mutations of Mycobacterium tuberculosis. Infect Drug Resist 2023; 16:4311-4323. [PMID: 37424666 PMCID: PMC10327919 DOI: 10.2147/idr.s410779] [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: 03/02/2023] [Accepted: 06/20/2023] [Indexed: 07/11/2023] Open
Abstract
Background The currently used conventional susceptibility testing for drug-resistant Mycobacterium tuberculosis (M.TB) is limited due to being time-consuming and having low efficiency. Herein, we propose the use of a microfluidic-based method to rapidly detect drug-resistant gene mutations using Kompetitive Allele-Specific PCR (KASP). Methods A total of 300 clinical samples were collected, and DNA extraction was performed using the "isoChip®" Mycobacterium detection kit. Phenotypic susceptibility testing and Sanger sequencing were performed to sequence the PCR products. Allele-specific primers targeting 37 gene mutation sites were designed, and a microfluidic chip (KASP) was constructed using 112 reaction chambers to simultaneously detect multiple mutations. Chip validation was performed using clinical samples. Results Phenotypic susceptibility of clinical isolates revealed 38 rifampicin (RIF)-resistant, 64 isoniazid (INH)-resistant, 48 streptomycin (SM)-resistant and 23 ethambutol (EMB)-resistant strains, as well as 33 multi-drug-resistant TB (MDR-TB) strains and 20 strains fully resistant to all four drugs. Optimization of the chip-based detection system for drug resistance detection showed satisfactory specificity and maximum fluorescence at a DNA concentration of 1×101 copies/µL. Further analysis revealed that 76.32% of the RIF-resistant strains harbored rpoB gene mutations (sensitivity, 76.32%; specificity 100%), 60.93% of the INH-resistant strains had katG gene mutations (sensitivity, 60.93%; specificity, 100%), 66.66% of the SM-resistant strains carried drug resistance gene mutations (sensitivity, 66.66%; specificity, 99.2%), and 69.56% of the EMB-resistant strains had embB gene mutations (sensitivity, 69.56%; specificity, 100%). Further, the overall agreement between the microfluidic chip and Sanger sequencing was satisfactory, with a turnaround time of the microfluidic chip was approximately 2 hours, much shorter than the conventional DST method. Conclusion The proposed microfluidic-based KASP assay provides a cost-effective and convenient method for detecting mutations associated with drug resistance in M. tuberculosis. It represents a promising alternative to the traditional DST method, with satisfactory sensitivity and specificity and a much shorter turnaround time.
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Affiliation(s)
- Shan Chen
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, People’s Republic of China
| | - Houming Liu
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, People’s Republic of China
| | - Tianpin Li
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, People’s Republic of China
| | - Wenjie Lai
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, People’s Republic of China
| | - Lei Liu
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, People’s Republic of China
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, People’s Republic of China
| | - Jiuxin Qu
- Department of Clinical Laboratory, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen, Guangdong Province, 518112, People’s Republic of China
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Saxena S, Punjabi K, Ahamad N, Singh S, Bendale P, Banerjee R. Nanotechnology Approaches for Rapid Detection and Theranostics of Antimicrobial Resistant Bacterial Infections. ACS Biomater Sci Eng 2022; 8:2232-2257. [PMID: 35546526 DOI: 10.1021/acsbiomaterials.1c01516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
As declared by WHO, antimicrobial resistance (AMR) is a high priority issue with a pressing need to develop impactful technologies to curb it. The rampant and inappropriate use of antibiotics due to the lack of adequate and timely diagnosis is a leading cause behind AMR evolution. Unfortunately, populations with poor economic status and those residing in densely populated areas are the most affected ones, frequently leading to emergence of AMR pathogens. Classical approaches for AMR diagnostics like phenotypic methods, biochemical assays, and molecular techniques are cumbersome and resource-intensive and involve a long turnaround time to yield confirmatory results. In contrast, recent emergence of nanotechnology-assisted approaches helps to overcome challenges in classical approaches and offer simpler, more sensitive, faster, and more affordable solutions for AMR diagnostics. Nanomaterial platforms (metallic, quantum-dot, carbon-based, upconversion, etc.), nanoparticle-based rapid point-of-care platforms, nano-biosensors (optical, mechanical, electrochemical), microfluidic-assisted devices, and importantly, nanotheranostic devices for diagnostics with treatment of AMR infections are examples of rapidly growing nanotechnology approaches used for AMR management. This review comprehensively summarizes the past 10 years of research progress on nanotechnology approaches for AMR diagnostics and for estimating antimicrobial susceptibility against commonly used antibiotics. This review also highlights several bottlenecks in nanotechnology approaches that need to be addressed prior to considering their translation to clinics.
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Affiliation(s)
- Survanshu Saxena
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Kapil Punjabi
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Nadim Ahamad
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Subhasini Singh
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Prachi Bendale
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Rinti Banerjee
- Nanomedicine Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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Keikha M, Karbalaei M. High resolution melting assay as a reliable method for diagnosing drug-resistant TB cases: a systematic review and meta-analysis. BMC Infect Dis 2021; 21:989. [PMID: 34551717 PMCID: PMC8456628 DOI: 10.1186/s12879-021-06708-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/11/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) is one of the most contagious infectious diseases worldwide. Currently, drug-resistant Mycobacterium tuberculosis (Mtb) isolates are considered as one of the main challenges in the global TB control strategy. Rapid detection of resistant strains effectively reduces morbidity and mortality of world's population. Although both culture and conventional antibiotic susceptibility testing are time-consuming, recent studies have shown that high resolution melting (HRM) assay can be used to determine the types of antibiotic resistance. In the present meta-analysis, we evaluated the discriminative power of HRM in detecting all drug-resistance cases of TB. METHODS A systematic search was performed using databases such as Cochrane Library, Scopus, PubMed, Web of Science, and Google Scholar. Related studies on the effect of HRM in the diagnosis of drug-resistant (DR) TB cases were retrieved by April 2021. We used Meta-Disc software to evaluate the pooled diagnostic sensitivity and specificity of HRM for the detection of each type of drug-resistant cases. Finally, diagnostic value of HRM was characterized by summary receiver operating characteristic (SROC) curve and the area under the curve (AUC) method. RESULTS Overall 47 studies (4,732 Mtb isolates) met our criteria and were included in the present meta-analysis. Sensitivity, specificity, and AUC of HRM were measured for antibiotics such as isoniazid (93%, 98%, 0.987), rifampin (94%, 97%, 0963), ethambutol (82%, 87%, 0.728), streptomycin (82%, 95%, 0.957), pyrazinamide (72%, 84%, 0.845), fluoroquinolones (86%, 99%, 0.997), MDR-TB (90%, 98%, 0.989), and pan-drug-resistant TB (89%, 95%, 0.973). CONCLUSIONS The HRM assay has high accuracy for the identification of drug-resistant TB, particularly firs-line anti-TB drugs. Therefore, this method is considered as an alternative option for the rapid diagnosis of DR-TB cases. However, due to heterogeneity of included studies, the results of HRM assays should be interpreted based on conventional drug susceptibility testing.
