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Kim D, Shin JI, Yoo IY, Jo S, Chu J, Cho WY, Shin SH, Chung YJ, Park YJ, Jung SH. GenoMycAnalyzer: a web-based tool for species and drug resistance prediction for Mycobacterium genomes. BMC Genomics 2024; 25:387. [PMID: 38643090 PMCID: PMC11031912 DOI: 10.1186/s12864-024-10320-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) is a useful tool for species identification and drug resistance prediction, and many clinical laboratories are transitioning to WGS as a routine diagnostic tool. However, user-friendly and high-confidence automated bioinformatics tools are needed to rapidly identify M. tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), detect drug resistance, and further guide treatment options. RESULTS We developed GenoMycAnalyzer, a web-based software that integrates functions for identifying MTBC and NTM species, lineage and spoligotype prediction, variant calling, annotation, drug-resistance determination, and data visualization. The accuracy of GenoMycAnalyzer for genotypic drug susceptibility testing (gDST) was evaluated using 5,473 MTBC isolates that underwent phenotypic DST (pDST). The GenoMycAnalyzer database was built to predict the gDST for 15 antituberculosis drugs using the World Health Organization mutational catalogue. Compared to pDST, the sensitivity of drug susceptibilities by the GenoMycAnalyzer for first-line drugs ranged from 95.9% for rifampicin (95% CI 94.8-96.7%) to 79.6% for pyrazinamide (95% CI 76.9-82.2%), whereas those for second-line drugs ranged from 98.2% for levofloxacin (95% CI 90.1-100.0%) to 74.9% for capreomycin (95% CI 69.3-80.0%). Notably, the integration of large deletions of the four resistance-conferring genes increased gDST sensitivity. The specificity of drug susceptibilities by the GenoMycAnalyzer ranged from 98.7% for amikacin (95% CI 97.8-99.3%) to 79.5% for ethionamide (95% CI 76.4-82.3%). The incorporated Kraken2 software identified 1,284 mycobacterial species with an accuracy of 98.8%. GenoMycAnalyzer also perfectly predicted lineages for 1,935 MTBC and spoligotypes for 54 MTBC. CONCLUSIONS GenoMycAnalyzer offers both web-based and graphical user interfaces, which can help biologists with limited access to high-performance computing systems or limited bioinformatics skills. By streamlining the interpretation of WGS data, the GenoMycAnalyzer has the potential to significantly impact TB management and contribute to global efforts to combat this infectious disease. GenoMycAnalyzer is available at http://www.mycochase.org .
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Affiliation(s)
- Doyoung Kim
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jeong-Ih Shin
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Integrated Research Center for Genomic Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sungjin Jo
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyon Chu
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | | | | | - Yeun-Jun Chung
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Integrated Research Center for Genomic Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Departments of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Hyun Jung
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea.
- Integrated Research Center for Genomic Polymorphism, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea.
- Departments of Biochemistry, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seoch-Gu, Seoul, 06591, Republic of Korea.
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da Silva WMV, Duarte MH, de Carvalho LD, de Souza Caldas PC, Campos CED, Redner P, Ramos JP. Discovery of a novel Mycobacterium asiaticum PRA-hsp65 pattern. INFECTION GENETICS AND EVOLUTION 2019; 76:104040. [PMID: 31533063 DOI: 10.1016/j.meegid.2019.104040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 09/07/2019] [Accepted: 09/12/2019] [Indexed: 11/16/2022]
Abstract
Twenty-one pulmonary sputum samples from nine Brazilian patients were analyzed by the PRA-hsp65 method for identification of Mycobacterium species and the results were compared by sequencing. We reported a mutation at the position 381, that generates a suppression cutting site in the BstEII enzyme, thus leading to a new PRA-hsp65 pattern for M. asiaticum identification.
