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Oliveira RSD, Chimara E, Brandão AP, Simeão FCDS, Souza ARD, Gallo JF, Pinhata JMW. Non-tuberculous mycobacteria hybridisation profiles in the GenoType MTBDR plus assay: experience from a diagnostic routine of a high-throughput laboratory. J Med Microbiol 2024; 73. [PMID: 38305283 DOI: 10.1099/jmm.0.001794] [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] [Indexed: 02/03/2024] Open
Abstract
Introduction. Disease caused by non-tuberculous mycobacteria (NTM) is an emergent problem. Because NTM pulmonary disease and tuberculosis (TB) have similar clinical presentations, many cases of NTM may be misdiagnosed as TB before laboratory identification of the NTM species.Hypothesis/Gap Statement. Clinical laboratories should always perform differentiation between Mycobacterium tuberculosis complex (MTBC) and NTM to guide patients' correct treatment.Aim. To describe the characteristics and to identify mycobacterial isolates presumptively classified as MTBC by macroscopic characteristics in culture media that tested negative in GenoType MTBDRplus.Methodology. All cultures from February 2019 to December 2021 showing MTBC macroscopic characteristics were processed by GenoType MTBDRplus. MTBC-negative cultures underwent species identification by immunochromatography, line probe assays and PRA-hsp65. Patients' data were obtained from Brazilian surveillance systems.Results. Only 479 (3.1%) of 15 696 isolates presumptively identified as MTBC were not confirmed by GenoType MTBDRplus and were then subjected to identification. A total of 344 isolates were shown to be NTM, of which 309 (64.5%) and 35 (7.3%) were identified to the species and genus levels, respectively. Of the 204 NTM isolates with MTBC characteristics, the most frequent species were M. fortuitum (n=52, 25.5%), M. abscessus complex (MABC; n=27, 13.2%) and M. avium complex (MAC; n=26, 12.7%). Regarding the GenoType MTBDRplus results from NTM isolates, there were diverse hybridisation profiles with rpoB gene's different wild-type (WT) probes. Seventy-six (16.1%) of the 473 patients were classified as having NTM disease, the most frequent being MAC (n=15, 19.7%), MABC (n=13, 17.1%), M. kansasii (n=10, 13.2%) and M. fortuitum (n=6, 7.9%).Conclusion. Because the signs and symptoms of pulmonary TB are similar to those of pulmonary mycobacteriosis and treatment regimens for TB and NTM are different, identifying the disease-causing species is paramount to indicate the correct management. Thus, in the laboratory routine, when an isolate presumptively classified as MTBC is MTBC-negative, it is still essential to perform subsequent identification.
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Affiliation(s)
- Rosângela Siqueira de Oliveira
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Erica Chimara
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Angela Pires Brandão
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
- Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, 21040-360, Rio de Janeiro, RJ, Brazil
| | - Fernanda Cristina Dos Santos Simeão
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Andreia Rodrigues de Souza
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Juliana Failde Gallo
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
| | - Juliana Maira Watanabe Pinhata
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), Av. Dr. Arnaldo, 351, 9º andar, 01246-000, São Paulo, SP, Brazil
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Pedace CS, Gonçalves MG, Souza AR, Dos Santos Simeão FC, de Carvalho NFG, Gallo JF, Chimara E. Development of multiplex real-time PCR for detection of clarithromycin resistance genes for the Mycobacterium abscessus group. J Med Microbiol 2023; 72. [PMID: 36920844 DOI: 10.1099/jmm.0.001670] [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: 03/16/2023] Open
Abstract
Introduction. The M. abscessus molecular identification and its drug-resistance profile are important to choose the correct therapy.Aim. This work developed a multiplex real-time PCR (mqPCR) for detection of clarithromycin resistance genes for the Mycobacterium abscessus group.Methodology. Isolates received by Adolfo Lutz Institute from 2010 to 2012, identified by PCR restriction enzyme analysis of a fragment of the hsp65 gene (PRA-hsp65) as M. abscessus type 1 (n=135) and 2 (n=71) were used. Drug susceptibility test (DST) for CLA were performed with reading on days 3 and 14. Subespecies identification by hsp65 and rpoB genes sequencing and erm(41) and rrl genes for mutation detection and primer design were performed. erm(41) gene deletion was detected by conventional PCR. Primers and probes were designed for five detections: erm(41) gene full size and with deletion; erm(41) gene T28 and C28; rrl gene A2058.Results. In total, 191/206 (92.7 %) isolates were concordant by all methods and 13/206 (6.3 %) were concordant only between molecular methods. Two isolates (1.0 %) were discordant by mqPCR compared to rrl gene sequencing. The mqPCR obtained 204/206 (99.0 %) isolates in agreement with the gold standard, with sensitivity and specificity of 98 and 100 %, respectively, considering the gold standard method and 92 and 93 % regarding DST.Conclusion. The mqPCR developed by us proved to be an easy-to-apply tool, minimizing time, errors and contamination.
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Affiliation(s)
- Carolina Salgado Pedace
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Maria Gisele Gonçalves
- Immunology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 10th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Andréia Rodrigues Souza
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Fernanda Cristina Dos Santos Simeão
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Natalia Fernandes Garcia de Carvalho
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Juliana Failde Gallo
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
| | - Erica Chimara
- Tuberculosis and Mycobacteriosis Branch, Bacteriology Center, Adolfo Lutz Institute, Avenida Doutor Arnaldo, 351 - 9th floor - Pacaembu, 01246000, São Paulo, Brazil
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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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Zhang L, Li Y, Yang H, Mu Y, Jiang J, Duan X. Mycobacterium chelonae Infection After a Cat Bite: A Rare Case Report. Clin Cosmet Investig Dermatol 2022; 15:1847-1851. [PMID: 36111182 PMCID: PMC9469770 DOI: 10.2147/ccid.s375826] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/25/2022] [Indexed: 12/03/2022]
Abstract
We describe a 62-year-old woman with a 1-month-old unhealed cat bite wound caused by Mycobacterium chelonae presenting with persistent infection despite treatment with cefazolin and amoxicillin. This is the first reported case of M. chelonae infection caused by a cat bite. Cat bites are affected by the cat’s food microbiome, so clinicians should consider the cat’s diet if wounds are not responding as expected to first-line therapy.
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Affiliation(s)
- Lei Zhang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Yixiong Li
- Department of Anorectal, The First Affiliated Hospital of Chengdu Medical College, Chengdu, People's Republic of China
| | - Hao Yang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Yunzhu Mu
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Jingjing Jiang
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
| | - Xi Duan
- Department of Dermatology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan Province, People's Republic of China
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Emikoglu Cerit SKB, Tarhan GL, Ceyhan I. Investigation of species distribution of nontuberculosis mycobacteria isolated from sputum samples in patients with suspected pulmonary tuberculosis. Int J Mycobacteriol 2022; 11:145-149. [PMID: 35775546 DOI: 10.4103/ijmy.ijmy_51_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: 11/04/2022] Open
Abstract
Aims Rapid and accurate identification of mycobacteria is important for the species-specific treatment of the disease. The aim of this study was the identification at the species level of 34 nontuberculous mycobacteria strains isolated from respiratory tract samples and 14 reference strains as by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Materials and Methods Isolates derived from clinical specimens were subcultured in the Lowenstein-Jensen medium. Deoxyribonucleic acid isolation was carried out using the boiling method. PCR amplification was performed using primers specific to the hsp65 gene region. The PCR products were digested BstEII and HaEIII enzymes. All samples were studied comparatively by two different centers. Results In our study, the most common species were found to be Mycobacterium intracellulare in 23.52% (8/34). The performance of the PCR-RFLP method in detecting mycobacteria was found to be 82.35%. Conclusions The PCR-RFLP method is a rapid, cheap, and practical method for the identification of mycobacteria.
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Affiliation(s)
| | - G Lnur Tarhan
- Department of Medical Microbiology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey
| | - Ismail Ceyhan
- Department of Public Health Nursing, Health Science Faculty, Ankara Yildirim Beyazit University, Ankara, Turkey
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Coelho AGV, Chiou AC, Pedro HDSP, Nardi SMT, Chimara E. Epidemiological profile and follow-up of patients with pulmonary disease by non-tuberculous mycobacteria in Baixada Santista area, São Paulo. EINSTEIN-SAO PAULO 2022; 20:eAO5510. [PMID: 35170707 PMCID: PMC8827356 DOI: 10.31744/einstein_journal/2022ao5510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 07/15/2020] [Indexed: 11/05/2022] Open
Abstract
Objective To present the frequency and species diversity of non-tuberculous mycobacteria, estimate the prevalence of non-tuberculous mycobacterial pulmonary disease, describe the epidemiological profile, and determine the follow-up of patients with non-tuberculous mycobacterial pulmonary disease living in a region with a high burden of tuberculosis. Methods This a retrospective cohort observational study using data records obtained from the Instituto Adolfo Lutz - Santos and from the São Paulo Sistema de Vigilância de Tuberculose do Estado de São Paulo in the period between 2000 and 2009. The studied variables were: socio-demographic characteristics, current and past history of tuberculosis, aspects related to diagnosis, and treatment and associated diseases. Results We included 319 non-tuberculous mycobacteria isolates in the study, corresponding to 257 patients. The species Mycobacterium kansasii (28.5%) and Mycobacterium fortuitum (16.6%) presented the higher occurrence. In 10.9% (24) of the patients, there was a criterion for confirming a case of pulmonary disease due to non-tuberculous mycobacteria. In relation to gender and age, male and individuals over 50 years old were the most frequent. Considering the confirmed cases, 47.8% had a past history of tuberculosis. Conclusion The lack of information about the cases is evident, since pulmonary disease due to non-tuberculous mycobacteria is not mandatory. The therapeutic regimen according to the identified species is fundamental for success in combating the infections caused by non-tuberculous mycobacteria. Besides that, information about the regional epidemiology of pulmonary disease caused by non-tuberculous mycobacteria and the search for associations with other comorbidities are important to establish the correct treatment. In order to improve surveillance of pulmonary diseases by non-tuberculous mycobacteria, we suggest the implantation of a sentinel surveillance and of population-based studies.
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Garcia Carvalho NF, Pedace CS, Barbosa de Almeida AR, Dos Santos Simeão FC, Chimara E. Evaluation of drug susceptibility in nontuberculous mycobacteria using the SLOMYCO and RAPMYCO sensititre plates. Int J Mycobacteriol 2021; 10:379-387. [PMID: 34916455 DOI: 10.4103/ijmy.ijmy_219_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Non-tuberculous Mycobacteria (NTM) cause different forms of diseases. According to recent guideline by ATS/ERS/ESCMID/IDSA, drug susceptibility test (DST) is an important requirement to choose adequate treatment. The minimum inhibitory concentration (MIC) test is the recommended method. Sensititre SLOMYCO and RAPMYCO commercial panels were developed to perform mycobacteria DST easier. However, there are only two comparative studies between SLOMYCO and the MIC method and none for the RAPMYCO panel. The present study aimed to evaluate the Sensititre SLOMYCO and RAPMYCO plates in determining drug susceptibility compared to the gold standard method (MIC). Methods The tests were carried out with clinical isolates received in the diagnostic routine of the Tuberculosis Laboratory at Institute Adolfo Lutz from the most frequent species in the state of São Paulo, Brazil. Reference strains were tested for repeatability and reproducibility analyses. MIC and Sensititre plates readings were compared with and without resazurin stain. Agreement between results was defined as MIC within the same dilution or dilution variation resulting the same category in both tests. Results were classified by categorical errors. Results The RAPMYCO panel had 100% agreement for the drugs amikacin, doxycycline, ciprofloxacin and trimethoprim/sulfamethoxazole, 83.3% for clarithromycin and moxifloxacin and 60% for cefoxitin. The SLOMYCO panel had 80% agreement for amikacin and moxifloxacin and 60% for clarithromycin, rifabutin, rifampicin and ciprofloxacin. The repeatability and reproducibility with RAPMYCO and SLOMYCO plates showed a high level of agreement for the drugs tested, being higher with the use of resazurin. However, an evaluation on routine condition is needed. Conclusions The present study found that the fewer steps in the tests with Sensititre plates and reading with resazurin allow its use with greater safety and efficiency in the laboratory routine. The results presented here will facilitate the execution of a validation for complete incorporation of Sensititre plates into a diagnostic routine.