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Affiliation(s)
- Masoud Keikha
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Karbalaei
- Department of Microbiology and Virology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran.
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Evidence for Expanding the Role of Streptomycin in the Management of Drug-Resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2020; 64:AAC.00860-20. [PMID: 32540971 DOI: 10.1128/aac.00860-20] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/06/2020] [Indexed: 01/09/2023] Open
Abstract
In 2019, the WHO tuberculosis (TB) treatment guidelines were updated to recommend only limited use of streptomycin, in favor of newer agents or amikacin as the preferred aminoglycoside for drug-resistant Mycobacterium tuberculosis However, the emergence of resistance to newer drugs, such as bedaquiline, has prompted a reanalysis of antitubercular drugs in search of untapped potential. Using 211 clinical isolates of M. tuberculosis from South Africa, we performed phenotypic drug susceptibility testing (DST) to aminoglycosides by both critical concentration and MIC determination in parallel with whole-genome sequencing to identify known genotypic resistance elements. Isolates with low-level streptomycin resistance mediated by gidB were frequently misclassified with respect to streptomycin resistance when using the WHO-recommended critical concentration of 2 μg/ml. We identified 29 M. tuberculosis isolates from South Africa with low-level streptomycin resistance concomitant with high-level amikacin resistance, conferred by gidB and rrs 1400, respectively. Using a large global data set of M. tuberculosis genomes, we observed 95 examples of this corresponding resistance genotype (gidB-rrs 1400), including identification in 81/257 (31.5%) of extensively drug resistant (XDR) isolates. In a phylogenetic analysis, we observed repeated evolution of low-level streptomycin and high-level amikacin resistance in multiple countries. Our findings suggest that current critical concentration methods and the design of molecular diagnostics need to be revisited to provide more accurate assessments of streptomycin resistance for gidB-containing isolates. For patients harboring isolates of M. tuberculosis with high-level amikacin resistance conferred by rrs 1400, and for whom newer agents are not available, treatment with streptomycin may still prove useful, even in the face of low-level resistance conferred by gidB.
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Mbano IM, Mandizvo T, Rogich J, Kunota TTR, Mackenzie JS, Pillay M, Balagaddé FK. Light Forge: A Microfluidic DNA Melting-based Tuberculosis Test. J Appl Lab Med 2020; 5:440-453. [PMID: 32445364 PMCID: PMC7192548 DOI: 10.1093/jalm/jfaa019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/15/2019] [Indexed: 01/09/2023]
Abstract
BACKGROUND There is a well-documented lack of rapid, low-cost tuberculosis (TB) drug resistance diagnostics in low-income settings across the globe. It is these areas that are plagued with a disproportionately high disease burden and in greatest need of these diagnostics. METHODS In this study, we compared the performance of Light Forge, a microfluidic high-resolution melting analysis (HRMA) prototype for rapid low-cost detection of TB drug resistance with a commercial HRMA device, a predictive "nearest-neighbor" thermodynamic model, DNA sequencing, and phenotypic drug susceptibility testing (DST). The initial development and assessment of the Light Forge assay was performed with 7 phenotypically drug resistant strains of Mycobacterium tuberculosis (M.tb) that had their rpoB gene subsequently sequenced to confirm resistance to Rifampin. These isolates of M.tb were then compared against a drug-susceptible standard, H37Rv. Seven strains of M.tb were isolated from clinical specimens and individually analyzed to characterize the unique melting profile of each strain. RESULTS Light Forge was able to detect drug-resistance linked mutations with 100% concordance to the sequencing, phenotypic DST and the "nearest neighbor" thermodynamic model. Researchers were then blinded to the resistance profile of the seven M.tb strains. In this experiment, Light Forge correctly classified 7 out of 9 strains as either drug resistant or drug susceptible. CONCLUSIONS Light Forge represents a promising prototype for a fast, low-cost diagnostic alternative for detection of drug resistant strains of TB in resource constrained settings.
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Affiliation(s)
- Ian M Mbano
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Tawanda Mandizvo
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Jerome Rogich
- University of Massachusetts Medical School, Worcester, MA
| | - Tafara T R Kunota
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Jared S Mackenzie
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
| | - Manormoney Pillay
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Frederick K Balagaddé
- Africa Health Research Institute, Nelson R. Mandela School of Medicine, University of KwaZulu Natal, Durban, South Africa
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Filipenko ML, Dymova MA, Cherednichenko AG, Khrapov EA, Mishukova OV, Schwartz YS. Detection of Mutations in Mycobacterium tuberculosis pncA Gene by Modified High-Resolution Melting Curve Analysis of PCR Products. Bull Exp Biol Med 2019; 168:264-269. [PMID: 31782002 DOI: 10.1007/s10517-019-04688-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Indexed: 11/29/2022]
Abstract
We developed a protocol for detection of mutations in the pncA gene associated with M. tuberculosis resistance to pyrazinamide by analyzing melting curves of 7 overlapping amplicons with artificial heteroduplex formation (H-HRM) formed by co-amplification of wild-type DNA and test DNA and compared its efficiency and robustness with those of classical HRM analysis. Using HRM and H-HRM, we analyzed 35 PZAR DNA isolates carrying mutations in the pncA gene, 3 PZAR isolates without mutations in the pncA gene, and 20 PZAS isolates without mutations in the pncA gene were analyzed. The sensitivity and specificity of HRM for detection of mutations in the pncA gene were moderate: 88.57% (CI 73.26%-96.80%) and 82.61% (CI 61.22%-95.05%), respectively. The sensitivity of the H-HRM test was 97.14% (CI 85.08%-99.93%) and specificity was 95.65% (CI 78.05%-99.89%), with a significant improvement in accuracy - 96.55% vs. 93.85% for HRM. In general, despite addition stage of equalizing the concentrations of the test and control mycobacterial DNA, H-HRM showed greater stability and reproducibility at standard settings of the melting curve analysis software.
