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Evaluation of Two Protein Extraction Protocols Based on Freezing and Mechanical Disruption for Identifying Nontuberculous Mycobacteria by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry from Liquid and Solid Cultures. J Clin Microbiol 2018; 56:JCM.01548-17. [PMID: 29367300 DOI: 10.1128/jcm.01548-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/19/2018] [Indexed: 01/30/2023] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has proved to be a useful diagnostic method for identifying conventional bacteria. In the case of mycobacteria, a good protein extraction protocol is essential in order to obtain reliable identification results. To date, no such protocol has been definitively established. The aim of this study was to compare the manufacturer's recommended protein extraction protocol (protocol A) with two novel protocols (protocols B and C), which apply different freezing temperatures and mechanical disruption times using an automatic tissue homogenizer. A total of 302 clinical isolates, comprising 41 nontuberculous mycobacteria (NTM) species, were grown in parallel on solid and liquid media and analyzed: 174 isolates were slow-growing mycobacteria (SGM) and 128 isolates were rapid-growing mycobacteria (RGM). Overall, MALDI-TOF MS identified a higher number of NTM isolates from solid than from liquid media, especially with protocol C (83.4 and 68.2%, respectively; P < 0.05). From solid media, this protein extraction method identified 57.9 and 3.9% more isolates than protocols A (P < 0.001) and B (P < 0.05), respectively. In the case of liquid media, protocol C identified 49.7 and 6.3% more isolates than protocols A and B, respectively (P < 0.001). With regard to the growth rate, MALDI-TOF MS identified more RGM isolates than SGM isolates in all of the protocols studied. In conclusion, the application of freezing and automatic tissue homogenizer improved protein extraction of NTM and boosted identification rates. Consequently, MALDI-TOF MS, which is a cheap and simple method, could be a helpful tool for identifying NTM species in clinical laboratories.
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Shukla S, Shukla SK, Sharma R. Species identification of aquatic mycobacterium isolates by sequencing and PCR-RFLP of the 16S–23S rDNA internal transcribed spacer (ITS) region. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2017.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Evaluation of Whole-Genome Sequencing for Mycobacterial Species Identification and Drug Susceptibility Testing in a Clinical Setting: a Large-Scale Prospective Assessment of Performance against Line Probe Assays and Phenotyping. J Clin Microbiol 2018; 56:JCM.01480-17. [PMID: 29167290 PMCID: PMC5786738 DOI: 10.1128/jcm.01480-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/11/2017] [Indexed: 11/20/2022] Open
Abstract
Use of whole-genome sequencing (WGS) for routine mycobacterial species identification and drug susceptibility testing (DST) is becoming a reality. We compared the performances of WGS and standard laboratory workflows prospectively, by parallel processing at a major mycobacterial reference service over the course of 1 year, for species identification, first-line Mycobacterium tuberculosis resistance prediction, and turnaround time. Among 2,039 isolates with line probe assay results for species identification, 74 (3.6%) failed sequencing or WGS species identification. Excluding these isolates, clinically important species were identified for 1,902 isolates, of which 1,825 (96.0%) were identified as the same species by WGS and the line probe assay. A total of 2,157 line probe test results for detection of resistance to the first-line drugs isoniazid and rifampin were available for 728 M. tuberculosis complex isolates. Excluding 216 (10.0%) cases where there were insufficient sequencing data for WGS to make a prediction, overall concordance was 99.3% (95% confidence interval [CI], 98.9 to 99.6%), sensitivity was 97.6% (91.7 to 99.7%), and specificity was 99.5% (99.0 to 99.7%). A total of 2,982 phenotypic DST results were available for 777 M. tuberculosis complex isolates. Of these, 356 (11.9%) had no WGS comparator due to insufficient sequencing data, and in 154 (5.2%) cases the WGS prediction was indeterminate due to discovery of novel, previously uncharacterized mutations. Excluding these data, overall concordance was 99.2% (98.7 to 99.5%), sensitivity was 94.2% (88.4 to 97.6%), and specificity was 99.4% (99.0 to 99.7%). Median processing times for the routine laboratory tests versus WGS were similar overall, i.e., 20 days (interquartile range [IQR], 15 to 31 days) and 21 days (15 to 29 days), respectively (P = 0.41). In conclusion, WGS predicts species and drug susceptibility with great accuracy, but work is needed to increase the proportion of predictions made.
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Choi SG, Choi MS. Isolation of Nontuberculous Mycobacteria (NTM) from Air Conditioner Dust. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2017. [DOI: 10.15324/kjcls.2017.49.4.435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Seung Gu Choi
- Department of Clinical Laboratory Science, Shinhan University, Uijeongbu, Korea
| | - Myeong Sik Choi
- Department of Public Health Science, Graduate School of Dankook University, Cheonan, Korea
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Chikamatsu K, Aono A, Hata H, Igarashi Y, Takaki A, Yamada H, Sakashita K, Mitarai S. Evaluation of PyroMark Q24 pyrosequencing as a method for the identification of mycobacteria. Diagn Microbiol Infect Dis 2017; 90:35-39. [PMID: 29107416 DOI: 10.1016/j.diagmicrobio.2017.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 11/16/2022]
Abstract
We evaluated PyroMark Q24 (QIAGEN) pyrosequencing as a method for the identification of mycobacteria, with potential application in clinical practice. Sequence data from the hypervariable region A of the 16S rRNA gene (43 and 35bp sequences) were obtained using PyroMark Q24, and a similarity search was performed automatically with PyroMark IdentiFire software. Of the 148 mycobacterial type strains tested, 138 (93.2%) were accurately identified to single or clade species level, including complex level. From the remaining 10 strains, 3 (Mycobacterium gilvum, Mycobacterium goodi, and Mycobacterium thermoresistible) showed poor sequencing quality of homopolymers. For 6 other strains (Mycobacterium cosmeticum, Mycobacterium flavescens, Mycobacterium pallens, Mycobacterium hodleri, Mycobacterium xenopi, and Mycobacterium crocinum), the sequences were unreadable from the middle, and Sanger sequencing indicated biallelic site. Finally, a 40bp sequence for Mycobacterium gordonae could not be obtained despite repeated attempts. PyroMark Q24 provided accurate identification of multiple mycobacterial strains isolated from common clinical settings, but additional gene sequencing is required to distinguish species identified as a group or complex.
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Affiliation(s)
- Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan.
| | - Akio Aono
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Hiroyuki Hata
- Kyokuto Pharmaceutical Industrial Co., Ltd., Tokyo, Japan
| | - Yuriko Igarashi
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Akiko Takaki
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Kentaro Sakashita
- Basic Mycobacteriology, Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan; Basic Mycobacteriology, Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
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Rodriguez-Temporal D, Perez-Risco D, Struzka EA, Mas M, Alcaide F. Impact of updating the MALDI-TOF MS database on the identification of nontuberculous mycobacteria. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:597-602. [PMID: 28480547 DOI: 10.1002/jms.3944] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 05/03/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Conventional identification of mycobacteria species is slow, laborious and has low discriminatory power. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved highly effective for identifying conventional bacteria, and it may also be useful for identifying mycobacteria. The aim of this study was to evaluate and compare MALDI-TOF MS with currently recommended molecular methods for the identification of nontuberculous mycobacteria (NTM), applying Mycobacteria Libraries v3.0 (ML3.0) and v2.0 (ML2.0). A total of 240 clinical isolates of 41 NTM species grown on solid media were analysed: 132 isolates of slow-growing mycobacteria and 108 of rapid-growing mycobacteria. MALDI-TOF MS, using ML3.0, identified 192 (80%) NTM isolates with a score ≥1.7, encompassing 35 (85.4%) different species, that is, 17 (7.1%; p = 0.0863) isolates and 15 (36.6%; p = 0.0339) species more than currently recommended molecular techniques (polymerase chain reaction reverse hybridization). All these isolates were correctly identified according to molecular identification methods. The application of ML3.0 also identified 15 (6.2%) NTM isolates more than ML2.0 (p < 0.01). The scores obtained with MALDI-TOF MS using ML3.0 (mean score: 1.960) were higher in 147 (61.2%) isolates than when using ML2.0 (mean score: 1.797; p < 0.01). Three of the species analysed were not included in either database, so they were not recognized by this system. In conclusion, MALDI-TOF MS identified more isolates and species than the recommended polymerase chain reaction reverse hybridization assays. Although the new ML3.0 is not the definitive database, it yielded better results than ML2.0. This shows that the updating of the MALDI-TOF MS database plays an essential role in mycobacterial identification. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- D Rodriguez-Temporal
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - D Perez-Risco
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
| | - E A Struzka
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - M Mas
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - F Alcaide
- Department of Microbiology, Hospital Universitari de Bellvitge-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, Universitat de Barcelona, Hospitalet de Llobregat, Barcelona, Spain
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O’Brien CR, Malik R, Globan M, Reppas G, McCowan C, Fyfe JA. Feline leprosy due to Candidatus 'Mycobacterium tarwinense':Further clinical and molecular characterisation of 15 previously reported cases and an additional 27 cases. J Feline Med Surg 2017; 19:498-512. [PMID: 28438086 PMCID: PMC10816531 DOI: 10.1177/1098612x17706467] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVES This paper, the first in a series of three on 'feline leprosy', provides a detailed description of disease referable to Candidatus 'Mycobacterium tarwinense', the most common cause of feline leprosy in Victoria, Australia. METHODS Cases were sourced retrospectively and prospectively for this observational study, describing clinical, geographical and molecular microbiological data for cats definitively diagnosed with Candidatus 'M tarwinense' infection. RESULTS A total of 145 cases of feline leprosy were scrutinised; 114 'new' cases were sourced from the Victorian Infectious Diseases Reference Laboratory records, veterinary pathology laboratories or veterinarians, and 31 cases were derived from six published studies. Forty-two cats were definitively diagnosed with Candidatus 'M tarwinense' infection. Typically, cats were between 3 and 11 years of age, with no gender predilection, and were generally systemically well. All had outdoor access. Most cats underwent surgical resection of lesions with adjunctive medical therapy, often utilising a combination of oral clarithromycin and rifampicin for at least 3 months. Prognosis for recovery was generally good. Resolution of lesions was not observed in the absence of treatment, but a number of untreated cats continued to enjoy an acceptable quality of life despite persistence of the disease, which extended locally but did not appear to disseminate to internal organs. Preliminary results of draft genome sequencing confirmed that the species is a member of the Mycobacterium simiae complex. CONCLUSIONS AND RELEVANCE Candidatus 'M tarwinense', a fastidious member of the M simiae complex, is capable of causing feline leprosy with a tendency to produce lesions on the head, particularly involving the eyes and periocular skin. The disease has an indolent clinical course and generally responds favourably to therapy despite lesions often containing large numbers of organisms. Detailed genomic analysis may yield clues as to the environmental niche and culture requirement of this elusive organism. Prospective treatment trials and/or drug susceptibility testing in specialised systems would further inform treatment recommendations.