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Affiliation(s)
| | | | | | | | - Erica Chimara
- Tuberculosis and Mycobacteriosis Laboratory, Institute Adolfo Lutz, São Paulo, Brazil
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de Almeida CAS, Dos Santos CR, Benites NR, Jordão RS, Chimara É, Benesi FJ, de Azevedo SS, Ribeiro MG, Pinheiro SR. Intradermal comparative cervical tuberculin test in the diagnosis of caprine tuberculosis. Braz J Microbiol 2021; 53:421-431. [PMID: 34767242 DOI: 10.1007/s42770-021-00650-9] [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: 06/03/2021] [Accepted: 11/03/2021] [Indexed: 11/29/2022] Open
Abstract
Tuberculosis remains one of the most important infectious diseases with well-known zoonotic nature that affect humans, wildlife, and domestic animals, including goats. Nonetheless, no intradermal tuberculin test has been standardized for caprine diagnosis of tuberculosis. The present study investigated the intradermal comparative cervical tuberculin test (ICCTT) in the diagnosis of tuberculosis among 60 goats from farms with history of tuberculosis. The cutoff applied to goats was based on a study where goats had been experimentally infected with Mycobacterium bovis and Mycobacterium avium. Clinical examination, bacteriological culture, and histopathological staining were assessed to the diagnosis. Isolates compatible with mycobacteria were subjected for molecular diagnosis based on gyrB-restriction fragment length polymorphism (RFLP) analysis and PCR restriction-enzyme analysis (PRA) of hsp65 gene by BstEII and HaeIII, namely PRA-hsp65 assay. From all goats, 60% (n = 36/60), 3.3% (n = 2/60), and 36.7% (n = 22/60) showed positive, inconclusive, and negative reactions, respectively. Out of 36 goats with ICCTT positive, 75% (n = 27/36) had isolation of mycobacteria and were detected M. bovis by gyrB-RFLP. Molecular diagnosis and histopathological findings compatible with tuberculosis showed 86.1% (n = 31/36) concordance with the ICCTT. When compared ICCTT with M. bovis isolation, gyrB-RFLP, and histopathology, the better arithmetic means of sensitivity and specificity were 2.5 mm for ICCTT compared with M. bovis isolation and gyrB-RFLP, and 4.55 mm when compared with histopathology. Both receiver operating characteristic (ROC) curves presented statistical significance (P < 0.001). The identification of other mycobacteria, e.g., M. kansasii, M. flavescens, M. avium, M. florentinum, M. lentiflavum, M. simiae, and Corynebacterium pseudotuberculosis, not influenced positive results in ICCTT. The concordance between bacteriological, histopathological, and molecular identification with ICCTT findings indicate that the tuberculin test may be used as a valuable tool for diagnosis of caprine tuberculosis and reinforce the importance of association of methods to diagnostic of the disease from animal origin.
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Affiliation(s)
| | - Caio R Dos Santos
- Animal Pathology Department, School of Veterinary Medicine and Animal Sciences, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Nilson Roberti Benites
- Department of Preventive Veterinary Medicine and Animal Science, USP, São Paulo, SP, Brazil
| | - Ricardo S Jordão
- Biological Institute of São Paulo, Secretariat of Agriculture and Supply of State of São Paulo, São Paulo, SP, Brazil
| | - Érica Chimara
- Tuberculosis and Mycobacteriosies Laboratory, Adolfo Lutz Institute, São Paulo, SP, Brazil
| | | | - Sergio S de Azevedo
- Veterinary Medicine Academic Unit, Federal University of Campina Grande, UFCG, Paraíba, PB, Brazil
| | - Márcio Garcia Ribeiro
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Sciences, São Paulo State University-UNESP, Botucatu, SP, Brazil
| | - Sônia Regina Pinheiro
- Department of Preventive Veterinary Medicine and Animal Science, USP, São Paulo, SP, Brazil
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Jia X, Yang L, Li C, Xu Y, Yang Q, Chen F. Combining comparative genomic analysis with machine learning reveals some promising diagnostic markers to identify five common pathogenic non-tuberculous mycobacteria. Microb Biotechnol 2021; 14:1539-1549. [PMID: 34019733 PMCID: PMC8313281 DOI: 10.1111/1751-7915.13815] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/02/2021] [Indexed: 11/29/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) can cause various respiratory diseases and even death in severe cases, and its incidence has increased rapidly worldwide. To date, it's difficult to use routine diagnostic methods and strain identification to precisely diagnose various types of NTM infections. We combined systematic comparative genomics with machine learning to select new diagnostic markers for precisely identifying five common pathogenic NTMs (Mycobacterium kansasii, Mycobacterium avium, Mycobacterium intracellular, Mycobacterium chelonae, Mycobacterium abscessus). A panel including six genes and two SNPs (nikA, benM, codA, pfkA2, mpr, yjcH, rrl C2638T, rrl A1173G) was selected to simultaneously identify the five NTMs with high accuracy (> 90%). Notably, the panel only containing the six genes also showed a good classification effect (accuracy > 90%). Additionally, the two panels could precisely differentiate the five NTMs from M. tuberculosis (accuracy > 99%). We also revealed some new marker genes/SNPs/combinations to accurately discriminate any one of the five NTMs separately, which provided the possibility to diagnose one certain NTM infection precisely. Our research not only reveals novel promising diagnostic markers to promote the development of precision diagnosis in NTM infectious, but also provides an insight into precisely identifying various genetically close pathogens through comparative genomics and machine learning.
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Affiliation(s)
- Xinmiao Jia
- Medical Research CenterState Key laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalPeking Union Medical CollegeBeijing100730China
- Department of Clinical LaboratoryState Key laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijing100730China
| | - Linfang Yang
- Departments of DermatologyAffiliated Xingtai People’s Hospital of Hebei Medical UniversityXingtai, Hebei054001China
| | - Cuidan Li
- CAS Key Laboratory of Genome Sciences & InformationChina National Center for BioinformationChinese Academy of SciencesBeijing Institute of GenomicsBeijing100101China
| | - Yingchun Xu
- Department of Clinical LaboratoryState Key laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijing100730China
| | - Qiwen Yang
- Department of Clinical LaboratoryState Key laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalPeking Union Medical CollegeChinese Academy of Medical SciencesBeijing100730China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & InformationChina National Center for BioinformationChinese Academy of SciencesBeijing Institute of GenomicsBeijing100101China
- University of Chinese Academy of SciencesBeijing100049China
- State Key Laboratory of Pathogenesis, PreventionTreatment of High Incidence Diseases in Central AsiaXinjiangChina
- Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijingChina
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Identification of the Mycobacterial Strains Isolated From Clinical Specimens Using hsp65 PCR-RFLP Method. MEDICAL BULLETIN OF SISLI ETFAL HOSPITAL 2020; 54:364-370. [PMID: 33312037 PMCID: PMC7729718 DOI: 10.14744/semb.2019.66587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/30/2019] [Indexed: 11/20/2022]
Abstract
Objectives It is important to identify mycobacteria at the species level, to distinguish pathogen from non-pathogenic species, to choose the appropriate treatment regimen and to collect epidemiological data. For the identification of mycobacteria, which are time-consuming and laborious with traditional methods, faster, more sensitive and reliable methods are needed. This study aims to investigate the suitability of the hsp65 Polymerase chain reaction-restriction fragment polymorphism (PCR-RFLP) method for routine laboratory use. Methods In this study, 141 mycobacterial isolates were obtained from 1632 samples, which were sent to the Medical Microbiology Laboratory. Results In the culture, mycobacteria were identified as 138 M. tuberculosis complex (MTBC) and three non-tuberculosis mycobacteria (NTM) by conventional methods. Using the hsp65 PCR-RFLP method, 137 isolates were identified as MTBC, four isolates as NTM. An isolate that was evaluated as MTBC because it was PNB sensitive by the conventional method was determined as NTM with the hsp65 method. In the identification of non-tuberculosis mycobacteria with the hsp65 PCR-RFLP method, one isolate was identified as M. abcessus and three isolates were identified as M. avium complex. Conclusion In our study, it was concluded that the hsp65 PCR-RFLP method, which allows identification of mycobacteria, including NTMs, is a method that is cheap, easy and suitable for routine use to provide rapid information to the clinic. The scope of the agar and database used in the method is effective in the definition of the correct species.
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Sharma M, Malhotra B, Tiwari J, Bhargava S. Profile of Nontuberculous Mycobacteria in Patients Suspected of Tuberculosis and Drug-Resistant Tuberculosis. J Lab Physicians 2020; 12:203-211. [PMID: 33268938 PMCID: PMC7684985 DOI: 10.1055/s-0040-1721160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Objective Infections due to nontuberculous mycobacteria (NTM) is increasing globally and may present as drug-resistant tuberculosis (DRTB). In India, data on NTM prevalence and species diversity is limited. Present study was conducted to detect the prevalence and profile of NTM among patients suspected of DRTB using paraffin slide culture (PSC)and mycobacteria growth indicator tube (MGIT) culture methods for isolation of NTM. Material and Method A total of 2,938 samples suspected of TB/DRTB were cultured on PSC and MGIT960. Species identification of mycobacterial isolate was done by sequencing of 16s ribosomal RNA gene. Result Among 2938 samples, 35 (1.19%) were found positive for NTM by PSC and 9 (0.30%) were found positive by MGIT. The diversity of NTM species was high (13 species). Out of 35 NTM isolates by PSC, maximum 34.29% (12) isolates were found to be Mycobacterium fortuitum , followed by 11.43% (4) Mycobacterium abscessus and Mycobacterium chelonae , and 42.85% (15) were other species viz. 8.57% (3) were Mycobacterium intracellulare and Mycobacterium kansasii , 5.71% (2) were Mycobacterium peregrinum , and 2.85% (1) were Mycobacterium flavescens, Mycobacterium farcinogenes, Mycobacterium moriokanese, Mycobacterium wolinskyi, Mycobacterium simiae, Mycobacterium goodii , and Mycobacterium terrae each. Coinfection of Mycobacterium tuberculosis (MTB) and NTM was found in 60% (21) samples. Conclusion Prevalence of NTM was low among multidrug resistant tuberculosis/TB suspected patients, similar to other studies done in India. PSC was found better than MGIT for the isolation of NTM, though poor separation of NTM and MTB on subculture may have led to false negativity in cases of coinfection. About 13 species were isolated; M. fortuitum was the most common of all. Since coinfection of NTM and TB can also occur, samples of patients suspected of NTM should be cultured on PSC even if positive for MTB.