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Affiliation(s)
- M L Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - M A Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A G Cherednichenko
- Novosibirsk Research Institute of Tuberculosis, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - E A Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O V Mishukova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ya Sh Schwartz
- Novosibirsk Research Institute of Tuberculosis, Ministry of Health of the Russian Federation, Novosibirsk, Russia
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Lu Y, Chen S, Wei L, Sun L, Liu H, Xu Y. A Microfluidic-Based SNP Genotyping Method for Hereditary Hearing-Loss Detection. Anal Chem 2019; 91:6111-6117. [PMID: 30917650 DOI: 10.1021/acs.analchem.9b00652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shan Chen
- Laboratory of ShenZhen Third People’s Hospital, ShenZhen, GuangDong 518112, China
| | - Li Wei
- CapitalBio Technology, Beijing 101111, China
| | - Lanhua Sun
- CapitalBio Technology, Beijing 101111, China
| | - Houming Liu
- Laboratory of ShenZhen Third People’s Hospital, ShenZhen, GuangDong 518112, China
| | - Youchun Xu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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Zhao C, Wang X, Zhang C, Liu B, Jing H, Ming L, Jiang H, Zheng Y, Liu P, Liu G, Jiang Y. Development of a TaqMan Array card to target 21 purulent meningitis-related pathogens. BMC Infect Dis 2019; 19:289. [PMID: 30922257 PMCID: PMC6438039 DOI: 10.1186/s12879-019-3856-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/27/2019] [Indexed: 02/08/2023] Open
Abstract
Background Purulent meningitis (PM) is a serious life-threatening infection of the central nervous system (CNS) by bacteria or fungi and associated with high mortality and high incidence of CNS sequelae in children. However, the conventional cerebrospinal fluid (CSF) culture method is time-consuming and has a low sensitivity. Methods Our study developed a real-time PCR-based purulent meningitis-TaqMan array card (PM-TAC) that targeted 21 PM-related pathogens and could produce results within 3 h. Primers and probes were adapted from published sources possibly. The performance of them were evaluated and optimized and then they were spotted on TAC. Results The PM-TAC showed a sensitivity and specificity of 95 and 96%, respectively. For all of the 21 targeted pathogens, the PM-TAC assay had a LOD ranging from 5 copies/reaction to 100 copies/reaction, an intra-assay variation of 0.07–4.45%, and an inter-assay variation of 0.11–6.81%. Of the 15 CSF samples collected from patients with PM after empiric antibiotic therapies, the positive rate was 53.3% (8/15) for our PM-TAC assay but was only 13.3% (2/15) for the CSF culture method. Of the 17 CSF samples showing negative CSF culture, the PM-TAC assay identified a case of Neisseria meningitidis infection. Furthermore, all of the 10 CSF samples from patients without CNS infection showed negative for the PM-TAC assay. Conclusions Our PM-TAC assay also demonstrated that the pathogen loads in the CSF samples correlated with the severity of PM. Thus, the PM-TAC may be helpful to improve the prognosis of PM and clinical outcomes from antibiotic therapies. Electronic supplementary material The online version of this article (10.1186/s12879-019-3856-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chengna Zhao
- Anhui Medical University, Hefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xi Wang
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China
| | - Chao Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bing Liu
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China
| | - Hongbo Jing
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Lihua Ming
- Chest Hospital of Xinjiang, Urumqi, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Gang Liu
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China.
| | - Yongqiang Jiang
- Anhui Medical University, Hefei, China. .,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
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Wu X, Lu W, Shao Y, Song H, Li G, Li Y, Zhu L, Chen C. pncA gene mutations in reporting pyrazinamide resistance among the MDR-TB suspects. INFECTION GENETICS AND EVOLUTION 2018; 72:147-150. [PMID: 30447296 DOI: 10.1016/j.meegid.2018.11.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/29/2018] [Accepted: 11/11/2018] [Indexed: 10/27/2022]
Abstract
Mutations in pncA gene contributing to PZA resistance was not clearly elucidated in China. To reveal the correlated mutations of pncA gene on pyrazinamide (PZA) resistance. 148 Mycobacterium tuberculosis clinical isolates were included from multi-drug resistant tuberculosis suspects. The MGIT 960 test and microscopic observation drug susceptibility (MODS) assay were adopted for PZA phenotype drug susceptibility test. 120 isolates with consistent MGIT 960 and MODS results were selected for pncA gene sequencing. 68 samples (56.7%) were resistant to PZA while leaving 52 PZA susceptible samples. Out of the 68 PZA resistant isolates, 49 (72.1%) harbored mutations of pncA, and 4 (7.7%) of the 52 PZA susceptible samples harbored mutations of pncA as well. Compared to the phenotype drug resistant pattern of PZA, the mutations of pncA gene reached a sensitivity of 0.72 to report PZA resistance and a specificity of 0.92 to predict PZA susceptibility. Those mutations, Gln10Pro, Asp12Ala, Tyr41Stop, Gly97Asp, Val128Gly and FSC131(ins) exceeding 5% of the total PZA resistant isolates of each, might be helpful but not adequate in PZA molecular susceptibility test design and development.
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Affiliation(s)
- Xiaoyuan Wu
- Central Laboratory, Nanjing Chest Hospital, Medicine School of Southeast University, Nanjing, Jiangsu, China
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Yan Shao
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Honghuan Song
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Guoli Li
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Yan Li
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China
| | - Cheng Chen
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, China; Key Laboratory of Public Health Safety (Fudan University), Ministry of Education, Shanghai, China.