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Affiliation(s)
- Carolyn R O’Brien
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC 3030, Australia
| | - Richard Malik
- Centre for Veterinary Education, The University of Sydney, NSW 2006, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory, Melbourne, VIC 3000, Australia
| | - George Reppas
- Vetnostics, 60 Waterloo Road, North Ryde, NSW 2113, Australia
| | - Christina McCowan
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, VIC 3030, Australia
- Department of Environment and Primary Industries, Bundoora, VIC 3083, Australia
| | - Janet A Fyfe
- Victorian Infectious Diseases Reference Laboratory, Melbourne, VIC 3000, Australia
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Abstract
ABSTRACT
Mycobacterium marinum
is a well-known pathogenic mycobacterium for skin and soft tissue infections and is associated with fishes and water. Among nontuberculous mycobacteria (NTM), it is the leading cause of extrarespiratory human infections worldwide. In addition, there is a specific scientific interest in
M. marinum
because of its genetic relatedness to
Mycobacterium tuberculosis
and because experimental infection of
M. marinum
in fishes mimics tuberculosis pathogenesis. Microbiological characteristics include the fact that it grows in 7 to 14 days with photochromogenic colonies and is difficult to differentiate from
Mycobacterium ulcerans
and other mycolactone-producing NTM on a molecular basis. The diagnosis is highly suspected by the mode of infection, which is related to the hobby of fishkeeping, professional handling of marine shells, or swimming in nonchlorinated pools. Clinics distinguished skin and soft tissue lesions (typically sporotrichoid or subacute hand nodules) and lesions disseminated to joint and bone, often related with the local use of corticosteroids. In clinical microbiology, microscopy and culture are often negative because growth requires low temperature (30°C) and several weeks to succeed in primary cultivation. The treatment is not standardized, and no randomized control trials have been done. Therapy is a combination of surgery and antimicrobial agents such as cyclines and rifampin, with successful outcome in most of the skin diseases but less frequently in deep tissue infections. Prevention can be useful with hand protection recommendations for professionals and all persons manipulating fishes or fish tank water and use of alcohol disinfection after contact.
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Dastranj M, Farahani A, Hashemi Shahraki A, Atashi S, Mohajeri P. Molecular identification and distribution of non-tuberculous mycobacteria isolated from clinical specimens by PCR-sequencing method in West of Iran. CLINICAL RESPIRATORY JOURNAL 2017; 12:996-1002. [PMID: 28224727 DOI: 10.1111/crj.12617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/23/2017] [Accepted: 02/13/2017] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND AIMS Infections by non-tuberculous mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis. METHODS A cross-sectional study was conducted on 45 diverse isolates collected from sputum in 2 years 2014-2015 using standard decontamination procedure. All mycobacterial isolates were grown on LJ medium and also conventional tests for preliminary identification of mycobacteria rely on traits and then DNA extraction. PCR was performed, and sequencing of 16S rRNA and rpoB genes was applied for NTM strains identification. RESULTS A total of 45 isolates collected, 37 samples (83%) were evaluated as NTM. All NTM strains using molecular methods by sequencing 16S rRNA and rpoB gene were identified, by this way 12 different species have been identified which sequencing of rpoB was able to identify all species. The major species obtained were Mycobacterium simiae (22%), M. fortuitum (19%), and M. abscessus (13%). CONCLUSIONS The results of our study showed that the patients were infected by a wide range of atypical mycobacteria. It was concluded that 16S rRNA gene sequencing coupled with rpoB marker is a high discriminatory power in identification of NTM. The presence of various species in clinical samples in Iran emphasizes the use of molecular method like sequence analysis of genes is necessary for reliable identification.
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Affiliation(s)
- Mahsa Dastranj
- Microbiology Department, Kurdistan Science and Research Branch, Islamic Azad University, Sanandaj, Iran
| | - Abbas Farahani
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Sara Atashi
- West Tuberculosis Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parviz Mohajeri
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Shirudi Shahid Boulevard, Daneshgah Street, Kermanshah, 67148-69914, Iran
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Kim SH, Shin JH. Identification of nontuberculous mycobacteria using multilocous sequence analysis of 16S rRNA, hsp65, and rpoB. J Clin Lab Anal 2017; 32. [PMID: 28230286 DOI: 10.1002/jcla.22184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 01/24/2017] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The isolation of nontuberculous mycobacteria (NTM) from clinical specimens has increased, and they now are considered significant opportunistic pathogens. The aims of this study were to develop a database and interpretive criteria for identifying individual species. In addition, using clinical isolates, we evaluated the clinical usefulness of 16S rRNA, hsp65, and rpoB as target genes for this method. METHODS The sequences of NTM for 16S rRNA, hsp65, and rpoB were collected from GenBank and checked by manual inspection. Clinical isolates collected between 2005 and 2010 were used for DNA extraction, polymerase chain reaction, and sequencing of these three genes. We constructed a database for the genes and evaluated the clinical utility of multilocus sequence analysis (MLSA) using 109 clinical isolates. RESULTS A total 131, 130, and 122 sequences were collected from GenBank for 16S rRNA, hsp65, and rpoB, respectively. The percent similarities of the three genes ranged from 96.57% to 100% for the 16S rRNA gene, 89.27% to 100% for hsp65, and 92.71% to 100% for rpoB. When we compared the sequences of 109 clinical strains with those of the database, the rates of species-level identification were 71.3%, 86.79%, and 81.55% with 16S rRNA, hsp65, and rpoB, respectively. We could identify 97.25% of the isolates to the species level when we used MLSA. CONCLUSION There were significant differences among the utilities of the three genes for species identification. The MLSA technique would be helpful for identification of NTM.