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Affiliation(s)
- Megha Sharma
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| | - Bharti Malhotra
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
| | - Jitendra Tiwari
- Department of Microbiology, Government Medical College, Bharatpur, Rajasthan, India
| | - Shipra Bhargava
- Department of Microbiology, SMS Medical College, Jaipur, Rajasthan, India
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Moreno-Izquierdo C, Zurita J, Contreras-Yametti F, Jara-Palacios M. Mycobacterium abscessus subspecies abscessus infection associated with cosmetic surgical procedures: Cases series. IDCases 2020; 22:e00992. [PMID: 33194548 PMCID: PMC7644577 DOI: 10.1016/j.idcr.2020.e00992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/03/2020] [Accepted: 10/10/2020] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium abscessus is a drug-resistant nontuberculous mycobacterium (NTM). Cutaneous & subcutaneous NTM infections post-cosmetic surgery are poorly diagnosed. Initial surgical evaluation facilitates early suspicion of M. abscessus infection. Rapidly evolving infection & negative culture/antibiotic response are indicators. Amikacin, imipenem, & clarithromycin combination may treat M. abscessus infection.
Background Mycobacterium abscessus is one of the most pathogenic and drug-resistant opportunistic microorganisms among the nontuberculous mycobacteria (NTM) involved in skin and soft tissue infections (SSTI) associated with cosmetic surgical procedures. However, NTM infection is often wrongly diagnosed initially causing prolonged suffering. Here is described the author’s experience working with patients who developed M. abscessus SSTI after cosmetic procedures. Methods Patients who developed NTM infection after undergoing cosmetic procedures, and who presented at the Hospital Metropolitano and Hospital Vozandes (Quito, Ecuador) between 2013–2016. A review of patient medical records was performed. Results Five patients with culture proven M. abscessus subspecies abscessus SSTI after cosmetic surgeries were identified. All patients were treated with aggressive surgical debridement and antibiotics. Conclusions A rapidly spreading wound infection presenting two or more weeks after a cosmetic procedure that fails to respond to standard antimicrobial therapy should raise suspicion for NTM infection. Samples for acid-fast bacilli smear, cultures, and PCR from infected tissue should be taken. Surgical drainage and debridement are recommended along with a long course of antibiotics. In the absence of clinical trials, a combination of amikacin, imipenem, and clarithromycin may be an adequate initial treatment for M. abscessus subspecies abscessus SSTI in immunocompetent patients.
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Affiliation(s)
- C. Moreno-Izquierdo
- Escuela de Medicina, Facultad de Ciencias Médicas, de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
- Servicio de Microbiología y Tuberculosis, Hospital Vozandes, Quito, Ecuador
- Servicio de Infectología, Hospital Metropolitano, Quito, Ecuador
- Corresponding author at: Escuela de Medicina, Facultad de Ciencias Médicas, de la Salud y de la Vida, Universidad Internacional del Ecuador, Ecuador.
| | - J. Zurita
- Servicio de Microbiología y Tuberculosis, Hospital Vozandes, Quito, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - F.I. Contreras-Yametti
- Escuela de Medicina, Facultad de Ciencias Médicas, de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - M.A. Jara-Palacios
- Escuela de Medicina, Facultad de Ciencias Médicas, de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
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Zurita J, Sevillano G, González C, Lascano Y. Segniliparus rugosus from the sputum of a child with cystic fibrosis in Ecuador: challenges in bacterial identification. New Microbes New Infect 2020; 35:100668. [PMID: 32461807 PMCID: PMC7240726 DOI: 10.1016/j.nmni.2020.100668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 03/10/2020] [Indexed: 11/17/2022] Open
Abstract
Using sequencing analyses of the 16S rRNA gene, we identified Segniliparus rugosus in an 8-year-old child with cystic fibrosis. We describe the difficulties we encountered in identifying this bacterium. To the best of our knowledge, this is the first reported case of S. rugosus in Ecuador.
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Affiliation(s)
- J. Zurita
- Biomedical Research Unit, Zurita & Zurita Laboratorios, Quito, Ecuador
- Corresponding author. Zurita & Zurita Laboratories, Quito, Ecuador.
| | - G. Sevillano
- Biomedical Research Unit, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - C. González
- Biomedical Research Unit, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Y. Lascano
- Department of Paediatric Pneumology, Hospital Carlos Andrade Marin, Quito, Ecuador
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Prevalence and risk factors of pulmonary nontuberculous mycobacterial infections in the Zhejiang Province of China. Epidemiol Infect 2019; 147:e269. [PMID: 31506134 PMCID: PMC6807301 DOI: 10.1017/s0950268819001626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Risk factors and prevalence of pulmonary nontuberculous mycobacterial (NTM) diseases were retrospectively evaluated in 1208 suspected pulmonary TB patients seeking care at the Affiliated Hospital of Hangzhou Normal University between July 2018 and December 2018. Further analysis of 390 culture-positive cases demonstrated that 358 (358/390, 91.8%) were infected with Mycobacterium tuberculosis (MTB), 24 (24/390, 6.2%) with NTM and eight (8/390, 2.0%) with both MTB and NTM. M. intracellulare was the most prevalent NTM isolated (16/24, 66.7%), followed by M. abscessus (3/24), M. kansasii (2/24), M. avium (1/24), M. szulgai (1/24) and M. fortuitum (1/24). The difference between NTM and TB case rates for the ⩾65-year-old age group significantly exceeded the difference for the reference group (patients aged 25-44 years) (OR (95% CI): 4.63 (1.03-20.90)). Pulmonary NTM diseases incidence positively correlated with prior TB history (OR (95% CI): 12.92 (3.24-31.82)). Moreover, pulmonary NTM patients were significantly more likely to exhibit underlying bronchiectasis than pulmonary TB patients (OR (95% CI): 18.89 (7.54-47.88)). In conclusion, approximately one-tenth of culture-positive suspected pulmonary TB patients are infected with NTM (most frequently M. intracellulare) in Zhejiang Province, China. The elderly and those with bronchiectasis or a history of TB are at the greatest risk of contracting pulmonary NTM disease.
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Carvalho NFGD, Pavan F, Sato DN, Leite CQF, Arbeit RD, Chimara E. Genetic correlates of clarithromycin susceptibility among isolates of the Mycobacterium abscessus group and the potential clinical applicability of a PCR-based analysis of erm(41). J Antimicrob Chemother 2019; 73:862-866. [PMID: 29272470 DOI: 10.1093/jac/dkx476] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/19/2017] [Indexed: 11/12/2022] Open
Abstract
Objectives To define the genetic basis of clarithromycin resistance among isolates of the Mycobacterium abscessus group (MAG). Methods We analysed 133 isolates identified as MAG. Species identification was confirmed by sequencing the rpoB gene. Clarithromycin susceptibility testing was performed according to CLSI recommendations, with an extended 14 day incubation. Known resistance genotypes of erm(41) and rrl were identified by sequencing; the presence of deletions in erm(41) was detected by PCR. Results The 133 MAG isolates included 82 M. abscessus, 27 Mycobacterium massiliense and 24 Mycobacterium bolletii. After the 3 day incubation, only five isolates demonstrated clarithromycin resistance (R); after 14 days of extended incubation, an additional 92 exhibited inducible resistance (IR), with the remaining being susceptible (S). The distribution of susceptibility phenotypes varied among the species. Among M. abscessus isolates, 11% were S, 84% IR and 5% R; among M. bolletii isolates, 96% were IR and 4% R; and among M. massiliense isolates 100% were S. Sequencing of rrl identified only a single isolate with the A2058G mutation. Deletions in erm(41) were present in 30 susceptible isolates; among the remaining 103 isolates, 97 were R or IR (sensitivity, 83%; specificity, 100%; positive predictive value, 100%; negative predictive value, 94%). Among the six susceptible isolates without deletions, all carried the erm(41) T28C point mutation. Conclusions A significant proportion of MAG isolates demonstrate inducible resistance to clarithromycin that is only detectable with an extended 14 day incubation. Further, the majority of clarithromycin-susceptible MAG isolates have characteristic deletions in erm(41) that can rapidly and reliably be detected by a simple PCR.
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Affiliation(s)
- Natalia F G de Carvalho
- Tuberculosis and Mycobacteriosis Laboratory, Bacteriology Center, Instituto Adolfo Lutz, São Paulo, Brazil
| | - Fernando Pavan
- Faculdade de Ciências Farmacêuticas, UNESP, Araraquara, Brazil
| | - Daisy N Sato
- Faculdade de Ciências Farmacêuticas, UNESP, Araraquara, Brazil
| | | | - Robert D Arbeit
- Division of Infectious Diseases, Tufts Medical Center, Boston, MA, USA
| | - Erica Chimara
- Tuberculosis and Mycobacteriosis Laboratory, Bacteriology Center, Instituto Adolfo Lutz, São Paulo, Brazil
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Starkova DA, Iwamoto T, Vyazovaya AA, Molchanov VM, Zhuravlev VY, Vishnevsky BI, Narvskaya OV. Single Nucleotide Polymorphisms in hsp65 and MACPPE12 Genes of Mycobacterium avium subsp. hominissuis. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Marques LRM, Ferrazoli L, Chimara É. Pulmonary nontuberculous mycobacterial infections: presumptive diagnosis based on the international microbiological criteria adopted in the state of São Paulo, Brazil, 2011-2014. J Bras Pneumol 2019; 45:e20180278. [PMID: 31038648 PMCID: PMC6733752 DOI: 10.1590/1806-3713/e20180278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/20/2019] [Indexed: 11/26/2022] Open
Abstract
Objective: Pulmonary nontuberculous mycobacterial infections are caused by nontuberculous mycobacteria (NTM), the microbiological diagnosis of which involves the isolation and identification of the same species in at least two sputum samples, one BAL fluid sample, or one lung biopsy sample. The objective of the present study was to determine the frequency at which the various NTM species are identified among selected individuals and in potential cases of pulmonary nontuberculous mycobacterial infection. Methods: This was a retrospective analysis of the data on species isolated from respiratory specimens collected from 2,843 individuals between 2011 and 2014. Potential NTM infection cases were identified on the basis of the international microbiological criteria adopted in the state of São Paulo. Results: A total of 50 species were identified using the molecular method PCR-restriction enzyme analysis. Samples collected from 1,014 individuals were analyzed in relation to the microbiological criteria, and 448 (44.18%) had a presumptive diagnosis of pulmonary nontuberculous mycobacterial infection, the species identified most frequently being, in descending order, Mycobacterium kansasii, M. abscessus, M. intracellulare, M. avium, and M. szulgai. Conclusions: Although various NTM species were identified among the individuals studied, those presumptively identified most frequently on the basis of the microbiological criteria adopted in the state of São Paulo were the ones that are most commonly associated with pulmonary nontuberculous mycobacterial infection worldwide or in specific geographic regions.
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Affiliation(s)
| | - Lucilaine Ferrazoli
- . Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo (SP) Brasil
| | - Érica Chimara
- . Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz, São Paulo (SP) Brasil
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Fogelson SB, Camus AC, Lorenz WW, Vasireddy R, Vasireddy S, Smith T, Brown-Elliott BA, Wallace RJ, Hasan NA, Reischl U, Sanchez S. Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns. PLoS One 2019; 14:e0214274. [PMID: 30908517 PMCID: PMC6433289 DOI: 10.1371/journal.pone.0214274] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 03/11/2019] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium chelonae is a member of the Mycobacterium chelonae-abscessus complex and a cause of opportunistic disease in fish, reptiles, birds, and mammals including humans. Isolates in the complex are often difficult to identify and have differing antimicrobial susceptibilities. Thirty-one previously identified rapidly-growing, non-tuberculous Mycobacterium sp. isolates cultured from biofilms, fish, reptiles, mammals, including humans, and three ATCC reference strains were evaluated with nine M. chelonae-abscessus complex whole genome sequences from GenBank by phylogenomic analysis, targeted gene comparisons, and in-vitro antimicrobial susceptibility patterns to assess strain variation among isolates from different sources. Results revealed minimal genetic variation among the M. chelonae strains. However, the core genomic alignment and SNP pattern of the complete 16S rRNA sequence clearly separated the turtle type strain ATCC 35752T from the clinical isolates and human reference strain “M. chelonae chemovar niacinogenes” ATCC 19237, providing evidence of two distinct subspecies. Concatenation of the partial rpoB (752 bp) and complete hsp65 (1,626 bp) sequence produced the same species/subspecies delineations as the core phylogeny. Partial rpoB and hsp65 sequences identified all the clinical isolates to the appropriate species level when respective cut-offs of 98% and 98.4% identity to the M. chelonae type strain ATCC 35752T were employed. The human strain, ATCC19237, was the most representative strain for the evaluated human, veterinary, and environmental strains. Additionally, two isolates were identified as Mycobacterium saopaulense, its first identification in a non-fish or non-human host.