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Mbelele PM, Mohamed SY, Sauli E, Mpolya EA, Mfinanga SG, Addo KK, Heysell SK, Mpagama SG. Meta-narrative review of molecular methods for diagnosis and monitoring of multidrug-resistant tuberculosis treatment in adults. Int J Mycobacteriol 2018; 7:299-309. [PMID: 30531026 PMCID: PMC6548176 DOI: 10.4103/ijmy.ijmy_135_18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Early and accurate diagnosis and rigorous clinical and microbiological monitoring of multidrug-resistant tuberculosis (MDR-TB) treatment can curb morbidity and mortality. While others are still under evaluation, the World Health Organization has recommended few novel molecular methods for MDR-TB diagnosis only. We present current molecular methods for diagnosis and monitoring of MDR-TB treatment in TB-endemic settings. A systematic meta-narrative review was conducted according to the RAMESES recommendations. Electronic databases were searched for relevant articles published in English language from January 2013 to June 2018. Based on predefined criteria, two independent reviewers extracted the key messages from relevant articles. Disagreement between them was resolved through discussion and the involvement of a third reviewer, if needed. Key messages were synthesized to create the meta-narratives for method's accuracy, drug-susceptibility capability, and laboratory infrastructure required. We included 33 articles out of 1213 records retrieved, of which 16 (48%) and 12 (36%) were conducted in high- and low-TB-endemic settings, respectively. Xpert® MTB/RIF, GenoType MTBDRplus, GenoType MTBDRsl, FlouroType™ MTBDR, TB TaqMan® array card, and DNA sequencers can accurately guide effective treatment regimens. Molecular bacterial load assay quantifies mycobactericidal impact of these regimens. Although they present inherent advantages compared to the current standard of care, they carry important limitations to implementation and/or scale-up. Therefore, considerable effort must now be directed to implementation and health systems research to maximize these forecasted benefits for individual patient's health outcomes.
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Affiliation(s)
- Peter M. Mbelele
- Kibong’oto Infectious Diseases Hospital, Sanya Juu,
Siha, Kilimanjaro
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
| | - Sagal Y. Mohamed
- Division of Infectious Diseases and International Health,
University of Virginia, Charlottesville, Virginia, USA
| | - Elingarami Sauli
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
| | - Emmanuel A. Mpolya
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
| | - Sayoki G. Mfinanga
- Muhimbili Centre, National Institute for Medical Research,
Dar es Salaam, Tanzania
| | - Kennedy K. Addo
- Department of Bacteriology, Noguchi Memorial Institute for
Medical Research, University of Ghana, Accra, Ghana
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health,
University of Virginia, Charlottesville, Virginia, USA
| | - Stellah G. Mpagama
- Kibong’oto Infectious Diseases Hospital, Sanya Juu,
Siha, Kilimanjaro
- Department of Global Health and Biomedical Sciences, School
of Life Science and Bioengineering, Nelson Mandela-African Institution for Science
and Technology, Arusha
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12
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Sakai F, Sonaty G, Watson D, Klugman KP, Vidal JE. Development and characterization of a synthetic DNA, NUversa, to be used as a standard in quantitative polymerase chain reactions for molecular pneumococcal serotyping. FEMS Microbiol Lett 2018; 364:4082726. [PMID: 28903467 PMCID: PMC5812490 DOI: 10.1093/femsle/fnx173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/04/2017] [Indexed: 01/18/2023] Open
Abstract
Identification of Streptococcus pneumoniae and its more than 90 serotypes is routinely conducted by culture and Quellung reactions. Quantitative polymerase chain reactions (qPCRs) have been developed for molecular detection, including a pan-pneumococcus lytA assay, and assays targeting 79 serotypes. Reactions require genomic DNA from every target to prepare standards, which can be time consuming. In this study, we have developed a synthetic DNA molecule as a surrogate for genomic DNA and present new single-plex qPCR reactions to increase molecular detection to 94 pneumococcal serotypes. Specificity of these new reactions was confirmed with a limit of detection between 2 and 20 genome equivalents/reaction. A synthetic DNA (NUversa, ∼8.2 kb) was then engineered to contain all available qPCR targets for serotyping and lytA. NUversa was cloned into pUC57-Amp-modified to generate pNUversa (∼10.2 kb). Standards prepared from pNUversa and NUversa were compared against standards made out of genomic DNA. Linearity [NUversa (R2 > 0.982); pNUversa (R2 > 0.991)] and efficiency of qPCR reactions were similar to those utilizing chromosomal DNA (R2 > 0.981). Quantification with plasmid pNUversa was affected, however, whereas quantification with synthetic NUversa was comparable to that of genomic DNA. Therefore, NUversa may be utilized as DNA standard in single-plex assays of the currently known 94 pneumococcal serotypes.
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Affiliation(s)
- Fuminori Sakai
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - Griffin Sonaty
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - David Watson
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA.,Bill and Melinda Gates Foundation, 500 Fifth Avenue North, Seattle, WA 98109, USA
| | - Jorge E Vidal
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, 1518 Clifton Rd NE Room 6007, Atlanta, GA 30322, USA
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13
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Rapid Microarray-Based Detection of Rifampin, Isoniazid, and Fluoroquinolone Resistance in Mycobacterium tuberculosis by Use of a Single Cartridge. J Clin Microbiol 2018; 56:JCM.01249-17. [PMID: 29212699 PMCID: PMC5786735 DOI: 10.1128/jcm.01249-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/23/2017] [Indexed: 02/07/2023] Open
Abstract
The rapid and robust identification of mutations in Mycobacterium tuberculosis complex (MTBC) strains mediating multidrug-resistant (MDR) and extensively drug-resistant (XDR) phenotypes is crucial to combating the MDR tuberculosis (TB) epidemic. Currently available molecular anti-TB drug susceptibility tests either are restricted to a single target or drug (i.e., the Xpert MTB/RIF test) or present a risk of cross-contamination due to the design limitations of the open platform (i.e., line probe assays). With a good understanding of the technical and commercial boundaries, we designed a test cartridge based on an oligonucleotide array into which dried reagents are introduced and which has the ability to identify MTBC strains resistant to isoniazid, rifampin, and the fluoroquinolones. The melting curve assay interrogates 43 different mutations in the rifampin resistance-determining region (RRDR) of rpoB, rpoB codon 572, katG codon 315, the inhA promoter region, and the quinolone resistance-determining region (QRDR) of gyrA in a closed cartridge system within 90 min. Assay performance was evaluated with 265 clinical MTBC isolates, including MDR/XDR, non-MDR, and fully susceptible isolates, from a drug resistance survey performed in Swaziland in 2009 and 2010. In 99.5% of the cases, the results were consistent with data previously acquired utilizing Sanger sequencing. The assay, which uses a closed cartridge system in combination with a battery-powered Alere q analyzer and which has the potential to extend the current gene target panel, could serve as a rapid and robust point-of-care test in settings lacking a comprehensive molecular laboratory infrastructure to differentiate TB patients infected with MDR and non-MDR strains and to assist clinicians with their early treatment decisions.