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Affiliation(s)
- Si Hyun Kim
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, South Korea.,Paik Institute for Clinical Research, Inje University College of Medicine, Busan, South Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, South Korea.,Paik Institute for Clinical Research, Inje University College of Medicine, Busan, South Korea
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Varghese B, Enani M, Shoukri M, AlThawadi S, AlJohani S, Al- Hajoj S. Emergence of Rare Species of Nontuberculous Mycobacteria as Potential Pathogens in Saudi Arabian Clinical Setting. PLoS Negl Trop Dis 2017; 11:e0005288. [PMID: 28076350 PMCID: PMC5261817 DOI: 10.1371/journal.pntd.0005288] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/24/2017] [Accepted: 12/28/2016] [Indexed: 12/29/2022] Open
Abstract
Background Clinical relevance of nontuberculous mycobacteria (NTM) is increasing worldwide including in Saudi Arabia. A high species diversity of NTM’s has been noticed in a recent study. However, the identification in diagnostic laboratories is mostly limited to common species. The impact of NTM species diversity on clinical outcome is so far neglected in most of the clinical settings. Methodology/Principal Findings During April 2014 to September 2015, a nationwide collection of suspected NTM clinical isolates with clinical and demographical data were carried out. Primary identification was performed by commercial line probe assays. Isolates identified up to Mycobacterium species level by line probe assays only were included and subjected to sequencing of 16S rRNA, rpoB, hsp65 and 16S-23S ITS region genes. The sequence data were subjected to BLAST analysis in GenBank and Ez-Taxon databases. Male Saudi nationals were dominated in the study population and falling majorly into the 46–59 years age group. Pulmonary cases were 59.3% with a surprising clinical relevance of 75% based on American Thoracic Society guidelines. Among the 40.7% extra-pulmonary cases, 50% of them were skin infections. The identification revealed 16 species and all of them are reporting for the first time in Saudi Arabia. The major species obtained were Mycobacterium monascence (18.5%), M. cosmeticum (11.1%), M. kubicae (11.1%), M. duvalli (7.4%), M.terrae (7.4%) and M. triplex (7.4%). This is the first report on clinical relevance of M. kubicae, M. tusciae, M.yongonense, M. arupense and M.iranicum causing pulmonary disease and M. monascence, M. duvalli, M. perigrinum, M. insubricum, M. holsaticum and M. kyorinense causing various extra-pulmonary diseases in Saudi Arabia. Ascites caused by M. monascence and cecum infection by M. holsaticum were the rarest incidents. Conclusions/Significance To the first time in the country, clinical significance of various rare NTM’s are well explored and the finding warrants a new threat to the Saudi Arabian clinical settings. Nontuberculous mycobacteria (NTM) are ubiquitous in nature and they are opportunistic pathogens. In the last decade, infections caused by NTM’s increased—around the world in immune-suppressed and immune-competent individuals and Saudi Arabia is not an exception. Developments in diagnostic technologies increased the identification of several new or rare species of NTM’s. Indeed, the species diversity of NTM has a direct impact on clinical outcome and therapies. Saudi Arabian clinics so far report only the common species of NTM’s and rare species are mostly neglected due to the lack of proper infrastructure or ignorance. To the first time in the country, an exploration on the existence of clinically relevant rare NTM species was conducted on a nationwide level. The findings showed a huge diversity of rare NTM species causing both pulmonary and extra-pulmonary diseases. Clinical relevance of pulmonary infection based on American Thoracic Society guidelines was confirmed as an aggressive 75%, which is really alarming. Interestingly, 16 species of NTM’s were isolated in the study, and all of them are reporting for the first time in country. Overall finding shows Saudi Arabia faces serious threat from rare NTM species with high clinical significance and warrants the immediate need for more advanced infrastructure.
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Affiliation(s)
- Bright Varghese
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- * E-mail: (BV); (SAH)
| | - Mushira Enani
- Medical Specialties Department, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Mohammed Shoukri
- National Biotechnology Centre, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sahar AlThawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and research Centre, Riyadh, Saudi Arabia
| | - Sameera AlJohani
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Sahal Al- Hajoj
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- * E-mail: (BV); (SAH)
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Kim SJ, Yoon SH, Choi SM, Lee J, Lee CH, Han SK, Yim JJ. Characteristics associated with progression in patients with of nontuberculous mycobacterial lung disease : a prospective cohort study. BMC Pulm Med 2017; 17:5. [PMID: 28056937 PMCID: PMC5216528 DOI: 10.1186/s12890-016-0349-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/12/2016] [Indexed: 12/11/2022] Open
Abstract
Background Patients with distinctive morphotype were more susceptible to nontuberculous mycobacterial lung disease (NTM-LD). However, little is known about the association between body morphotype and progression of NTM-LD. The aim of this study was to elucidate predictors of NTM-LD progression, focusing on body morphotype and composition. Methods Data from patients with NTM-LD who participated in NTM cohort which started in 1 July 2011 were analyzed. Patients with more than 6 months of follow up were included for analysis. NTM-LD progression was defined as clinician-initiated anti-NTM treatment, based on symptomatic and radiologic aggravation. Body morphotype and composition was measured at entry to the cohort using bioelectrical impedance analysis. Results NTM-LD progressed in 47 out of 150 patients with more than 6 months of follow up. Patients with middle (adjusted hazard ratio [aHR], 2.758; 95% confidence interval [CI], 1.112–6.843) or lowest tertile (aHR, 3.084; 95% CI, 1.241–7.668) of abdominal fat ratio had a higher risk of disease progression compared with the highest tertile. Other predictors for disease progression were presence of cavity on chest computed tomography (aHR, 4.577; 95% CI, 2.364–8.861), and serum albumin level <3.5 g/dL (aHR, 12.943; 95% CI, 2.588–64.718). Conclusions Progression of NTM-LD is associated with body composition. Lower abdominal fat ratio is an independent predictor of NTM-LD progression. Trial registration ClinicalTrials.gov, NCT01616745 Registered 25 March 2012
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Affiliation(s)
- Soo Jung Kim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, School of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Soon Ho Yoon
- Department of Radiology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun Mi Choi
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 110-744, Republic of Korea
| | - Jinwoo Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 110-744, Republic of Korea
| | - Chang-Hoon Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 110-744, Republic of Korea
| | - Sung Koo Han
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 110-744, Republic of Korea
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 110-744, Republic of Korea.
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Cerna-Cortes JF, Cortes-Cueto AL, Cano-Gaona MR, Leon-Montes N, Helguera-Repetto AC, Rivera-Gutierrez S, Salas-Rangel LP, Castro-Rosas J, Gonzalez-Y-Merchand JA. Microbiological Quality and Occurrence of Nontuberculous Mycobacteria in Fresh-Squeezed Orange Juice Samples Purchased from Street Vendors in Mexico City. J Food Prot 2016; 79:2190-2195. [PMID: 28221956 DOI: 10.4315/0362-028x.jfp-16-197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Nontuberculous mycobacteria (NTM) are potentially pathogenic agents commonly found in a natural ecosystem. For this reason, food is considered another source of NTM transmission for humans. The aims of this study were to evaluate the microbiological quality and the occurrence of NTM in fresh-squeezed orange juice samples purchased from street vendors. All 102 samples analyzed were positive for aerobic mesophilic bacteria (AMB), with limits ranging from 1.8 to 6.2 log CFU/ml. A total of 55 (54%), 25 (25%), and 13 (13%) orange juice samples were positive for total coliforms (TC), fecal coliforms (FC), and Escherichia coli , respectively. TC, FC, and E. coli were present with limits ranging from <3 to >1,100 most probable number (MPN)/ml, <3 to 460 MPN/ml, and <3 to 11 MPN/ml, respectively. Six orange juice samples harbored NTM. These NTM were identified by using three molecular markers (hsp65, rrs, and rpoB genes) and corresponded to the fast-growing mycobacteria: Mycobacterium fortuitum (n = 3), Mycobacterium rhodesiae (n = 1), Mycobacterium obuense (n = 1), and a mixture of M. fortuitum and Mycobacterium mucogenicum in an additional sample (n = 1). No correlation was found between the presence NTM in orange juice samples with the presence and concentration of the indicator microorganisms (aerobic mesophilic bacteria, TC, and FC). Overall, these results suggest that fresh-squeezed orange juice might represent a vehicle for NTM transmission in humans. Therefore, prevention of contamination by humans (proper handling and washing of oranges) during juice preparation should be recommended.
