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Ghazvini K, Khoshbakht R, Tadayon K, Mosavari N, BahramiTaghanaki HR, Mohammadi GR, Rashti Baf M, Nourian K, Samiei A, Ghavidel M. Genotyping of Mycobacterium tuberculosis complex isolated from humans and animals in northeastern Iran. Sci Rep 2023; 13:6746. [PMID: 37185604 PMCID: PMC10127167 DOI: 10.1038/s41598-023-33740-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The objective of this study was to genotype Mycobacterium tuberculosis complex isolated from humans and cattle in northern Iran. Over the course of one year, a total of 120 human and 21 cattle isolates were tested using region of difference (RD)-based polymerase chain reaction (PCR) and mycobacterial interspersed repetitive unites-variable number tandem repeats (MIRU-VNTR). In M. tuberculosis, out of 120 isolates investigated, the most common genotype detected was NEW-1 (53.3%), followed by CAS/ Delhi (24.1%), Haarlem (5%), Beijing (4.16%), Uganda I (4.16%), S (3.3%), Ural (0.83%), TUR (0.83%), Uganda II (0.83%), Lam (0.83%) and Cameroon (0.83%). The HGDI rate was 0.9981 and the clustering rate was 10.83. Of the isolates, QUB26 had the highest allele diversity (h: 0.76), while the loci Mtub29 and MIRU24 had the lowest (h: 0). In M. Bovis, out of 123 collected tissue samples, 21 (17%) grew on culture media. The HGDI rate was 0.71 and clustering rate was 85.7%. The locus ETRC had the highest allele diversity (h: 0.45). The findings of this study suggest that there is high genetic diversity among M. tuberculosis isolates in Khorasan Razavi Province, which is consistent with similar results from other studies in other provinces in Iran and neighboring countries. This indicates that the prevalent genotypes in this study are spreading in the Middle East region. Furthermore, considering that M. Bovis isolates were identified in two clusters, it seems that all of them have a common origin and are circulating among the livestock farms in the province.
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Affiliation(s)
- Kiarash Ghazvini
- Antimicrobial Resistance Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reza Khoshbakht
- Department of Laboratory Sciences, School of Paramedical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Keyvan Tadayon
- Department of Microbiology, Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nader Mosavari
- PPD Tuberculin Department, Razi Vaccine and Serum Research Institute, (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | | | - Gholam Reza Mohammadi
- Department of Clinical Sciences, School of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Rashti Baf
- Deputy of Veterinary Administration of Khorasan Razavi Province, Mashhad, Iran
| | - Kimiya Nourian
- Department of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amin Samiei
- Tuberculosis and Leprosy Coordinator at Health Chancellor, Health Center of Khorasan State, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahdis Ghavidel
- Shahid Hasheminejad Hospital, Mashhad University of Medical Sciences, Mashhad, Iran.
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Chu P, Shi J, Dong F, Yang H, Zhao S, Liu G, Zheng H, Liu J, Li H, Lu J. Bacteremia tuberculosis among HIV‐negative children in China. Pediatr Investig 2022; 6:197-206. [PMID: 36203521 PMCID: PMC9523815 DOI: 10.1002/ped4.12342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/21/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Ping Chu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute Beijing Children's Hospital, Capital Medical University, National Center for Children's Health Beijing China
- Beijing Advanced Innovation Center for Big Data‐Based Precision Medicine Beihang University & Capital Medical University Beijing China
| | - Jin Shi
- Department of Tuberculosis Beijing Tuberculosis and Thoracic Tumor Research Institute Beijing Chest Hospital Capital Medical University Beijing China
| | - Fang Dong
- Department of Laboratory Medicine Beijing Children's Hospital Capital Medical University, National Center for Children's Health Beijing China
| | - Hui Yang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute Beijing Children's Hospital, Capital Medical University, National Center for Children's Health Beijing China
| | - Shunying Zhao
- Department 2 of Respiratory Medicine Beijing Children's Hospital Capital Medical University National Center for Children's Health Beijing China
| | - Gang Liu
- Department of Infectious Disease Beijing Children's Hospital, Capital Medical University, National Center for Children's Health Beijing China
| | - Huyong Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center Beijing Children's Hospital Capital Medical University, National Center for Children's Health Beijing China
| | - Jinrong Liu
- Department 2 of Respiratory Medicine Beijing Children's Hospital Capital Medical University National Center for Children's Health Beijing China
| | - Huimin Li
- Department 2 of Respiratory Medicine Beijing Children's Hospital Capital Medical University National Center for Children's Health Beijing China
| | - Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute Beijing Children's Hospital, Capital Medical University, National Center for Children's Health Beijing China
- Beijing Advanced Innovation Center for Big Data‐Based Precision Medicine Beihang University & Capital Medical University Beijing China
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In Vitro Susceptibility Testing of GSK656 against Mycobacterium Species. Antimicrob Agents Chemother 2020; 64:AAC.01577-19. [PMID: 31791947 DOI: 10.1128/aac.01577-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 11/25/2019] [Indexed: 02/03/2023] Open
Abstract
In this study, we aimed to assess the in vitro susceptibility to GSK656 among multiple mycobacterial species and to investigate the correlation between leucyl-tRNA synthetase (LeuRS) sequence variations and in vitro susceptibility to GSK656 among mycobacterial species. A total of 187 mycobacterial isolates, comprising 105 Mycobacterium tuberculosis isolates and 82 nontuberculous mycobacteria (NTM) isolates, were randomly selected for the determination of in vitro susceptibility. For M. tuberculosis, 102 of 105 isolates had MICs of ≤0.5 mg/liter, demonstrating a MIC50 of 0.063 mg/liter and a MIC90 of 0.25 mg/liter. An epidemiological cutoff value of 0.5 mg/liter was proposed for identification of GSK656-resistant M. tuberculosis strains. For NTM, the MIC50 and MIC90 values were >8.0 mg/liter for both Mycobacterium intracellulare and Mycobacterium avium In contrast, all Mycobacterium abscessus isolates had MICs of ≤0.25 mg/liter, yielding a MIC90 of 0.063 mg/liter. LeuRS from M. abscessus showed greater sequence similarity to M. tuberculosis LeuRS than to LeuRSs from M. avium and M. intracellulare Sequence alignment revealed 28 residues differing between LeuRSs from M. avium and M. intracellulare and LeuRSs from M. tuberculosis and M. abscessus; among them, 15 residues were in the drug binding domain. Structure modeling revealed that several different residues were close to the tRNA-LeuRS interface or the entrance of the drug-tRNA binding pocket. In conclusion, our data demonstrate significant species diversity in in vitro susceptibility to GSK656 among various mycobacterial species. GSK656 has potent efficacy against M. tuberculosis and M. abscessus, whereas inherent resistance was noted for M. intracellulare and M. avium.
