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Castro-Rodriguez B, Franco-Sotomayor G, Rodriguez-Pazmiño ÁS, Cardenas-Franco GE, Orlando SA, Hermoso de Mendoza J, Parra-Vera H, García-Bereguiain MÁ. Rapid and accurate identification and differentiation of Mycobacterium tuberculosis and non-tuberculous mycobacteria using PCR kits available in a high-burden setting. Front Public Health 2024; 12:1358261. [PMID: 38628855 PMCID: PMC11018931 DOI: 10.3389/fpubh.2024.1358261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
Infections caused by mycobacteria, including Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), are a major public health issue worldwide. An accurate diagnosis of mycobacterial species is a challenge for surveillance and treatment, particularly in high-burden settings usually associated with low- and middle-income countries. In this study, we analyzed the clinical performance of two commercial PCR kits designed for the identification and differentiation of MTBC and NTM, available in a high-burden setting such as Ecuador. A total of 109 mycobacteria isolates were included in the study, 59 of which were previously characterized as M. tuberculosis and the other 59 as NTM. Both kits displayed great clinical performance for the identification of M. tuberculosis, with 100% sensitivity. On the other hand, for NTM, one of the kits displayed a good clinical performance with a sensitivity of 94.9% (CI 95%: 89-100%), while the second kit had a reduced sensitivity of 77.1% (CI 95%: 65-89%). In conclusion, one of the kits is a fast and reliable tool for the identification and discrimination of MTBC and NTM from clinical isolates.
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Affiliation(s)
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
- Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | | | - Solón Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
- Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - Henry Parra-Vera
- Centro de Investigación Microbiológica (CIM), Guayaquil, Ecuador
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Radulski Ł, Krajewska-Wędzina M, Lipiec M, Weiner M, Zabost A, Augustynowicz-Kopeć E. Mycobacterial Infections in Invasive Turtle Species in Poland. Pathogens 2023; 12:pathogens12040570. [PMID: 37111456 PMCID: PMC10143171 DOI: 10.3390/pathogens12040570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Over the last 30 years, the number of invasive turtle species living in the wild has significantly increased in Poland. This proliferation carries many threats, which mainly include the displacement of native species of animals from their natural habitats. Turtles can also be reservoirs for pathogens, including bacteria from the Mycobacterium genus. In order to confirm or rule out the presence of acid-fast mycobacteria in the population of invasive turtle species, samples from carapace, plastron, internal organs and mouth cavity swabs from 125 animals were tested. Twenty-eight mycobacterial strains were isolated in culture, which were classified as atypical following multiplex-PCR reactions. The GenoType Mycobacterium Common Mycobacteria (CM) test, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, PCR-restriction fragment length polymorphism (PRA)-hsp65 and DNA sequencing were used to identify the species of isolates. Of the 28 strains, 11 were identified as M. fortuitum, 10 as M. chelonae, 3 as M. avium ssp. avium, 2 as M. nonchromogenicum and 1 each of M. neoaurum and M. scrofulaceum. The results of the research will also strengthen the understanding that these animals can be vectors for pathogens when living in the wild.
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Affiliation(s)
- Łukasz Radulski
- County Veterinary Inspectorate in Puławy, C.K. Norwida 17, 24-100 Puławy, Poland
| | - Monika Krajewska-Wędzina
- National Veterinary Research Institute, 24-100 Puławy, Poland
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Institute of Preclinical Veterinary Sciences, University of Life Sciences, 20-033 Lublin, Poland
| | - Marek Lipiec
- National Veterinary Research Institute, 24-100 Puławy, Poland
| | - Marcin Weiner
- Pope John Paul II State School of Higher Education, Sidorska 95/97, 21-500 Biała Podlaska, Poland
| | - Anna Zabost
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland
| | - Ewa Augustynowicz-Kopeć
- Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, 01-138 Warsaw, Poland
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Ledesma Y, Echeverría G, Claro-Almea FE, Silva D, Guerrero-Freire S, Rojas Y, Bastidas-Caldes C, Navarro JC, de Waard JH. The Re-Identification of Previously Unidentifiable Clinical Non-Tuberculous Mycobacterial Isolates Shows Great Species Diversity and the Presence of Other Acid-Fast Genera. Pathogens 2022; 11:pathogens11101159. [PMID: 36297216 PMCID: PMC9610484 DOI: 10.3390/pathogens11101159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 01/24/2023] Open
Abstract
Non-tuberculous mycobacteria that cannot be identified at the species level represent a challenge for clinical laboratories, as proper species assignment is key to implementing successful treatments or epidemiological studies. We re-identified forty-eight isolates of Ziehl-Neelsen (ZN)-staining-positive "acid-fast bacilli" (AFB), which were isolated in a clinical laboratory and previously identified as Mycobacterium species but were unidentifiable at the species level with the hsp65 PCR restriction fragment length polymorphism analysis (PRA). As most isolates also could not be identified confidently via 16S, hsp65, or rpoB DNA sequencing and a nBLAST search analysis, we employed a phylogenetic method for their identification using the sequences of the 16S rDNA, which resulted in the identification of most AFB and a Mycobacterium species diversity not found before in our laboratory. Most were rare species with only a few clinical reports. Moreover, although selected with the ZN staining as AFB, not all isolates belonged to the genus Mycobacterium, and we report for the first time in Latin America the isolation of Nocardia puris, Tsukamurella pulmosis, and Gordonia sputi from sputum samples of symptomatic patients. We conclude that ZN staining does not differentiate between the genus Mycobacterium and other genera of AFB. Moreover, there is a need for a simple and more accurate tree-based identification method for mycobacterial species. For this purpose, and in development in our lab, is a web-based identification system using a phylogenetic analysis (including all AFB genera) based on 16S rDNA sequences (and in the future multigene datasets) and the closest relatives.
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Affiliation(s)
- Yanua Ledesma
- Laboratorios de Investigación, Facultad de Ciencias de Salud, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Gustavo Echeverría
- Instituto de Investigación en Salud Pública y Zoonosis-CIZ, Universidad Central del Ecuador, Quito 170521, Ecuador
- Programa de Doctorado, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Franklin E. Claro-Almea
- Servicio Autónomo Instituto de Biomedicina Dr. Jacinto Convit, Universidad Central de Venezuela, Caracas 1010, Venezuela
| | - Douglas Silva
- Servicio Autónomo Instituto de Biomedicina Dr. Jacinto Convit, Universidad Central de Venezuela, Caracas 1010, Venezuela
| | - Salomé Guerrero-Freire
- Laboratorios de Investigación, Facultad de Ciencias de Salud, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
- Programa de Doctorado, Facultad de Ciencias Veterinarias, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
| | - Yeimy Rojas
- Grupo de Microbiología Aplicada, Universidad Regional Amazónica Ikiam, Tena 150102, Ecuador
| | - Carlos Bastidas-Caldes
- One Health Research Group, Facultad de Ingeniería y Ciencias Aplicadas, Biotecnología, Universidad de las Américas, Quito 170125, Ecuador
- Programa de Doctorado en Salud Pública y Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres 10003, España
| | - Juan Carlos Navarro
- Grupo de Enfermedades Emergentes, Ecoepidemiologia y Biodiversidad, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito 170107, Ecuador
| | - Jacobus H. de Waard
- Laboratorios de Investigación, Facultad de Ciencias de Salud, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
- Instituto de Investigación en Salud Pública y Zoonosis-CIZ, Universidad Central del Ecuador, Quito 170521, Ecuador
- Servicio Autónomo Instituto de Biomedicina Dr. Jacinto Convit, Universidad Central de Venezuela, Caracas 1010, Venezuela
- Correspondence:
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Aghajani J, Farnia P, Farnia P, Ghanavi J, Saif S, Marjani M, Tabarsi P, Moniri A, Abtahian Z, Hoffner S, Velayati AA. Effect of COVID-19 pandemic on incidence of mycobacterial diseases among suspected tuberculosis pulmonary patients in Tehran, Iran. Int J Mycobacteriol 2022; 11:415-422. [PMID: 36510928 DOI: 10.4103/ijmy.ijmy_167_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Recent pandemic of coronavirus SARS-CoV-2 (COVID-19) caused limitations in the country's strategies to fight against mycobacterial infections. The aim of this study was to compare the suspected tuberculosis (TB) pulmonary patients before and during the COVID-19 pandemic (January 2018-December 2021) who were referred to the National Reference TB Laboratory (NRL TB), Tehran, Iran. The mycobacterial isolated strains were identified and compared with previous data. Methods A total of 16,899 clinical samples collected from 7041 suspected pulmonary TB patients were received from 2018 to 2021. Primary isolation of Mycobacterium isolates was done on Löwenstein-Jensen medium. Then, the DNA was extracted from acid-fast bacillus culture-positive samples and identification was performed by IS6110, Hsp65, and 16S-23S rRNA genes using polymerase chain reaction (PCR), PCR-restriction fragment length polymorphism, and nested PCR methods. Results A total of 11679 specimens (69.1%) from 4866 suspected TB patients were collected in 2018-2019 and 5220 specimens (30.8%; from 2175 patients) in 2020-2021. Out of 11679 specimens, 2046 samples that belong to 852 patients were infected with Mycobacterium tuberculosis, and the remaining were non-TB Mycobacterium (NTM) species (n = 244) isolated from 102 patients. The cultures for 12894 specimens were either negative (76.3%) or contaminated (845/16899; 5%). A comparison of the total number of patients who were referred for diagnosis and treatment (954/666 patients, P > 0.05) showed a 30.1% reduction during the COVID-19 pandemic. Although, with these low number of patients, the significant increases of NTM species (P < 0.05) among suspected TB pulmonary patients were observed. Besides, new species of NTM, for example, Mycobacterium peregrinum and Mycobacterium montefiorense, were detected. For the past 20 years, these two species were not reported from pulmonary patients in Iran. Conclusions During the pandemic of COVID-19, the TB diagnosis network became irregular, as a consequence, many patients could not reach the treatment center, and this could increase the circulation of mycobacterial diseases (TB and NTM). The study shows the emergence of new opportunistic NTM species also.