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14
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Advances in point-of-care technologies for molecular diagnostics. Biosens Bioelectron 2017; 98:494-506. [DOI: 10.1016/j.bios.2017.07.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022]
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15
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Maitra A, Kamil TK, Shaik M, Danquah CA, Chrzastek A, Bhakta S. Early diagnosis and effective treatment regimens are the keys to tackle antimicrobial resistance in tuberculosis (TB): A report from Euroscicon's international TB Summit 2016. Virulence 2017; 8:1005-1024. [PMID: 27813702 PMCID: PMC5626228 DOI: 10.1080/21505594.2016.1256536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/27/2016] [Indexed: 12/22/2022] Open
Abstract
To say that tuberculosis (TB) has regained a strong foothold in the global human health and wellbeing scenario would be an understatement. Ranking alongside HIV/AIDS as the top reason for mortality due to a single infectious disease, the impact of TB extends far into socio-economic context worldwide. As global efforts led by experts and political bodies converge to mitigate the predicted outcome of growing antimicrobial resistance, the academic community of students, practitioners and researchers have mobilised to develop integrated, inter-disciplinary programmes to bring the plans of the former to fruition. Enabling this crucial requirement for unimpeded dissemination of scientific discovery was the TB Summit 2016, held in London, United Kingdom. This report critically discusses the recent breakthroughs made in diagnostics and treatment while bringing to light the major hurdles in the control of the disease as discussed in the course of the 3-day international event. Conferences and symposia such as these are the breeding grounds for successful local and global collaborations and therefore must be supported to expand the understanding and outreach of basic science research.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Tengku Karmila Kamil
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Monisha Shaik
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Cynthia Amaning Danquah
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Alina Chrzastek
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK
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16
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Banu S, Pholwat S, Foongladda S, Chinli R, Boonlert D, Ferdous SS, Rahman SMM, Rahman A, Ahmed S, Houpt ER. Performance of TaqMan array card to detect TB drug resistance on direct specimens. PLoS One 2017; 12:e0177167. [PMID: 28472124 PMCID: PMC5417650 DOI: 10.1371/journal.pone.0177167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/24/2017] [Indexed: 12/31/2022] Open
Abstract
Culture based phenotypic drug susceptibility testing (DST) for Mycobacterium tuberculosis (TB) is time consuming therefore rapid genotypic methods are increasingly being utilized. We previously developed and evaluated on TB isolates a rapid genotypic TaqMan array card (TAC) that detects mutations in several resistance-associated genes using dozens of primer pairs, probes, and high resolution melt analysis, with >96% accuracy versus Sanger sequencing. In this study we examined the performance of TAC on sputum, comparing results between 71 paired sputum and TB isolates of which 62 were MDR-TB. We also adapted the TAC to include wild-type probes and broadened coverage for rpoB and gyrA mutations. TAC was 89% successful at detecting wild-type or mutations within inhA, katG, rpoB, eis, gyrA, rplC, and pncA on smear positive sputa and 33% successful on smear negative sputa. The overall accuracy of these detections as compared to the TAC results of the paired isolate was 95% ± 7 (average sensitivity 98% ± 3; specificity 92% ± 14). Accuracy of sputum TAC results versus phenotypic DST for isoniazid, rifampin, ofloxacin/moxifloxacin, and pyrazinamide was 85% ± 12. This was similar to that of the isolate TAC results (accuracy 88% ± 13), thus inaccuracies primarily reflected intrinsic genotypic-phenotypic discordance. The TAC is a rapid, modular, comprehensive, and accurate TB DST for the major first and second line TB drugs and could be used for supplemental testing of GeneXpert resistant smear positive sputum.
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Affiliation(s)
- Sayera Banu
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Suporn Foongladda
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Rattapha Chinli
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Duangjai Boonlert
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sara Sabrina Ferdous
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - S. M. Mazidur Rahman
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Arfatur Rahman
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Shahriar Ahmed
- Mycobacteriology Laboratory, Infectious Diseases Division, International Center for Diarrhoeal Diseases Research, Dhaka, Bangladesh
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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17
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Pholwat S, Liu J, Stroup S, Jacob ST, Banura P, Moore CC, Huang F, Laufer MK, Houpt E, Guler JL. The Malaria TaqMan Array Card Includes 87 Assays for Plasmodium falciparum Drug Resistance, Identification of Species, and Genotyping in a Single Reaction. Antimicrob Agents Chemother 2017; 61:e00110-17. [PMID: 28264857 PMCID: PMC5404514 DOI: 10.1128/aac.00110-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/02/2017] [Indexed: 11/20/2022] Open
Abstract
Antimalarial drug resistance exacerbates the global disease burden and complicates eradication efforts. To facilitate the surveillance of resistance markers in countries of malaria endemicity, we developed a suite of TaqMan assays for known resistance markers and compartmentalized them into a single array card (TaqMan array card, TAC). We included 87 assays for species identification, for the detection of Plasmodium falciparum mutations associated with chloroquine, atovaquone, pyrimethamine, sulfadoxine, and artemisinin resistance, and for neutral single nucleotide polymorphism (SNP) genotyping. Assay performance was first optimized using DNA from common laboratory parasite lines and plasmid controls. The limit of detection was 0.1 to 10 pg of DNA and yielded 100% accuracy compared to sequencing. The tool was then evaluated on 87 clinical blood samples from around the world, and the malaria TAC once again achieved 100% accuracy compared to sequencing and in addition detected the presence of mixed infections in clinical samples. With its streamlined protocol and high accuracy, this malaria TAC should be a useful tool for large-scale antimalarial resistance surveillance.
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Affiliation(s)
- Suporn Pholwat
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Shevin T Jacob
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
| | - Patrick Banura
- Department of Community Health, Masaka Regional Referral Hospital, Masaka, Uganda
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Fang Huang
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Miriam K Laufer
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Jennifer L Guler
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
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18
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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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19
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Microfluidics: innovative approaches for rapid diagnosis of antibiotic-resistant bacteria. Essays Biochem 2017; 61:91-101. [PMID: 28258233 DOI: 10.1042/ebc20160059] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/14/2017] [Accepted: 01/18/2017] [Indexed: 11/17/2022]
Abstract
The emergence of antibiotic-resistant bacteria has become a major global health concern. Rapid and accurate diagnostic strategies to determine the antibiotic susceptibility profile prior to antibiotic prescription and treatment are critical to control drug resistance. The standard diagnostic procedures for the detection of antibiotic-resistant bacteria, which rely mostly on phenotypic characterization, are time consuming, insensitive and often require skilled personnel, making them unsuitable for point-of-care (POC) diagnosis. Various molecular techniques have therefore been implemented to help speed up the process and increase sensitivity. Over the past decade, microfluidic technology has gained great momentum in medical diagnosis as a series of fluid handling steps in a laboratory can be simplified and miniaturized on to a small platform, allowing marked reduction of sample amount, high portability and tremendous possibility for integration with other detection technologies. These advantages render the microfluidic system a great candidate to be developed into an easy-to-use sample-to-answer POC diagnosis suitable for application in remote clinical settings. This review provides an overview of the current development of microfluidic technologies for the nucleic acid based and phenotypic-based detections of antibiotic resistance.