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Affiliation(s)
- Jorge F Cerna-Cortes
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas-Instituto Politecnico Nacional, Prolongacion Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomas, México, D.F., C.P. 11340, México
| | - Ana Laura Cortes-Cueto
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas-Instituto Politecnico Nacional, Prolongacion Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomas, México, D.F., C.P. 11340, México
| | - Maria Rosalia Cano-Gaona
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas-Instituto Politecnico Nacional, Prolongacion Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomas, México, D.F., C.P. 11340, México
| | - Nancy Leon-Montes
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas-Instituto Politecnico Nacional, Prolongacion Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomas, México, D.F., C.P. 11340, México
| | - Addy C Helguera-Repetto
- Departamento de Inmunobioquimica, Torre de Investigación, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Montes Urales 800, Colonia Lomas de Virreyes, México, D.F., C.P. 11000, Mexico
| | - Sandra Rivera-Gutierrez
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas-Instituto Politecnico Nacional, Prolongacion Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomas, México, D.F., C.P. 11340, México
| | - Laura P Salas-Rangel
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas-Instituto Politecnico Nacional, Prolongacion Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomas, México, D.F., C.P. 11340, México
| | - Javier Castro-Rosas
- Centro de Investigaciones Quimicas, Instituto de Ciencias Básicas e Ingenieria, Universidad Autonoma del Estado de Hidalgo, Centro Universitario, Carretera Pachuca-Tulancingo km 4.5, Mineral de la Reforma, Hidalgo, C.P. 42183, México
| | - Jorge A Gonzalez-Y-Merchand
- Departamento de Microbiologia, Escuela Nacional de Ciencias Biologicas-Instituto Politecnico Nacional, Prolongacion Carpio y Plan de Ayala S/N, Col. Casco de Santo Tomas, México, D.F., C.P. 11340, México
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64
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Park J, Cho J, Lee CH, Han SK, Yim JJ. Progression and Treatment Outcomes of Lung Disease Caused by Mycobacterium abscessus and Mycobacterium massiliense. Clin Infect Dis 2016; 64:301-308. [PMID: 28011609 DOI: 10.1093/cid/ciw723] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 10/23/2016] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Mycobacterium abscessus and Mycobacterium massiliense are grouped as the Mycobacterium abscessus complex. The aim of this study was to elucidate the differences between M. abscessus and M. massiliense lung diseases in terms of progression rate, treatment outcome, and the predictors thereof. METHODS Between 1 January 2006 and 30 June 2015, 56 patients and 54 patients were diagnosed with M. abscessus and M. massiliense lung diseases, respectively. The time to progression requiring treatment and treatment outcomes were compared between the 2 groups of patients, and predictors of progression and sustained culture conversion with treatment were analyzed. In addition, mediation analysis was performed to evaluate the effect of susceptibility to clarithromycin on treatment outcomes. RESULTS During follow-up, 21 of 56 patients with M. abscessus lung diseases and 21 of 54 patients with M. massiliense lung diseases progressed, requiring treatment. No difference was detected in the time to progression between the 2 patient groups. Lower body mass index, bilateral lung involvement, and fibrocavitary-type disease were identified as predictors of disease progression. Among the patients who began treatment, infection with M. massiliense rather than M. abscessus and the use of azithromycin rather than clarithromycin were associated with sustained culture conversion. The difference in treatment outcomes was partly mediated by the organism's susceptibility to clarithromycin. CONCLUSIONS Progression rates were similar but treatment outcomes differed significantly between patients with lung disease caused by M. abscessus and M. massiliense. This difference in treatment outcomes was partly explained by the susceptibility of these organisms to clarithromycin.
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Affiliation(s)
- Jimyung Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jaeyoung Cho
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Chang-Hoon Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Koo Han
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
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65
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Yang M, Huh HJ, Kwon HJ, Kim JY, Song DJ, Koh WJ, Ki CS, Lee NY. Comparative evaluation of the AdvanSure Mycobacteria GenoBlot assay and the GenoType Mycobacterium CM/AS assay for the identification of non-tuberculous mycobacteria. J Med Microbiol 2016; 65:1422-1428. [PMID: 27902391 DOI: 10.1099/jmm.0.000376] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, to assess the performance of the AdvanSure Mycobacteria GenoBlot assay (AdvanSure assay), we compared its performance with that of the GenoType Mycobacterium CM/AS assay (GenoType assay) for the identification of non-tuberculous mycobacteria (NTM). Twenty-four reference strains and 103 consecutive clinical NTM isolates were analysed. The accuracy rates for the 24 reference strains were 87.5 and 95.8 % for the AdvanSure and GenoType assays, respectively. For the 103 clinical isolates, a 91.3 % (94/103) concordance rate was observed between the two assays. The majority (7/9) of discrepancies were isolates identified as Mycobacterium avium complex (MAC) by only the AdvanSure assay. All of these isolates except one were confirmed as MAC by sequence-based typing. The AdvanSure assay showed comparable performance to the GenoType assay and can be useful as a routine method for NTM identification in the clinical setting, especially where MAC is the main cause of NTM infection.
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Affiliation(s)
- Mina Yang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyeon Jeong Kwon
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Dong Joon Song
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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66
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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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67
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Kim HY, Lee SY, Kim BJ, Kook YH. Allele-specific duplex polymerase chain reaction to differentiate Mycobacterium abscessus subspecies and to detect highly clarithromycin-resistant isolates. Indian J Med Microbiol 2016; 34:369-74. [PMID: 27514964 DOI: 10.4103/0255-0857.188355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
On the basis of the structural differences of erm, we used a duplex polymerase chain reaction (PCR) to differentiate Mycobacterium abscessus subsp. abscessus and subsp. massiliense isolates and to detect the point mutations of 23S rRNA gene that confer a high level of resistance to clarithromycin. Subsp. massiliense strains occupying almost half of the clinical isolates can be simply identified, and their clarithromycin susceptibility can be rapidly determined.
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Affiliation(s)
- H Y Kim
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Institute of Endemic Diseases, Seoul 110 799, Republic of Korea
| | - S Y Lee
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Institute of Endemic Diseases, Seoul 110 799, Republic of Korea
| | - B J Kim
- Department of Microbiology and Immunology; Department of Biomedical Sciences, Seoul National University College of Medicine, Institute of Endemic Diseases; Seoul National University Medical Research Center; Cancer Research Institute, Seoul National University College of Medicine, Seoul 110 799, Republic of Korea
| | - Y H Kook
- Department of Microbiology and Immunology, Seoul National University College of Medicine, Institute of Endemic Diseases; Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul 110 799, Republic of Korea
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68
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Bromberg R, Grishin NV, Otwinowski Z. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput Biol 2016; 12:e1004985. [PMID: 27336403 PMCID: PMC4918981 DOI: 10.1371/journal.pcbi.1004985] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/10/2016] [Indexed: 01/20/2023] Open
Abstract
Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. Due to their lack of distinct morphological features, bacteria and archaea were extremely difficult to classify until technology was developed to obtain their DNA sequences; these sequences could then be compared to estimate evolutionary relationships. Now, due to technological advances, there is a flood of available sequences from a wide variety of organisms. These advances have spurred the development of algorithms which can estimate evolutionary relationships using whole genomes, in contrast to the more traditional methods which used single genes earlier and now typically use groups of conserved genes. However, there are many challenges when attempting to infer evolutionary relationships, in particular horizontal gene transfer, where DNA is transferred from one organism to another, resulting in an organism’s genome containing DNA that does not reflect its evolution by descent. We developed a new whole-genome method for estimating evolutionary distances which identifies and corrects for horizontal transfer. We found that for SlopeTree and all other whole-genome methods we applied, horizontal transfer causes some evolutionary distances to be grossly underestimated, and that our correction corrects for this.
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Affiliation(s)
- Raquel Bromberg
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Zbyszek Otwinowski
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- * E-mail:
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69
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Sakyi SA, Aboagye SY, Darko Otchere I, Yeboah-Manu D. Clinical and Laboratory Diagnosis of Buruli Ulcer Disease: A Systematic Review. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2016; 2016:5310718. [PMID: 27413382 PMCID: PMC4931084 DOI: 10.1155/2016/5310718] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/25/2016] [Indexed: 01/08/2023]
Abstract
Background. Buruli ulcer (BU) is a necrotizing cutaneous infection caused by Mycobacterium ulcerans. Early diagnosis is crucial to prevent morbid effects and misuse of drugs. We review developments in laboratory diagnosis of BU, discuss limitations of available diagnostic methods, and give a perspective on the potential of using aptamers as point-of-care. Methods. Information for this review was searched through PubMed, web of knowledge, and identified data up to December 2015. References from relevant articles and reports from WHO Annual Meeting of the Global Buruli Ulcer initiative were also used. Finally, 59 articles were used. Results. The main laboratory methods for BU diagnosis are microscopy, culture, PCR, and histopathology. Microscopy and PCR are used routinely for diagnosis. PCR targeting IS2404 is the gold standard for laboratory confirmation. Culture remains the only method that detects viable bacilli, used for diagnosing relapse and accrued isolates for epidemiological investigation as well as monitoring drug resistance. Laboratory confirmation is done at centers distant from endemic communities reducing confirmation to a quality assurance. Conclusions. Current efforts aimed at developing point-of-care diagnostics are saddled with major drawbacks; we, however, postulate that selection of aptamers against MU target can be used as point of care.
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Affiliation(s)
- Samuel A. Sakyi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Molecular Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Samuel Y. Aboagye
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
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Densmore CL, Iwanowicz LR, Henderson AP, Iwanowicz DD, Odenkirk JS. Mycobacterial infection in Northern snakehead (Channa argus) from the Potomac River catchment. JOURNAL OF FISH DISEASES 2016; 39:771-775. [PMID: 26471857 DOI: 10.1111/jfd.12412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/24/2015] [Accepted: 07/24/2015] [Indexed: 06/05/2023]
Affiliation(s)
- C L Densmore
- United States Geological Survey, Leetown Science Center, Kearneysville, WV, USA
| | - L R Iwanowicz
- United States Geological Survey, Leetown Science Center, Kearneysville, WV, USA
| | - A P Henderson
- United States Geological Survey, Leetown Science Center, Kearneysville, WV, USA
| | - D D Iwanowicz
- United States Geological Survey, Leetown Science Center, Kearneysville, WV, USA
| | - J S Odenkirk
- Virginia Department of Game and Inland Fisheries, Fredericksburg, VA, USA
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71
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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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Nasr Esfahani B, Moghim S, Ghasemian Safaei H, Moghoofei M, Sedighi M, Hadifar S. Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene. Jundishapur J Microbiol 2016; 9:e30763. [PMID: 27284397 PMCID: PMC4898205 DOI: 10.5812/jjm.30763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 01/18/2016] [Accepted: 02/01/2016] [Indexed: 11/16/2022] Open
Abstract
Background Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3% - 100%), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation. Objectives In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran. Materials and Methods From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software. Results Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50% were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98% and M. gordonae in another cluster with a bootstrap value of 90%. In the fast-growing group, one cluster with a bootstrap value of 89% was defined, including all fast-growing members present in this study. Conclusions The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85% - 100%); the resulting tree has high validity.