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Affiliation(s)
- Jafar Aghajani
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Poopak Farnia
- Department of Biotechnology, School of Advanced Technology in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parissa Farnia
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jalaledin Ghanavi
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shima Saif
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Marjani
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afshin Moniri
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Abtahian
- Clinical Tuberculosis and Epidemiology Research Center, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sven Hoffner
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - Ali Akbar Velayati
- Mycobacteriology Research Centre, National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Clarke C, Kerr TJ, Warren RM, Kleynhans L, Miller MA, Goosen WJ. Identification and Characterisation of Nontuberculous Mycobacteria in African Buffaloes ( Syncerus caffer), South Africa. Microorganisms 2022; 10:microorganisms10091861. [PMID: 36144463 PMCID: PMC9503067 DOI: 10.3390/microorganisms10091861] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 12/04/2022] Open
Abstract
Diagnosis of bovine tuberculosis (bTB) may be confounded by immunological cross-reactivity to Mycobacterium bovis antigens when animals are sensitised by certain nontuberculous mycobacteria (NTMs). Therefore, this study aimed to investigate NTM species diversity in African buffalo (Syncerus caffer) respiratory secretions and tissue samples, using a combination of novel molecular tools. Oronasal swabs were collected opportunistically from 120 immobilised buffaloes in historically bTB-free herds. In addition, bronchoalveolar lavage fluid (BALF; n = 10) and tissue samples (n = 19) were obtained during post-mortem examination. Mycobacterial species were identified directly from oronasal swab samples using the Xpert MTB/RIF Ultra qPCR (14/120 positive) and GenoType CMdirect (104/120 positive). In addition, all samples underwent mycobacterial culture, and PCRs targeting hsp65 and rpoB were performed. Overall, 55 NTM species were identified in 36 mycobacterial culture-positive swab samples with presence of esat-6 or cfp-10 detected in 20 of 36 isolates. The predominant species were M. avium complex and M. komanii. Nontuberculous mycobacteria were also isolated from 6 of 10 culture-positive BALF and 4 of 19 culture-positive tissue samples. Our findings demonstrate that there is a high diversity of NTMs present in buffaloes, and further investigation should determine their role in confounding bTB diagnosis in this species.
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Güven Gökmen T, Yakici G, Kalayci Y, Turut N, Meral Ocal M, Haligür M, Günaydin E, Köksal F. Molecular characterization of Mycobacterium bovis strains isolated from cattle and humans by spoligotyping and 24-locus MIRU-VNTR, and prevalence of positive IGRA in slaughterhouse workers in Southern Turkey. IRANIAN JOURNAL OF VETERINARY RESEARCH 2022; 23:210-218. [PMID: 36425601 PMCID: PMC9681978 DOI: 10.22099/ijvr.2022.42580.6186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/09/2022] [Accepted: 06/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Mycobacterium bovis is a zoonotic member of the Mycobacterium tuberculosis complex with a wide range of hosts, mainly cattle. Molecular epidemiological studies should be conducted to determine the transmission route, zoonotic risk factors, and phylogenetic relationships of M. bovis strains. Aims: This study aimed to characterize bovine and human M. bovis isolates by molecular methods. METHODS Molecular characterization and clonal relationship of strains isolated from tissue and organ samples of 76 cattle with positive tuberculin tests were collected from a slaughterhouse, and four M. bovis strains isolated from clinical materials of patients with suspected pulmonary TB isolates were analyzed using 24-locus MIRU-VNTR and spoligotyping methods. QuantiFERON-TB Gold Plus (QFT-Plus; Qiagen) was used to determine the prevalence of latent TB infection among 21 slaughterhouse personnel including 7 veterinarians, 12 butchers, 1 caretaker, and 1 veterinary technician. RESULTS SB0288/SIT685 type was detected in both cattle and humans by the spoligotyping method. When evaluating MIRU-VNTR, the presence of a 100% compatible pattern between human and bovine isolates was not detected, but some human samples were found to be 91.6% similar to a bovine sample. In addition, 21 slaughterhouse workers were screened with the interferon gamma-released assay (IGRA) and a 23.8% positivity was detected. CONCLUSION Clonal similarity was determined between the bovine and human isolates using the MIRU-VNTR and spoligotyping methods and IGRA positivity in the occupational group suggested that M. bovis might be associated with pulmonary tuberculosis in humans.
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Affiliation(s)
- T. Güven Gökmen
- Department of Microbiology, Ceyhan Veterinary Faculty, Cukurova University, 01330, Adana, Turkey
| | - G. Yakici
- Tuberculosis Region Laboratory, Tropical Disease and Research Center, Cukurova University, 01330, Adana, Turkey
| | - Y. Kalayci
- Microbiology Laboratory, Adana City Hospital, 01230, Adana, Turkey
| | - N. Turut
- MSc, Microbiology Laboratory, Adana Veterinary Control Institute, 01250, Adana, Turkey
| | - M. Meral Ocal
- Department of Microbiology, Medicine Faculty, Cukurova University, 01330, Adana, Turkey
| | - M. Haligür
- Department of Pathology, Ceyhan Veterinary Faculty, Cukurova University, 01330, Adana, Turkey
| | - E. Günaydin
- Department of Microbiology, Veterinary Faculty, Kastamonu University, 37150, Kastamonu, Turkey
| | - F. Köksal
- Department of Microbiology, Medicine Faculty, Cukurova University, 01330, Adana, Turkey
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Characterization of Clinical Isolates of Mycobacterium simiae Using Drug Susceptibility Tests and Molecular Analyses. Curr Microbiol 2021; 78:2324-2331. [PMID: 33847796 DOI: 10.1007/s00284-021-02486-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Mycobacterium simiae is an emerging nontuberculous mycobacterium (NTM) and an opportunistic pathogen which is described mainly in Asia and presents in the environment that can cause pulmonary infection. The objective of this study is to characterize M. simiae clinical isolates using mycobacterial interspersed repetitive unit variable-number tandem repeats (MIRU-VNTR) typing for the differentiation of the strains. A total of 169 clinical isolates of NTM were recovered from patients suspected of having tuberculosis (TB)-like and related infections. After isolation and identification of mycobacterial strains by conventional biochemical and PCR-based tests, M. simiae strains were confirmed using restriction fragment length polymorphism (RFLP)-based identification assay. Furthermore, drug susceptibility and MIRU-VNTR typing was performed using on the clinical isolates of M. simiae. Out of 169 NTM strains, 92 (54.4%) isolates were identified as M. simiae. Antibiotic susceptibility experiments indicated that all 92 M. simiae isolates were resistant to first line antimycobacterial agents. Moreover, 8 (8.6%) M. simiae isolates were resistant to ciprofloxacin; and 6 (6.5%) were resistant to both amikacin and kanamycin, while the remaining were susceptible to second line antimycobacterial agents. MIRU-VNTR analysis showed that the M. simiae isolates were classified in four distinct M. simiae clusters and two single types. The minimum spanning analysis revealed that the isolates were grouped in three complexes. The data suggested that MIRI-VNTR typing is useful for typing of M. simiae isolates, however, MIRU-16 locus was absolutely absent in M. simiae.
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Kunduracılar H. Identification of mycobacteria species by molecular methods. Int Wound J 2019; 17:245-250. [PMID: 31863568 DOI: 10.1111/iwj.13238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/05/2019] [Accepted: 09/15/2019] [Indexed: 11/28/2022] Open
Abstract
In this study, mycobacteria, which were previously identified as Mycobacterium tuberculosis complex (MTC), and mycobacteria other than tuberculosis (MOTT) with cord factor and the p-nitro-alpha-acetyl-amino-beta-hydroxypropiophenone (NAP) test were reanalysed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis method in order to confirm the identification, and at the same time, species accepted as MOTT were identified. Although the results of the NAP test were obtained within 3-5 days, the PCR-RFLP results were obtained in 1 day. Ten species identified as MTC with the NAP test and cord factor were confirmed with the PCR-RFLP method. Fourteen species accepted as MOTT were identified as Mycobacterium species with the evaluation of the bands observed after the restriction of PCR product with the PCR-RFLP method. These were as follows: three species Mycobacterium intracellulare type I, two species Mycobacterium phlei, two species Mycobacterium kansasii, one species Mycobacterium fortuitum type I, one species Mycobacterium gordonae type I, one species Mycobacterium abscessus type I, one species Mycobacterium scrofulaceum, one species Mycobacterium szulgai type I, one species Mycobacterium avium type II, and one species Mycobacterium terrae. Hence, the results of both the cord factor and the NAP test were confirmed with the molecular method, and at the same time, mycobacteria species identification was made by determining the fastest, easiest, and the most accurate result-giving method. Because PCR-RFLP is a very rapid method that provides exact identification of mycobacteria species, it can be performed in routine procedures.
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Chen CJ, Yang YC, Huang HH, Chang TC, Lu PL. Evaluation of a membrane hybridization array for detection of Mycobacterium tuberculosis complex and resistance to isoniazid and rifampin in sputum specimens, mycobacterial liquid cultures, and clinical isolates. Kaohsiung J Med Sci 2019; 35:615-623. [PMID: 31433118 DOI: 10.1002/kjm2.12119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/16/2019] [Indexed: 11/07/2022] Open
Abstract
The gold standard of antituberculosis susceptibility testing is based on culture method which takes weeks. Rapid detection of resistance to isoniazid (INH) and rifampin (RIF) to avoid inappropriate regimens and to prevent transmission of resistant strains are important. A membrane array (BluePoint MTBDR) was developed to identify Mycobacterium tuberculosis complex (MTBC) and the genetic mutations responsible for resistance to RIF and INH. We aimed to evaluate the performance of this array for diagnosing drug-resistant MTBC. A total of 261 acid-fast bacilli positive sputum specimens, 1025 positive mycobacteria growth indicator tube (MGIT) cultures and 544 clinical isolates were analyzed. Antituberculosis susceptibility testing was the gold standard and was performed on MTBC isolated from positive MGIT cultures and on 544 clinical isolates. The sensitivity and specificity of the array to detect MTBC were 62.2% and 88.1% for sputum specimens, 100% and 97.9% for MGIT cultures. For detection of drug-resistant MTBC in positive MGIT tubes, the sensitivities of the array were 100% for RIF and 97.1% for INH, while the specificities were 99.7% and 100%, respectively. Interestingly, we noticed four genotypically RIF-resistant but phenotypically RIF-susceptible isolates and eight genotypically INH resistant but phenotypically INH-susceptible isolates. Comparing with conventional culture methods for species identification and drug susceptibility testing, the BluePoint MTBDR assay demonstrated to be a rapid test with high sensitivity and specificity to identify MTBC and to detect isoniazid and rifampin resistance when it is applied to broth culture specimens and clinical isolates.