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Affiliation(s)
- Susan B. Fogelson
- University of Georgia, College of Veterinary Medicine, Department of Pathology, Athens, GA, United States of America
- * E-mail:
| | - Alvin C. Camus
- University of Georgia, College of Veterinary Medicine, Department of Pathology, Athens, GA, United States of America
| | - W. Walter Lorenz
- University of Georgia, Institute of Bioinformatics, Athens, GA, United States of America
| | - Ravikiran Vasireddy
- University of Texas Health Science Center at Tyler, Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, Tyler, TX, United States of America
| | - Sruthi Vasireddy
- University of Texas Health Science Center at Tyler, Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, Tyler, TX, United States of America
| | - Terry Smith
- University of Texas Health Science Center at Tyler, Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, Tyler, TX, United States of America
| | - Barbara A. Brown-Elliott
- University of Texas Health Science Center at Tyler, Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, Tyler, TX, United States of America
| | - Richard J. Wallace
- University of Texas Health Science Center at Tyler, Mycobacteria/Nocardia Research Laboratory, Department of Microbiology, Tyler, TX, United States of America
| | - Nabeeh A. Hasan
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, United States of America
| | - Udo Reischl
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, Regensburg, Germany
| | - Susan Sanchez
- University of Georgia, College of Veterinary Medicine, Department of Infectious Diseases, Athens, GA, United States of America
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Krooks J, Weatherall A, Markowitz S. Complete Resolution of Mycobacterium marinum Infection with Clarithromycin and Ethambutol: A Case Report and a Review of the Literature. THE JOURNAL OF CLINICAL AND AESTHETIC DERMATOLOGY 2018; 11:48-51. [PMID: 30666280 PMCID: PMC6334835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A 70-year-old, immunocompetent male presented with mildly painful and pruritic erythematous patches and vesicles on the right dorsal aspect of the distal middle finger present for four weeks. Other skin lesions or systemic symptoms were notably absent. The patient failed to respond to valacyclovir, topical triamcinolone acetonide ointment, trimethoprim-sulfamethoxazole, and cephalexin for presumptive diagnoses of recurrent herpetic whitlow, dyshidrotic eczema, and blistering distal dactylitis, respectively. Furthermore, biopsy findings were inconsistent with eczema, psoriasis, or viral or fungal infection as potential etiologies. Mycobacterium marinum infection was then considered due to the patient's observation that the lesion appeared three weeks after purchasing a home fish tank. Mycobacterium marinum, referred to as "fish tank granuloma" as a result of its typical association with aquarium exposure, is usually diagnosed clinically and treated empirically due to the organism's slow-growing nature. In light of the infection's low prevalence, large studies regarding treatment options are limited. Our patient's lesion resolved within two weeks of treatment with clarithromycin (500mg twice a day) and ethambutol (15mg/kg once a day), which was then continued for two more months. Prior to this treatment, the patient's lesion had cleared completely with minocycline; we attribute recurrence to not continuing therapy past lesion resolution.
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Affiliation(s)
- Jolie Krooks
- Ms. Krooks, Dr. Weatherall, and Dr. Markowitz are with the Florida Atlantic University Charles E. Schmidt College of Medicine in Boca Raton, Florida
| | - Angela Weatherall
- Ms. Krooks, Dr. Weatherall, and Dr. Markowitz are with the Florida Atlantic University Charles E. Schmidt College of Medicine in Boca Raton, Florida
| | - Stuart Markowitz
- Ms. Krooks, Dr. Weatherall, and Dr. Markowitz are with the Florida Atlantic University Charles E. Schmidt College of Medicine in Boca Raton, Florida
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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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Hospital bronchoscopy-related pseudo-outbreak caused by a circulating Mycobacterium abscessus subsp. massiliense. J Hosp Infect 2018; 100:e138-e141. [DOI: 10.1016/j.jhin.2018.07.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/30/2018] [Indexed: 11/19/2022]
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Siqueira FDS, Rossi GG, Machado AK, Alves CFS, Flores VC, Somavilla VD, Agertt VA, Siqueira JD, Dias RDS, Copetti PM, Sagrillo MR, Back DF, de Campos MMA. Sulfamethoxazole derivatives complexed with metals: a new alternative against biofilms of rapidly growing mycobacteria. BIOFOULING 2018; 34:893-911. [PMID: 30418037 DOI: 10.1080/08927014.2018.1514497] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Biofilms are considered important sources of infections on biomedical surfaces, and most infections involving biofilm formation are associated with medical device implants. Therefore, there is an urgent need for new antimicrobial compounds that can combat microbial resistance associated with biofilm formation. In this context, this work aimed to evaluate the antibiofilm action of sulfamethoxazole complexed with Au, Cd, Cu, Ni and Hg on rapidly growing mycobacteria (RGM), as well as to evaluate their safety through cytotoxic assays. The results demonstrate potentiation of the novel compounds in antibiofilm activity, mainly in the complex with Au, which was able to completely inhibit biofilm formation and had the capacity to destroy the biofilm at all the concentrations tested. All cytotoxic data suggest that the majority of sulfamethoxazole metallic derivatives are antimicrobial alternatives, as well as safe molecules, which could be used as potential therapeutic agents for bacterial and biofilm elimination.
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Affiliation(s)
- Fallon Dos Santos Siqueira
- a Graduate Program in Pharmaceutical Sciences , Universidade Federal de Santa Maria , Santa Maria , Brazil
| | - Grazielle Guidolin Rossi
- a Graduate Program in Pharmaceutical Sciences , Universidade Federal de Santa Maria , Santa Maria , Brazil
| | | | | | - Vanessa Costa Flores
- a Graduate Program in Pharmaceutical Sciences , Universidade Federal de Santa Maria , Santa Maria , Brazil
| | - Viviane Drescher Somavilla
- a Graduate Program in Pharmaceutical Sciences , Universidade Federal de Santa Maria , Santa Maria , Brazil
| | - Vanessa Albertina Agertt
- a Graduate Program in Pharmaceutical Sciences , Universidade Federal de Santa Maria , Santa Maria , Brazil
| | | | - Renne de Sousa Dias
- c Graduate Program in Chemistry , Universidade Federal de Santa Maria , Santa Maria , Brazil
| | | | | | - Davi Fernando Back
- c Graduate Program in Chemistry , Universidade Federal de Santa Maria , Santa Maria , Brazil
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Puga FG, Pocente RHC, Chimara E, Bollela VR. HIV-negative pulmonary disease caused by nontuberculous mycobacteria in Southern Brazil: clinical and microbiological characterization. J Thorac Dis 2018; 10:1903-1911. [PMID: 29707345 DOI: 10.21037/jtd.2018.03.66] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Background Nontuberculous mycobacteria (NTM) have been identified with increasing frequency in the clinical practice. The aim of this study was to characterize NTM isolates in respiratory specimens from patients with pulmonary disease and to correlate this with clinical/radiological findings, decision to start treatment and outcomes. Methods A cross-sectional descriptive study was performed and included all patients who had at least one NTM isolated in respiratory specimens between 2011 and 2014. NTM culture was performed in liquid medium followed by immunochromatographic identification (anti-MPT64). Species identification was based on nucleic acid amplification followed by restriction analysis of a 441 bp fragment of the hsp65 gene (hsp65 PRA) and patients' records were reviewed. Results From 14,394 cultures in 4 years, 590 (4.10%) grew NTM and 305 (51.7%) isolates were characterized till species level, representing 290 patients including those with and without human immunodeficiency virus (HIV) infection. Two hundred and eleven non-HIV patients had NTM isolated from respiratory specimens, 49 (23.2%) had criteria for active disease based on the American Thoracic Society (ATS) 2007. The majority was men above 51 years old and M. intracellulare was detected in 59.2% (29/49), followed by M. avium 14.3% (7/49), and M. abscessus 12.2% (6/49). Conclusions Old age, nodular and nodular/bronchiectasis radiographic pattern, previous tuberculosis (TB) treatment and M. intracellulare were more frequent among NTM-disease patients compared to those only colonized. Positive culture and maintenance of clinical symptoms (poor outcome) was a rule when M. abscessus caused NTM-disease. Positive acid-fast smear in respiratory specimen is a strong predictor of disease.
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Affiliation(s)
- Fernanda Guioti Puga
- Ribeirão Preto School of Medicine, University of São Paulo (FMRP-USP), Ribeirão Preto, Brazil
| | | | - Erica Chimara
- Adolfo Lutz Institute, Central Mycobacteria Laboratory, São Paulo, Brazil
| | - Valdes Roberto Bollela
- Ribeirão Preto School of Medicine, University of São Paulo (FMRP-USP), Ribeirão Preto, Brazil
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Watanabe Pinhata JM, Lemes RA, Simeão FCDS, Souza ARD, Chimara E, Ferrazoli L. Use of an immunochromatographic assay for rapid identification of Mycobacterium tuberculosis complex clinical isolates in routine diagnosis. J Med Microbiol 2018; 67:683-686. [PMID: 29570446 DOI: 10.1099/jmm.0.000726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Accurate identification of Mycobacterium tuberculosis complex (MTBC) isolates is essential for tuberculosis (TB) control, especially in a high-burden country such as Brazil. Conventional identification methods are laborious and time-consuming, while rapid molecular methods are expensive and require skilled personnel and appropriate physical laboratory infrastructure. Immunochromatographic assays (ICAs) have been shown to provide a rapid and reliable TB diagnosis at a low cost. The use of the SD Bioline TB Ag MPT64 ICA (MPT64 assay) for rapid identification of MTBC clinical isolates in the routine diagnosis of a large-volume reference TB laboratory was evaluated. We analysed 375 isolates on solid and liquid media concurrently with conventional phenotypic methods, the PRA-hsp65 molecular technique and the MPT64 assay. The sensitivity, specificity and accuracy of the ICA were 97.7, 100 and 98.1 %, respectively. The MPT64 assay yielded rapid and accurate results, enabling the treatment to be initiated early and also impacting on TB control.