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Kargarpour Kamakoli M, Hadifar S, Khanipour S, Farmanfarmaei G, Fateh A, Siadat SD, Vaziri F. Comparison of MIRU-VNTR genotyping between old and fresh clinical samples in tuberculosis. Infect Dis (Lond) 2019; 51:659-667. [PMID: 31314640 DOI: 10.1080/23744235.2019.1638963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Background: Twenty-four loci mycobacterial interspersed repetitive unit-variable number tandem repeat analysis (MIRU-VNTR) is extensively used for genotyping and detection of polyclonal infections in tuberculosis. The aim of the present study was to compare the direct and indirect MIRU-VNTR genotyping and detection of polyclonal infections between old and fresh clinical samples. Method: Two series of TB samples were collected for comparison. After genomic DNA extraction from clinical samples and their respective cultures, 24 loci MIRU-VNTR was performed. Results: In the 14 old samples, no mixed infections were observed, in clinical samples and their respective cultures. In nine fresh samples, 44.4% of mixed infection was observed in the clinical samples, but no mixed infections were observed in their respective cultures. Surprisingly, in the old samples, 92.86% of samples (13/14) had an allelic change between clinical samples and their respective cultures. On the other hand, in fresh samples, only one sample (1/9) had an allelic change between clinical samples and their respective cultures. Conclusions: We concluded that 24 loci MIRU-VNTR undoubtedly is successful in direct genotyping of clinical samples, especially for the fresh samples. However, selecting starting material, such as clinical sample or respective culture can be controversial for the old samples. Regarding polyclonal infections, the fresh samples gives us a better view to detect these infections, especially in the clinical sample.
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Affiliation(s)
- Mansour Kargarpour Kamakoli
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Shima Hadifar
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Sharareh Khanipour
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Ghazaleh Farmanfarmaei
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Abolfazl Fateh
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Seyed Davar Siadat
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Farzam Vaziri
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
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Genetic diversity of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in the capital of Iran. Mol Phylogenet Evol 2018; 132:46-52. [PMID: 30513341 DOI: 10.1016/j.ympev.2018.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 11/24/2018] [Accepted: 11/26/2018] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Evaluation of the genetic diversity of Mycobacterium tuberculosis (M.tb) and determining if the association between a specific genotype and the site of infection is crucial. Accordingly, the current study aimed at comparing predominant M.tb genotypes in pulmonary (PTB) and extrapulmonary tuberculosis (EPTB) isolates circulating in the capital of Iran. METHODS The genetic diversity of culture-confirmed PTB and EPTB isolates were evaluated by Spoligotyping and MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat) typing methods. Genotyping data were analyzed with SITVIT, MIRU-VNTRplus, and TBminer databases. To assess adjusted associations, chi-square/the Fisher exact test and multiple logistic regression model were applied. RESULTS URAL2 (NEW-1) (28/88; 31.8%) and CAS1-DELHI (25/84; 29.8%) genotypes were predominant in EPTB and PTB strains, respectively. Based on MIRU-VNTR typing, 158 different MIRU-VNTR patterns were identified. Clustering rate and minimum estimate of the proportion of TB caused by recent transmission was 4.1% and 8.1%, respectively. CONCLUSIONS The current study provided new insight into circulating genotypes of M.tb in PTB and EPTB patients in Tehran, Iran. This low percentage of TB transmission rate, demonstrated that mode of TB transmission was mainly associated with reactivation of latent TB rather than recently transmitted infection in this region. There was no significant difference in the association between the genotypes of M.tb strains and the site of the disease.
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Challenge in direct Spoligotyping of Mycobacterium tuberculosis: a problematic issue in the region with high prevalence of polyclonal infections. BMC Res Notes 2018; 11:486. [PMID: 30016972 PMCID: PMC6050728 DOI: 10.1186/s13104-018-3579-z] [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: 04/19/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Based on our recent studies the prevalence of polyclonal infection in tuberculosis clinical specimens is more than 50% in Tehran, Iran. With this background, Spoligotyping was performed on clinical specimens and their respective cultures, and we examined whether mixed infections interfere with the results or not. RESULTS Based on the Spoligotyping pattern, among the fourteen patients, 57.1% had different genotypes in clinical samples and their respective cultures. These discrepant patterns were suggestive of polyclonal infections in clinical samples with possible overlapping Spoligotype patterns. We propose that in societies with high mixed infections (e.g. Iran), direct Spoligotyping on clinical samples can be controversial.
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He P, Wang H, Luo J, Yan Y, Chen Z. A Real-Time PCR with Melting Curve Analysis for Molecular Typing of Vibrio parahaemolyticus. Curr Microbiol 2018; 75:1206-1213. [PMID: 29796853 DOI: 10.1007/s00284-018-1511-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/16/2018] [Indexed: 12/19/2022]
Abstract
Foodborne disease caused by Vibrio parahaemolyticus is a serious public health problem in many countries. Molecular typing has a great scientific significance and application value for epidemiological research of V. parahaemolyticus. In this study, a real-time PCR with melting curve analysis was established for molecular typing of V. parahaemolyticus. Eighteen large variably presented gene clusters (LVPCs) of V. parahaemolyticus which have different distributions in the genome of different strains were selected as targets. Primer pairs of 18 LVPCs were distributed into three tubes. To validate this newly developed assay, we tested 53 Vibrio parahaemolyticus strains, which were classified in 13 different types. Furthermore, cluster analysis using NTSYS PC 2.02 software could divide 53 V. parahaemolyticus strains into six clusters at a relative similarity coefficient of 0.85. This method is fast, simple, and conveniently for molecular typing of V. parahaemolyticus.