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Affiliation(s)
- Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Hajieh Ghasemian Safaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Mohsen Moghoofei
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, IR Iran
| | - Mansour Sedighi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Shima Hadifar
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
- Corresponding author: Shima Hadifar, Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran. Tel: +98-3137922493, Fax: +98-3136688597, E-mail:
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Kim BJ, Kim BR, Lee SY, Kim GN, Kook YH, Kim BJ. Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis. PLoS One 2016; 11:e0152703. [PMID: 27031100 PMCID: PMC4816341 DOI: 10.1371/journal.pone.0152703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/17/2016] [Indexed: 12/30/2022] Open
Abstract
Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950T and Mycobacterium yongonense DSM 45126T. Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126T than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum.
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Affiliation(s)
- Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ga-Na Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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Jung YJ, Kim JY, Song DJ, Koh WJ, Huh HJ, Ki CS, Lee NY. Evaluation of three real-time PCR assays for differential identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria species in liquid culture media. Diagn Microbiol Infect Dis 2016; 85:186-91. [PMID: 27105774 DOI: 10.1016/j.diagmicrobio.2016.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/02/2016] [Accepted: 03/13/2016] [Indexed: 11/29/2022]
Abstract
We evaluated the analytical performance of M. tuberculosis complex (MTBC)/nontuberculous mycobacteria (NTM) PCR assays for differential identification of MTBC and NTM using culture-positive liquid media. Eighty-five type strains and 100 consecutive mycobacterial liquid media cultures (MGIT 960 system) were analyzed by a conventional PCR assay (MTB-ID(®) V3) and three real-time PCR assays (AdvanSure™ TB/NTM real-time PCR, AdvanSure; GENEDIA(®) MTB/NTM Detection Kit, Genedia; Real-Q MTB & NTM kit, Real-Q). The accuracy rates for reference strains were 89.4%, 100%, 98.8%, and 98.8% for the MTB-ID V3, AdvanSure, Genedia, and Real-Q assays, respectively. Cross-reactivity in the MTB-ID V3 assay was mainly attributable to non-mycobacterium Corynebacterineae species. The diagnostic performance was determined using clinical isolates grown in liquid media, and the overall sensitivities for all PCR assays were higher than 95%. In conclusion, the three real-time PCR assays showed better performance in discriminating mycobacterium species and non-mycobacterium Corynebacterineae species than the conventional PCR assay.
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Affiliation(s)
- Yu Jung Jung
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Ji-Youn Kim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Dong Joon Song
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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75
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Rodríguez-García A, Fernández-Alegre E, Morales A, Sola-Landa A, Lorraine J, Macdonald S, Dovbnya D, Smith MCM, Donova M, Barreiro C. Complete genome sequence of 'Mycobacterium neoaurum' NRRL B-3805, an androstenedione (AD) producer for industrial biotransformation of sterols. J Biotechnol 2016; 224:64-5. [PMID: 26988397 DOI: 10.1016/j.jbiotec.2016.03.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/10/2016] [Indexed: 11/28/2022]
Abstract
Microbial bioconversion of sterols into high value steroid precursors, such as 4-androstene-3,17-dione (AD), is an industrial challenge. Genes and enzymes involved in sterol degradation have been proposed, although the complete pathway is not yet known. The genome sequencing of the AD producer strain 'Mycobacterium neoaurum' NRRL B-3805 (formerly Mycobacterium sp. NRRL B-3805) will serve to elucidate the critical steps for industrial processes and will provide the basis for further genetic engineering. The genome comprises a circular chromosome (5 421 338bp), is devoid of plasmids and contains 4844 protein-coding genes.
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Affiliation(s)
- Antonio Rodríguez-García
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real 1, 24006 León, Spain; Área de Microbiología, Departamento de Biología Molecular, Universidad de León, Campus de Vegazana, 24071 León, Spain
| | - Estela Fernández-Alegre
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real 1, 24006 León, Spain
| | - Alejandro Morales
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real 1, 24006 León, Spain
| | - Alberto Sola-Landa
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real 1, 24006 León, Spain
| | - Jess Lorraine
- Department of Biology, University of York, Wentworth Way, YO10 5DD, United Kingdom
| | - Sandy Macdonald
- Department of Biology, University of York, Wentworth Way, YO10 5DD, United Kingdom
| | - Dmitry Dovbnya
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki 5, 142290 Pushchino, Moscow Region, Russia
| | - Margaret C M Smith
- Department of Biology, University of York, Wentworth Way, YO10 5DD, United Kingdom
| | - Marina Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Prospekt Nauki 5, 142290 Pushchino, Moscow Region, Russia
| | - Carlos Barreiro
- INBIOTEC (Instituto de Biotecnología de León), Parque Científico de León, Avda. Real 1, 24006 León, Spain.
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Mycobacterium arupense, Mycobacterium heraklionense, and a Newly Proposed Species, "Mycobacterium virginiense" sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis. J Clin Microbiol 2016; 54:1340-51. [PMID: 26962085 DOI: 10.1128/jcm.00198-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/01/2016] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium terrae complex has been recognized as a cause of tenosynovitis, with M. terrae and Mycobacterium nonchromogenicum reported as the primary etiologic pathogens. The molecular taxonomy of the M. terrae complex causing tenosynovitis has not been established despite approximately 50 previously reported cases. We evaluated 26 isolates of the M. terrae complex associated with tenosynovitis or osteomyelitis recovered between 1984 and 2014 from 13 states, including 5 isolates reported in 1991 as M. nonchromogenicum by nonmolecular methods. The isolates belonged to three validated species, one new proposed species, and two novel related strains. The majority of isolates (20/26, or 77%) belonged to two recently described species: Mycobacterium arupense (10 isolates, or 38%) and Mycobacterium heraklionense (10 isolates, or 38%). Three isolates (12%) had 100% sequence identity to each other by 16S rRNA and 99.3 to 100% identity by rpoB gene region V sequencing and represent a previously undescribed species within the M. terrae complex. There were no isolates of M. terrae or M. nonchromogenicum, including among the five isolates reported in 1991. The 26 isolates were susceptible to clarithromycin (100%), rifabutin (100%), ethambutol (92%), and sulfamethoxazole or trimethoprim-sulfamethoxazole (70%). The current study suggests that M. arupense, M. heraklionense, and a newly proposed species ("M. virginiense" sp. nov.; proposed type strain MO-233 [DSM 100883, CIP 110918]) within the M. terrae complex are the major causes of tenosynovitis and osteomyelitis in the United States, with little change over 20 years. Species identification within this complex requires sequencing methods.
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77
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Koizumi Y, Shimizu K, Shigeta M, Minamiguchi H, Hodohara K, Andoh A, Tanaka T, Chikamatsu K, Mitarai S, Mikamo H. Mycobacterium shigaense Causes Lymph Node and Cutaneous Lesions as Immune Reconstitution Syndrome in an AIDS Patient: The Third Case Report of a Novel Strain Non-tuberculous Mycobacterium. Intern Med 2016; 55:3375-3381. [PMID: 27853087 PMCID: PMC5173512 DOI: 10.2169/internalmedicine.55.6996] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A 40-year-old man complaining of progressive body weight loss was diagnosed to have acquired immunodeficiency syndrome. Within 2 weeks after the initiation of combination antiretroviral therapy, he developed fever, massive cervical lymphadenopathy and a protruding subcutaneous abscess. A lymph node biopsy and abscess drainage revealed non-caseous granuloma and mycobacterium. The mycobacterium belonged to Runyon II group, but it showed no matches to any previously reported species. According to sequence analyses, the strain was identified as Mycobacterium shigaense. After six months of antimycobacterial treatment, the lesions were all successfully cured. This is the third case report of the novel mycobacterium, M. shigaense, presenting in associatioin with immune reconstitution syndrome.