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Affiliation(s)
- William Marco Vicente da Silva
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil.
| | - Mayara Henrique Duarte
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Luciana Distásio de Carvalho
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Paulo Cesar de Souza Caldas
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Carlos Eduardo Dias Campos
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Paulo Redner
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
| | - Jesus Pais Ramos
- National Reference Laboratory for Tuberculosis, Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Fiocruz, RJ, Brazil
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Arttawejkul P, Kongpolprom N. A case of pulmonary infection caused by Mycobacterium asiaticum: Difficulties on diagnostic and therapeutic approaches. Respir Med Case Rep 2018; 24:150-152. [PMID: 29984149 PMCID: PMC6010662 DOI: 10.1016/j.rmcr.2018.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/11/2018] [Accepted: 05/11/2018] [Indexed: 11/16/2022] Open
Abstract
A 56-year-old previously healthy female presented with chronic productive cough and fever. Chest X-ray revealed right middle lung opacities. Sputum acid fast bacilli smear was positive, however polymerase chain reaction was negative for Mycobacterium tuberculosis. Further investigations were pursued, which identified Mycobacterium asiaticum. Appropriate therapy with isoniazid, rifampin and clarithromycin for total 18 months (including pyrazinamide and ethambutol for first 4 months) resulted in clinical and radiographic improvement. Recognition of the possibility of this rarely described pulmonary pathogen is essential for successful treatment.
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Affiliation(s)
- Pureepat Arttawejkul
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Thai Red Cross, Thailand
| | - Napplika Kongpolprom
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Thai Red Cross, Thailand
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Abstract
In Queensland, Australia, all cases of mycobacterial infection (tuberculosis [TB] and nontuberculous mycobacteria [NTM]) are notifiable under the Queensland Public Health Act (2005). This process originally emerged to avoid NTM confounding with notification of cases of TB, but has facilitated awareness of the increasing incidence and changing epidemiology of NTM. Although initially not a public health priority, the notification process has facilitated research that has led to an appreciation of both public health and environmental health issues associated with these pathogens. When reports of NTM infections were low in frequency, reporting was managed largely by clinicians specializing in TB. However, as reports of NTM isolates surpassed those for TB, the workload associated with clinical reporting exceeded resources. The Communicable Diseases Branch transitioned to digital reporting of laboratory isolates of mycobacteria, thereby enabling weekly and quarterly reporting of data, and generation of more detailed annual reports. The reports now include species and geographic distributions by health service district, allowing identification of clusters requiring further investigation and systematic reviews of different species. With ecological and climate change, the distribution and virulence of these emerging pathogens are evolving. Evidence of transmission of highly virulent and antibiotic-resistant clones of Mycobacterium abscessus among patients with cystic fibrosis internationally heightens the need for timely reporting to public health authorities. Ongoing systematic monitoring by public health authorities will be crucial to our understanding of NTM diseases.
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Rashid A, Nanjappa S, Greene JN. Infectious Causes of Right Middle Lobe Syndrome. Cancer Control 2017; 24:60-65. [PMID: 28178715 DOI: 10.1177/107327481702400110] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Right middle lobe (RML) syndrome is defined as recurrent or chronic obstruction or infection of the middle lobe of the right lung. Nonobstructive causes of middle lobe syndrome include inflammatory processes and defects in the bronchial anatomy and collateral ventilation. We report on 2 case patients with RML syndrome, one due to infection with Mycobacterium avium complex followed by M asiaticum infection and the other due to allergic bronchopulmonary aspergillosis. A history of atopy, asthma, or chronic obstructive pulmonary disease has been reported in up to one-half of those with RML. The diagnosis can be made by plain radiography, computed tomography, and bronchoscopy. Medical treatment consists of bronchodilators, mucolytics, and antimicrobials. Patients whose disease is unresponsive to treatment and those with obstructive RML syndrome can be offered surgical treatment.
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Affiliation(s)
| | - Sowmya Nanjappa
- Department of Internal Hospital Medicine, Moffitt Cancer Center and University of South Florida Morsani College of Medicine, Tampa, FL
| | - John N Greene
- Department of Infectious Diseases, Moffitt Cancer Center, Tampa, FL.