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Affiliation(s)
- Peiyan He
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Jiaxing, 314050, Zhejiang, China
| | - Henghui Wang
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Jiaxing, 314050, Zhejiang, China
| | - Jianyong Luo
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Jiaxing, 314050, Zhejiang, China
| | - Yong Yan
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Jiaxing, 314050, Zhejiang, China
| | - Zhongwen Chen
- Jiaxing Center for Disease Control and Prevention, No. 486, Wen Qiao Road, Jiaxing, 314050, Zhejiang, China.
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A 10-Year Comparative Analysis Shows that Increasing Prevalence of Rifampin-Resistant Mycobacterium tuberculosis in China Is Associated with the Transmission of Strains Harboring Compensatory Mutations. Antimicrob Agents Chemother 2018; 62:AAC.02303-17. [PMID: 29378712 DOI: 10.1128/aac.02303-17] [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] [Received: 11/08/2017] [Accepted: 01/20/2018] [Indexed: 11/20/2022] Open
Abstract
In this work, we conducted bacterial population profile studies to assess trends of rifampin (RIF) resistance of Mycobacterium tuberculosis isolates collected across China from 2005 to 2015. Totals of 273 and 269 randomly selected M. tuberculosis isolates from 2005 and 2015, respectively, were analyzed. The rates of RIF resistance (36.4%), isoniazid resistance (39.0%), and levofloxacin resistance (25.7%) in 2015 were significantly higher than those in 2005 (28.2%, 30.0%, and 15.4%, respectively; P < 0.05). Genotypic data revealed 256 (95.2%) Beijing-type isolates in 2015, a rate significantly higher than that in 2005 (86.4%) (P < 0.01). A higher proportion of mutations was identified within the rifampin resistance-determining region (RRDR) of rpoB in isolates from 2015 (99.0%) than in 2005 isolates (85.7%, P < 0.01). In addition, a significantly higher proportion of RIF-resistant isolates carrying compensatory mutations was observed in 2015 (31.6%) than in 2005 (7.8%). Notably, the great majority of these compensatory mutations (91.9%) were observed in isolates that harbored a mutation of codon 531 of the rpoB gene. In conclusion, our data demonstrate that resistance to RIF, isoniazid, and levofloxacin has become significantly more prevalent during the past decade. In addition, the prevalence of the Beijing genotype significantly increased from 2005 to 2015. Notably, a significantly increased frequency of strains with mutations in rpoC or rpoA is observed among those that have codon 531 mutations, which suggests that they may be compensatory and may play a role in facilitating transmission.
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Lian DS, Zeng HS. Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis. Compr Rev Food Sci Food Saf 2017; 16:1281-1295. [DOI: 10.1111/1541-4337.12297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Dong-Sheng Lian
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
| | - Hua-Song Zeng
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
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Lin HC, Perng CL, Lai YW, Lin FG, Chiang CJ, Lin HA, Jou R, Chiueh TS. Molecular screening of multidrug-resistance tuberculosis by a designated public health laboratory in Taiwan. Eur J Clin Microbiol Infect Dis 2017; 36:2431-2439. [PMID: 28840388 PMCID: PMC5688198 DOI: 10.1007/s10096-017-3082-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 07/31/2017] [Indexed: 11/29/2022]
Abstract
This manuscript describes our experience in early identifying MDR-TB cases in high-risk populations by setting up a single-referral molecular diagnosis laboratory in Taiwan. Taiwan Centers for Disease Control designated a single-referral laboratory to provide the GenoType MTBDRplus test for screening high-risk MDR-TB populations nationwide in 2012-2015. A total of 5,838 sputum specimens from 3,308 patients were tested within 3 days turnaround time. Compared with the conventional culture and drug susceptibility testing, the overall performance of the GenoType MTBDRplus test for detecting TB infection showed accuracy of 70.7%, sensitivity of 85.9%, specificity of 65.7%, positive predictive value of 45.5%, and negative predictive value of 93.3%. And the accuracy of detecting rifampin (RIF) resistance, isoniazid (INH) resistance, and MDR-TB (resistant to at least RIF and INH) were 96.5%, 95.2%, and 97.7%, respectively. MDR-TB contacts presented a higher rate of mutated codons 513-519, GenoType MTBDRplus banding pattern: rpoB WT3(-), and rpoB WT4(-) than the treatment failure group. The MDR-TB contact group also had a higher rate of inhA C15T mutation, banding pattern: inhA WT1(-), and inhA MUT1(+) than the recurrent group. Resistance profiles of MDR-TB isolates also varied geographically. The referral molecular diagnosis system contributed to rapid detection and initiation of appropriate therapy.
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Affiliation(s)
- H-C Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - C-L Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - Y-W Lai
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan, Republic of China
| | - F-G Lin
- School of Public Health, National Defense Medical Center, Taipei, Taiwan, Republic of China
| | - C-J Chiang
- Chest Hospital, Ministry of Health and Welfare, Tainan, Taiwan, Republic of China
| | - H-A Lin
- Division of Infection, Department of Medicine, Tri-Service General Hospital SongShan Branch, Taipei, Taiwan, Republic of China
| | - R Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, No. 161, Kun-Yang Street, Taipei, 11561, Republic of China. .,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan, Republic of China.
| | - T-S Chiueh
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan, Republic of China. .,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan, Republic of China. .,Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, No. 5 Fu-Hsing Street, Kuei-Shan, TaoYuan City, 33305, Taiwan, Republic of China.
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Lian DS, Zhao SJ. Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease. Clin Chem Lab Med 2017; 54:707-38. [PMID: 26352354 DOI: 10.1515/cclm-2015-0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.