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Affiliation(s)
- Chao-Ju Chen
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yuan-Chieh Yang
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hsin-Hui Huang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tsung Chain Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Liang Lu
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Zhou L, Ma C, Xiao T, Li M, Liu H, Zhao X, Wan K, Wang R. A New Single Gene Differential Biomarker for Mycobacterium tuberculosis Complex and Non-tuberculosis Mycobacteria. Front Microbiol 2019; 10:1887. [PMID: 31456790 PMCID: PMC6700215 DOI: 10.3389/fmicb.2019.01887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/30/2019] [Indexed: 12/28/2022] Open
Abstract
Background Tuberculosis (TB) and non-tuberculous mycobacteriosis are serious threats to health worldwide. A simple non-sequencing method is needed for rapid diagnosis, especially in less experienced hospitals, but there is no specific biomarker commonly used for all mycobacteria. The ku gene of the prokaryotic error-prone non-homologous end joining system (NHEJ) has the potential to be a highly specific detection biomarker for mycobacteria. Methods A total of 7294 mycobacterial genomes and 14 complete genomes of other families belonging to Corynebacteriales with Mycobacteriaceae were downloaded and analyzed for the existence and variation of the ku gene. Mycobacterium tuberculosis complex (MTBC) and non-tuberculosis mycobacteria (NTM)- specific primers were designed and the actual amplification and identification efficiencies were tested with 150 strains of 40 Mycobacterium species and 10 kinds of common respiratory pathogenic bacteria. Results The ku gene of the NHEJ system was ubiquitous in all genome sequenced Mycobacterium species and absent in other families of Corynebacteriales. On the one hand, as a single gene non-sequencing biomarker, its specific primers could effectively distinguish mycobacteria from other bacteria, MTBC from NTM, which would make the clinical detection of mycobacteria easy and have great clinical practical value. On the other hand, the sequence of ku gene can effectively distinguish NTM to species level with high resolution. Conclusion The Ku protein existed before the differentiation of Mycobacterium species, which was an important protein involved in maintaining of the genome’s integrity and related to the special growth stage of mycobacteria. It was rare in prokaryotes. These features made it a highly special differential biomarker for Mycobacterium.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,College of Pharmacy, Guizhou University, Guiyang, China
| | - Cuidie Ma
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Tongyang Xiao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruibai Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Nontuberculous Mycobacteria Persistence in a Cell Model Mimicking Alveolar Macrophages. Microorganisms 2019; 7:microorganisms7050113. [PMID: 31035520 PMCID: PMC6560506 DOI: 10.3390/microorganisms7050113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 12/15/2022] Open
Abstract
Nontuberculous Mycobacteria (NTM) respiratory infections have been gradually increasing. Here, THP-1 cells were used as a model to evaluate intracellular persistence of three NTM species (reference and clinical strains) in human alveolar macrophages. The contribution of phagosome acidification, nitric oxide (NO) production and cell dead on NTM intracellular fate was assessed. In addition, strains were characterized regarding their repertoire of virulence factors by whole-genome sequencing. NTM experienced different intracellular fates: M. smegmatis and M. fortuitum ATCC 6841 were cleared within 24h. In contrast, M. avium strains (reference/clinical) and M. fortuitum clinical strain were able to replicate. Despite this fact, unexpectedly high percentages of acidified phagosomes were found harbouring rab7, but not CD63. All NTM were able to survive in vitro at acidic pHs, with the exception of M. smegmatis. Our data further suggested a minor role for NO in intracellular persistence and that apoptosis mediated by caspase 8 and 3/7, but not necrosis, is triggered during NTM infection. Insights regarding the bacteria genomic backbone corroborated the virulence potential of M. avium and M. fortuitum. In conclusion, the phenotypic traits detected contrast with those described for M. tuberculosis, pointing out that NTM adopt distinct strategies to manipulate the host immune defense and persist intracellularly.
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Hung JH, Ko WC, Chen CY, Lin SH, Wu CL, Hsu SM, Teng YT, Wang SH, Tseng SH, Huang FC, Lai CC, Chen CL, Lai CH, Chen PL, Jou-Chen Huang E. Postoperative Mycobacteroides abscessus subsp. abscessus endophthalmitis: Clinical analysis of 12 clustered adults and a proposed therapeutic algorithm. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 53:766-777. [PMID: 30661953 DOI: 10.1016/j.jmii.2018.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/23/2018] [Accepted: 12/30/2018] [Indexed: 11/19/2022]
Abstract
PURPOSE Postoperative endophthalmitis caused by nontuberculous mycobacterium is a rare but devastating complication after intraocular surgery. However, optimal treatment strategies remain undetermined in view of its rarity. METHODS We investigated the cases of culture-proven postoperative Mycobacteroides abscessus subsp. abscessus endophthalmitis in southern Taiwan, focusing on clinical manifestations and microbiological study, and aimed to describe clinical staging and to propose a therapeutic modality for this disease. RESULTS Twelve cases, including two published cases, were treated in two medical centers in southern Taiwan between Aug. 2011 and Dec. 2016, and all ever received cataract surgery at one clinic. Their disease courses could be categorized into four distinct stages, i.e., the initial, quiescent, recurrent, and end stage, and some cases experienced 1-4 cycles of quiescent-recurrent stages. Although all eyes ended up with phthisis or were eviscerated, the affected eyes receiving pars plana vitrectomy (PPV) tended to become quiescent and survived longer than those without PPV (adjusted hazard ratio: 13.9, p < 0.05). Eight isolates of eight patients were available for microbiological study. All isolates were susceptible to amikacin, and inducible clarithromycin resistance was observed in 100% of isolates. CONCLUSION Despite the preservation of vision in postoperative M.abscessus endophthalmitis remained a challenge, a stage-based approach is proposed, which may facilitate decision-makings for the future study.
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Affiliation(s)
- Jia-Horung Hung
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Internal Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Diagnostic Microbiology and Antimicrobial Resistance Laboratory, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chau-Yin Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Biostatistics Consulting Center, National Cheng Kung University Hospital, Tainan, Taiwan; Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Lin Wu
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Min Hsu
- Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Ti Teng
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Hao Wang
- Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sung-Huei Tseng
- Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Fu-Chin Huang
- Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chun-Chieh Lai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Lung Chen
- Department of Ophthalmology, Chang Gung Memorial Hospital, Chiayi, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chien-Hsiung Lai
- Department of Ophthalmology, Chang Gung Memorial Hospital, Chiayi, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Internal Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Diagnostic Microbiology and Antimicrobial Resistance Laboratory, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Taiwan.
| | - Evelyn Jou-Chen Huang
- Department of Ophthalmology, Taipei Medical University Hospital, Taipei, Taiwan; Department of Ophthalmology, School of Medicine, College of Medicine, Taipei Medical University, Taiwan.
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Carneiro MDS, Nunes LDS, David SMMD, Dias CF, Barth AL, Unis G. Nontuberculous mycobacterial lung disease in a high tuberculosis incidence setting in Brazil. ACTA ACUST UNITED AC 2019; 44:106-111. [PMID: 29791549 PMCID: PMC6044650 DOI: 10.1590/s1806-37562017000000213] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 10/15/2017] [Indexed: 11/05/2022]
Abstract
Objective: The incidence of lung disease caused by nontuberculous mycobacteria (NTM) has been increasing worldwide. In Brazil, there are few studies about nontuberculous mycobacterial lung disease (NTMLD), and its prevalence is yet to be known. Our objective was to determine the specific etiology of the disease in the state of Rio Grande do Sul, Brazil, as well as the frequency and diversity of NTM species in our sample of patients. Methods: This is a retrospective analysis of the medical records of patients diagnosed with NTMLD treated in a referral center located in the city of Porto Alegre, Brazil, between 2003 and 2013. Results: Our sample comprised 100 patients. The most prevalent NTM species were Mycobacterium avium complex (MAC), in 35% of the cases; M. kansasii, in 17%; and M. abscessus, in 12%. A total of 85 patients had received previous treatment for tuberculosis. Associated conditions included structural abnormalities in the lungs, such as bronchiectasis, in 23% of the cases; COPD, in 17%; and immunosuppressive conditions, such as AIDS, in 24%. Conclusions: MAC and M. kansasii were the most prevalent species involved in NTMLD in the state, similarly to what occurs in other regions of Brazil. Data on regional epidemiology of NTMLD, its specific etiology, and associated conditions are essential to establish appropriate treatment, since each species requires specific regimens. Most patients with NTMLD had received previous tuberculosis treatment, which might lead to development of resistance and late diagnosis.
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Affiliation(s)
- Maiara Dos Santos Carneiro
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Luciana de Souza Nunes
- Laboratório de Pesquisa em Resistência Bacteriana, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brasil
| | | | | | - Afonso Luís Barth
- Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gisela Unis
- Hospital Sanatório Partenon, Porto Alegre, RS, Brasil
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Appak Ö, Türkel S, Esen N, Özkütük AA. Comparison of polymerase chain reaction-restriction enzyme analysis method and DNA sequence analysis results in the identification of non-tuberculous mycobacteria. Acta Microbiol Immunol Hung 2018; 65:515-527. [PMID: 30010392 DOI: 10.1556/030.65.2018.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The typing of non-tuberculous mycobacteria (NTM) is important from a clinical and epidemiological perspective. The polymerase chain reaction-restriction enzyme analysis (PRA) method and DNA sequence analysis method were utilized to target a gene region that codes the 65-kDa heat-shock protein for typing 150 suspected NTM samples isolated from the respiratory tract. Mycobacterium abscessus, Mycobacterium xenopi, Mycobacterium fortuitum, and Mycobacterium peregrinum were most frequently found by both methods. Six isolates that could not be defined by the PRA method were defined as Nocardia cyriacigeorgica, Nocardia abscessus, and Mycobacterium intracellulare by DNA sequence analysis. Discordance between the results of the two methods was observed for only one isolate. The isolate that was defined as Mycobacterium gordonae type 6 by the PRA method was defined as Mycobacterium senegalense by sequence analysis. The PRA method is simple and gives rapid results. Compared with DNA sequence analysis, it gives consistent and reliable results up to a ratio of 90%. DNA sequence analysis is the gold standard method in which all strains can be defined. However, given our laboratory conditions, its disadvantage is that it takes longer to reach a diagnosis than through the PRA method.
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Affiliation(s)
- Özgür Appak
- 1 Department of Medical Microbiology, Dokuz Eylul University, İzmir, Turkey
| | - Selçuk Türkel
- 2 Department of Medical Microbiology, Training and Research Hospital, Aksaray University, Aksaray, Turkey
| | - Nuran Esen
- 1 Department of Medical Microbiology, Dokuz Eylul University, İzmir, Turkey
| | - Ayşe Aydan Özkütük
- 1 Department of Medical Microbiology, Dokuz Eylul University, İzmir, Turkey
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Basein T, Gardiner BJ, Andujar Vazquez GM, Joel Chandranesan AS, Rabson AR, Doron S, Snydman DR. Microbial Identification Using DNA Target Amplification and Sequencing: Clinical Utility and Impact on Patient Management. Open Forum Infect Dis 2018; 5:ofy257. [PMID: 30539032 PMCID: PMC6284463 DOI: 10.1093/ofid/ofy257] [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: 07/25/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022] Open
Abstract
Broad-range polymerase chain reaction (PCR) is increasingly used in patients with culture-negative infections; however, few studies have assessed the diagnostic utility of this test in this context. We performed a retrospective cohort study of patients who had clinical specimens sent for broad-range PCR, aiming to evaluate performance and determine impact on patient management. Organisms were identified in 21/71 samples. High numbers of polymorphonuclear leukocytes on Gram stain (odds ratio [OR], 4.17; P = .04) and acute inflammation on histopathology (OR, 5.69; P = .02) were significantly associated with a positive result. Management was altered in 18 patients, 11 with positive and 7 with negative results. Overall, broad-range PCR assay had the highest impact in patients with microscopic evidence of inflammation. Physicians ordering this complex, difficult to interpret, and expensive test should carefully consider all available clinical information on an individualized basis to optimize its performance.