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Affiliation(s)
- Yusuke Koizumi
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, Japan
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78
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Choo SW, Ang MY, Dutta A, Tan SY, Siow CC, Heydari H, Mutha NVR, Wee WY, Wong GJ. MycoCAP - Mycobacterium Comparative Analysis Platform. Sci Rep 2015; 5:18227. [PMID: 26666970 PMCID: PMC4678330 DOI: 10.1038/srep18227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/09/2015] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium spp. are renowned for being the causative agent of diseases like leprosy, Buruli ulcer and tuberculosis in human beings. With more and more mycobacterial genomes being sequenced, any knowledge generated from comparative genomic analysis would provide better insights into the biology, evolution, phylogeny and pathogenicity of this genus, thus helping in better management of diseases caused by Mycobacterium spp.With this motivation, we constructed MycoCAP, a new comparative analysis platform dedicated to the important genus Mycobacterium. This platform currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive web-based tools have been integrated in MycoCAP particularly for comparative analysis including the PGC tool for comparison between two genomes, PathoProT for comparing the virulence genes among the Mycobacterium strains and the SuperClassification tool for the phylogenic classification of the Mycobacterium strains and a specialized classification system for strains of Mycobacterium abscessus. We hope the broad range of functions and easy-to-use tools provided in MycoCAP makes it an invaluable analysis platform to speed up the research discovery on mycobacteria for researchers. Database URL: http://mycobacterium.um.edu.my
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Affiliation(s)
- Siew Woh Choo
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Mia Yang Ang
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Avirup Dutta
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Shi Yang Tan
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Cheuk Chuen Siow
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Hamed Heydari
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Molecular Genetics, University of Toronto, ON M5S3E, Canada
| | - Naresh V R Mutha
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wei Yee Wee
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Guat Jah Wong
- Genome Informatics Research Laboratory, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
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79
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A cluster of central line-associated bloodstream infections due to rapidly growing nontuberculous mycobacteria in patients with hematologic disorders at a Japanese tertiary care center: an outbreak investigation and review of the literature. Infect Control Hosp Epidemiol 2015; 36:76-80. [PMID: 25627764 DOI: 10.1017/ice.2014.14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Rapidly growing nontuberculous mycobacteria (RGM) are considered rare pathogens, causing central line-associated bloodstream infection. We identified an outbreak of central line-associated bloodstream infection due to RGM at a hematology-oncology ward during a 5-month period. DESIGN Outbreak investigation and literature review. SETTING A Japanese tertiary care center. PATIENTS Adults who were hospitalized at the hematology-oncology ward from October 15, 2011, through February 17, 2012. RESULTS A total of 5 patients with a bloodstream infection due to RGM (4 cases of Mycobacterium mucogenicum and 1 case of Mycobacterium canariasense infection) were identified; of these, 3 patients had acute myeloid leukemia, 1 had acute lymphocytic leukemia, and 1 had aplastic anemia. Four of the 5 patients received cord blood transplantation prior to developing the bloodstream infection. All central venous catheters in patients with a bloodstream infection were removed. These patients promptly defervesced after catheter removal and their care was successfully managed without antimicrobial therapy. Surveillance cultures from the environment and water detected M. mucogenicum and M. canariasense in the water supply of the hematology-oncology ward. The isolates from the bloodstream infection and water sources were identical on the basis of 16S-rRNA gene sequencing. CONCLUSIONS The source of RGM in the outbreak of bloodstream infections likely was the ward tap water supply. Awareness of catheter-related bloodstream infections due to nontuberculous mycobacteria should be emphasized, especially where immunocompromised patients are at risk. Also, using antimicrobials after catheter removal to treat central line-associated bloodstream infection due to RGM may not be necessary. Infect Control Hosp Epidemiol 2015;36(1): 76-80.
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Identification of ISMyo2, a novel insertion sequence element of IS21 family and its diagnostic potential for detection of Mycobacterium yongonense. BMC Genomics 2015; 16:794. [PMID: 26472562 PMCID: PMC4608216 DOI: 10.1186/s12864-015-1978-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/29/2015] [Indexed: 11/21/2022] Open
Abstract
Background Mycobacterium yongonense, as a novel member of the M. avium complex (MAC), was recently reported to be isolated from human specimens in South Korea and Italy. Due to its close relatedness to other MAC members, particularly M. intracellulare in taxonomic aspects, the development of a novel diagnostic method for its specific detection is necessary for clinical or epidemiologic purposes. Methods Using the Mycobacterium yongonense genome information, we have identified a novel IS-element, ISMyo2. Targeting the ISMyo2 sequence, we developed a real-time PCR method and applied the technique to Mycobacterial genomic DNA. Results To identify proper nucleic acid targets for the diagnosis, comparisons of all insertion sequence (IS) elements of 3 M. intracellulare and 3 M. yongonense strains, whose complete genome sequences we reported recently, led to the selection of a novel target gene, the M. yongonense-specific IS element, ISMyo2 (2,387 bp), belonging to the IS21 family. Next, we developed a real-time PCR method using SYBR green I for M. yongonense-specific detection targeting ISMyo2, producing a 338-bp amplicon. When this assay was applied to 28 Mycobacterium reference strains and 63 MAC clinical isolates, it produced amplicons in only the 6 M. yongonense strains, showing a sensitivity of 100 fg of genomic DNA, suggesting its feasibility as a diagnostic method for M. yongonense strains. Conclusions We identified a novel ISMyo2 IS element belonging to the IS21 family specific to M. yongonense strains via genome analysis, and a real-time PCR method based on its sequences was developed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1978-2) contains supplementary material, which is available to authorized users.
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81
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Hadifar S, Moghim S, Fazeli H, GhasemianSafaei H, Havaei SA, Farid F, Esfahani BN. Molecular typing of Iranian mycobacteria isolates by polymerase chain reaction-restriction fragment length polymorphism analysis of 360-bp rpoB gene. Adv Biomed Res 2015; 4:152. [PMID: 26380237 PMCID: PMC4550954 DOI: 10.4103/2277-9175.161579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 02/15/2015] [Indexed: 11/30/2022] Open
Abstract
Background: Diagnosis and typing of Mycobacterium genus provides basic tools for investigating the epidemiology and pathogenesis of this group of bacteria. Polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) is an accurate method providing diagnosis and typing of species of mycobacteria. The present study is conducted by the purpose of determining restriction fragment profiles of common types of mycobacteria by PRA method of rpoB gene in this geographical region. Materials and Methods: Totally 60 clinical and environmental isolates from February to October, 2013 were collected and subcultured and identified by phenotypic methods. A 360 bp fragment of the rpoB gene amplified by PCR and products were digested by MspI and HaeIII enzymes. Results: In the present study, of all mycobacteria isolates identified by PRA method, 13 isolates (21.66%) were Mycobacterium tuberculosis, 34 isolates (56.66%) were rapidly growing Nontuberculosis Mycobacteria (NTM) that including 26 clinical isolates (43.33%) and 8 environmental isolates (13.33%), 11 isolates (18.33%) were clinical slowly growing NTM. among the clinical NTM isolates, Mycobacterium fortuitum Type I with the frequency of 57.77% was the most prevalent type isolates. Furthermore, an unrecorded of the PRA pattern of Mycobacterium conceptionense (HeaIII: 120/90/80, MspI: 120/105/80) was found. This study demonstrated that the PRA method was high discriminatory power for identification and typing of mycobacteria species and was able to identify 96.6% of all isolates. Conclusion: Based on the result of this study, rpoB gene could be a potentially useful tool for identification and investigation of molecular epidemiology of mycobacterial species.
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Affiliation(s)
- Shima Hadifar
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Sharareh Moghim
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hossein Fazeli
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Hajieh GhasemianSafaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Fariba Farid
- Department of Health, Isfahan Provincial Health Office, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, I. R. Iran
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82
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Biogeography of Nocardiopsis strains from hypersaline environments of Yunnan and Xinjiang Provinces, western China. Sci Rep 2015; 5:13323. [PMID: 26289784 PMCID: PMC4542603 DOI: 10.1038/srep13323] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 07/23/2015] [Indexed: 12/19/2022] Open
Abstract
The genus Nocardiopsis is a widespread group within the phylum Actinobacteria and has been isolated from various salty environments worldwide. However, little is known about whether biogeography affects Nocardiopsis distribution in various hypersaline environments. Such information is essential for understanding the ecology of Nocardiopsis. Here we analyzed 16S rRNA, gyrB, rpoB and sodA genes of 78 Nocardiopsis strains isolated from hypersaline environments in Yunnan and Xinjiang Provinces of western China. The obtained Nocardiopsis strains were classified into five operational taxonomic units, each comprising location-specific phylo- and genotypes. Statistical analyses showed that spatial distance and environmental factors substantially influenced Nocardiopsis distribution in hypersaline environments: the former had stronger influence at large spatial scales, whereas the latter was more influential at small spatial scales.