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Pang Y, Zhang Z, Wang Y, Wang S, Song Y, Zhao B, Zhou Y, Ou X, Li Q, Xia H, Zheng Y, Fang X, Zhao Y. Genotyping and Prevalence of Pyrazinamide- and Moxifloxacin-Resistant Tuberculosis in China, 2000 to 2010. Antimicrob Agents Chemother 2017; 61:e02170-16. [PMID: 27919887 PMCID: PMC5278687 DOI: 10.1128/aac.02170-16] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 11/23/2016] [Indexed: 11/20/2022] Open
Abstract
We investigated the prevalence, trends, and risk factors for pyrazinamide (PZA) and moxifloxacin (MOX) resistance among tuberculosis (TB) cases in China and also analyzed the population structure of Mycobacterium tuberculosis strains. All the M. tuberculosis strains enrolled in this study were collected from the national TB prevalence surveys. Each strain was genotyped by analyzing the regions of RD105 and IS6110 in the NTF region. The Bactec MGIT 960 system was used to detect the drug susceptibility of M. tuberculosis isolates to PZA and MOX. Based on the genotyping results, 241 (66.4%) strains were classified as Beijing genotype in 2000, which was significantly lower than in 2010 (76.2%, P < 0.01). The proportion of the modern Beijing genotype increased significantly from 49.6% in 2000 to 68.1% in 2010 (P < 0.01), while no significant difference was observed in the rate of ancient Beijing genotype between 2000 and 2010 (P = 0.676). In addition, we found that the proportion of PZA resistance in 2010 (15.0%) was significantly higher than that in 2000 (9.6%, P = 0.04). For MOX, there were more MOX-resistant isolates detected in 2010 (7.7%) than in 2000 (3.0%). In conclusion, our data demonstrate that the Beijing genotype was the predominant M. tuberculosis lineage during the past decade. The proportion of Beijing genotype isolates significantly increased from 2000 to 2010, largely due to an increase in the modern Beijing sublineage. In addition, resistance to PZA and MOX increased significantly in China between 2000 and 2010.
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Affiliation(s)
- Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhijian Zhang
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yufeng Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qiang Li
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zheng
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangqun Fang
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Wang J, Dong P, Wu W, Pan X, Liang X. High-throughput thermal stability assessment of DNA hairpins based on high resolution melting. J Biomol Struct Dyn 2016; 36:1-13. [PMID: 28024437 DOI: 10.1080/07391102.2016.1266967] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
On the basis of high-resolution melting, a high-throughput approach to measure melting temperatures (Tms) of short DNA hairpins was developed. With this method, Tms of thousands of triloop, tetraloop, and pentaloop hairpins involving various loop sequences and various closing base pairs (cbp) were obtained in hours. The stability of triloop hairpins decreased with the change of cbp (5'-3') in the order of c-g > g-c > t-a ≥ a-t, showing that the cbp of 5'-Pyr-Pur-3' (Pyr = pyrimidine, Pur = purine) contributed more stability than 5'-Pur-Pyr-3'. For tetraloop hairpins, GNNA, GNAB, and CNNG (N = A, G, C, or T; B = G, C, or T) were found to be highly stable irrespective of the cbp type. TNNA was also stable in both g-c and a-t families, while CGNA only in the c-g family. Pentaloop hairpins of cTGNAGg, cGNYNAg (Y = T or C) and cCGNNAg were exceptionally stable motifs. In most cases, pyrimidine-rich loops were more favorable to stabilize the whole structure than purine-rich ones. The present approach showed a good performance in assessing the thermal stability of large amounts of DNA hairpins comprehensively. These data are useful to understand the sequence dependence of the stability of DNA secondary structures and promising to improve the structure simulation by consummating basic databases.
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Affiliation(s)
- Jing Wang
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Ping Dong
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Wei Wu
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xiaoming Pan
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
| | - Xingguo Liang
- a College of Food Science and Engineering , Ocean University of China , Qingdao 266003 , China
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Factors Associated with Missed Detection of Mycobacterium tuberculosis by Automated BACTEC MGIT 960 System. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5972021. [PMID: 28078294 PMCID: PMC5204086 DOI: 10.1155/2016/5972021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/03/2016] [Indexed: 01/29/2023]
Abstract
Despite the demonstration of excellent performance, mycobacterial growth in BACTEC MGIT 960 can go undetected. The aim of this study was to investigate the prevalence of “false-negative” culture sample in Beijing and the potential factors associated with the detection failures by MGIT 960. Of the 577 sputum samples tested, 141 (24.4%) were culture-positive for mycobacteria, of which 133 (94.3%) were automatically determined by MGIT 960 system and 8 (5.7%) were positive for visual growth (false negative by MGIT). Statistical analysis showed that positive grade of specimen had no influence on the false-negative rate by MGIT 960 system (χ2 = 2.207, P = 0.820). In addition, the mean time to detection (TTD) was 241.4 (range: 224–261) hours for false-negative group and 186.8 (range: 173–199) hours for positive group. The difference in TTD between false-negative and positive groups was statistically significant (P < 0.01). In conclusion, our data demonstrate that the automatic MGIT missed a small portion of bacteriological mycobacterial patients. In addition, the poor growth rate rather than the low grade of AFB smear is associated with the detection failure by MGIT. Our findings highlight the notion that manual inspection for all instrument-negative MGIT tubes will bring about considerable benefit to patients and clinicians.
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15
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Galarza M, Fasabi M, Levano KS, Castillo E, Barreda N, Rodriguez M, Guio H. High-resolution melting analysis for molecular detection of multidrug resistance tuberculosis in Peruvian isolates. BMC Infect Dis 2016; 16:260. [PMID: 27278526 PMCID: PMC4899911 DOI: 10.1186/s12879-016-1615-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 06/03/2016] [Indexed: 12/30/2022] Open
Abstract
Background The emergence of multidrug-resistant strains is a major health problem especially for countries with high TB incidence such as Peru. In this study, we evaluated High Resolution Melting (HRM) assay in Peruvian isolates for the detection of mutations within rpoB, katG genes and promoter region inhA to determine isoniazid and rifampicin resistance in Mycobacterium tuberculosis (Mtb). Methods DNA samples extracted from a total of 167 clinical isolates of Mtb, 89 drug-sensitive and 78 multidrug-resistant, were blindly analyzed by HRM analysis and verified by DNA sequencing. Results The HRM analysis generated patterns that were specific to distinguish between sensitive and resistance isolates. The sensitivity and specificity of the HRM assays in comparison with drug susceptibility testing (DST) for detection of rifampicin resistance were 98.7 % and 97.5 %, and for isoniazid resistance were 98.7 % and 100 %. Conclusion This study suggests that HRM Analysis could help with rapid diagnosis of MDR-TB cases in Peru.