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Affiliation(s)
- Tinzar Basein
- Division of Geographic Medicine and Infectious Diseases
| | | | | | | | - Arthur R Rabson
- Department of Pathology, Tufts Medical Center and Tufts University School of Medicine, Boston, Massachusetts
| | - Shira Doron
- Division of Geographic Medicine and Infectious Diseases
| | - David R Snydman
- Division of Geographic Medicine and Infectious Diseases.,Tufts Clinical and Translational Science Institute, Tufts University, Boston, Massachusetts
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Azadi D, Motallebirad T, Ghaffari K, Shojaei H. Mycobacteriosis and Tuberculosis: Laboratory Diagnosis. Open Microbiol J 2018; 12:41-58. [PMID: 29785215 PMCID: PMC5897959 DOI: 10.2174/1874285801812010041] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/11/2018] [Accepted: 03/15/2018] [Indexed: 12/22/2022] Open
Abstract
Background Tuberculosis is one of the most important infectious diseases that has claimed its victims throughout much of known human history. With Koch's discovery of the tubercle bacillus as the etiologic agent of the disease, his sanitary and hygienic measures, which were based on his discovery and the development of a vaccine against tuberculosis by Albert Calmette and Camille Guérin in 1921, an attenuated Mycobacterium bovis strain, bacilli Calmette-Guérin (BCG), and the discovery of the first antibiotic against tuberculosis, streptomycin by Selman Waksman in 1943, soon led to the opinion that appropriate control measures had become available for tuberculosis and it had been assumed that the disease could ultimately be eradicated.The emergence of resistant strains of this bacteria and widespread distribution of the disease in the world, and the emergence of the AIDS epidemic destroyed any possibility of global control of tuberculosis in the foreseeable future. Objectives The purpose of this review is to highlight the current scientific literature on mycobacterial infections and provide an overview on the laboratory diagnosis of tuberculosis and non-tuberculosis infections based on conventional phenotypic and modern molecular assays. Method In this study, a number of 65 papers comprising 20 reviews, 9 case reports, and 36 original research in association with mycobacteriosis and the laboratory diagnosis of mycobacterial infections, were reviewed. Results Based on our analysis on the published documents methods applied for the laboratory diagnosis of tuberculosis are continually assessed and developed in order to achieve more rapid, less expensive, and accurate results. Acid-fast staining and culture for mycobacteria remain at the core of any diagnostic algorithm with the sensitivity of 20-70% and specificity of 95-98% for AFB microscopy and the sensitivity of 95% and the specificity of 98% for culture based diagnosis. Following growth in culture, molecular tests such as nucleic acid hybridization probes and DNA sequencing may be used for definitive species identification. Nucleic acid amplification methods provide the means for direct detection of Mycobacterium tuberculosis in respiratory specimens without the prerequisite to isolate or culture the organism, leading to more rapid diagnosis and better patient care. Conclusion As the researchers in a developing country, we strongly believe that despite significant advances in laboratory capacity, in many countries reliable confirmation of suspected mycobacterial diseases is hindered by a lack of knowledge on proper standardized methods, sufficient funds, suitably trained staff and laboratory supplies.
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Affiliation(s)
- Davood Azadi
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
| | - Tahereh Motallebirad
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan Iran
| | - Kazem Ghaffari
- Department of Laboratory Sciences, Khomein University of Medical Sciences, Khomein, Iran
| | - Hasan Shojaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan Iran
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17
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Rapid identification of mycobacteria from positive MGIT broths of primary cultures by MALDI-TOF mass spectrometry. PLoS One 2018; 13:e0192291. [PMID: 29394275 PMCID: PMC5796708 DOI: 10.1371/journal.pone.0192291] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/22/2018] [Indexed: 02/06/2023] Open
Abstract
Background Rapid identification of mycobacteria is important for timely treatment and the implementation of public health measures. The MGIT system ensures rapid detection of mycobacteria, but identification is usually delayed by days to weeks due to further subculture on solid medium. Matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF MS) was demonstrated to effectively identify mycobacteria isolates subcultured from solid or liquid media. Reports of identification directly from MGIT broths of both sterile and non-sterile clinical specimens, omitting the subculture step, were limited and not satisfactory before. Our identification method dramatically shortened delay from detection to identification of mycobacteria. Methodology We assessed the performance of the Vitek MS IVD version 3.0 for direct identification of NTM and M.tuberculosis from primary MGIT cultures, and assessed two sample preparation methods. Results Direct identification of NTM from positive MGIT broths, using MALDI-TOF VITEK MS with IVD v.3.0, generated high rates of acceptable results reaching 96.4% (80/83), and up to 100% (83/83) for sample preparations including a 0.1% SDS washing step. The sensitivity of VITEK MS to identify M.tuberculosis from MGIT tubes was 58/72 (80.6%), when using immunochromatography (ICA) test as gold standard. A characteristic colony clumping, wool-like appearance was observed in 48, and all 58 (100%) were correctly identified as M.tuberculosis using MALDI-TOF. The detection rate of M.tuberculosis complex was low (10/24, 41.6%) in the 24 MGIT tubes that was polymicrobial. Our method significantly reduced both the reagent cost and turnaround time. Conclusions Based on a simplified protocol, we showed that MALDI-TOF MS can be used for rapid identification of NTM directly from primary MGIT cultures within the routine clinical laboratory workflow. However, we recommend an initial ICA test to screen for M.tuberculosis complex, due to a low identification rate of M. tuberculosis in the presence of polymicrobial cultures using MALDI-TOF.
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Fatahi-Bafghi M. Nocardiosis from 1888 to 2017. Microb Pathog 2017; 114:369-384. [PMID: 29146497 DOI: 10.1016/j.micpath.2017.11.012] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 01/11/2023]
Abstract
The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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19
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Torres-Coy JA, Carrera C, Rodríguez-Castillo BA, Ramírez-Murga R, Ortiz-Cáceres W, Pérez-Alfonzo R, de Waard JH. Mycobacterium szulgai
: an unusual cause of skin and soft tissue infection after breast augmentation. Int J Dermatol 2017; 56:e122-e124. [DOI: 10.1111/ijd.13605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/18/2017] [Accepted: 02/20/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Jesus A. Torres-Coy
- Laboratorio de Tuberculosis; Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”; Caracas Venezuela
| | - Carolina Carrera
- Centro Clínico de Dermatología y Enfermedades Tropicales; Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”; Caracas Venezuela
| | | | - Rosalicia Ramírez-Murga
- Laboratorio de Tuberculosis; Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”; Caracas Venezuela
| | - William Ortiz-Cáceres
- Centro Clínico de Dermatología y Enfermedades Tropicales; Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”; Caracas Venezuela
| | - Ricardo Pérez-Alfonzo
- Centro Clínico de Dermatología y Enfermedades Tropicales; Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”; Caracas Venezuela
| | - Jacobus H. de Waard
- Laboratorio de Tuberculosis; Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”; Caracas Venezuela
- Instituto de Biomedicina “Dr. Jacinto Convit”; Facultad de Medicina; Universidad Central de Venezuela; Caracas Venezuela
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Kontos F, Mavromanolakis DN, Zande MC, Gitti ZG. Isolation of Mycobacterium kumamotonense from a patient with pulmonary infection and latent tuberculosis. Indian J Med Microbiol 2016; 34:241-4. [PMID: 27080783 DOI: 10.4103/0255-0857.180356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Mycobacterium kumamotonense is a novel, slow-growing non-chromogenic nontuberculous mycobacterium, which belongs to Mycobacterium terrae complex. We report, for the first time in Greece, the isolation of M. kumamotonense from an immunocompetent patient with pulmonary infection and latent tuberculosis. M. kumamotonense was identified by sequencing analysis of 16S rDNA and 65-kDa heat shock protein genes while by commercial molecular assays it was misidentified as Mycobacterium celatum. Antibiotic susceptibility testing was performed by the reference broth microdilution method. The strain was susceptible to amikacin, clarithromycin, rifampin, ciprofloxacin, moxifloxacin, rifabutin, ethambutol and linezolid.
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Affiliation(s)
- Fanourios Kontos
- Department of the Clinical Microbiology Laboratory, Medical School of Athens, Attikon University Hospital, Athens, Greece
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Identification of Species of Nontuberculous Mycobacteria Clinical Isolates from 8 Provinces of China. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2153910. [PMID: 27882322 PMCID: PMC5110891 DOI: 10.1155/2016/2153910] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/29/2016] [Indexed: 01/15/2023]
Abstract
Pulmonary diseases caused by nontuberculous mycobacteria (NTM) are increasing in incidence and prevalence worldwide. In this study, we identified NTM species of the clinical isolates from 8 provinces in China, in order to preliminarily provide some basic scientific data in the different species and distribution of NTM related to pulmonary disease in China. A total of 523 clinical isolates from patients with tuberculosis (TB) diagnosed clinically from 2005 to 2012 were identified to the species using conventional and molecular methods, including multilocus PCR, rpoB and hsp65 PCR-PRA, hsp65, rpoB, and 16S-23S internal transcribed spacer region sequencing. The isolates were identified into 3 bacterium genera, including NTM, Gordonia bronchialis, and Nocardia farcinica, and, for the 488 NTM isolates, 27 species were identified. For all the 27 species of NTM which were found to cause pulmonary infections in humans, the most prevalent species was M. intracellulare, followed by M. avium and M. abscessus. And seven other species were for the first time identified in patients with TB in China. NTM species identification is very important for distinguishing between tuberculosis and NTM pulmonary diseases, and the species diversity drives the creation of diverse and integrated identification methods with higher accuracy and efficacy.