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83
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Kim K, Hong SH, Kim BJ, Kim BR, Lee SY, Kim GN, Shim TS, Kook YH, Kim BJ. Separation of Mycobacterium abscessus into subspecies or genotype level by direct application of peptide nucleic acid multi-probe- real-time PCR method into sputa samples. BMC Infect Dis 2015; 15:325. [PMID: 26259717 PMCID: PMC4531893 DOI: 10.1186/s12879-015-1076-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/31/2015] [Indexed: 11/30/2022] Open
Abstract
Background Recently, we introduced a novel peptide nucleic acid (PNA) multi-probe real time PCR method targeting the hsp65 gene (hsp65 PNA RT-PCR) to distinguish Mycobacterium abscessus groups. Methods Here, we evaluated the usefulness of the hsp65 PNA RT-PCR for the direct identification of the M. abscessus group at the subspecies and genotype levels from sputa samples. The method was applied to total sputa DNA from 60 different patients who were identified as having mycobacterial infections via rpoB PCR restriction analysis of the same cultures. Results The hsp65 PNA RT-PCR method had higher sensitivity than the multi-probe real-time PCR assay targeting hsp65 (HMPRT-PCR) for the detection of M. abscessus from sputum [96.7 % (29/30 samples) vs. 70 % (21/30 samples); 100 % specificity]. Conclusions These results suggest that the PNA-based method is feasible for the detection of M. abscessus members not only from cultures but also directly from sputa. Electronic supplementary material The online version of this article (doi:10.1186/s12879-015-1076-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kijeong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, 156-756, Republic of Korea.
| | - Seok-Hyun Hong
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Ga-Na Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Tae Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Liver Research Institute, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul, 110-799, Republic of Korea.
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84
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Morimoto K, Kazumi Y, Shiraishi Y, Yoshiyama T, Murase Y, Ikushima S, Kurashima A, Kudoh S, Goto H, Maeda S. Clinical and microbiological features of definiteMycobacterium gordonaepulmonary disease: the establishment of diagnostic criteria for low-virulence mycobacteria. Trans R Soc Trop Med Hyg 2015. [DOI: 10.1093/trstmh/trv058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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85
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Meghdadi H, Khosravi AD, Ghadiri AA, Sina AH, Alami A. Detection of Mycobacterium tuberculosis in extrapulmonary biopsy samples using PCR targeting IS6110, rpoB, and nested-rpoB PCR Cloning. Front Microbiol 2015; 6:675. [PMID: 26191059 PMCID: PMC4490800 DOI: 10.3389/fmicb.2015.00675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/22/2015] [Indexed: 12/14/2022] Open
Abstract
Present study was aimed to examine the diagnostic utility of polymerase chain reaction (PCR) and nested PCR techniques for the detection of Mycobacterium tuberculosis (MTB) DNA in samples from patients with extra pulmonary tuberculosis (EPTB). In total 80 formalin-fixed, paraffin-embedded (FFPE) samples comprising 70 samples with definite diagnosis of EPTB and 10 samples from known non- EPTB on the basis of histopathology examination, were included in the study. PCR amplification targeting IS6110, rpoB gene and nested PCR targeting the rpoB gene were performed on the extracted DNAs from 80 FFPE samples. The strong positive samples were directly sequenced. For negative samples and those with weak band in nested-rpoB PCR, TA cloning was performed by cloning the products into the plasmid vector with subsequent sequencing. The 95% confidence intervals (CI) for the estimates of sensitivity and specificity were calculated for each method. Fourteen (20%), 34 (48.6%), and 60 (85.7%) of the 70 positive samples confirmed by histopathology, were positive by rpoB-PCR, IS6110-PCR, and nested-rpoB PCR, respectively. By performing TA cloning on samples that yielded weak (n = 8) or negative results (n = 10) in the PCR methods, we were able to improve their quality for later sequencing. All samples with weak band and 7 out of 10 negative samples, showed strong positive results after cloning. So nested-rpoB PCR cloning revealed positivity in 67 out of 70 confirmed samples (95.7%). The sensitivity of these combination methods was calculated as 95.7% in comparison with histopathology examination. The CI for sensitivity of the PCR methods were calculated as 11.39-31.27% for rpoB-PCR, 36.44-60.83% for IS6110- PCR, 75.29-92.93% for nested-rpoB PCR, and 87.98-99.11% for nested-rpoB PCR cloning. The 10 true EPTB negative samples by histopathology, were negative by all tested methods including cloning and were used to calculate the specificity of the applied methods. The CI for 100% specificity of each PCR method were calculated as 69.15-100%. Our results indicated that nested-rpoB PCR combined with TA cloning and sequencing is a preferred method for the detection of MTB DNA in EPTB samples with high sensitivity and specificity which confirm the histopathology results.
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Affiliation(s)
- Hossein Meghdadi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
| | - Azar D Khosravi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran ; Health Research Institute, Infectious and Tropical Diseases Research Center, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
| | - Ata A Ghadiri
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran ; Cell and Molecular Research Center, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
| | | | - Ameneh Alami
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences , Ahvaz, Iran
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Lin L, Yin X, Wang Q. Rapid differentiation of mycobacteria by simplex real-time PCR with melting temperature calling analysis. J Appl Microbiol 2015; 119:853-8. [PMID: 26119243 DOI: 10.1111/jam.12884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 05/27/2015] [Accepted: 06/05/2015] [Indexed: 12/01/2022]
Abstract
AIMS This study aimed to develop a rapid, simple and cost-effective method for the differentiation of Mycobacterium species. METHODS AND RESULTS A total of 80 clinical mycobacterial isolates belonging to 12 different species and 16 reference strains of 16 different species were differentiated by the simplex real-time PCR coupled with melting temperature calling analysis. By comparing their melting profiles with those of the reference strains, all clinical mycobacterial isolates were differentiated as Mycobacterium tuberculosis complex or nontuberculous mycobacteria, and the latter were further divided into five groups. In comparison with 16S-23S internal transcribed spacer sequencing method as the gold standard method, both sensitivity and specificity of the assay were 100% when it was used for the differentiation between Myco. tuberculosis complex and nontuberculous mycobacteria. CONCLUSIONS The simplex real-time PCR coupled with melting temperature calling analysis could be an alternative method for the differentiation between Myco. tuberculosis complex and nontuberculous mycobacteria. SIGNIFICANCE AND IMPACT OF THE STUDY Rapid differentiation of mycobacteria could shorten the diagnostic time of mycobacterial diseases. It is also helpful for achieving optimal therapy and appropriate patient management.
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Affiliation(s)
- L Lin
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - X Yin
- Clinical Laboratory, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong Province, China
| | - Q Wang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
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87
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Microbiological features and clinical relevance of new species of the genus Mycobacterium. Clin Microbiol Rev 2015; 27:727-52. [PMID: 25278573 DOI: 10.1128/cmr.00035-14] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are present in the environment, mainly in water, and are occasionally responsible for opportunistic infections in humans. Despite the fact that NTM are characterized by a moderate pathogenicity, the diseases caused by NTM at various body sites are increasing on a worldwide level. Among over 150 officially recognized NTM species, only two or three dozen are familiar to clinicians, and even to most microbiologists. In this paper, approximately 50 new species described in the last 8 years are reviewed, and their role in human infections is assessed on the basis of reported clinical cases. The small number of reports concerning most of the "new" mycobacterial species is responsible for the widespread conviction that they are very rare. Their role is actually largely underestimated, mainly because they often remain unrecognized and misidentified. Aiming to minimize such bias, emphasis has been placed on more common identification pitfalls. Together with new NTM, new members of the Mycobacterium tuberculosis complex described in the last few years are also an object of the present review.
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88
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Kim BJ, Kim JM, Kim BR, Lee SY, Kim G, Jang YH, Ryoo S, Jeon CO, Jin HM, Jeong J, Lee SH, Lim JH, Kook YH, Kim BJ. Mycobacterium anyangense sp. nov., a rapidly growing species isolated from blood of Korean native cattle, Hanwoo (Bos taurus coreanae). Int J Syst Evol Microbiol 2015; 65:2277-2285. [PMID: 25870258 DOI: 10.1099/ijs.0.000255] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
From the whole blood of Korean native cattle, Hanwoo (Bos taurus coreanae), a previously undescribed, rapidly growing, scotochromogenic isolate of the genus Mycobacterium is reported. Its 16S rRNA gene sequence, and the sequences of three other genes (hsp65, recA and rpoB) were unique and phylogenetic analysis based on 16S rRNA gene sequence (1420 bp) placed the organism into the rapidly growing Mycobacterium group close to Mycobacterium smegmatis (98.5% sequence similarity). However, phylogenetic analyses based on three different gene sequences (hsp65, recA and rpoB) revealed its location to be distinct from the branch of rapidly growing species. Culture and biochemical characteristics were generally similar to those of Mycobacterium fortuitum. Unique matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS profiles of lipids, unique fatty acid profile, unique mycolic acids profiles and a low DNA-DNA relatedness to M. fortuitum (23.6%) and M. smegmatis (39.7%) strongly supported the taxonomic status of this strain as a representative of a novel species of rapidly growing mycobacteria named Mycobacterium anyangense. The type strain is strain QIA-38(T) ( = JCM 30275(T) = KCTC 29443(T)).