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Affiliation(s)
- Marco Galarza
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Manuel Fasabi
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Kelly S Levano
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru
| | - Edith Castillo
- Laboratorio de Referencia Regional de Tuberculosis y Microbiología, DIRESA Callao, Lima, Peru
| | - Nadia Barreda
- Laboratorio de Referencia Regional de Tuberculosis y Microbiología, DIRESA Callao, Lima, Peru
| | - Mitzi Rodriguez
- Laboratorio de Referencia Regional de Tuberculosis y Microbiología, DIRESA Callao, Lima, Peru
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Instituto Nacional de Salud, Lima, Peru.
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16
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Haarlem 3 is the predominant genotype family in multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis in the capital of Iran: A 5-year survey. J Glob Antimicrob Resist 2016; 5:7-10. [PMID: 27436458 DOI: 10.1016/j.jgar.2016.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/16/2015] [Accepted: 01/20/2016] [Indexed: 11/23/2022] Open
Abstract
The objective of this study was to further understand the genetic diversity of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis isolates prevalent in Tehran, the capital city of Iran. From January 2010 to March 2015, a total of 723 M. tuberculosis strains were isolated from patients with pulmonary tuberculosis (TB). A total of 23 MDR, pre-XDR and XDR M. tuberculosis isolates were genotyped by spoligotyping and 24-loci mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing. The results showed that the MDR, pre-XDR and XDR M. tuberculosis strains mainly belonged to the Haarlem 3 genotype (11/23; 47.8%), followed by the Beijing family (9/23; 39.1%). In addition, the 23 strains were clustered into 21 genotypes using a 24-loci MIRU-VNTR. In conclusion, Haarlem 3 genotype was the predominant genotype among the isolates from MDR-TB cases in this study, which could be of special concern.
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17
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Wang LQ, Wang TY, Sun QL, Qie YQ. Correlation between thyroglobulin gene polymorphisms and autoimmune thyroid disease. Mol Med Rep 2015; 12:4469-4475. [PMID: 26099577 DOI: 10.3892/mmr.2015.3978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 05/19/2015] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to detect thyroglobulin (Tg) gene polymorphisms in a Han Chinese population from the Northern regions of Henan province, China, and to study the correlation between Tg gene polymorphisms and autoimmune thyroid disease (AITD). A total of 270 patients with AITD and 135 healthy controls were enrolled. Genomic DNA was extracted and fluorescence polymerase chain reaction analysis was performed; high‑resolution melting curve analysis (HRMA) was used to detect single‑nucleotide polymorphisms (SNPs) in exons 10, 12 and 33 of the Tg gene. SNPs were then correlated with AITD. Han people from the Northern regions of Henan displayed four Tg exon SNPs: E10SNP24 T/G, E10SNP158 T/C, E12SNP A/G and E33SNP C/T. Several allele and genotype frequencies differed between the AITD group and the healthy control group (Tg E10SNP: Allele T, P<0.01; allele G, P<0.01; and Tg genotype GG, P<0.01; genotype TG, P<0.01. Tg E12SNP: Allele A, P<0.01; allele G, P<0.01; Tg genotype GG, P<0.01; genotype AG, P<0.01). A statistically significant difference in the frequency of selected Tg SNPs haplotypes was also present between AITD patients and healthy controls (P<0.05). There was no significant difference in haplotypes between various types of AITD (hypothyroidism, hyperthyroidism and Hashimoto's disease). The Tg SNP frequency distribution was significantly different between Han populations of the Northern regions of Henan province and the Xi'an regions of Shaanxi province. The results of the present study suggested that specific Tg gene alleles or genotypes were correlated with AITD; specific Tg SNP haplotypes were associated with hypothyroidism, hyperthyroidism and Hashimoto's disease, and the Tg SNP frequency distribution differed depending on the geographical location of the Han Chinese populations.
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Affiliation(s)
- Li-Qiang Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Qiu-Li Sun
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Yong-Qiang Qie
- Department of Nuclear Medicine, Anyang Regional Hospital of Puyang City, Anyang, Henan 455000, P.R. China
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18
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Pang Y, Lu J, Yang J, Wang Y, Cohen C, Ni X, Zhao Y. A novel method for diagnosis of smear-negative tuberculosis patients by combining a random unbiased Phi29 amplification with a specific real-time PCR. Tuberculosis (Edinb) 2015; 95:411-4. [PMID: 25957821 DOI: 10.1016/j.tube.2015.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 03/27/2015] [Accepted: 03/29/2015] [Indexed: 11/18/2022]
Abstract
In this study, we develop a novel method for diagnosis of smear-negative tuberculosis patients by performing a random unbiased Phi29 amplification prior to the use of a specific real-time PCR. The limit of detection (LOD) of the conventional real-time PCR was 100 colony-forming units (CFU) of MTB genome/reaction, while the REPLI real-time PCR assay could detect 0.4 CFU/reaction. In comparison with the conventional real-time PCR, REPLI real-time PCR shows better sensitivity for the detection of smear-negative tuberculosis (P = 0.015).
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Affiliation(s)
- Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Jian Yang
- Shaanxi Tuberculosis Dispensary, Shaanxi, China
| | - Yufeng Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chad Cohen
- McGill International TB Centre, Montreal, Quebec, Canada
| | - Xin Ni
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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19
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Zhang Z, Lu J, Liu M, Wang Y, Qu G, Li H, Wang J, Pang Y, Liu C, Zhao Y. Genotyping and molecular characteristics of multidrug-resistant Mycobacterium tuberculosis isolates from China. J Infect 2015; 70:335-45. [DOI: 10.1016/j.jinf.2014.11.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 01/02/2023]
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20
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Zhang Z, Pang Y, Wang Y, Cohen C, Zhao Y, Liu C. Differences in risk factors and drug susceptibility between Mycobacterium avium and Mycobacterium intracellulare lung diseases in China. Int J Antimicrob Agents 2015; 45:491-5. [PMID: 25795316 DOI: 10.1016/j.ijantimicag.2015.01.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/15/2023]
Abstract
The aim of this study was to investigate the differences in risk factors and drug susceptibility between Mycobacterium avium and Mycobacterium intracellulare lung diseases in China. In total, 452 nontuberculous mycobacteria (NTM) strains isolated from patients with NTM lung diseases in four specialised TB hospitals were enrolled in this study. The minimum inhibitory concentration (MIC) was used to evaluate the drug susceptibility of M. avium and M. intracellulare isolates. In addition, demographic and clinical characteristics of patients with NTM lung diseases caused by M. avium and M. intracellulare were analysed. Of 452 NTM isolates, M. intracellulare (188; 41.6%) was the most frequently isolated organism. The percentages of moxifloxacin- and linezolid-resistant strains among the M. intracellulare isolates were significantly lower than those among the M. avium group (P=0.003 and P<0.001, respectively). In contrast, M. avium harboured a lower proportion of rifampicin-resistant strains than M. intracellulare (P=0.005). Among patients with M. intracellulare lung diseases, the percentages of patients aged >64 years and patients with chronic obstructive pulmonary disease (COPD) were significantly higher than among patients with M. avium (P=0.008 for age and P=0.001 for COPD). In conclusion, these data demonstrated that M. intracellulare was the most common NTM species in China. This study also revealed that M. intracellulare and M. avium differed in their drug susceptibility profiles. In addition, clinical cases of M. intracellulare lung diseases were more likely to be found in the aged population and among patients with COPD co-morbidity.