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A cluster of endophthalmitis caused by Mycobacterium abscessus after cataract surgery. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2016; 49:799-803. [DOI: 10.1016/j.jmii.2014.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/29/2014] [Accepted: 02/04/2014] [Indexed: 12/22/2022]
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Comparison of restriction enzyme pattern analysis and full gene sequencing of 16S rRNA gene for Nocardia species identification, the first report of Nocardia transvalensis isolated of sputum from Iran, and review of the literature. Antonie Van Leeuwenhoek 2016; 109:1285-98. [DOI: 10.1007/s10482-016-0746-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
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Early detection of Mycobacterium tuberculosis complex in BACTEC MGIT cultures using nucleic acid amplification. Eur J Clin Microbiol Infect Dis 2016; 35:977-84. [PMID: 27039339 DOI: 10.1007/s10096-016-2625-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
We evaluated the application of nucleic acid amplification (NAA) in liquid cultures for the early detection of Mycobacterium tuberculosis. The Cobas TaqMan MTB test, IS6110 real-time PCR, and hsp65 PCR-restriction fragment length polymorphism (RFLP) analysis were used to detect BACTEC MGIT 960 (MGIT) cultures on days 3, 5, 7, and 14. The procedure was initially tested with a reference strain, H37Rv (ATCC 27294). Subsequently, 200 clinical specimens, including 150 Acid Fast bacillus (AFB) smear-positive and 50 AFB smear-negative samples, were examined. The Cobas TaqMan MTB test and IS6110-based PCR analysis were able to detect M. tuberculosis after 1 day when the inoculum of H37Rv was >3 x 10(-2) CFU/ml. After a 5-day incubation in the MGIT system, all three NAA assays had a positive detection regardless of the inoculum size. After a 1-day incubation of the clinical specimens in the MGIT system, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the Cobas TaqMan MTB assay were 70.2%, 100%, 100%, and 82.3% respectively. For IS6110-based PCR analysis, these values were 63.1%, 100%, 100%, and 78.9%, and were 88.1%, 100%, 100%, and 92.1% respectively for hsp65 PCR-RFLP analysis. After a 3-day incubation, the specificity and PPV were 100% for all three NAA tests; the Cobas TaqMan MTB assay had the best sensitivity (97.6%) and NPV (98.3%). The sensitivity, specificity, PPV, and NPV for conventional culture analysis were 98.8%, 100%, 100%, and 99.1%. Thus, NAA may be useful for the early detection of M. tuberculosis after 3 days in MGIT.
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Haridy M, Fukuta M, Mori Y, Ito H, Kubo M, Sakai H, Yanai T. An outbreak of Mycobacterium genavense infection in a flock of captive diamond doves (Geopelia cuneata). Avian Dis 2015; 58:383-90. [PMID: 25518432 DOI: 10.1637/10775-011714-reg.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Two diamond doves (Geopelia cuneata) in a flock of 23 birds housed in an aviary in a zoo in central Japan were found dead as a result of mycobacteriosis. Fecal samples of the remaining doves were positive for mycobacterial infection, and thus they were euthanatized. Clinical signs and gross pathology, including weight loss and sudden death and slight enlargement of the liver and intestine, were observed in a small number of birds (3/23). Disseminated histiocytic infiltration of either aggregates or sheets of epithelioid cells containing acid-fast bacilli, in the absence of caseous necrosis, were observed in different organs of the infected doves, especially lungs (23/23), intestines (9/23), livers (7/23), and hearts (6/23). Mycobacterium sp. was isolated from the livers of three birds (3/23). DNA extracted from frozen liver and formalin-fixed, paraffin-embedded tissues (5/23) were used for amplification of the gene encoding mycobacterial 65-kDa heat shock protein (hsp65). The causative Mycobacterium species was identified by PCR-restriction fragment length polymorphism analysis. Mycobacterium genavense infection was confirmed in three of the diamond doves. Moreover, partial 16S rDNA gene sequencing revealed 100% identity across the three samples tested, and 99.77% nucleotide homology of the isolate sequence to M. genavense. The main route of M. genavense infection in the diamond doves was most likely airborne, suggesting a potential zoonotic risk of airborne transmission between humans and birds.
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Qvist T, Gilljam M, Jönsson B, Taylor-Robinson D, Jensen-Fangel S, Wang M, Svahn A, Kötz K, Hansson L, Hollsing A, Hansen CR, Finstad PL, Pressler T, Høiby N, Katzenstein TL. Epidemiology of nontuberculous mycobacteria among patients with cystic fibrosis in Scandinavia. J Cyst Fibros 2014; 14:46-52. [PMID: 25178871 PMCID: PMC4298356 DOI: 10.1016/j.jcf.2014.08.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/08/2014] [Accepted: 08/08/2014] [Indexed: 11/28/2022]
Abstract
Background Nontuberculous mycobacteria (NTM) are an emerging threat to cystic fibrosis (CF) patients but their epidemiology is not well described. Methods In this retrospective observational study we identified all Scandinavian CF patients with a positive NTM culture from airway secretions from 2000 to the end of 2012 and used national CF databases to describe microbiological and clinical characteristics. Results During the 13-year period 157 (11%) CF patients were culture positive for NTM at least once. Mycobacterium abscessus complex (MABSC) (45%) and Mycobacterium avium complex (MAC) (32%) were the predominant species with geographical differences in distribution. Younger patients were more prone to MABSC (p < 0.01). Despite treatment, less than one-third of MABSC patients with repeated positive cultures cleared their infection and a quarter had a lung transplant or died. Conclusion NTM are significant CF pathogens and are becoming more prevalent in Scandinavia. MABSC and MAC appear to target distinct patient groups. Having multiple positive cultures despite treatment conveys a poor outcome.
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Affiliation(s)
- Tavs Qvist
- Copenhagen CF Center, Department of Infectious Diseases, University Hospital Rigshospitalet, Denmark.
| | - Marita Gilljam
- Gothenburg CF Center, Department of Respiratory Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Bodil Jönsson
- Clinical Microbiology Laboratories, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | | | - Mikala Wang
- Department of Clinical Microbiology, Aarhus University Hospital, Denmark
| | - Anita Svahn
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Sweden
| | - Karsten Kötz
- Gothenburg CF Center, Department of Pediatrics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lennart Hansson
- Lund CF Center, Department of Respiratory Medicine and Allergology, Skane University Hospital, Sweden
| | | | - Christine R Hansen
- Department of Pediatrics, Copenhagen University Hospital Rigshospitalet, Denmark
| | - Pål L Finstad
- Norwegian Resource Centre for Cystic Fibrosis, Oslo University Hospital, Oslo, Norway
| | - Tania Pressler
- Copenhagen CF Center, Department of Infectious Diseases, University Hospital Rigshospitalet, Denmark
| | - Niels Høiby
- Department of Clinical Microbiology, Copenhagen University Hospital Rigshospitalet, Denmark
| | - Terese L Katzenstein
- Copenhagen CF Center, Department of Infectious Diseases, University Hospital Rigshospitalet, Denmark
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Sgarioni SA, Hirata RDC, Hirata MH, Leite CQF, de Prince KA, de Andrade Leite SR, Filho DV, Siqueira VLD, Caleffi-Ferracioli KR, Cardoso RF. Occurrence of Mycobacterium bovis and non-tuberculous mycobacteria (NTM) in raw and pasteurized milk in the northwestern region of Paraná, Brazil. Braz J Microbiol 2014; 45:707-11. [PMID: 25242962 PMCID: PMC4166303 DOI: 10.1590/s1517-83822014000200046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 09/09/2013] [Indexed: 11/22/2022] Open
Abstract
Milk is widely consumed in Brazil and can be the vehicle of agent transmission. In this study, was evaluated the occurrence of Mycobacterium bovis and non-tuberculous mycobacteria (NTM) in raw and pasteurized milk consumed in the northwestern region of Paraná, Brazil. Fifty-two milk samples (20 pasteurized and 32 raw) from dairy farms near the municipality of Maringa, Parana State, Brazil were collected. Milk samples were decontaminated using 5% oxalic acid method and cultured on Lowenstein-Jensen and Stonebrink media at 35 °C and 30 °C, with and without 5–10% CO2. Mycobacteria isolates were identified by morphological features, PCR-Restriction Fragment Length Polymorphism Analysis (PCR-PRA) and Mycolic acids analysis. Thirteen (25%) raw and 2 (4%) pasteurized milk samples were positive for acid fast bacilli growth. Nine different species of NTM were isolated (M. nonchromogenicum, M. peregrinum, M. smegmatis, M. neoaurum, M. fortuitum, M. chelonae, M. flavescens, M. kansasii and M. scrofulaceum). M. bovis was not detected. Raw and pasteurized milk may be considered one source for NTM human infection. The paper reinforces the need for intensification of measures in order to avoid the milk contamination and consequently prevent diseases in the south of Brazil.
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Affiliation(s)
- Sônia Aparecida Sgarioni
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá MaringáPR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Rosario Dominguez Crespo Hirata
- Departamento de Análises Clínicas e Toxicológicas Universidade de São Paulo São PauloSP Brazil Departamento de Análises Clínicas e Toxicológicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mario Hiroyuki Hirata
- Departamento de Análises Clínicas e Toxicológicas Universidade de São Paulo São PauloSP Brazil Departamento de Análises Clínicas e Toxicológicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Clarice Queico Fujimura Leite
- Faculdade de Ciências Farmacêutica da Universidade Estadual Paulista AraraquaraSP Brazil Faculdade de Ciências Farmacêutica da Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Karina Andrade de Prince
- Faculdade de Ciências Farmacêutica da Universidade Estadual Paulista AraraquaraSP Brazil Faculdade de Ciências Farmacêutica da Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Sergio Roberto de Andrade Leite
- Instituto de Química da Universidade Estadual Paulista AraraquaraSP Brazil Instituto de Química da Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Dirceu Vedovello Filho
- Secretaria de Saúde do Estado do Paraná MaringáPR Brazil Secretaria de Saúde do Estado do Paraná, Maringá, PR, Brazil
| | - Vera Lucia Dias Siqueira
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá MaringáPR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Katiany Rizzieri Caleffi-Ferracioli
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá MaringáPR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Rosilene Fressatti Cardoso
- Departamento de Análises Clínicas e Biomedicina Universidade Estadual de Maringá MaringáPR Brazil Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, Maringá, PR, Brazil
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Favaro L, Scanzio T, Varello K, Caffara M, Righetti M, Bozzetta E, Prearo M. Mixed mycobacterial infection in an adult koi carp Cyprinus carpio L. JOURNAL OF FISH DISEASES 2014; 37:753-755. [PMID: 23937602 DOI: 10.1111/jfd.12159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 06/28/2013] [Accepted: 06/30/2013] [Indexed: 06/02/2023]
Affiliation(s)
- L Favaro
- Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Torino, Italy
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Aubry A, Sougakoff W, Bodzongo P, Delcroix G, Armand S, Millot G, Jarlier V, Courcol R, Lemaître N. First evaluation of drug-resistant Mycobacterium tuberculosis clinical isolates from Congo revealed misdetection of fluoroquinolone resistance by line probe assay due to a double substitution T80A-A90G in GyrA. PLoS One 2014; 9:e95083. [PMID: 24743770 PMCID: PMC3990612 DOI: 10.1371/journal.pone.0095083] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/21/2014] [Indexed: 11/26/2022] Open
Abstract
Background Tuberculosis (TB) is one of the major public health problems in Congo. However, data concerning Mycobacterium tuberculosis drug resistance are lacking because of the insufficient processing capacity. So, the aim of this study was to investigate for the first time the resistance patterns and the strain lineages of a sample of M. tuberculosis complex (MTBC) isolates collected in the two main cities of Congo. Methods Over a 9-day period, 114 smear-positive sputa isolated from 114 patients attending centers for the diagnosis and treatment of TB in Brazzaville and Pointe Noire were collected for culture and drug susceptibility testing (DST). Detection of mutations conferring drug resistance was performed by using line probe assays (GenoType MTBDRplus and MTBDRsl) and DNA sequencing. Strain lineages were determined by MIRU-VNTR genotyping. Results Of the 114 sputa, 46 were culture positive for MTBC. Twenty-one (46%) were resistant to one or more first-line antiTB drugs. Of these, 15 (71%) were multidrug resistant (MDR). The most prevalent mutations involved in rifampin and isoniazid resistance, D516V (60%) in rpoB and S315T (87%) in katG respectively, were well detected by MTBDRplus assay. All the 15 MDR strains were susceptible to fluoroquinolone and injectable second-line drug. No mutation was detected in the rrs locus involved in resistance to amikacin and capreomycin by both the MTBDRsl assay and DNA sequencing. By contrast, 9 MDR strains belonging to the same cluster related to T-family were identified as being falsely resistant to fluoroquinolone by the MTBDRsl assay due to the presence of a double substitution T80A-A90G in GyrA. Conclusions Taken together, these data revealed a possible spread of a particular MDR clone in Congo, misidentified as fluoroquinolone resistant by MTBDRsl assay. Thus, this test cannot replace gold-standard culture method and should be interpreted carefully in view of the patient's native land.