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20
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Ebers A, Stroup S, Mpagama S, Kisonga R, Lekule I, Liu J, Heysell S. Determination of plasma concentrations of levofloxacin by high performance liquid chromatography for use at a multidrug-resistant tuberculosis hospital in Tanzania. PLoS One 2017; 12:e0170663. [PMID: 28141813 PMCID: PMC5283651 DOI: 10.1371/journal.pone.0170663] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 01/09/2017] [Indexed: 11/18/2022] Open
Abstract
Therapeutic drug monitoring may improve multidrug-resistant tuberculosis (MDR-TB) treatment outcomes. Levofloxacin demonstrates significant individual pharmacokinetic variability. Thus, we sought to develop and validate a high-performance liquid chromatography (HPLC) method with ultraviolet (UV) detection for levofloxacin in patients on MDR-TB treatment. The HPLC-UV method is based on a solid phase extraction (SPE) and a direct injection into the HPLC system. The limit of quantification was 0.25 μg/mL, and the assay was linear over the concentration range of 0.25—15 μg/mL (y = 0.5668x—0.0603, R2 = 0.9992) for the determination of levofloxacin in plasma. The HPLC-UV methodology achieved excellent accuracy and reproducibility along a clinically meaningful range. The intra-assay RSD% of low, medium, and high quality control samples (QC) were 1.93, 2.44, and 1.90, respectively, while the inter-assay RSD% were 3.74, 5.65, and 3.30, respectively. The mean recovery was 96.84%. This method was then utilized to measure levofloxacin concentrations from patients’ plasma samples from a retrospective cohort of consecutive enrolled subjects treated for MDR-TB at the national TB hospital in Tanzania during 5/3/2013–8/31/2015. Plasma was collected at 2 hours after levofloxacin administration, the time of estimated peak concentration (eCmax) treatment. Forty-one MDR-TB patients had plasma available and 39 had traceable programmatic outcomes. Only 13 (32%) patients had any plasma concentration that reached the lower range of the expected literature derived Cmax with the median eCmax being 5.86 (3.33–9.08 μg/ml). Using Classification and Regression Tree analysis, an eCmax ≥7.55 μg/mL was identified as the threshold which best predicted cure. Analyzing this CART derived threshold on treatment outcome, the time to sputum culture conversion was 38.3 ± 22.7 days vs. 47.8 ± 26.5 days (p = 0.27) and a greater proportion were cured, in 10 out of 15 (66.7%) vs. 6 out of 18 (33.3%) (p = 0.06) respectively. Furthermore, one patient with an eCmax/minimum inhibitory concentration (MIC) of only 1.13 acquired extensively drug resistant (XDR)-TB while undergoing treatment. The individual variability of levofloxacin concentrations in MDR-TB patients from Tanzania supports further study of the application of onsite therapeutic drug monitoring and MIC testing.
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Affiliation(s)
- Andrew Ebers
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, United States of America
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, United States of America
| | - Stellah Mpagama
- Kibong'oto Infectious Disease Hospital, Kilimanjaro, Tanzania
| | - Riziki Kisonga
- Kibong'oto Infectious Disease Hospital, Kilimanjaro, Tanzania
| | - Isaack Lekule
- Kibong'oto Infectious Disease Hospital, Kilimanjaro, Tanzania
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, United States of America
| | - Scott Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, United States of America
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Nayak S, Blumenfeld NR, Laksanasopin T, Sia SK. Point-of-Care Diagnostics: Recent Developments in a Connected Age. Anal Chem 2017; 89:102-123. [PMID: 27958710 PMCID: PMC5793870 DOI: 10.1021/acs.analchem.6b04630] [Citation(s) in RCA: 281] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Samiksha Nayak
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nicole R. Blumenfeld
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Tassaneewan Laksanasopin
- Biological Engineering Program, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok 10140, Thailand
| | - Samuel K. Sia
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
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22
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Foongladda S, Banu S, Pholwat S, Gratz J, O-Thong S, Nakkerd N, Chinli R, Ferdous SS, Rahman SMM, Rahman A, Ahmed S, Heysell S, Sariko M, Kibiki G, Houpt E. Comparison of TaqMan(®) Array Card and MYCOTB(TM) with conventional phenotypic susceptibility testing in MDR-TB. Int J Tuberc Lung Dis 2016; 20:1105-12. [PMID: 27393547 PMCID: PMC4937751 DOI: 10.5588/ijtld.15.0896] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 03/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although phenotypic drug susceptibility testing (DST) is endorsed as the standard for second-line drug testing of Mycobacterium tuberculosis, it is slow and laborious. METHODS We evaluated the accuracy of two faster, easier methodologies that provide results for multiple drugs: a genotypic TaqMan(®) Array Card (TAC) and the Sensititre(®) MYCOTB(TM) plate. Both methods were tested at three central laboratories in Bangladesh, Tanzania, and Thailand with 212 multidrug-resistant tuberculosis (MDR-TB) isolates and compared with the laboratories' phenotypic method in use. RESULTS The overall accuracy for ethambutol, streptomycin, amikacin, kanamycin, ofloxacin, and moxifloxacin vs. the phenotypic standard was 87% for TAC (range 70-99) and 88% for the MYCOTB plate (range 76-98). To adjudicate discordances, we re-defined the standard as the consensus of the three methods, against which the TAC and MYCOTB plate yielded 94-95% accuracy, while the phenotypic result yielded 93%. Some isolates with genotypic mutations and high minimum inhibitory concentration (MIC) were phenotypically susceptible, and some isolates without mutations and low MIC were phenotypically resistant, questioning the phenotypic standard. CONCLUSIONS In our view, the TAC, the MYCOTB plate, and the conventional phenotypic method have similar performance for second-line drugs; however, the former methods offer speed, throughput, and quantitative DST information.