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Affiliation(s)
- Juliana Maira Watanabe Pinhata
- Tuberculosis and Mycobacteriosis Core, Center of Bacteriology, Adolfo Lutz Institute, Av. Dr. Arnaldo 351, CEP: 01246-902, São Paulo, SP, Brazil
| | - Romilda Aparecida Lemes
- Tuberculosis and Mycobacteriosis Core, Center of Bacteriology, Adolfo Lutz Institute, Av. Dr. Arnaldo 351, CEP: 01246-902, São Paulo, SP, Brazil
| | - Fernanda Cristina Dos Santos Simeão
- Tuberculosis and Mycobacteriosis Core, Center of Bacteriology, Adolfo Lutz Institute, Av. Dr. Arnaldo 351, CEP: 01246-902, São Paulo, SP, Brazil
| | - Andréia Rodrigues de Souza
- Tuberculosis and Mycobacteriosis Core, Center of Bacteriology, Adolfo Lutz Institute, Av. Dr. Arnaldo 351, CEP: 01246-902, São Paulo, SP, Brazil
| | - Erica Chimara
- Tuberculosis and Mycobacteriosis Core, Center of Bacteriology, Adolfo Lutz Institute, Av. Dr. Arnaldo 351, CEP: 01246-902, São Paulo, SP, Brazil
| | - Lucilaine Ferrazoli
- Tuberculosis and Mycobacteriosis Core, Center of Bacteriology, Adolfo Lutz Institute, Av. Dr. Arnaldo 351, CEP: 01246-902, São Paulo, SP, Brazil
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Pinhata JMW, Felippe IM, Gallo JF, Chimara E, Ferrazoli L, de Oliveira RS. Growth characteristics of liquid cultures increase the reliability of presumptive identification of Mycobacterium tuberculosis complex. J Med Microbiol 2018; 67:828-833. [PMID: 29687767 DOI: 10.1099/jmm.0.000734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We evaluated the microscopic and macroscopic characteristics of mycobacteria growth indicator tube (MGIT) cultures for the presumptive identification of the Mycobacterium tuberculosis complex (MTBC) and assessed the reliability of this strategy for correctly directing isolates to drug susceptibility testing (DST) or species identification. A total of 1526 isolates of mycobacteria received at the Instituto Adolfo Lutz were prospectively subjected to presumptive identification by the observation of growth characteristics along with cord formation detection via microscopy. The presumptive identification showed a sensitivity, specificity and accuracy of 98.8, 92.5 and 97.9 %, respectively. Macroscopic analysis of MTBC isolates that would have been erroneously classified as non-tuberculous mycobacteria based solely on microscopic morphology enabled us to direct them rapidly to DST, representing a substantial gain to patients. In conclusion, the growth characteristics of mycobacteria in MGIT, when considered along with cord formation, increased the reliability of the presumptive identification, which has a great impact on the laboratory budget and turnaround times.
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Affiliation(s)
- Juliana Maira Watanabe Pinhata
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz - Av. Dr. Arnaldo, 351 - 9° andar - 01246-902 - São Paulo - SP, Brazil
| | - Isis Moreira Felippe
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz - Av. Dr. Arnaldo, 351 - 9° andar - 01246-902 - São Paulo - SP, Brazil
| | - Juliana Failde Gallo
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz - Av. Dr. Arnaldo, 351 - 9° andar - 01246-902 - São Paulo - SP, Brazil
| | - Erica Chimara
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz - Av. Dr. Arnaldo, 351 - 9° andar - 01246-902 - São Paulo - SP, Brazil
| | - Lucilaine Ferrazoli
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz - Av. Dr. Arnaldo, 351 - 9° andar - 01246-902 - São Paulo - SP, Brazil
| | - Rosangela Siqueira de Oliveira
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz - Av. Dr. Arnaldo, 351 - 9° andar - 01246-902 - São Paulo - SP, Brazil
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Identification of the Infection Source of an Outbreak of Mycobacterium Chelonae Keratitis After Laser in Situ Keratomileusis. Cornea 2018; 37:116-122. [PMID: 29111994 DOI: 10.1097/ico.0000000000001423] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE Nontuberculous mycobacteria keratitis is a rare but challenging complication of laser in situ keratomileusis (LASIK). This study was conducted to determine the source(s) of infection in a cluster of cases of keratitis after LASIK and to describe this outbreak and patients' outcomes. METHODS In this retrospective, case series, single-center study, 86 patients were included who underwent LASIK or photorefractive keratectomy between December 2011 and February 2012. Corneal scrapes from the affected eyes, samples of tap and distilled water, water from the reservoir of the distilling equipment, steamer, and autoclave cassette; antiseptic and anesthetic solutions and surgical instrument imprints were cultivated in liquid and on solid media. Gram-negative bacteria and yeasts were identified using automated systems and mycobacteria by polymerase chain reaction-restriction enzyme analysis of the hsp65 gene (PRA-hsp65) and DNA sequencing. Mycobacterial isolates were typed by pulsed-field gel electrophoresis. The cases and outcomes are described. The main outcome measure was identification of the source(s) of the mycobacterial infections. RESULTS Eight (15 eyes) of 86 patients (172 eyes) who underwent LASIK developed infections postoperatively; no patients who underwent photorefractive keratectomy developed infections. Mycobacterium chelonae was isolated from 4 eyes. The distilled water collected in the surgical facility contained the same M. chelonae strain isolated from the patients' eyes. Different gram-negative bacteria and yeasts were isolated from samples collected at the clinic but not from the patients' eyes. CONCLUSIONS Tap water distilled locally in surgical facilities may be a source of infection after ocular surgery and its use should be avoided.
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Verma AK, Sarin R, Arora VK, Kumar G, Arora J, Singh P, Myneedu VP. Amplification of Hsp 65 gene and usage of restriction endonuclease for identification of non tuberculous rapid grower mycobacterium. Indian J Tuberc 2018; 65:57-62. [PMID: 29332650 DOI: 10.1016/j.ijtb.2017.08.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 06/08/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The rapid grower mycobacteria have emerged as significant group of human pathogen amongst the Runyon group IV organisms that are capable of causing infection in both the healthy and immunocompromised hosts. Study aimed to identification of species amongst rapid grower non tuberculous mycobacterial isolates by polymerase chain reaction - restriction enzyme analysis (PRA). Analysis and comparison of results with standard biochemical tests. METHODS Rapid grower non tuberculous mycobacteria had been collected from liquid culture section during the study period. All isolates were identified by conventional biochemical tests. A 441bp fragment of hsp65 genes was amplified and digested by two restriction enzymes, BstEII and HaeIII. Digested products were analyzed using polyacrilamid gel electrophoresis (PAGE). RESULTS During study, 121 rapid grower mycobacterial isolates were subjected for species identification. Isolates were obtained from pulmonary samples (72) and extrapulmonary samples (49). In the PRA test 8 different types of rapid grower mycobacteria were identified after analyzing the fragments generated through restriction enzymes. Mycobacterium chelonae (57/121) was the most common isolate in pulmonary and extrapulmonary samples. Mycobacterium fortuitum (42), Mycobacterium abscessus (11), Mycobacterium immunogen (06), Mycobacterium peregrinum (02), Mycobacterium smegmatis (01), Mycobacterium wolinskyi (01), Mycobacterium goodii (01) were identified as other species of rapid grower non tuberculous mycobacteria. CONCLUSION PRA is a rapid and accurate system for the identification of species of non tuberculous mycobacteria. Results of PRA and biochemical tests are concordant up to 98%.
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Affiliation(s)
- Ajoy Kumar Verma
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Rohit Sarin
- Department of TB and Chest, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India.
| | - Vijay Kumar Arora
- Department of TB & Chest Medicine, Santosh Medical College and Hospital Ghaziabad, 201009, NCR Delhi, India
| | - Gavish Kumar
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Jyoti Arora
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Paras Singh
- Department of Molecular Medicine, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Vithal Prasad Myneedu
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
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Nasiri M, Dabiri H, Fooladi A, Amini S, Hamzehloo G, Feizabadi M. High rates of nontuberculous mycobacteria isolation from patients with presumptive tuberculosis in Iran. New Microbes New Infect 2017; 21:12-17. [PMID: 29188063 PMCID: PMC5695646 DOI: 10.1016/j.nmni.2017.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 11/19/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) can cause disease which can be indistinguishable from tuberculosis (TB), posing a diagnostic and therapeutic challenge, particularly in low- and middle-income settings. We aimed to investigate the mycobacterial agents associated with presumptive clinical pulmonary TB in Iran. A total of 410 mycobacterial isolates, obtained between March 2014 and January 2016, from 7600 clinical samples taken from consecutive cases of presumptive diagnosis of TB were identified. Phenotypic and molecular tests were used to identify the isolated organisms to the species level. Single-locus and multilocus sequence analysis based on 16S rRNA, rpoB, hsp65 and ITS locus were used to confirm the results. Of 410 consecutive strains isolated from suspected TB subjects, 62 isolates (15.1%) were identified as NTM. Patients with positive NTM cultures met American Thoracic Society diagnostic criteria for NTM disease. Mycobacterium simiae was the most frequently encountered (38.7%), followed by Mycobacterium fortuitum (19.3%), M. kansasii (17.7%) and M. avium complex (8.0%). Isolation of NTM, including M. simiae, from suspected TB cases is a serious public health problem and merits further attention by health authorities, physicians and microbiologists.
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Affiliation(s)
- M.J. Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Iran
| | - H. Dabiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Iran
| | - A.A.I. Fooladi
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Iran
| | - S. Amini
- Regional Tuberculosis Reference Laboratory, Iran
| | - G. Hamzehloo
- Regional Tuberculosis Reference Laboratory, Iran
| | - M.M. Feizabadi
- Department of Microbiology, School of Medicine, Iran
- Thoracic Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
- Corresponding author: M. M. Feizabadi, Department of Microbiology, Tehran University of Medical Sciences, School of Medicine, Tehran, IranDepartment of MicrobiologyTehran University of Medical SciencesSchool of MedicineTehranIran
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Wang H, Bédard E, Prévost M, Camper AK, Hill VR, Pruden A. Methodological approaches for monitoring opportunistic pathogens in premise plumbing: A review. WATER RESEARCH 2017; 117:68-86. [PMID: 28390237 PMCID: PMC5693313 DOI: 10.1016/j.watres.2017.03.046] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/19/2017] [Accepted: 03/22/2017] [Indexed: 05/06/2023]
Abstract
Opportunistic premise (i.e., building) plumbing pathogens (OPPPs, e.g., Legionella pneumophila, Mycobacterium avium complex, Pseudomonas aeruginosa, Acanthamoeba, and Naegleria fowleri) are a significant and growing source of disease. Because OPPPs establish and grow as part of the native drinking water microbiota, they do not correspond to fecal indicators, presenting a major challenge to standard drinking water monitoring practices. Further, different OPPPs present distinct requirements for sampling, preservation, and analysis, creating an impediment to their parallel detection. The aim of this critical review is to evaluate the state of the science of monitoring OPPPs and identify a path forward for their parallel detection and quantification in a manner commensurate with the need for reliable data that is informative to risk assessment and mitigation. Water and biofilm sampling procedures, as well as factors influencing sample representativeness and detection sensitivity, are critically evaluated with respect to the five representative bacterial and amoebal OPPPs noted above. Available culturing and molecular approaches are discussed in terms of their advantages, limitations, and applicability. Knowledge gaps and research needs towards standardized approaches are identified.