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Affiliation(s)
- Alexandra Aubry
- UPMC Université, Paris, France
- INSERM U1135, Paris, France
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Wladimir Sougakoff
- UPMC Université, Paris, France
- INSERM U1135, Paris, France
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | | | - Guy Delcroix
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
| | - Sylvie Armand
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
| | - Gérald Millot
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Vincent Jarlier
- UPMC Université, Paris, France
- INSERM U1135, Paris, France
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - René Courcol
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
- Université Lille Nord de France, Lille, France
- UDSL, F-59000 Lille, France
- INSERM U1019-UMR8204, Lille, France
| | - Nadine Lemaître
- Laboratoire de Bactériologie-Hygiène du CHRU, Lille, France
- Université Lille Nord de France, Lille, France
- UDSL, F-59000 Lille, France
- INSERM U1019-UMR8204, Lille, France
- * E-mail:
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Lima AS, Duarte RS, Montenegro LML, Schindler HC. Rapid detection and differentiation of mycobacterial species using a multiplex PCR system. Rev Soc Bras Med Trop 2014; 46:447-52. [PMID: 23982098 DOI: 10.1590/0037-8682-0097-2013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 07/22/2013] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION The early diagnosis of mycobacterial infections is a critical step for initiating treatment and curing the patient. Molecular analytical methods have led to considerable improvements in the speed and accuracy of mycobacteria detection. METHODS The purpose of this study was to evaluate a multiplex polymerase chain reaction system using mycobacterial strains as an auxiliary tool in the differential diagnosis of tuberculosis and diseases caused by nontuberculous mycobacteria (NTM) RESULTS: Forty mycobacterial strains isolated from pulmonary and extrapulmonary origin specimens from 37 patients diagnosed with tuberculosis were processed. Using phenotypic and biochemical characteristics of the 40 mycobacteria isolated in LJ medium, 57.5% (n=23) were characterized as the Mycobacterium tuberculosis complex (MTBC) and 20% (n=8) as nontuberculous mycobacteria (NTM), with 22.5% (n=9) of the results being inconclusive. When the results of the phenotypic and biochemical tests in 30 strains of mycobacteria were compared with the results of the multiplex PCR, there was 100% concordance in the identification of the MTBC and NTM species, respectively. A total of 32.5% (n=13) of the samples in multiplex PCR exhibited a molecular pattern consistent with NTM, thus disagreeing with the final diagnosis from the attending physician. CONCLUSIONS Multiplex PCR can be used as a differential method for determining TB infections caused by NTM a valuable tool in reducing the time necessary to make clinical diagnoses and begin treatment. It is also useful for identifying species that were previously not identifiable using conventional biochemical and phenotypic techniques.
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Affiliation(s)
- Andrea Santos Lima
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife,
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Escobar-Escamilla N, Ramírez-González JE, González-Villa M, Torres-Mazadiego P, Mandujano-Martínez A, Barrón-Rivera C, Bäcker CE, Fragoso-Fonseca DE, Olivera-Díaz H, Alcántara-Pérez P, Hernández-Solís A, Cícero-Sabido R, Cortés-Ortíz IA. Hsp65 phylogenetic assay for molecular diagnosis of nontuberculous mycobacteria isolated in Mexico. Arch Med Res 2013; 45:90-7. [PMID: 24333253 DOI: 10.1016/j.arcmed.2013.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/22/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND AND AIMS Nontuberculous mycobacteria (NTM) are mainly distributed as important emerging pathogens in patients with chronic or immunosuppressive diseases. Accurate identification of causative species is crucial for proper treatment and patient follow-up. However, several difficulties are associated with phenotypic and molecular diagnostic methods for precise identification at the species level due to shared metabolic and genetic characteristics. We undertook this study to evaluate the application of the phylogenetic method based on hsp65 gene into Telenti's PCR-restriction enzyme analysis (PRA) for molecular identification of NTM. METHODS The study population was comprised of 1646 Mycobacterium clinical isolates (AFB positive) collected from 2008-2011, of which 537 (32.6%) were MNT identified by PRA analysis. DNA sequencing of hsp65 in 53 isolates (10%) was performed. Sequence identification through NCBI-Basic Local Alignment Search Tool (BLAST) achieved correct identification in 23 isolates. Phylogenetic trees including hsp65 available GenBank sequences for all described genres of NTM and hsp65 obtained sequences were constructed using Mega 5.05 software. We compared sequence identification based on phylogenetic clustering and BLAST similarity search. RESULTS Phylogenetic clustering allowed more specific differentiation of closely related species and clearer identification in comparison with BLAST; 30 Mycobacterium species (this is the first report of isolation of some of these from clinical samples in Mexico) were identified in this way. CONCLUSIONS The proposed 440 bp hsp65 phylogenetic method allows a better identification tool to differentiate Mycobacterium species and is useful to complement diagnosis and epidemiological surveillance of NTM.
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Affiliation(s)
- Noé Escobar-Escamilla
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - José Ernesto Ramírez-González
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Maribel González-Villa
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Pilar Torres-Mazadiego
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - América Mandujano-Martínez
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | | | | | - David Esaú Fragoso-Fonseca
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Hiram Olivera-Díaz
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Patricia Alcántara-Pérez
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Alejandro Hernández-Solís
- Servicio de Neumología, Hospital General de México "Eduardo Liceaga", Secretaría de Salud, México, D.F., Mexico
| | - Raúl Cícero-Sabido
- Facultad de Medicina, Universidad Nacional Autónoma de México, México, D.F., Mexico
| | - Iliana Alejandra Cortés-Ortíz
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico.
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Evaluation of hsp65 nested PCR-restriction analysis (PRA) for diagnosing tuberculosis in a high burden country. BIOMED RESEARCH INTERNATIONAL 2013; 2013:391549. [PMID: 24260739 PMCID: PMC3821893 DOI: 10.1155/2013/391549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/08/2013] [Indexed: 11/17/2022]
Abstract
Current study evaluated the hsp65 Nested PCR Restriction Fragment Length Polymorphism Analysis (hsp65 Nested PCR-PRA) to detect and
identify Mycobacterium tuberculosis complex directly in clinical samples for a rapid and specific diagnosis of tuberculosis (TB). hsp65 Nested PCR-PRA was
applied directly to 218 clinical samples obtained from 127 patients suspected of TB or another mycobacterial infection from July 2009 to July 2010. The hsp65 Nested
PCR-PRA showed 100% sensitivity and 95.0 and 93.1% specificity in comparison with culture and microscopy (acid fast bacillus smear), respectively. hsp65 Nested
PCR-PRA was shown to be a fast and reliable assay for diagnosing TB, which may contribute towards a fast diagnosis that could help the selection of appropriate chemotherapeutic and early
epidemiological management of the cases which are of paramount importance in a high TB burden country.
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Kurokawa S, Kabayama J, Fukuyasu T, Hwang SD, Park CI, Park SB, del Castillo CS, Hikima JI, Jung TS, Kondo H, Hirono I, Takeyama H, Aoki T. Bacterial classification of fish-pathogenic Mycobacterium species by multigene phylogenetic analyses and MALDI Biotyper identification system. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:340-348. [PMID: 23229498 DOI: 10.1007/s10126-012-9492-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/19/2012] [Indexed: 06/01/2023]
Abstract
Mycobacterium marinum is difficult to distinguish from other species of Mycobacterium isolated from fish using biochemical methods. Here, we used genetic and proteomic analyses to distinguish three Mycobacterium strains: M. marinum strains MB2 and Europe were isolated from tropical and marine fish in Thailand and Europe, and Mycobacterium sp. 012931 strain was isolated from yellowtail in Japan. In phylogenetic trees based on gyrB, rpoB, and Ag85B genes, Mycobacterium sp. 012931 clustered with M. marinum strains MB2 and Europe, but in trees based on 16S rRNA, hsp65, and Ag85A genes Mycobacterium sp. 012931 did not cluster with the other strains. In proteomic analyses using a Bruker matrix-assisted laser desorption ionization Biotyper, the mass profile of Mycobacterium sp. 012931 differed from the mass profiles of the other two fish M. marinum strains. Therefore, Mycobacterium sp. 012931 is similar to M. marinum but is not the same, suggesting that it could be a subspecies of M. marinum.