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Affiliation(s)
- S Foongladda
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - S Banu
- International Center for Diarrheal Diseases and Research, Dhaka, Bangladesh
| | - S Pholwat
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - J Gratz
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - S O-Thong
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - N Nakkerd
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - R Chinli
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - S S Ferdous
- International Center for Diarrheal Diseases and Research, Dhaka, Bangladesh
| | - S M M Rahman
- International Center for Diarrheal Diseases and Research, Dhaka, Bangladesh
| | - A Rahman
- International Center for Diarrheal Diseases and Research, Dhaka, Bangladesh
| | - S Ahmed
- International Center for Diarrheal Diseases and Research, Dhaka, Bangladesh
| | - S Heysell
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - M Sariko
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - G Kibiki
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | - E Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
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23
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Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study. J Clin Microbiol 2016; 54:2058-67. [PMID: 27225403 PMCID: PMC4963505 DOI: 10.1128/jcm.00535-16] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/19/2016] [Indexed: 11/20/2022] Open
Abstract
Increasingly complex drug-resistant tuberculosis (DR-TB) is a major global health concern and one of the primary reasons why TB is now the leading infectious cause of death worldwide. Rapid characterization of a DR-TB patient's complete drug resistance profile would facilitate individualized treatment in place of empirical treatment, improve treatment outcomes, prevent amplification of resistance, and reduce the transmission of DR-TB. The use of targeted next-generation sequencing (NGS) to obtain drug resistance profiles directly from patient sputum samples has the potential to enable comprehensive evidence-based treatment plans to be implemented quickly, rather than in weeks to months, which is currently needed for phenotypic drug susceptibility testing (DST) results. In this pilot study, we evaluated the performance of amplicon sequencing of Mycobacterium tuberculosis DNA from patient sputum samples using a tabletop NGS technology and automated data analysis to provide a rapid DST solution (the Next Gen-RDST assay). One hundred sixty-six out of 176 (94.3%) sputum samples from the Republic of Moldova yielded complete Next Gen-RDST assay profiles for 7 drugs of interest. We found a high level of concordance of our Next Gen-RDST assay results with phenotypic DST (97.0%) and pyrosequencing (97.8%) results from the same clinical samples. Our Next Gen-RDST assay was also able to estimate the proportion of resistant-to-wild-type alleles down to mixtures of ≤1%, which demonstrates the ability to detect very low levels of resistant variants not detected by pyrosequencing and possibly below the threshold for phenotypic growth methods. The assay as described here could be used as a clinical or surveillance tool.
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24
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Desjardins CA, Cohen KA, Munsamy V, Abeel T, Maharaj K, Walker BJ, Shea TP, Almeida DV, Manson AL, Salazar A, Padayatchi N, O'Donnell MR, Mlisana KP, Wortman J, Birren BW, Grosset J, Earl AM, Pym AS. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. Nat Genet 2016; 48:544-51. [PMID: 27064254 PMCID: PMC4848111 DOI: 10.1038/ng.3548] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 03/18/2016] [Indexed: 12/19/2022]
Abstract
A more complete understanding of the genetic basis of drug resistance in Mycobacterium tuberculosis is critical for prompt diagnosis and optimal treatment, particularly for toxic second-line drugs such as D-cycloserine. Here we used the whole-genome sequences from 498 strains of M. tuberculosis to identify new resistance-conferring genotypes. By combining association and correlated evolution tests with strategies for amplifying signal from rare variants, we found that loss-of-function mutations in ald (Rv2780), encoding L-alanine dehydrogenase, were associated with unexplained drug resistance. Convergent evolution of this loss of function was observed exclusively among multidrug-resistant strains. Drug susceptibility testing established that ald loss of function conferred resistance to D-cycloserine, and susceptibility to the drug was partially restored by complementation of ald. Clinical strains with mutations in ald and alr exhibited increased resistance to D-cycloserine when cultured in vitro. Incorporation of D-cycloserine resistance in novel molecular diagnostics could allow for targeted use of this toxic drug among patients with susceptible infections.
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Affiliation(s)
| | - Keira A Cohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Vanisha Munsamy
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, the Netherlands
| | - Kashmeel Maharaj
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Bruce J Walker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Terrance P Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Deepak V Almeida
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Abigail L Manson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alex Salazar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, the Netherlands
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Max R O'Donnell
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University College of Physicians and Surgeons, New York, New York, USA
- Department of Epidemiology, Columbia Mailman School of Public Health, New York, New York, USA
| | - Koleka P Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Jennifer Wortman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Bruce W Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jacques Grosset
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alexander S Pym
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
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25
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Zimenkov DV, Kulagina EV, Antonova OV, Zhuravlev VY, Gryadunov DA. Simultaneous drug resistance detection and genotyping of Mycobacterium tuberculosis using a low-density hydrogel microarray. J Antimicrob Chemother 2016; 71:1520-31. [PMID: 26929267 DOI: 10.1093/jac/dkw015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/11/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Nucleic acid amplification tests are widely used in TB diagnostics. Priority tasks in their development consist of increasing the specificity and sensitivity of the detection of resistance to a wide spectrum of anti-TB drugs. METHODS We developed a multiplexed assay allowing the detection of 116 drug resistance-determining mutations in the rpoB, katG, inhA, ahpC, gyrA, gyrB, rrs, eis and embB genes in the Mycobacterium tuberculosis complex genome and six SNPs to identify the main lineages circulating in Russia. The assay is based on the amplification of 17 fragments of the genome using the universal primer adapter technique and heat pulses at the elongation step, followed by hybridization on a microarray. RESULTS The method was evaluated using 264 pairs of clinical samples and corresponding isolates. A significant proportion (25%) of smear-negative samples were correctly analysed by microarray analysis in addition to 96% of smear-positive samples. The sensitivity and specificity of the assay exceeded 90% for rifampicin, isoniazid, ofloxacin and second-line injection drugs. In agreement with previous studies, the specificity of ethambutol resistance was as low as 57%, while the sensitivity was 89.9%. Strong association of the Beijing lineage with a resistant phenotype was observed. Euro-American lineage strains, excluding Ural and LAM, were predominantly associated with the susceptible phenotype. CONCLUSIONS The developed test has a high sensitivity and specificity and can be directly applied to clinical samples. The combination of mutation-based drug resistance profiling and basic genotyping could be useful for clinical microbiology studies and epidemiological surveillance of the M. tuberculosis complex.