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Affiliation(s)
- Hong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Emilie Bédard
- Department of Civil Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - Anne K Camper
- Center for Biofilm Engineering and Department of Civil Engineering, Montana State University, Bozeman, MT 59717, USA
| | - Vincent R Hill
- Waterborne Disease Prevention Branch, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30329, USA
| | - Amy Pruden
- Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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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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Pseudooutbreak of rapidly growing mycobacteria due to Mycobacterium abscessus subsp bolletii in a digestive and respiratory endoscopy unit caused by the same clone as that of a countrywide outbreak. Am J Infect Control 2016; 44:e221-e226. [PMID: 27524260 DOI: 10.1016/j.ajic.2016.06.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 11/21/2022]
Abstract
BACKGROUND The nontuberculous mycobacteria (NTM) are widely spread. In Brazil, 2,520 cases of rapidly growing mycobacteria (RGM) infections after medical procedures were reported, with 5.4% of cases related to nonsurgical invasive procedures and with an occurrence of 1 clone (BRA100) of Mycobacterium abscessus subsp bolletii. OBJECTIVE To describe a pseudooutbreak of M abscessus subsp bolletii in an endoscopy and bronchoscopy unit. METHODS The alert for a pseudooutbreak was given when 3 patients, in the same week, had a positive bronchoalveolar lavage culture for M abscessus subsp bolletii. The patients had no symptoms/signs of mycobacterial infection; thus, contamination of bronchoscopes was suspected. Samples for culturing were collected from bronchoscopes, digestive endoscopes, automated disinfection machines, and the water supply. Clinical samples were identified by polymerase chain reaction restriction-enzyme analysis (PRA) of the hsp65 gene and their pulsed-field gel electrophoresis pattern was compared with environmental samples. RESULTS The investigation demonstrated a contamination of bronchoscopes, digestive endoscopes, and disinfection machines. Molecular typing demonstrated that all strains belonged to the same clone (MAB01), identical to clone BRA100. DISCUSSION Cross-transmission due to poor disinfection as well as resistance to glutaraldehyde may play roles in the spread of MAB01 M abscessus subsp bolletii, which may have a unique resistance to the environment and adaption to human hosts. However the water supply may have played a role. Attention is needed to ensure the quality of water used to rinse disinfected equipment.
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Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
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rpoB Gene Sequencing for Identification of Rapidly Growing Mycobacteria. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2016. [DOI: 10.5812/pedinfect.40001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Gallo JF, Pinhata JMW, Chimara E, Gonçalves MG, Fukasawa LO, Oliveira RSD. Performance of an in-house real-time polymerase chain reaction for identification of Mycobacterium tuberculosis isolates in laboratory routine diagnosis from a high burden setting. Mem Inst Oswaldo Cruz 2016; 111:545-50. [PMID: 27598243 PMCID: PMC5027861 DOI: 10.1590/0074-02760160048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/30/2016] [Indexed: 01/15/2023] Open
Abstract
Brazil is one of the high burden countries for tuberculosis, and a rapid diagnosis is essential for effective control of the disease. In the present study, an in-house real-time polymerase chain reaction (PCR) assay targeting the mpt64 gene for identification of Mycobacterium tuberculosis complex isolates was evaluated under routine diagnosis conditions in a reference laboratory. From May 2011 to July 2012, 1,520 isolates of mycobacteria were prospectively submitted for phenotypic and/or PRA-hsp65 identification and to real-time PCR. The mpt64 real-time PCR showed 99.7% sensitivity and 96% specificity and detected 79.4% of the cases missed by phenotypic and PRA-hsp65 identification. The in-house real-time PCR assay showed high sensitivity and specificity and was successfully implemented in the routine diagnosis of tuberculosis in a reference laboratory from a high burden setting.
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Affiliation(s)
- Juliana Failde Gallo
- Instituto Adolfo Lutz, Centro de Bacteriologia, Núcleo de Tuberculose e Micobacterioses, São Paulo, SP, Brasil
| | | | - Erica Chimara
- Instituto Adolfo Lutz, Centro de Bacteriologia, Núcleo de Tuberculose e Micobacterioses, São Paulo, SP, Brasil
| | - Maria Gisele Gonçalves
- Instituto Adolfo Lutz, Centro de Imunologia, Laboratório de Diagnóstico Molecular de Infecções Bacterianas, São Paulo, SP, Brasil
| | - Lucila Okuyama Fukasawa
- Instituto Adolfo Lutz, Centro de Imunologia, Laboratório de Diagnóstico Molecular de Infecções Bacterianas, São Paulo, SP, Brasil
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Lima-Junior JD, Viana-Niero C, Conde Oliveira DV, Machado GE, Rabello MCDS, Martins-Junior J, Martins LF, Digiampietri LA, da Silva AM, Setubal JC, Russell DA, Jacobs-Sera D, Pope WH, Hatfull GF, Leão SC. Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U. BMC Microbiol 2016; 16:111. [PMID: 27316672 PMCID: PMC4912749 DOI: 10.1186/s12866-016-0734-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 06/08/2016] [Indexed: 01/13/2023] Open
Abstract
Background A large collection of sequenced mycobacteriophages capable of infecting a single host strain of Mycobacterium smegmatis shows considerable genomic diversity with dozens of distinctive types (clusters) and extensive variation within those sharing evident nucleotide sequence similarity. Here we profiled the mycobacterial components of a large composting system at the São Paulo zoo. Results We isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc2155 as a host. None of these eight phages infected any of mycobacterial strains isolated from the same materials. The phage isolates span considerable genomic diversity, including two phages (Barriga, Nhonho) related to Subcluster A1 phages, two Cluster B phages (Pops, Subcluster B1; Godines, Subcluster B2), three Subcluster F1 phages (Florinda, Girafales, and Quico), and Madruga, a relative of phage Patience with which it constitutes the new Cluster U. Interestingly, the two Subcluster A1 phages and the three Subcluster F1 phages have genomic relationships indicating relatively recent evolution within a geographically isolated niche in the composting system. Conclusions We predict that composting systems such as those used to obtain these mycobacteriophages will be a rich source for the isolation of additional phages that will expand our view of bacteriophage diversity and evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0734-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James Daltro Lima-Junior
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Cristina Viana-Niero
- Departmento de Ciências Biológicas, Universidade Federal de São Paulo, campus Diadema, São Paulo, Brazil
| | - Daniel V Conde Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gabriel Esquitini Machado
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Joaquim Martins-Junior
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Layla Farage Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | | | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.,Virginia Bioinformatics Institute, Blacksburg, VA, 24060, USA
| | - Daniel A Russell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Welkin H Pope
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 1524, USA
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
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Garcia de Carvalho NF, Sato DN, Pavan FR, Ferrazoli L, Chimara E. Resazurin Microtiter Assay for Clarithromycin Susceptibility Testing of Clinical Isolates of Mycobacterium abscessus Group. J Clin Lab Anal 2016; 30:751-5. [PMID: 27169515 DOI: 10.1002/jcla.21933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/09/2015] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Mycobacterium abscessus group has heterogeneous susceptibility pattern among species. The species is most common cause of nosocomial infections. Macrolides minimum Inhibitory concentration (MIC) determination is essential for the treatment. METHODS Thirty-six strains were randomly selected for performing Resazurin Microtiter Assay (REMA) for clarithromycin testing in comparison to MIC test according to Clinical and Laboratory Standards Institute (2011) recommendation. REMA has been used for detection of drug resistance in M. tuberculosis. Extended incubation was performed to detect induced resistance. RESULTS Thirty microliters of resazurin (0.01%) was added after visually taking MIC reading. Resistance was observed in 11.1% of M. bolletti and 4.8% of M. abscessus strains; and induced resistance was detected in 77.8% and 95.2% of M. bolletti and M. abscessus strains, respectively. All strains of M. massiliense were susceptible. The samples presented same MIC value both by visual reading and through resazurin. CONCLUSION The present study showed 100% concordance between both readings, with REMA providing easier to read and report results benefit. This change in reading can also reflect on the MIC determination and report, improving the test.
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Affiliation(s)
| | - Daisy Nakamura Sato
- Nucleo de Tuberculose e Micobacterioses, Instituto Adolfo Lutz, Sao Paulo, Brazil
| | - Fernando R Pavan
- Laboratório de Micobacteriologia, Faculdade de Ciências Farmacêuticas, Universidade Estadual Paulista "Júlio de Mesquita Filho,", Araraquara, Brazil
| | - Lucilaine Ferrazoli
- Nucleo de Tuberculose e Micobacterioses, Instituto Adolfo Lutz, Sao Paulo, Brazil
| | - Erica Chimara
- Nucleo de Tuberculose e Micobacterioses, Instituto Adolfo Lutz, Sao Paulo, Brazil.
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Rónai Z, Eszterbauer E, Csivincsik Á, Guti C, Dencső L, Jánosi S, Dán Á. Detection of wide genetic diversity and several novel strains among non-avium nontuberculous mycobacteria isolated from farmed and wild animals in Hungary. J Appl Microbiol 2016; 121:41-54. [DOI: 10.1111/jam.13152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/10/2016] [Accepted: 03/31/2016] [Indexed: 12/01/2022]
Affiliation(s)
- Z. Rónai
- National Food Chain Safety Office (NFCSO); Budapest Hungary
| | - E. Eszterbauer
- Institute for Veterinary Medical Research; Centre for Agricultural Research; Hungarian Academy of Sciences; Budapest Hungary
| | - Á. Csivincsik
- Diagnostic Imaging and Radiation Oncology; University of Kaposvar; Kaposvár Hungary
| | - C.F. Guti
- Institute for Veterinary Medical Research; Centre for Agricultural Research; Hungarian Academy of Sciences; Budapest Hungary
| | - L. Dencső
- National Food Chain Safety Office (NFCSO); Budapest Hungary
| | - S. Jánosi
- National Food Chain Safety Office (NFCSO); Budapest Hungary
| | - Á. Dán
- National Food Chain Safety Office (NFCSO); Budapest Hungary
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Khosravi AD, Hashemi Shahraki A, Hashemzadeh M, Sheini Mehrabzadeh R, Teimoori A. Prevalence of Non-Tuberculous Mycobacteria in Hospital Waters of Major Cities of Khuzestan Province, Iran. Front Cell Infect Microbiol 2016; 6:42. [PMID: 27148491 PMCID: PMC4829604 DOI: 10.3389/fcimb.2016.00042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/26/2016] [Indexed: 11/13/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are among the emerging pathogens in immunocompromised individuals including hospitalized patients. So, it is important to consider hospitals water supplies as a source for infection. The aim of this study was to determine the prevalence of NTM in the hospital aquatic systems of Khuzestan, South west of Iran. In total, 258 hospital water samples were collected and examined. After initial sample processing, sediment of each sample were inoculated into two Lowenstein-Jensen medium. The positive cultures were studied with phenotypic tests including growth rate, colony morphology, and pigmentation, with subsequent PCR- restriction enzyme analysis (PRA) and rpoB gene sequence analysis. Mycobacterial strains were isolated from 77 samples (29.8%), comprising 52 (70.1%) rapid growing, and 25 (32.4%) slow growing mycobacteria. Based on the overall results, M. fortuitum (44.1%) was the most common mycobacterial species in hospital water samples, followed by M. gordonae (n = 13, 16.8%) and M. senegalense (n = 5, 7.7%). In conclusion, current study demonstrated the NTM strains as one of the major parts of hospital water supplies with probable potential source for nosocomial infections. This finding also help to shed light on to the dynamics of the distribution and diversity of NTM in the water system of hospitals in the region of study.