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Chin'ombe N, Muzividzi B, Munemo E, Nziramasanga P. Molecular Identification of Nontuberculous Mycobacteria in Humans in Zimbabwe Using 16S Ribosequencing. Open Microbiol J 2016; 10:113-23. [PMID: 27335623 PMCID: PMC4899540 DOI: 10.2174/1874285801610010113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/27/2016] [Accepted: 01/29/2016] [Indexed: 12/26/2022] Open
Abstract
Background: Several nontuberculous mycobacteria (NTM) were previously isolated from diverse environments such as water, soil, sewage, food and animals. Some of these NTM are now known to be opportunistic pathogens of humans. Objective: The main purpose of the study was to identify NTM isolates stored at the National Microbiology Reference Laboratory (NMRL) and were previously isolated from humans during a national tuberculosis (TB) survey. Methods: Pure NTM cultures already isolated from human sputum samples during the national TB survey were retrieved from the NMRL and used for this study. DNA was extracted from the samples and 16S ribosomal RNA gene amplified by polymerase chain reaction. The amplicons were sequenced and bioinformatics tools were used to identify the NTM species. Results: Out of total of 963 NTM isolates stored at the NMRL, 81 were retrieved for speciation. Forty isolates (49.4%) were found to belong to Mycobacterium avium-intracellulare complex (MAC) species. The other 41 isolates (50.6%) were identified as M. lentiflavum (6.2%), M. terrae complex (4.9%), M. paraense (4.9%), M. kansasii (3.7%), M. moriokaense (3.7%), M. asiaticum (2.5%), M. novocastrense (2.5%), M. brasiliensis (2.5%), M. elephantis (2.5%), M. paraffinicum (1.2%), M. bohemicum (1.2%), M. manitobense (1.2%), M. intermedium (1.2%), M. tuberculosis complex (1.2%), M. parakoreense (1.2%), M. florentinum (1.2%), M. litorale (1.2%), M. fluoranthenivorans (1.2%), M. sherrisii (1.2%), M. fortuitum (1.2%) and M septicum (1.2%). Two isolates (2.5%) could not be identified, but were closely related to M. montefiorense and M. phlei respectively. Interestingly, the MAC species were the commonest NTM during the survey. Conclusion: The study emphasizes the importance of identifying species of NTM in Zimbabwe. Future studies need to ascertain their true diversity and clinical relevance.
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Affiliation(s)
- Nyasha Chin'ombe
- Molecular Microbiology Laboratory, Department of Medical Microbiology, University of Zimbabwe, P O Box A178, Avondale, Harare, Zimbabwe
| | - Boniface Muzividzi
- National Microbiology Reference Laboratory, P.O. Box ST 749, Southerton, Harare, Zimbabwe
| | - Ellen Munemo
- National Microbiology Reference Laboratory, P.O. Box ST 749, Southerton, Harare, Zimbabwe
| | - Pasipanodya Nziramasanga
- Molecular Microbiology Laboratory, Department of Medical Microbiology, University of Zimbabwe, P O Box A178, Avondale, Harare, Zimbabwe
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Comparison of methods for the isolation of mycobacteria from water treatment plant sludge. Antonie van Leeuwenhoek 2015; 107:1165-79. [DOI: 10.1007/s10482-015-0408-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/18/2015] [Indexed: 11/25/2022]
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Croce O, Robert C, Raoult D, Drancourt M. Draft Genome Sequence of Mycobacterium asiaticum Strain DSM 44297. GENOME ANNOUNCEMENTS 2014; 2:e00320-14. [PMID: 24744338 PMCID: PMC3990754 DOI: 10.1128/genomea.00320-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 04/03/2014] [Indexed: 11/20/2022]
Abstract
We report the draft genome sequence of Mycobacterium asiaticum strain DSM 44297, a tropical mycobacterium seldom responsible for human infection. The genome of M. asiaticum has a size of 5,935,986 bp, with a 66.03% G+C content, encoding 5,591 proteins and 81 RNAs.
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Tortoli E. Epidemiology of cervico-facial pediatric lymphadenitis as a result of nontuberculous mycobacteria. Int J Mycobacteriol 2012; 1:165-9. [PMID: 26785617 DOI: 10.1016/j.ijmyco.2012.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 10/29/2012] [Indexed: 11/28/2022] Open
Abstract
Cervical lymphadenitis as a result of nontuberculous mycobacteria, otherwise known as scrofula, is a disease occurring almost exclusively in immunocompetent young children. The most frequent mycobacterial species responsible is Mycobacterium avium, but a large number of other species may also be involved. The epidemiology of such disease is revised here, and the impact of different species as causative agents of adenitis is also discussed.