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Affiliation(s)
- Zhijian Zhang
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian District, Beijing 100853, China
| | - Yu Pang
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian District, Beijing 100853, China; National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District, Beijing 102206, China.
| | - Yufeng Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District, Beijing 102206, China
| | - Chad Cohen
- McGill International TB Centre, Montreal, Quebec, Canada
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District, Beijing 102206, China.
| | - Changting Liu
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, 28 Fuxing Road, Haidian District, Beijing 100853, China.
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21
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Keeratipibul S, Silamat P, Phraephaisarn C, Srisitthinam D, Takahashi H, Chaturongkasumrit Y, Vesaratchavest M. Genotyping ofSalmonella entericaSerovar Typhimurium Isolates by Multilocus Variable Number of Tandem Repeat High-Resolution Melting Analysis (MLV-HRMA). Foodborne Pathog Dis 2015; 12:8-20. [DOI: 10.1089/fpd.2014.1761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Suwimon Keeratipibul
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Panusanun Silamat
- Department of Food Technology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Daranee Srisitthinam
- Department of Research and Development, Betagro Science Center Co. Ltd., Pathum Thani, Thailand
| | - Hajime Takahashi
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yuphakhun Chaturongkasumrit
- Department of Food Science and Technology, Faculty of Marine Science, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Mongkol Vesaratchavest
- Department of Research and Development, Betagro Science Center Co. Ltd., Pathum Thani, Thailand
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22
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Zhang D, An J, Wang Y, Pang Y. Genetic diversity of multidrug-resistant tuberculosis in a resource-limited region of China. Int J Infect Dis 2014; 29:7-11. [DOI: 10.1016/j.ijid.2014.05.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/02/2014] [Accepted: 05/21/2014] [Indexed: 10/24/2022] Open
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Zhang D, Liu B, Wang Y, Pang Y. Rapid molecular screening for multidrug-resistant tuberculosis in a resource-limited region of China. Trop Med Int Health 2014; 19:1259-66. [PMID: 25040060 DOI: 10.1111/tmi.12359] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To investigate the molecular characteristics of MDR and XDR strains circulating in Chongqing, China. METHODS The drug target genes conferring for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), ofloxacin (OFLX) and kanamycin (KAN) resistance were screened by DNA sequencing to determine the mutation frequencies in this area. RESULTS Drug susceptibility of 208 MDR isolates revealed that 132 (63.46%) were resistant to streptomycin (SM), 96 (46.15%) to ethambutol (EMB), 51 (24.52%) to ofloxacin (OFLX), and 26 (12.50%) to kanamycin (KAN); six (2.88%) isolates had XDR profiles. In comparison with the drug susceptibility phenotype, the sensitivity of drug resistance by DNA sequencing was 91.83% for RIF, 87.50% for INH, 66.67% for EMB, 74.51% for OFLX and 53.85% for KAN resistance. 12.50% of EMB- and 1.27% of OFLX-susceptible isolates were harboured genetic mutations in embB and gyrA, respectively. CONCLUSION Our findings demonstrate that the hot-spot regions localised in rpoB, katG and inhA genes serve as excellent markers for the corresponding drug resistance, while EMB, OFLX or KAN drug-resistant TB cases may not be identifiable by scanning embB, gyrA, rrs and eis promoter in Chongqing, indicating that further studies on the drug resistance mechanisms of EMB, OFLX and KAN are urgently needed to elucidate the low sensitivity between genomic substitutions and drug-resistant phenotype.
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Affiliation(s)
- Dan Zhang
- Yongchuan Hospital, Chongqing Medical University, Chongqing, China
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24
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Molecular and phenotypic characterization of multidrug-resistant Mycobacterium tuberculosis isolates resistant to kanamycin, amikacin, and capreomycin in China. Eur J Clin Microbiol Infect Dis 2014; 33:1959-66. [DOI: 10.1007/s10096-014-2144-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/28/2014] [Indexed: 10/25/2022]
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25
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Lu J, Liu M, Wang Y, Pang Y, Zhao Z. Mechanisms of fluoroquinolone monoresistance inMycobacterium tuberculosis. FEMS Microbiol Lett 2014; 353:40-8. [DOI: 10.1111/1574-6968.12401] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery; Beijing Pediatric Research Institute; Beijing Children's Hospital affiliated to Capital Medical University; Beijing China
- National Center for Tuberculosis Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing China
| | - Min Liu
- Liaoning Provincial Center for Disease Control and Prevention; Shenyang China
| | - Yufeng Wang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery; Beijing Pediatric Research Institute; Beijing Children's Hospital affiliated to Capital Medical University; Beijing China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention; Chinese Center for Disease Control and Prevention; Beijing China
| | - Zhuo Zhao
- Liaoning Provincial Center for Disease Control and Prevention; Shenyang China
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26
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Molecular characteristics of MDR Mycobacterium tuberculosis strains isolated in Fujian, China. Tuberculosis (Edinb) 2014; 94:159-61. [DOI: 10.1016/j.tube.2013.03.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 03/07/2013] [Accepted: 03/23/2013] [Indexed: 11/23/2022]
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27
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Zhang Z, Pang Y, Wang Y, Liu C, Zhao Y. Beijing genotype of Mycobacterium tuberculosis is significantly associated with linezolid resistance in multidrug-resistant and extensively drug-resistant tuberculosis in China. Int J Antimicrob Agents 2013; 43:231-5. [PMID: 24439458 DOI: 10.1016/j.ijantimicag.2013.12.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/12/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022]
Abstract
Linezolid (LNZ) is a promising antimicrobial agent for the treatment of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB). To investigate the efficacy of LNZ among MDR-TB and XDR-TB in China, the LNZ susceptibility of 158 MDR-TB isolates from the national drug resistance survey was determined by the minimum inhibitory concentration method. The 158 MDR-TB isolates were also sequenced in the 23S rRNA, rplC and rplD genes conferring LNZ resistance and were typed using spoligotyping to identify the Beijing genotype of Mycobacterium tuberculosis. Overall, the prevalence of LNZ-resistant isolates was 10.8% (17/158) among MDR-TB isolates circulating in China. Beijing genotype was significantly associated with LNZ resistance in MDR-TB and XDR-TB (odds ratio=4.66, 95% confidence interval 1.03-21.16; P=0.033). In addition, a higher frequency of LNZ-resistant isolates was observed among XDR-TB strains (60%) compared with the MDR (5.6%; P<0.001) and pre-XDR groups (12.2%; P=0.004). Mutations in 23S rRNA and rplC were responsible for only 29.4% of LNZ-resistant M. tuberculosis among MDR-TB isolates, and a novel non-synonymous substitution His155Asp in rplC was first identified to be contributing to low-level LNZ resistance (2μg/mL) in M. tuberculosis. The unsatisfactory correlation between mutant genotypes highlights the urgent need to investigate another mechanism for LNZ resistance that has not yet been described.