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Affiliation(s)
- Satoru Kurokawa
- Animal Health Department of Research and Development Agricultural and Veterinary Division, Meiji Seika Pharma, 2-4-16, Kyobashi, Chuo-ku, Tokyo, 104-8002, Japan
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Evaluation of a membrane array for detection of Mycobacterium tuberculosis complex and nontuberculous mycobacteria in positive liquid cultures. Diagn Microbiol Infect Dis 2013; 75:337-41. [DOI: 10.1016/j.diagmicrobio.2013.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 01/02/2013] [Accepted: 01/08/2013] [Indexed: 01/15/2023]
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Moghim S, Sarikhani E, Nasr Esfahani B, Faghri J. Identification of Nontuberculous Mycobacteria Species Isolated from Water Samples Using Phenotypic and Molecular Methods and Determination of their Antibiotic Resistance Patterns by E- Test Method, in Isfahan, Iran. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2012; 15:1076-82. [PMID: 23493797 PMCID: PMC3586926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2011] [Accepted: 12/24/2011] [Indexed: 12/03/2022]
Abstract
INTRODUCTION Many studies have shown epidemiological links between strains isolated in tap water, and those isolated from patients. Molecular methods linked to PCR are more reliable and faster for identification of non- tuberculous mycobacteria (NTM). In this study molecular methods were used for identification and typing of NTM. MATERIALS AND METHODS Five hundred ml of 85 water samples was passed through 0.45 μm filters. The filters were transferred directly onto 7H10 Middle Brook solid media, containing 15% OADC. PCR for 16S rRNA was done and the PCR product (1500 bp) was sequenced. PRA of the hsp65 gene was investigated to identify the species of isolates. For evaluation of susceptibility of NTM to antimycobacterial agents, E-test method was used. RESULT The genus of 26 isolated NTM was confirmed by 16s rRNA sequence based method. Nineteen isolates of Mycobacteria were differentiated using hsp65 genes PRA. The dominant isolates were M. fortuitum (26.7%), M. chelonae like organism (13.3%) and M. mucogenicum (13.3%). Seventy one percent of NTM species were resistant to isoniazid, 64% to rifampin, 57% to ethambutol, 35% to tetracycline, 14 % to azithromycin and 7.1 % to amikacin. CONCLUSION The results showed that E-test method is not a proper technique for antimycobacterial assay because some NTM species are slow in growing and have no growth on Muller Hinton agar. Regarding the 16S rRNA sequence analysis, the identification of isolates was restricted to the genus level, because 99% similarity within 16S rRNA of two isolates may or may not determine the same species.
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Affiliation(s)
- Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ensieh Sarikhani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jamshid Faghri
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Chowdhury IH, Sen A, Bahar B, Hazra A, Chakraborty U, Choudhuri S, Goswami A, Pal NK, Bhattacharya B. A molecular approach to identification and profiling of first-line-drug-resistant mycobacteria from sputum of pulmonary tuberculosis patients. J Clin Microbiol 2012; 50:2082-4. [PMID: 22461679 PMCID: PMC3372138 DOI: 10.1128/jcm.06093-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 03/15/2012] [Indexed: 11/20/2022] Open
Abstract
Conventional and molecular techniques were applied to detect and characterize drug resistance of mycobacteria in the sputum samples of clinically confirmed tuberculosis. The sensitivities of mycobacterium detection by ZN staining, culture, multiplex PCR, and restriction fragment length polymorphism (RFLP) were 27.7%, 19.9%, 92.9%, and 95.7%, respectively, but all were 100% specific. The conventional and multiple-allele-specific PCR (MAS-PCR) methods enabled establishment of the drug resistance in 19.3% and 86.9% cases, respectively. We demonstrated that molecular techniques have potential in the accurate diagnosis of tuberculosis.
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Affiliation(s)
| | | | - Bojlul Bahar
- Cell and Molecular Biology Laboratory, School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
| | | | - Urmita Chakraborty
- Department of Microbiology, Institute of Postgraduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Avranil Goswami
- Department of Microbiology, Institute of Postgraduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Nishith Kumar Pal
- Department of Microbiology, Institute of Postgraduate Medical Education and Research (IPGME&R), Kolkata, India
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Honarvar B, Movahedan H, Mahmoodi M, Sheikholeslami FM, Farnia P. Mycobacterium aurum keratitis: An unusual etiology of a sight-threatening infection. Braz J Infect Dis 2012. [DOI: 10.1016/s1413-8670(12)70308-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Comparison of the (CCG)4-based PCR and MIRU-VNTR for molecular typing of Mycobacterium avium strains. Mol Biol Rep 2012; 39:7681-6. [PMID: 22350162 DOI: 10.1007/s11033-012-1603-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/02/2012] [Indexed: 10/14/2022]
Abstract
Mycobacterium avium, a member of the group of non-tuberculous mycobacteria, is most often responsible for the serious diseases in humans and is frequently isolated from NTM-caused pulmonary events. In this connection the epidemiological aspect is also of great importance. Here we present a useful genetic assay that uses (CCG)(4)-based PCR for genotyping M. avium. After applying this test to 33 strains of M. avium, we found a discriminatory index of 0.979. The accuracy of this analysis was supported by a reasonable reproducibility of 95.1%. These results were compared with the Mycobacterial Intergenic Repeat Unit-Variable Number Tandem Repeats (MIRU-VNTR) typing scheme which had slightly lower discriminatory index of 0.945 however, the method was able to cluster different strains compared to CCG-PCR. Taking into account high discriminatory index and reproducibility, this test scheme has the potential as a screening tool in the investigation of M. avium infections, especially if combined with MIRU-VNTR.
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Chia JH, Wu TL, Su LH, Kuo AJ, Lai HC. Direct identification of mycobacteria from smear-positive sputum samples using an improved multiplex polymerase chain reaction assay. Diagn Microbiol Infect Dis 2012; 72:340-9. [PMID: 22280996 DOI: 10.1016/j.diagmicrobio.2011.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 11/22/2011] [Accepted: 12/10/2011] [Indexed: 11/26/2022]
Abstract
The rapid identification of mycobacteria from smear-positive sputum samples is very important. To identify the Mycobacterium tuberculosis complex (MTBC) and frequently isolated nontuberculous mycobacteria strains directly from smear-positive sputum samples, an improved multiplex polymerase chain reaction (PCR) assay was developed. Nine pairs of primers targeting the 16S-23S rDNA internal transcribed spacer-1, hsp65, and the early secretory antigen (ESAT-6) gene sequences were developed, and their efficacy was evaluated in comparison to traditional culturing and 16S rRNA gene sequencing methods. A total of 200 smear- and culture-positive sputum specimens collected between November 2005 and May 2006 were used for the analysis. The results of the assay showed an accurate identification rate for acid-fast bacilli (AFB) 3+, AFB 2+, and AFB rare/1+ samples of 98%, 95%, and 53%, respectively. The improved multiplex PCR method saves time and has advantages for identifying mycobacteria from AFB 2+ and 3+ sputum samples. The method is suitable for use in countries with a high MTBC prevalence rate.
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Affiliation(s)
- Ju-Hsin Chia
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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41
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Kazumi Y, Mitarai S. The evaluation of an identification algorithm for Mycobacterium species using the 16S rRNA coding gene and rpoB. Int J Mycobacteriol 2012; 1:21-8. [PMID: 26786945 DOI: 10.1016/j.ijmyco.2012.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Conventional biochemical tests are the standard for the identification of Mycobacterium species, but molecular identifications are becoming more prevalent. The rpoB gene encodes the β-subunit of RNA polymerase and is utilized for the identification of Mycobacterium species. In the present study, a stepwise Mycobacterium species identification algorithm using the 16S rRNA encoding gene and rpoB analysis was evaluated for its effectiveness. METHODS A total of 172 clinical Mycobacterium isolates were tested, and concordant results were obtained with 108 strains by using the conventional method and molecular methods (AccuProbe or DDH method). RESULTS In these 108 strains, 4 strains were identified by 16S rRNA gene analysis, but rpoB indicated no identical Mycobacterium species with more than 99% similarity. The remaining 64 strains were not identified by conventional method and commercial kits. Forty-two showed concordant results with 16S rRNA and rpoB analysis, and 13 strains were identified by 16S rRNA gene analysis although rpoB indicated no identical Mycobacterium species. On the other hand, 4 strains included 2 strains of Gordona and 2 strains of M. celatum type II which were identified by rpoB but not by 16S rRNA gene analysis. Finally, 5 strains could not be identified by analysis of either gene. The rpoB analysis can differentiate M. kansasii from M. gastri; M. malmoense from M. szulgai; M. abscessus from M. chelonae; M. peregrinum from M. septicum; M. porcinum from M. fortuitum; and M. farucinogense from M. senegalense-pairs that are not differentiated by 16S rRNA analysis. Additionally, Nocardia asteroids, Rhodococcus equi, Gordona aichiense, G. aurantiaca, G. bronchialis and G. terrae are able to be analyzed by using rpoB. CONCLUSIONS The 16S rRNA gene identification is a rapid and prevalent method but still has some limitations. Therefore, the stepwise combination of rpoB with 16S rRNA gene analysis is an effective system for the identification of Mycobacterium species.
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Affiliation(s)
- Yuko Kazumi
- Molecular Epidemiology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Tokyo, Japan
| | - Satoshi Mitarai
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Tokyo, Japan.
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42
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García-Martos P, García-Agudo L. [Infections due to rapidly growing mycobacteria]. Enferm Infecc Microbiol Clin 2011; 30:192-200. [PMID: 22133415 DOI: 10.1016/j.eimc.2011.09.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 08/30/2011] [Accepted: 09/10/2011] [Indexed: 01/07/2023]
Abstract
Rapidly growing mycobacteria (RGM) are ubiquitous in nature and widely distributed in water, soil and animals. During the past three decades we have observed a notable increment of infections caused by RGM, both localized and disseminated, as well as nosocomial outbreaks of contaminated medical equipment. The microbiological diagnosis of RGM infections includes direct microscopic observation and culture. The taxonomic identification is performed by phenotypic, biochemical, chromatographic and molecular biology techniques. The treatment differs from that of other mycobacteriosis like tuberculosis, owing to the variable in vitro susceptibility of the species of this group. The RGM are resistant to conventional antituberculous drugs, but can be susceptible to broad spectrum antimicrobial agents. In this study we comment on the significant aspects of human infections by RGM, including their biology, epidemiology, pathology, microbiological diagnosis, taxonomic identification, antimicrobial susceptibility and treatment.
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Affiliation(s)
- Pedro García-Martos
- Unidad de Micobacterias, Servicio de Microbiología, Hospital Universitario Puerta del Mar, Cádiz, Spain.
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43
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Esparcia Ó, Español M, Garrigó M, Moreno C, Montemayor M, Navarro F, Coll P. [Use of different PCR-based techniques integrated into a non-tuberculous identification algorithm]. Enferm Infecc Microbiol Clin 2011; 30:3-10. [PMID: 21924798 DOI: 10.1016/j.eimc.2011.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/11/2011] [Accepted: 06/16/2011] [Indexed: 10/17/2022]
Abstract
INTRODUCTION The aim of the present work was to demonstrate the utility of a non-tuberculous mycobacteria (NTM) identification algorithm, which integrates different PCR-based techniques and basic phenotypic features. Moreover, the algorithm for pattern restriction analysis of hsp65 (hsp65 PRA) interpretation has been updated. METHODS The workflow chosen consisted of the identification by a DNA hybridization probe method, followed by PCR-restriction enzyme analysis of hsp65 (hsp65 PRA) in those isolates that cannot be identified by hybridization probes. If necessary, 16S rRNA gene and hsp65 gene sequencing were used for speciation. RESULTS A total of 236 NTM were collected, in which 102 (43.2%) isolates were identified by DNA specific probes and 76 (32.2%) isolates were identified with hsp65 PRA. Partial sequencing of the 16S rRNA gene was used for species identification of the remaining 58 (24.5%) isolates. Fifty-three (22.4%) were identified using this method. Five isolates (2.1%) were submitted for partial sequencing of hsp65 gene and one isolate was identified with this method. Four strains (1.7%) could not be identified at species level. Three new PRA patterns were found. Seven isolates tested positive with the AccuProbe Mycobacterium avium complex identification test but did not test positive with the M. avium or Mycobacterium intracellulare specific probes. Five and two of these isolates were identified as M. intracellulare and Mycobacterium colombiense, respectively. CONCLUSION This approach allowed us to identify almost all NTM isolates found in this study, including some recently described species.