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Affiliation(s)
- Enrico Tortoli
- Emerging Bacterial Pathogens Unit, San Gabriele Building, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milano, Italy.
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Muwonge A, Kankya C, Johansen TB, Djønne B, Godfroid J, Biffa D, Edvardsen V, Skjerve E. Non-tuberculous mycobacteria isolated from slaughter pigs in Mubende district, Uganda. BMC Vet Res 2012; 8:52. [PMID: 22564290 PMCID: PMC3490772 DOI: 10.1186/1746-6148-8-52] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 05/07/2012] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The importance of infections caused by non-tuberculous mycobacteria (NTM) in animals and humans has gained considerable recognition during the past few years. In the developed world, where pig production is extensively practiced, studies on mycobacterial infections and related control strategies have received increasing attention. The infections are reported to be caused by a wide spectrum of NTM. Unfortunately, these infections have been less recognized in sub-Saharan Africa owing to lack of awareness and systematic studies. In this study we aimed at isolating and identifying species of mycobacteria involved in causing infections in slaughter pigs in Mubende district of Uganda. Furthermore we wanted to identify factors associated with infection prevalence in the study area. METHODS A total of 363 lymph nodes were collected and cultured for the presence of mycobacteria. Isolates were identified by 16S rDNA gene sequencing. A questionnaire survey was administered to identify production related factors associated with infection prevalence. Data were assembled and analysed using descriptive statistics and mixed effects logistic regression analysis. RESULTS Mycobacteria were detected in 39 % (143/363) of the examined lymph nodes, 63 % (59/93) of lymph nodes with gross lesions typical of mycobacteriosis and 31% (84/270) of lymph nodes with no visible lesions. Nineteen per cent of the isolated mycobacteria were identified as Mycobacterium (M) avium, of these 78% and 22% were M. avium sub sp. Hominissuis and avium respectively. Other mycobacterial species included M. senuense (16%), M. terrae (7%) and M. asiaticum (6%). This study found free range systems (OR = 3.0; P = 0.034) and use of water from valley dams (OR = 2.0; P = 0.049) as factors associated with high prevalence of mycobacteria in slaughter pigs. CONCLUSIONS This study demonstrated a high prevalence of NTM infections among slaughter pigs in Mubende district of Uganda. M. avium was the most prevalent of all NTM isolated and identified. Free range system of pig management and valley dam water were the most significant factors associated with NTM prevalence in Mubende district. These findings could be of a major public health concern given that it is in a predominantly pork consuming population with 18% HIV/AIDS prevalence. Therefore, stringent post-mortem inspection at the slaughter houses is of paramount importance to reduce human exposure.
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Affiliation(s)
- Adrian Muwonge
- Centre for Epidemiology and Biostatistics, Norwegian School of Veterinary Science, P.O. Box 8146 Dep, 0033, Oslo, Norway
| | - Clovice Kankya
- Centre for Epidemiology and Biostatistics, Norwegian School of Veterinary Science, P.O. Box 8146 Dep, 0033, Oslo, Norway
- Department of Biosecurity, Ecosystems and Public Health (BEP), College Of Veterinary Medicine, Animal Resources & Biosecurity Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Tone B Johansen
- Norwegian Veterinary Institute, P.O. Box 750, N-0106, Oslo, Norway
| | - Berit Djønne
- Norwegian Veterinary Institute, P.O. Box 750, N-0106, Oslo, Norway
| | - Jacques Godfroid
- Section for Arctic Veterinary Medicine, Norwegian School of Veterinary Science, Stakkevollveien 9010, Tromsø, Norway
| | - Demelash Biffa
- College of Medicine, University of Arizona, 1656 E. Mabel St, P.O. Box 245221, Tucson, AZ, 85724, USA
| | - Vigdis Edvardsen
- Norwegian Veterinary Institute, P.O. Box 750, N-0106, Oslo, Norway
| | - Eystein Skjerve
- Centre for Epidemiology and Biostatistics, Norwegian School of Veterinary Science, P.O. Box 8146 Dep, 0033, Oslo, Norway
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