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Affiliation(s)
- Zhijian Zhang
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, 28# Fuxing Road, Haidian District, Beijing 100853, China
| | - Yu Pang
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, 28# Fuxing Road, Haidian District, Beijing 100853, China; National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District, Beijing 102206, China.
| | - Yufeng Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District, Beijing 102206, China
| | - Changting Liu
- Respiratory Diseases Department of Nanlou, Chinese People's Liberation Army General Hospital, 28# Fuxing Road, Haidian District, Beijing 100853, China.
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District, Beijing 102206, China.
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28
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Prevalence and molecular characterization of fluoroquinolone-resistant Mycobacterium tuberculosis isolates in China. Antimicrob Agents Chemother 2013; 58:364-9. [PMID: 24165186 DOI: 10.1128/aac.01228-13] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
China is one of the countries with the highest burdens of multidrug-resistant (MDR) and fluoroquinolone (FQ)-resistant tuberculosis (TB) globally. Nevertheless, knowledge about the prevalence and molecular characterization of FQ-resistant Mycobacterium tuberculosis isolates from this region remains scant. In this study, 138 M. tuberculosis isolates determined by the agar proportion susceptibility method to be resistant to ofloxacin (OFX) were enrolled from a national drug resistance survey of China. All these strains were tested for susceptibility to ofloxacin, levofloxacin, moxifloxacin, gatifloxacin, and sparfloxacin using liquid Middlebrook 7H9 medium. The entire gyrA and gyrB genes conferring FQ resistance were sequenced, and spoligotyping was performed to distinguish different genotypes. Overall, the prevalence of resistance in China was highest for ofloxacin (3.76%), intermediate for levofloxacin (3.18%) and moxifloxacin (3.12%), and lowest for sparfloxacin (1.91%) and gatifloxacin (1.33%). Mutations in the gyrA gene were observed in 89 (64.5%) out of the 138 OFX-resistant M. tuberculosis strains. Positions 94 and 90 were the most frequent sites of mutation conferring FQ resistance on these strains, accounting for high-level FQ resistance. Furthermore, the Beijing genotype showed no association with high-level FQ resistance or distribution in hot spots in the quinolone resistance-determining region (QRDR) of gyrA. Our findings provide essential implications for the feasibility of genotypic tests relying on detection of mutations in the QRDR of gyrA and the shorter first-line treatment regimens based on FQs in China.
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29
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Combining COLD-PCR and high-resolution melt analysis for rapid detection of low-level, rifampin-resistant mutations in Mycobacterium tuberculosis. J Microbiol Methods 2013; 93:32-6. [DOI: 10.1016/j.mimet.2013.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 01/06/2013] [Accepted: 01/11/2013] [Indexed: 12/17/2022]
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30
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Pang Y, Song Y, Xia H, Zhou Y, Zhao B, Zhao Y. Risk factors and clinical phenotypes of Beijing genotype strains in tuberculosis patients in China. BMC Infect Dis 2012; 12:354. [PMID: 23245430 PMCID: PMC3538705 DOI: 10.1186/1471-2334-12-354] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 11/19/2012] [Indexed: 01/05/2023] Open
Abstract
Background Beijing genotype strains are the most predominant strains in China. The aim of this study was to explore risk factors and clinical phenotypes associated with infection with Beijing genotype strains among tuberculosis patients in China. Methods Using data and strains derived from the first Chinese national drug resistance base-line survey, we performed a statistical analysis of the relationship between different genotypes, demographic characteristics and clinical phenotypes. Result Of patients infected with the 3634 strains for which detailed information was available, we found that people in young age groups [aged under 25 years, OR (95% CI): 1.30(1.03-1.62)], urban people [OR (95% CI): 1.18 (0.47-0.94)], or of Hui ethnicity [OR (95% CI): 1.96 (1.10-3.50)] or those needing retreatment [OR (95% CI): 1.22 (1.03-1.43)] were more likely to be infected with Beijing genotype strains compared with patients who were rural, or of Han ethnicity or those with new TB cases. In contrast, Uyghur [OR (95% CI): 0.45 (0.30-0.67)], or Zhuang ethnicities [OR (95% CI): 0.30 (0.19-0.48)], presented lower than average risk in infections with the Beijing genotype strain. In addition, a higher proportion of patients with hemoptysis [OR (95% CI): 0.81 (0.69-0.94)] and chest pain [OR (95% CI): 0.79 (0.69-0.91)] were infected with non-Beijing genotype strains than with Beijing genotype strains. Conclusions In China, young age group, urban people, Hui ethnicity and the earlier treated patients are all high risk factors for infection with Beijing genotype strains, while Uyghur and Zhuang ethnicity are lower than average risk factors for infection. The high rate of chest symptoms occurring in non-Beijing genotype infected patients indicates that more attention should be paid to basic research on non-Beijing genotype strains.