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Affiliation(s)
- Azar Dokht Khosravi
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
| | - Abdolrazagh Hashemi Shahraki
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
- Department of Epidemiology, Pasteur Institute of IranTehran, Iran
| | - Mohammad Hashemzadeh
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
- Student Research Committee, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
| | - Rasa Sheini Mehrabzadeh
- Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical SciencesAhvaz, Iran
| | - Ali Teimoori
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical ScienceAhvaz, Iran
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Riello FN, Brígido RTS, Araújo S, Moreira TA, Goulart LR, Goulart IMB. Diagnosis of mycobacterial infections based on acid-fast bacilli test and bacterial growth time and implications on treatment and disease outcome. BMC Infect Dis 2016; 16:142. [PMID: 27039183 PMCID: PMC4818481 DOI: 10.1186/s12879-016-1474-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The establishment of therapeutic regimens for mycobacteriosis depends on the accurate identification of Mycobacterium species, and misdiagnosis can result in inappropriate treatment and increased mortality of patients. Differential diagnosis among Mycobacterium species has been made by conventional phenotypic and biochemical tests after a long culture period. Specialized molecular diagnostics of mycobacteria allows rapid detection and species identification; however, such tests are not available in public health programs. Our aim was to demonstrate the clinical implications of erroneous diagnosis by performing molecular genotyping of mycobacterial infections in patients that were diagnosed based on symptoms, culture and bacilloscopy. METHODS Culture samples of mycobacterial infections from 55 patients clinically diagnosed as tuberculosis in 2013 and 2014, based on conventional methods, were identified by PCR -RFLP and results are discussed. RESULTS We have confirmed 35 (63.6%) positive samples as M. tuberculosis, but 18 (32.7%) were identified as non-tuberculous mycobacteria (M. avium type 1, M. avium type 2, M. kansasii type 1 type 1, M. mucogenicum, M. chelonae, M. terrae type 3, and 1 unknown RFLP pattern) and two were negative. Regarding clinical diagnosis, 61.8% (34/55) was classified as pulmonary tuberculosis. It is important to emphasize that 36.4% (20/55) of samples were misdiagnosed by conventional methods, and 11 (61.1%) of the HIV positive patients (18/55) were NTM-coinfected. CONCLUSION The identification of species in mycobacterial infections is essential for correct diagnosis and choice of treatment regimen, and misdiagnosis by conventional tools can lead to chronic disease, increased resistance and death.
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Affiliation(s)
- Fabiane N. Riello
- />National Reference Center for Sanitary Dermatology and Leprosy (CREDESH) Clinical Hospital Federal University of Uberlândia, Uberlândia, Minas Gerais Brazil
| | - Rebecca T. S. Brígido
- />National Reference Center for Sanitary Dermatology and Leprosy (CREDESH) Clinical Hospital Federal University of Uberlândia, Uberlândia, Minas Gerais Brazil
| | - Sergio Araújo
- />National Reference Center for Sanitary Dermatology and Leprosy (CREDESH) Clinical Hospital Federal University of Uberlândia, Uberlândia, Minas Gerais Brazil
| | - Tomaz A. Moreira
- />Laboratory of Clinical Analysis, Clinics’ Hospital of the Federal University of Uberlândia, Uberlândia, Minas Gerais Brazil
| | - Luiz Ricardo Goulart
- />Federal University of Uberlandia, Institute of Genetics and Biochemistry, Laboratory of Nanobiotechnology, Campus Umuarama, Block 2E, Room 248, CEP 38400-902 Uberlandia, Minas Gerais Brazil
| | - Isabela M. B. Goulart
- />National Reference Center for Sanitary Dermatology and Leprosy (CREDESH) Clinical Hospital Federal University of Uberlândia, Uberlândia, Minas Gerais Brazil
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Nour-Neamatollahie A, Ebrahimzadeh N, Siadat SD, Vaziri F, Eslami M, Akhavan Sepahi A, Khanipour S, Masoumi M, Sakhaee F, Ghazanfari Jajin M, Bahrmand A, Fateh A. Distribution of non-tuberculosis mycobacteria strains from suspected tuberculosis patients by heat shock protein 65 PCR-RFLP. Saudi J Biol Sci 2016; 24:1380-1386. [PMID: 28855835 PMCID: PMC5562452 DOI: 10.1016/j.sjbs.2016.02.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Revised: 01/24/2016] [Accepted: 02/01/2016] [Indexed: 12/03/2022] Open
Abstract
The genus Mycobacterium contains more than 150 species. Non-tuberculosis mycobacteria (NTM) often cause extrapulmonary and pulmonary disease. Mycobacteria detection at species level is necessary and provides useful information on epidemiology and facilitates successful treatment of patients. This retrospective study aimed to determine the incidence of the NTM isolates and Mycobacterium tuberculosis (Mtb) in clinical specimens collected from Iranian patients during February 2011–December 2013, by PCR–restriction fragment length polymorphism analysis (PRA) of the hsp65 gene. We applied conventional biochemical test and hsp65–PRA identification assay to identify species of mycobacteria in specimens from patients suspected of having mycobacterial isolates. This method was a sensitive, specific and effective assay for detecting mycobacterial species and had a 100% sensitivity and specificity for Mtb and Mycobacterium avium complex (MAC) species. Using PRA for 380 mycobacterial selected isolates, including 317 Mtb, four Mycobacterium bovis and of the 59 clinical isolates, the most commonly identified organism was Mycobacterium kansasii (35.6%), followed by Mycobacterium simiae (16.9%), Mycobacterium gordonae (16.9%), Mycobacterium fortuitum (5.1%), Mycobacterium intracellulare (5.1%), Mycobacterium avium (5.1%), Mycobacterium scrofulaceum (3.4%), Mycobacterium gastri (3.4%), Mycobacterium flavescens (3.4%), Mycobacterium chelonae (3.4%) and Mycobacterium nonchromogenicum (1.7%). PRA method, in comparison with classical methods, is rapid, useful and sensitive for the phylogenetic analysis and species detection of mycobacterial strains. Mycobacterium kansasii is the most common cause of infection by NTM in patients with non-HIV and HIV which demonstrated a high outbreak and diversity of NTM strains in our laboratory.
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Affiliation(s)
- Ali Nour-Neamatollahie
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Department of Microbiology, College of Basic Science, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Nayereh Ebrahimzadeh
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Eslami
- Young Researchers and Elite Club, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Abbas Akhavan Sepahi
- Department of Microbiology, College of Basic Science, Islamic Azad University, Tehran North Branch, Tehran, Iran
| | - Sharareh Khanipour
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Sakhaee
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | | | - Ahmadreza Bahrmand
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Departments of Mycobacteriology & Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Romero JJ, Herrera P, Cartelle M, Barba P, Tello S, Zurita J. Panniculitis caused by Mycobacterium monacense mimicking erythema induratum: a case in Ecuador. New Microbes New Infect 2016; 10:112-5. [PMID: 26933504 PMCID: PMC4765770 DOI: 10.1016/j.nmni.2016.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/02/2016] [Accepted: 01/14/2016] [Indexed: 11/24/2022] Open
Abstract
We report the first case of recently characterized species M. monacense associated with chronic nodular vasculitis, infecting a young woman. This case represents the first isolation of M. monacense from Ecuador. The isolate was identified by conventional and molecular techniques.
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Affiliation(s)
- J J Romero
- Hospital Vozandes, Ecuador; Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Ecuador
| | | | - M Cartelle
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Ecuador
| | - P Barba
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Ecuador
| | - S Tello
- Laboratorio de Patología, Hospital AXXIS, Quito, Ecuador
| | - J Zurita
- Hospital Vozandes, Ecuador; Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Ecuador; Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Ecuador
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Wachholz PA, Sette CS, Caitano do Nascimento D, Soares CT, Diório SM, Masuda PY. Mycobacterium peregrinum Skin Infection: Case Report. J Cutan Med Surg 2015; 20:249-51. [PMID: 26627593 DOI: 10.1177/1203475415616963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mycobacterium peregrinum is a rapidly growing mycobacterium (RGM) that rarely causes skin infections. The correct identification of the specific RGM infecting the skin will enhance therapeutic success. OBJECTIVE To highlight the importance of rapid and precise identification of the Mycobacterium involved in skin infections in order to enhance therapeutic success. METHODS We describe an RGM skin infection in an immunocompetent patient. RESULTS Classic methods (biochemical tests and culture) of RGM identification are time-consuming, and the histopathological features are not specific. Some molecular methods are reliable but expensive. The PRAhsp-65 is a simple procedure that is helpful in identifying the specific agent of an RGM. CONCLUSION Although skin infections caused by M peregrinum are rare, they represent a substantial clinical challenge. Specific and more effective treatment options depend on the development of precise and rapid methods for identifying mycobacterial species.
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Rapid detection of Mycobacterium tuberculosis complex by real-time PCR in sputum samples and its use in the routine diagnosis in a reference laboratory. J Med Microbiol 2015; 64:1040-1045. [DOI: 10.1099/jmm.0.000121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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44
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Hernández-Toloza JE, Rincón-Serrano MDP, Celis-Bustos YA, Aguillón CI. [Identification of mycobacteria to the species level by molecular methods in the Public Health Laboratory of Bogotá, Colombia]. Enferm Infecc Microbiol Clin 2015; 34:17-22. [PMID: 25888362 DOI: 10.1016/j.eimc.2015.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Global epidemiology of non-tuberculous mycobacteria (NTM) is unknown due to the fact that notification is not required in many countries, however the number of infection reports and outbreaks caused by NTM suggest a significant increase in the last years. Traditionally, mycobacteria identification is made through biochemical profiles which allow to differentiate M. tuberculosis from NTM, and in some cases the mycobacteria species. Nevertheless, these methods are technically cumbersome and time consuming. On the other hand, the introduction of methods based on molecular biology has improved the laboratory diagnosis of NTM. OBJECTIVE To establish the NTM frequency in positive cultures for acid-fast bacilli (AAFB) which were sent to Laboratorio de Salud Pública de Bogotá over a 12 month period. MATERIALS AND METHODS A total of 100 positive cultures for acid-fast bacilli from public and private hospitals from Bogotá were identified by both biochemical methods and the molecular methods PRA (PCR-restriction enzyme analysis) and multiplex-PCR. Furthermore, low prevalence mycobacteria species and non-interpretable results were confirmed by 16SrDNA sequentiation analysis. RESULTS Identification using the PRA method showed NMT occurrence in 11% of cultures. In addition, this molecular methodology allowed to detect the occurrence of more than one mycobacteria in 4% of the cultures. Interestingly, a new M. kubicae pattern of PCR-restriction analysis is reported in our study. CONCLUSION Using a mycobacteria identification algorithm, which includes the molecular method PRA, improves the diagnostic power of conventional methods and could help to advance both NTM epidemiology knowledge and mycobacteriosis control.
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Muricy ECM, Lemes RA, Bombarda S, Ferrazoli L, Chimara E. Differentiation between Nocardia spp. and Mycobacterium spp.: Critical aspects for bacteriological diagnosis. Rev Inst Med Trop Sao Paulo 2015; 56:397-401. [PMID: 25229219 PMCID: PMC4172110 DOI: 10.1590/s0036-46652014000500005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 03/07/2014] [Indexed: 11/22/2022] Open
Abstract
New methodologies were developed for the identification of Nocardia but the initial diagnosis still requires a fast and accurate method, mainly due to the similarity to Mycobacterium, both clinical and bacteriologically. Growth on Löwenstein-Jensen (LJ) medium, presence of acid-fast bacilli through Ziehl-Neelsen staining, and colony morphology can be confusing aspects between Nocardia and Mycobacterium. This study describes the occurrence of Nocardia spp. in a mycobacterial-reference laboratory, observing the main difficulties in differentiating Nocardia spp. from Mycobacterium spp., and correlating isolates with nocardiosis cases. Laboratory records for the period between 2008 and 2012 were analyzed, and the isolates identified as Nocardia sp. or as non-acid-fast filamentous bacilli were selected. Epidemiological and bacteriological data were analyzed as well. Thirty-three isolates identified as Nocardia sp. and 22 as non-acid-fast bacilli were selected for this study, and represented 0.12% of isolates during the study period. The presumptive identification was based on macroscopic and microscopic morphology, resistance to lysozyme and restriction profiles using the PRA-hsp65 method. Nocardia spp. can grow on media for mycobacteria isolation (LJ and BBL MGIT™) and microscopy and colony morphology are very similar to some mycobacteria species. Seventeen patients (54.8%) were reported and treated for tuberculosis, but presented signs and symptoms of nocardiosis. It was concluded that the occurrence of Nocardia sp. during the study period was 0.12%. Isolates with characteristics of filamentous bacilli, forming aerial hyphae, with colonies that may be pigmented, rough and without the BstEII digestion pattern in PRA-hsp65 method are suggestive of Nocardia spp. For a mycobacterial routine laboratory, a flow for the presumptive identification of Nocardia is essential, allowing the use of more accurate techniques for the correct identification, proper treatment and better quality of life for patients.