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Affiliation(s)
- Danila V Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 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
| | | | - Dmitry A Gryadunov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
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26
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Ison SA, Delannoy S, Bugarel M, Nagaraja TG, Renter DG, den Bakker HC, Nightingale KK, Fach P, Loneragan GH. Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique. Appl Environ Microbiol 2016; 82:640-9. [PMID: 26567298 PMCID: PMC4711113 DOI: 10.1128/aem.03182-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition of a Shiga toxin-encoding gene. Targeted amplicon sequencing using next-generation sequencing technology of 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) and three SNPs differentiating Shiga toxin-positive (stx-positive) strains from Shiga toxin-negative (stx-negative) strains were used to infer the phylogenetic relationships of 178 E. coli O26:H11 strains (6 stx-positive strains and 172 stx-negative AEEC strains) from cattle feces to 7 publically available genomes of human clinical strains. The AEEC cattle strains displayed synonymous SNP genotypes with stx2-positive sequence type 29 (ST29) human O26:H11 strains, while stx1 ST21 human and cattle strains clustered separately, demonstrating the close phylogenetic relatedness of these Shiga toxin-negative AEEC cattle strains and human clinical strains. With the exception of seven stx-negative strains, five of which contained espK, three stx-related SNPs differentiated the STEC strains from non-STEC strains, supporting the hypothesis that these AEEC cattle strains could serve as a potential reservoir for new or existing pathogenic human strains. Our results support the idea that targeted amplicon sequencing for SNP genotyping expedites strain identification and genetic characterization of E. coli O26:H11, which is important for food safety and public health.
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Affiliation(s)
- Sarah A Ison
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Sabine Delannoy
- ANSES Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Marie Bugarel
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Tiruvoor G Nagaraja
- Department of Diagnostic Medicine Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - David G Renter
- Department of Diagnostic Medicine Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Henk C den Bakker
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Kendra K Nightingale
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
| | - Patrick Fach
- ANSES Food Safety Laboratory, Platform IdentyPath, Université Paris-Est, Maisons-Alfort, France
| | - Guy H Loneragan
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, Texas, USA
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27
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Heaney J, Rolfe K, Gleadall NS, Greatorex JS, Curran MD. Low-Density TaqMan® Array Cards for the Detection of Pathogens. METHODS IN MICROBIOLOGY 2015; 42:199-218. [PMID: 38620215 PMCID: PMC7172410 DOI: 10.1016/bs.mim.2015.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Real-time PCR assays have revolutionised diagnostic microbiology over the past 15 years or more. Adaptations and improvements over that time frame have led to the development of multiplex assays. However, limitations in terms of available fluorophores has meant the number of assays which can be combined has remained in single figures. This latter limitation has led to the focus tending to be on individual pathogens and their detection. This chapter describes the development of TaqMan® Array Cards (TACs), technology which allows the detection of multiple pathogens (up to 48 targets) from a single nucleic acid extract, utilising small volumes and real-time PCR. This in turn lends itself to a syndromic approach to infectious disease diagnosis. Using the examples of TACs we have developed in our own laboratory, as well as others, we explain the design, optimisation and use of TACs for respiratory, gastrointestinal and liver infections. Refinement of individual assays is discussed as well as the incorporation of appropriate internal and process controls onto the array cards. Finally, specific examples are given of instances where the assays have had a direct, positive impact on patient care.
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Affiliation(s)
- Jude Heaney
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Institute of Hepatology, Foundation for Liver Research, London, United Kingdom
| | - Kathryn Rolfe
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
| | - Nicholas S. Gleadall
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
| | - Jane S. Greatorex
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
| | - Martin D. Curran
- Public Health England, Cambridge University Hospitals NHS, Cambridge, United Kingdom
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28
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Colman RE, Schupp JM, Hicks ND, Smith DE, Buchhagen JL, Valafar F, Crudu V, Romancenco E, Noroc E, Jackson L, Catanzaro DG, Rodwell TC, Catanzaro A, Keim P, Engelthaler DM. Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing. PLoS One 2015; 10:e0126626. [PMID: 25970423 PMCID: PMC4430321 DOI: 10.1371/journal.pone.0126626] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/03/2015] [Indexed: 12/20/2022] Open
Abstract
Undetected and untreated, low-levels of drug resistant (DR) subpopulations in clinical Mycobacterium tuberculosis (Mtb) infections may lead to development of DR-tuberculosis, potentially resulting in treatment failure. Current phenotypic DR susceptibility testing has a theoretical potential for 1% sensitivity, is not quantitative, and requires several weeks to complete. The use of "single molecule-overlapping reads" (SMOR) analysis with next generation DNA sequencing for determination of ultra-rare target alleles in complex mixtures provides increased sensitivity over standard DNA sequencing. Ligation free amplicon sequencing with SMOR analysis enables the detection of resistant allele subpopulations at ≥0.1% of the total Mtb population in near real-time analysis. We describe the method using standardized mixtures of DNA from resistant and susceptible Mtb isolates and the assay's performance for detecting ultra-rare DR subpopulations in DNA extracted directly from clinical sputum samples. SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations. This will provide insights into interventions aimed at suppressing minor DR subpopulations before they become clinically significant.
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MESH Headings
- Antitubercular Agents/pharmacology
- Antitubercular Agents/therapeutic use
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Frequency
- Genetic Loci
- High-Throughput Nucleotide Sequencing
- Humans
- Microbial Sensitivity Tests
- Molecular Diagnostic Techniques
- Mycobacterium tuberculosis/genetics
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Rebecca E. Colman
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - James M. Schupp
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Nathan D. Hicks
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - David E. Smith
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Jordan L. Buchhagen
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Faramarz Valafar
- San Diego State University, San Diego, CA, United States of America
| | - Valeriu Crudu
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Elena Romancenco
- University of California San Diego, San Diego, CA, United States of America
| | - Ecaterina Noroc
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Lynn Jackson
- University of California San Diego, San Diego, CA, United States of America
| | - Donald G. Catanzaro
- University of Arkansas College of Education and Health Professions, Fayetteville, AR, United States of America
| | - Timothy C. Rodwell
- University of California San Diego, San Diego, CA, United States of America
| | - Antonino Catanzaro
- University of California San Diego, San Diego, CA, United States of America
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
- Center for Microbial Genetics & Genomics, Northern Arizona University, Flagstaff, AZ, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
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