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Affiliation(s)
- Óscar Esparcia
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Barcelona, España.
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García-Agudo L, Jesús I, Rodríguez-Iglesias M, García-Martos P. Evaluation of INNO-LiPA mycobacteria v2 assay for identification of rapidly growing mycobacteria. Braz J Microbiol 2011; 42:1220-6. [PMID: 24031745 PMCID: PMC3768772 DOI: 10.1590/s1517-838220110003000048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/25/2010] [Accepted: 05/16/2011] [Indexed: 11/22/2022] Open
Abstract
A total of 54 rapidly growing mycobacteria (RGM) isolated from patients attended in the two hospitals of Cádiz Bay (Spain) were selected during a seven-year-period (2000–2006) in order to evaluate the INNO-LiPA Mycobacteria v2 assay for mycobacterial identification, based on the reverse hybridization principle. The strains were cultured in Löwenstein-Jensen and Middlebrook 7H9 media and identified to the species level by sequencing of the 16S rRNA, PCR-restriction enzyme analysis of the hsp65 gene, conventional tests and INNO-LiPA Mycobacteria v2 assay. By the molecular methods we identified a total of 12 different species: 23 Mycobacterium fortuitum, 11 M. chelonae, 10 M. abscessus, 2 M. senegalense, 1 M. alvei, 1 M. brumae, 1 M. mageritense, 1 M. mucogenicum, 1 M. neoaurum, 1 M. peregrinum, 1 M. septicum and 1 M. smegmatis. Fifty two strains (96.3%) were correctly identified by conventional techniques and 47 strains (87.0%) by INNO-LiPA Mycobacteria v2 assay. We find INNO-LiPA Mycobacteria v2 assay simple to perform but it provides few advantages in comparison with conventional methods and sometimes needs complementary tests to identify Mycobacterium fortuitum complex, M. chelonae complex and specific species due to the great heterogeneity in the RGM group.
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Affiliation(s)
- Lidia García-Agudo
- Microbiology Service. Hospital de Puerto Real , Carretera Nacional IV km 665, 11510 Puerto Real, Cádiz , Spain
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Prosthetic joint infection caused by Mycobacterium alvei in an elderly patient. J Clin Microbiol 2011; 49:3096-8. [PMID: 21697319 DOI: 10.1128/jcm.00603-11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first case of prosthetic joint infection caused by Mycobacterium alvei, which was identified by PCR-restriction fragment length polymorphism and verified by analysis of nucleotide sequences of its amplified 16S ribosomal DNA. The pathogen was susceptible to linezolid, amikacin, ciprofloxacin, tigecycline, and trimethoprim-sulfamethoxazole. The clinical implications are discussed.
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Trinucleotide repeat sequence-based PCR as a potential approach for genotyping Mycobacterium gordonae strains. J Microbiol Methods 2011; 85:28-32. [PMID: 21276824 DOI: 10.1016/j.mimet.2011.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 12/14/2010] [Accepted: 01/03/2011] [Indexed: 11/20/2022]
Abstract
Diseases that are caused by non-tuberculous mycobacteria (NTM) continue to pose difficult clinical problems, and the epidemiological aspect of NTM-caused diseases is of great importance. In the case of Mycobacterium gordonae there is no adequate genotyping scheme. Here we present a potential rapid and reproducible genetic assay that uses trinucleotide repeat sequence-based PCR (TRS-PCR) for genotyping M. gordonae. The proposed method constitutes a useful single-primer PCR screen for genotyping this species. Among 10 TRS-containing primers, after applying (CAC)₄-based PCR to 36 strains of M. gordonae, we found a discriminatory index of 0.975. The accuracy of this analysis was supported by a reasonable reproducibility of 92%. These results were compared with the Enterobacterial Repetitive Intergenic Consensus Sequences (ERIC)-PCR typing scheme which had lower discriminatory index of 0.93 and its reproducibility was only 86.3%.
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Pedro HSP, Pereira MIF, Goloni MRA, Pires FC, Oliveira RS, da Rocha MAB, Conceição LM, Fraga VD, Fenley JC, Cordeschi T, Machado RLD, Franco C, Rossit ARB. Mycobacterium tuberculosis in a HIV-1-infected population from Southeastern Brazil in the HAART era. Trop Med Int Health 2010; 16:67-73. [DOI: 10.1111/j.1365-3156.2010.02681.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ong CS, Ngeow YF, Yap SF, Tay ST. Evaluation of PCR–RFLP analysis targeting hsp65 and rpoB genes for the typing of mycobacterial isolates in Malaysia. J Med Microbiol 2010; 59:1311-1316. [DOI: 10.1099/jmm.0.021139-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, PCR–RFLP analysis (PRA) targeting hsp65 and rpoB gene regions was evaluated for the identification of mycobacterial species isolated from Malaysian patients. Overall, the hsp65 PRA identified 92.2 % of 90 isolates compared to 85.6 % by the rpoB PRA. With 47 rapidly growing species, the hsp65 PRA identified fewer (89.4 %) species than the rpoB PRA (95.7 %), but with 23 slow-growing species the reverse was true (91.3 % identification by the hsp65 PRA but only 52.5 % by the rpoB PRA). There were 16 isolates with discordant PRA results, which were resolved by 16S rRNA and hsp65 gene sequence analysis. The findings in this study suggest that the hsp65 PRA is more useful than the rpoB PRA for the identification of Mycobacterium species, particularly with the slow-growing members of the genus. In addition, this study reports 5 and 12 novel restriction patterns for inclusion in the hsp65 and rpoB PRA algorithms, respectively.
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Affiliation(s)
- Chia-Sui Ong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yun-Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sook-Fan Yap
- Department of Pathology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sun-Tee Tay
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Huang WC, Chiou CS, Chen JH, Shen GH. Molecular epidemiology of Mycobacterium abscessus infections in a subtropical chronic ventilatory setting. J Med Microbiol 2010; 59:1203-1211. [PMID: 20616186 DOI: 10.1099/jmm.0.020586-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of this study was to investigate the high level of pulmonary Mycobacterium abscessus infections and implement a surveillance programme among 43 ventilator-dependent patients, 15 with pulmonary M. abscessus infections, in a hospital long-term respiratory care ward (RCW) in central Taiwan. M. abscessus isolates were obtained from 35 patients in the RCW of hospital A, 6 patients in the RCWs of another three hospitals (B, C and D), and from 4 water sources in two of the hospitals (A and B). Strains were characterized by methods including hsp65 PCR-RFLP and PFGE. The patients were followed-up by chest X-ray for 1 year. All clinical isolates were type I and II, and belonged to ten distinct clusters of PFGE patterns. Five clinical strains in two hospitals belonged to a single cluster, whilst four clinical strains in the other two hospitals belonged to a single unique cluster. The strains from hospital A fell into nine clusters and were distinct from the strains isolated from the water supply. Patients infected with type I strains showed a significantly more rapid progression of disease. The number of different strains involved suggested either that there had been a polyclonal outbreak or that a high level of endemic infections was present in the RCW of hospital A. This and the lack of homology between the clinical and environmental isolates from hospital A raised the possibility that pulmonary M. abscessus infections may have been spread by the movement of patients between RCWs, a routine practice in Taiwan's integrated delivery system.
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Affiliation(s)
- Wei-Chang Huang
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, ROC
| | - Chien-Shun Chiou
- Central Region Laboratory, Center of Research and Diagnostics, Centers for Disease Control, Taichung, Taiwan, ROC
| | - Jiann-Hwa Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Gwan-Han Shen
- Institute of Respiratory Therapy, China Medical University, Taichung, Taiwan, ROC.,Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan, ROC.,Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, ROC
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Marumo K, Nakamura H, Tazawa S, Kazumi Y, Kawano R, Shirata C, Taguchi K, Kikuchi T, Nagashima G. Isolation of novel mycobacteria contaminating an aquarium fish tank in a Japanese university hospital. J Appl Microbiol 2010; 109:558-566. [PMID: 20148998 DOI: 10.1111/j.1365-2672.2010.04680.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To better understand nontuberculous mycobacteria (NTM) contamination in a hospital setting, six freshwater fish gut homogenates and water in an aquarium fish tank placed on the reception counter of a nursing station were cultured for mycobacteria. METHODS AND RESULTS By direct sequencing of 16s rRNA, rpoB and hsp65, scotochromogenic and nonchromogenic Mycobacterium szulgai isolates containing hsp65 type II (GenBank accession nos. FJ384762 and FJ384764, respectively), Mycobacterium gordonae isolates containing rpoB clusters B and E (GenBank accession no. FJ384766), and Mycobacterium kansasii isolates containing hsp65 type VI were collected from the gut homogenates and water from the fish tank. However, no isolates were obtained from the tap water used to refill the fish tank. A randomly amplified polymorphic DNA (RAPD) analysis using a 10-mer primer (5'-TGGTCGCGGC) showed that some NTM from the fish tank water were identical to those obtained from the gut homogenates. CONCLUSIONS Fish and water in the tank were contaminated by the novel NTM. SIGNIFICANCE AND IMPACT OF THE STUDY These findings could help to elucidate infection routes and contamination sources of novel NTM from water sources.
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Affiliation(s)
- K Marumo
- Department of Clinical Pathology, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan., Infection Control Team, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan
| | - H Nakamura
- Infection Control Team, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan., Division of Central Clinical laboratory, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan
| | - S Tazawa
- Infection Control Team, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan., Division of Central Clinical laboratory, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan
| | - Y Kazumi
- Bacteriology Division, The Research Institute of Tuberculosis, Japan Antituberculosis Association, Kiyose-shi, Tokyo, Japan
| | - R Kawano
- Infection Control Team, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan., Division of Nursing, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan
| | - C Shirata
- Division of Nursing, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan
| | - K Taguchi
- Department of Clinical Pathology, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan., Infection Control Team, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan
| | - T Kikuchi
- Infection Control Team, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan., Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Aoba-ku, Yokohama, Japan
| | - G Nagashima
- Department of Neurosurgery, St. Marianna University School of Medicine Toyoko Hospital, Nakahara-ku, Kawasaki, Japan
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