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Affiliation(s)
| | | | - Sidney Bombarda
- Epidemiological Surveillance Center Prof. Alexandre Vranjac, São Paulo, SP, Brazil
| | - Lucilaine Ferrazoli
- Tuberculosis and Mycobacteriosis Branch, Instituto Adolfo Lutz, São Paulo, SP, Brazil
| | - Erica Chimara
- Tuberculosis and Mycobacteriosis Branch, Instituto Adolfo Lutz, São Paulo, SP, Brazil
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Verma AK, Kumar G, Arora J, Singh P, Arora VK, Myneedu VP, Sarin R. Identification of mycobacterial species by PCR restriction enzyme analysis of thehsp65gene — an Indian experience. Can J Microbiol 2015; 61:293-6. [DOI: 10.1139/cjm-2014-0525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nowadays, nontuberculous mycobacteria (NTM) often cause pulmonary and extrapulmonary disease. Species identification of NTM determines the line of treatment and management of the disease. The routine diagnostic methods, i.e., smear microscopy and biochemical identification, of nontuberculous mycobacteria are tedious and time consuming and not all laboratories can perform these tests on a routine basis. A PCR targeting the hsp65 gene was implemented using standard strains and was applied to 109 clinical isolates. The PCR-amplified product was subjected to restriction enzyme analysis using BstEII and HaeIII. The results obtained were compared with that of biochemical tests. Of 109 NTM, 107 were identified to species level. PCR plus restriction enzyme analysis (PRA) identified 12 types of NTM. Common species identified were Mycobacterium chelonae (32), a rapid growing NTM, and Mycobacterium avium complex (21), among the slow growing NTM. PRA and biochemical identification showed 95.32% (102/107) concordant results. PRA is fast, cheap, and accurate for identification of potentially pathogenic NTM.
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Affiliation(s)
- Ajoy Kumar Verma
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Gavish Kumar
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Jyoti Arora
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Paras Singh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Vijay Kumar Arora
- Department of TB and Chest, Santosh Medical College and Hospital, Santosh University, Pratap Vihar, Ghaziabad 201009, Uttar Pradesh, New Delhi, India
| | - Vithal Prasad Myneedu
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
| | - Rohit Sarin
- Department of TB and Chest, National Institute of Tuberculosis and Respiratory Diseases, Sri Aurobindo Marg, New Delhi 110030, India
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Sette CS, Wachholz PA, Masuda PY, da Costa Figueira RBF, de Oliveira Mattar FR, Ura DG. Mycobacterium marinum infection: a case report. J Venom Anim Toxins Incl Trop Dis 2015; 21:7. [PMID: 25806076 PMCID: PMC4372314 DOI: 10.1186/s40409-015-0008-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/04/2015] [Indexed: 11/10/2022] Open
Abstract
The infection by Mycobacterium marinum in humans is relatively uncommon. When it occurs, it mainly affects the skin, usually with a chronic, indolent and benign evolution. The diagnosis requires a high index of suspicion, and a significant delay may be observed between the first symptoms to the final diagnosis. This present case reports a M. marinum infection in an immunocompetent patient that had a chronic undiagnosed injury on the dominant hand for at least five years. The patient had several medical consultations, without proper suspicion, hampering adequate diagnostic investigation. Histopathology detected tuberculoid granulomas, but showed no acid-fast bacilli. The culture in appropriate medium and the polymerase chain reaction-restriction enzyme analysis (PRA)-hsp65 confirmed the diagnosis. Treatment with clarithromycin (1 g/day) for three months was effective. Although uncommon, this infection is a contact zoonosis. Therefore, it is important for clinicians to be aware of this diagnosis and properly guide preventable measures to professionals that are in risk group.
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Affiliation(s)
- Christiane Salgado Sette
- Instituto Lauro de Souza Lima, Rodovia Comandante João Ribeiro de Barros, km 225/226, Bauru, SP CEP 17.034-971 Brazil
| | - Patrick Alexander Wachholz
- Department of Public Health, Botucatu Medical School, UNESP - Univ Estadual Paulista, Av. Prof. Montenegro Bairro: Distrito de Rubião Junior, s/n - 18618970 Botucatu, SP Brazil
| | - Paula Yoshiko Masuda
- Instituto Lauro de Souza Lima, Rodovia Comandante João Ribeiro de Barros, km 225/226, Bauru, SP CEP 17.034-971 Brazil
| | | | | | - Deise Godoy Ura
- Instituto Lauro de Souza Lima, Rodovia Comandante João Ribeiro de Barros, km 225/226, Bauru, SP CEP 17.034-971 Brazil
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Kwenda G, Churchyard GJ, Thorrold C, Heron I, Stevenson K, Duse AG, Marais E. Molecular characterisation of clinical and environmental isolates of Mycobacterium kansasii isolates from South African gold mines. JOURNAL OF WATER AND HEALTH 2015; 13:190-202. [PMID: 25719478 DOI: 10.2166/wh.2014.161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mycobacterium kansasii (M. kansasii) is a major cause of non-tuberculous mycobacterial pulmonary disease in the South African gold-mining workforce, but the source of infection and molecular epidemiology are unknown. This study investigated the presence of M. kansasii in gold and coal mine and associated hostel water supplies and compared the genetic diversity of clinical and environmental isolates of M. kansasii. Five M. kansasii and ten other potentially pathogenic mycobacteria were cultured mainly from showerhead biofilms. Polymerase chain reaction-restriction analysis of the hsp65 gene on 196 clinical and environmental M. kansasii isolates revealed 160 subtype I, eight subtype II and six subtype IV strains. Twenty-two isolates did not show the typical M. kansasii restriction patterns, suggesting that these isolates may represent new subtypes of M. kansasii. In contrast to the clonal population structure found amongst the subtype I isolates from studies in other countries, DNA fingerprinting of 114 clinical and three environmental subtype I isolates demonstrated genetic diversity amongst the isolates. This study demonstrated that showerheads are possible sources of M. kansasii and other pathogenic non-tuberculous mycobacterial infection in a gold-mining region, that subtype I is the major clinical isolate of M. kansasii strain and that this subtype exhibits genetic diversity.
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Affiliation(s)
- Geoffrey Kwenda
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa E-mail:
| | - Gavin J Churchyard
- Aurum Institute for Health Research, Parktown 2193, Johannesburg, South Africa
| | - Catherine Thorrold
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa E-mail:
| | - Ian Heron
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 OPZ, Scotland, UK
| | - Karen Stevenson
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 OPZ, Scotland, UK
| | - Adriano G Duse
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa E-mail:
| | - Elsé Marais
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa E-mail:
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49
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Furini AADC, Pedro HDSP, Rodrigues JF, Montenegro LML, Machado RLD, Franco C, Schindler HC, Batista IMFD, Rossit ARB. Detection of Mycobacterium tuberculosis complex by nested polymerase chain reaction in pulmonary and extrapulmonary specimens. J Bras Pneumol 2014; 39:711-8. [PMID: 24473765 PMCID: PMC4075904 DOI: 10.1590/s1806-37132013000600010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 09/24/2013] [Indexed: 12/01/2022] Open
Abstract
OBJECTIVE: To compare the performance of nested polymerase chain reaction (NPCR) with
that of cultures in the detection of the Mycobacterium
tuberculosis complex in pulmonary and extrapulmonary specimens.
METHODS: We analyzed 20 and 78 pulmonary and extrapulmonary specimens, respectively,
of 67 hospitalized patients suspected of having tuberculosis. An automated
microbial system was used for the identification of Mycobacterium spp.
cultures, and M. tuberculosis IS6110 was
used as the target sequence in the NPCR. The kappa statistic was used in
order to assess the level of agreement among the results. RESULTS: Among the 67 patients, 6 and 5, respectively, were diagnosed with pulmonary
and extrapulmonary tuberculosis, and the NPCR was positive in all of the
cases. Among the 98 clinical specimens, smear microscopy, culture, and NPCR
were positive in 6.00%, 8.16%, and 13.26%, respectively. Comparing the
results of NPCR with those of cultures (the gold standard), we found that
NPCR had a sensitivity and specificity of 100% and 83%, respectively, in
pulmonary specimens, compared with 83% and 96%, respectively, in
extrapulmonary specimens, with good concordance between the tests (kappa,
0.50 and 0.6867, respectively). CONCLUSIONS: Although NPCR proved to be a very useful tool for the detection of
M. tuberculosis complex, clinical, epidemiological, and
other laboratory data should also be considered in the diagnosis and
treatment of pulmonary and extrapulmonary tuberculosis.
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Affiliation(s)
| | | | | | | | | | - Célia Franco
- Regional Foundation School of Medicine, São José do Rio Preto, Brazil
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50
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Nunes LDS, Baethgen LF, Ribeiro MO, Cardoso CM, de Paris F, De David SMM, da Silva MG, Duarte RS, Barth AL. Outbreaks due to Mycobacterium abscessus subsp. bolletii in southern Brazil: persistence of a single clone from 2007 to 2011. J Med Microbiol 2014; 63:1288-1293. [PMID: 25038135 PMCID: PMC7304884 DOI: 10.1099/jmm.0.074906-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 07/16/2014] [Indexed: 11/18/2022] Open
Abstract
Outbreaks associated with rapidly growing mycobacteria (RGM) have been increasingly reported worldwide, including in Brazil. Among the RGM, the Mycobacterium abscessus complex is the most pathogenic and related to multidrug resistance. The aim of this study was to evaluate the antimicrobial susceptibility and molecular profile of RGM isolates involved in new postsurgical infection outbreaks in Brazil since 2007. Of the 109 cases reported in the state of Rio Grande do Sul between 2007 and 2011, 43 (39 %) had confirmed mycobacterial growth in culture. Clinical isolates were obtained from biopsy specimens or abscess aspirates. PRA-hsp65 restriction pattern identified the isolates as M. abscessus type 2, and partial rpoB sequencing confirmed the identification as M. abscessus subsp. bolletii. All isolates were susceptible to amikacin and resistant to ciprofloxacin, doxycycline, sulfamethoxazole, moxifloxacin and tobramycin. Most isolates (72 %) were fully susceptible to cefoxitin but six isolates (14 %) were fully resistant to clarithromycin. The latter differed from the susceptibility profiles of the previously described BRA100 clone from other Brazilian regions. Nevertheless, pulsed-field gel electrophoresis analysis revealed that these isolates belonged to a single BRA100 clone. In conclusion, our study reports the persistence of an emergent single and highly resistant clone of M. abscessus subsp. bolletii for several years even after national implementation of infection control measures.
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Affiliation(s)
- Luciana de S Nunes
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | | | | | - Fernanda de Paris
- Unidade de Pesquisa Biomédica, Serviço de Patologia Clínica, Hospital de Clínicas de Porto Alegre (HCPA), Brazil
| | | | - Marlei G da Silva
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Brazil
| | - Rafael S Duarte
- Instituto de Microbiologia, Universidade Federal do Rio de Janeiro (UFRJ), Brazil
| | - Afonso L Barth
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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