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Affiliation(s)
- Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
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31
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Study of the rifampin monoresistance mechanism in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2012. [PMID: 23208715 DOI: 10.1128/aac.01024-12] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rifampin (RIF) susceptibility is a key factor in determining the treatment effectiveness of the standardized treatment regimens. In Mycobacterium tuberculosis, both target gene mutation and the efflux pump play major roles in the resistance to antituberculosis drugs. By eliminating RIF-resistant strains with rpoB mutation, the choice of RIF-monoresistant strains may allow us to identify the RIF-specific efflux pump genes. This study explored the RIF monoresistance mechanism in M. tuberculosis. Data from DNA sequencing and MIC measurements revealed that specific mutations, including Ser531Leu and His526Asp in RpoB, show high-level drug resistance. Three-dimensional structure modeling provided further evidence that the affinity between RIF and RpoB mutants was in accordance with the drug resistance level of the corresponding isolates. Furthermore, transcription-level analysis among the nonmutated isolates indicated that three efflux pumps (Rv0783, Rv2936, and Rv0933) might be involved in exporting RIF from the cell. Compared to 8 μg/ml for wild-type Escherichia coli, the MICs for the transgenic E. coli strains with either Rv0783 or Rv2936 were 32 and 16 μg/ml, respectively. In conclusion, our study indicated that several RpoB mutant types, including Ser531Leu and His526Asp, show high-level RIF resistance attributed to low affinity between RpoB mutant proteins and RIF. In addition, this work demonstrates that Rv2936 and Rv0783 may be responsible for low-level resistance to RIF by exporting RIF from cells. The predicted structure of RpoB and the newly identified efflux pumps in this study will provide a novel approach to design new drugs and develop novel diagnosis technologies.
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Zhang D, An J, Wang J, Hu C, Wang Z, Zhang R, Wang Y, Pang Y. Molecular typing and drug susceptibility of Mycobacterium tuberculosis isolates from Chongqing Municipality, China. INFECTION GENETICS AND EVOLUTION 2012. [PMID: 23183314 DOI: 10.1016/j.meegid.2012.10.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
China's tuberculosis (TB) burden is second only to that of India worldwide. In Chongqing, the largest municipality in southwestern China, although the prevalence of both TB and drug-resistant TB is higher than in other municipalities, the molecular characteristics and drug susceptibility phenotypes are poorly known. In this study, 297 Mycobacterium tuberculosis isolates from Chongqing were genotyped with spacer oligonucleotide typing (spoligotyping) and 28-locus MIRU-VNTR (24-locus MIRU-VNTR scheme and 4 other loci). Spoligotyping results were compared with drug-resistant profiles. Patients who showed clustering by both spoligotyping and 28-locus MIRU-VNTR were interviewed to investigate their detailed contact history. Our data demonstrated that the Beijing genotype was the most prevalent genotype, and ST1 was the most predominant lineage in Chongqing. The Beijing genotype was significantly associated with ethambutol resistance and multidrug-resistant phenotypes. A combination of the 10 most polymorphic loci permitted to achieve higher discriminatory power than 24-VNTR. In addition, a presumed transmission pathway was observed in a cluster of patients with the same MIRU-VNTR profile. The 10-VNTR locus set is suitable for genotyping of Mycobacterium tuberculosis in Chongqing.
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Affiliation(s)
- Dan Zhang
- Yongchuan Hospital, Chongqing Medical University, Chongqing, China
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Perng CL, Chen HY, Chiueh TS, Wang WY, Huang CT, Sun JR. Identification of non-tuberculous mycobacteria by real-time PCR coupled with a high-resolution melting system. J Med Microbiol 2012; 61:944-951. [PMID: 22493281 DOI: 10.1099/jmm.0.042424-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are increasingly important opportunistic pathogens responsible for a variety of clinical diseases. The aim of this study was to evaluate a novel technique, real-time PCR coupled with high-resolution melting analysis (real-time PCR-HRMA), for NTM identification. Two pairs of unique primers targeted to the 16S rRNA gene and the 16S-23S internal transcribed spacer region were selected for further evaluation. A total of 149 mycobacterial clinical isolates were subjected to analysis using the real-time PCR-HRMA system. Overall, 134 NTM identified by the 16S rRNA full-gene sequencing method were categorized into four major groups: Mycobacterium avium complex, Mycobacterium chelonae group, Mycobacterium gordonae and Mycobacterium fortuitum group. Of the 134 prevalent mycobacterial isolates, 101 mycobacteria (75.4 %) could be identified correctly by the real-time PCR-HRMA system. The individual sensitivities for the M. avium complex, M. chelonae group, M. gordonae and M. fortuitum groups were 90.9, 89.1, 100 and 36.8 %, respectively. The specificity of identifying these groups varied from 96.4 to 100 %. When identification failed, mostly it was attributable to various species in the M. fortuitum group. The real-time PCR-HRMA system is therefore a rapid and sensitive method for identifying prevalent NTM in a clinical laboratory.
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Affiliation(s)
- Cherng-Lih Perng
- Graduate Institute of Pathology, National Defense Medical Center, Taipei, Taiwan, ROC.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hsing-Yu Chen
- Department of Clinical Pathology, Taipei City Hospital Renai Branch, Taipei, Taiwan, ROC
| | - Tzong-Shi Chiueh
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan, ROC.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Wei-Yao Wang
- Division of Infectious Disease, Fong-Yuan Hospital, Taichung, Taiwan, ROC.,Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chun-Ting Huang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
| | - Jun-Ren Sun
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan, ROC.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital and National Defense Medical Center, Taipei, Taiwan, ROC
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Douarre PE, Cashman W, Buckley J, Coffey A, O'Mahony JM. High resolution melting PCR to differentiate Mycobacterium avium subsp. paratuberculosis“cattle type” and “sheep type”. J Microbiol Methods 2012; 88:172-4. [DOI: 10.1016/j.mimet.2011.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 10/11/2011] [Indexed: 11/24/2022]
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