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Affiliation(s)
- Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Jae-Myung Kim
- Animal and Plant Health Research Department, Animal and Plant Quarantine Agency, Anyang 430-757, Republic of Korea
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - GaNa Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Yun-Ho Jang
- Animal and Plant Health Research Department, Animal and Plant Quarantine Agency, Anyang 430-757, Republic of Korea
| | - Soyoon Ryoo
- Animal and Plant Health Research Department, Animal and Plant Quarantine Agency, Anyang 430-757, Republic of Korea
| | - Che-Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Hyun-Mi Jin
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Joseph Jeong
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-714, Republic of Korea
| | - Seon Ho Lee
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-714, Republic of Korea
| | - Ji-Hun Lim
- Department of Laboratory Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 682-714, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, and Institute of Endemic Diseases, Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
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89
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Evaluation of the Ribosomal Protein S1 Gene (rpsA) as a Novel Biomarker for Mycobacterium Species Identification. BIOMED RESEARCH INTERNATIONAL 2015; 2015:271728. [PMID: 25945329 PMCID: PMC4402190 DOI: 10.1155/2015/271728] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 11/07/2014] [Indexed: 11/17/2022]
Abstract
Objectives. To evaluate the resolution and reliability of the rpsA gene, encoding ribosomal protein S1, as a novel biomarker for mycobacteria species identification. Methods. A segment of the rpsA gene (565 bp) was amplified by PCR from 42 mycobacterial reference strains, 172 nontuberculosis mycobacteria clinical isolates, and 16 M. tuberculosis complex clinical isolates. The PCR products were sequenced and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method. Results. Comparative sequence analysis of the rpsA gene provided the basis for species differentiation within the genus Mycobacterium. Slow- and rapid-growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. The sequences discrepancy was obvious between M. kansasii and M. gastri, M. chelonae and M. abscessus, M. avium and M. intracellulare, and M. szulgai and M. malmoense, which cannot be achieved by 16S ribosomal DNA (rDNA) homologue genes comparison. 183 of the 188 (97.3%) clinical isolates, consisting of 8 mycobacterial species, were identified correctly by rpsA gene blast. Conclusions. Our study indicates that rpsA sequencing can be used effectively for mycobacteria species identification as a supplement to 16S rDNA sequence analysis.
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90
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Choi SG, Song WH, Kim DJ, Lee JS. Study of Nontuberculous Mycobacteria Isolated from the Theater Environment. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2015. [DOI: 10.15324/kjcls.2015.47.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Seung-Gu Choi
- Department of Biomedical Laboratory Science, Shin Han University, Uijeongbu 480-701, Korea
| | - Woon-Heung Song
- Department of Biomedical Laboratory Science, Shin Han University, Uijeongbu 480-701, Korea
| | - Dae-Jeung Kim
- Department of Laboratory Medicine, Bundang Jesaeng general hospital, Seongnam 463-774, Korea
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91
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Macovei L, McCafferty J, Chen T, Teles F, Hasturk H, Paster BJ, Campos-Neto A. The hidden 'mycobacteriome' of the human healthy oral cavity and upper respiratory tract. J Oral Microbiol 2015; 7:26094. [PMID: 25683180 PMCID: PMC4329316 DOI: 10.3402/jom.v7.26094] [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: 09/22/2014] [Accepted: 01/19/2015] [Indexed: 12/23/2022] Open
Abstract
The incidence of opportunistic non-tuberculous mycobacteria (NTM) infections has increased considerably in the past decades causing an array of infections, including respiratory and soft-tissue infections. NTM are ubiquitous and can be found in numerous environments, including households and water plants. However, NTM have not been reported to be associated with the healthy human oral microbiome. Since the oral cavity and upper respiratory track are the main ports of entry of microorganisms into the human body, elucidating NTM diversity and prevalence will assist in the assessment of the potential risks of infection elicited by these opportunistic pathogens. Here, we report the identification of a ‘non-tuberculous mycobacteriome’ in healthy individuals. We employed a modified DNA extraction procedure in conjunction with mycobacterial-specific primers to screen niches in the oral cavity (buccal mucosa and dental plaque) and upper respiratory tract (nostrils and oropharynx) of 10 healthy subjects. A total of 50 prevalent operational taxonomic units sequenced on MiSeq (Illumina) using 16S rRNA V3–V4 region were detected across all screened niches, showing the presence of diverse NTM communities. NTM DNA was detected in the nostrils of all 10 subjects, in buccal mucosa of 8 subjects, in the oropharynx of 7 subjects, and in the dental plaques of 5 subjects. Results from quantitative PCR showed each individual harbored 103–104 predicted NTM per each screened niche. The modification of standard DNA isolation methods to increase sensitivity toward mycobacterial species represents an important step to advance the knowledge of the oral as well as the overall human microbiome. These findings clearly reveal for the first time that healthy individuals harbor a ‘non-tuberculous mycobacteriome’ in their oral cavity and upper respiratory tract and may have important implications in our understanding of infections caused by NTM.
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Affiliation(s)
| | | | - Tsute Chen
- The Forsyth Institute, Cambridge, MA, USA
| | - Flavia Teles
- The Forsyth Institute, Cambridge, MA, USA.,Harvard School of Dental Medicine, Boston, MA, USA
| | | | - Bruce J Paster
- The Forsyth Institute, Cambridge, MA, USA.,Harvard School of Dental Medicine, Boston, MA, USA
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92
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Guo F, Wang ZP, Yu K, Zhang T. Detailed investigation of the microbial community in foaming activated sludge reveals novel foam formers. Sci Rep 2015; 5:7637. [PMID: 25560234 PMCID: PMC4284521 DOI: 10.1038/srep07637] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 12/01/2014] [Indexed: 02/01/2023] Open
Abstract
Foaming of activated sludge (AS) causes adverse impacts on wastewater treatment operation and hygiene. In this study, we investigated the microbial communities of foam, foaming AS and non-foaming AS in a sewage treatment plant via deep-sequencing of the taxonomic marker genes 16S rRNA and mycobacterial rpoB and a metagenomic approach. In addition to Actinobacteria, many genera (e.g., Clostridium XI, Arcobacter, Flavobacterium) were more abundant in the foam than in the AS. On the other hand, deep-sequencing of rpoB did not detect any obligate pathogenic mycobacteria in the foam. We found that unknown factors other than the abundance of Gordonia sp. could determine the foaming process, because abundance of the same species was stable before and after a foaming event over six months. More interestingly, although the dominant Gordonia foam former was the closest with G. amarae, it was identified as an undescribed Gordonia species by referring to the 16S rRNA gene, gyrB and, most convincingly, the reconstructed draft genome from metagenomic reads. Our results, based on metagenomics and deep sequencing, reveal that foams are derived from diverse taxa, which expands previous understanding and provides new insight into the underlying complications of the foaming phenomenon in AS.
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Affiliation(s)
- Feng Guo
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Zhi-Ping Wang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Ke Yu
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - T Zhang
- Environmental Biotechnology Laboratory, Department of Civil Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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93
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Empirical treatment of highly suspected nontuberculous mycobacteria infections following aesthetic procedures. Arch Plast Surg 2014; 41:759-67. [PMID: 25396192 PMCID: PMC4228222 DOI: 10.5999/aps.2014.41.6.759] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/10/2014] [Accepted: 07/17/2014] [Indexed: 11/13/2022] Open
Abstract
Background Infection caused by nontuberculous mycobacteria (NTM) has been increasing. Awareness of this infection is crucial yet problematic. Delayed management may lead to destructive results. We empirically treated a series of patients with clinical suspicion of NTM infection prior to the identification of the pathogen. Methods A total of 12 patients who developed surgical site infections between January 2011 and February 2014 were reviewed. Patients with a skin and subcutaneous infection resistant to standard management over two weeks, and previous history of aesthetic procedures within three months were regarded as highly suspected of having an NTM infection. A variety of diagnostic modalities were examined simultaneously, along with starting empirical treatment including a combination of clarithromycin and moxifloxacin, and surgical debridement. Results All wounds healed completely within 4 weeks. The mean follow-up duration was 7.2 months, and none of the patients developed relapse. Specific NTM pathogens were identified in six patients. Eight patients showed caseating granuloma implying an NTM infection. One patient showed an uncommon Stenotrophomonas infection, which was successfully treated. Three patients had no evidence of a pathogen despite repeated microbial tests. Complications such as scarring, pigmentation, and disfigurement were common in all the patients. Conclusions NTM should be considered in the differential diagnosis of an unusual skin and soft-tissue infection. We propose an empirical regimen of clarithromycin and moxifloxacin as an efficient treatment option for an NTM infection.
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94
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Sano Y, Matsuda K, Osaki K, Miyasho T, Tsuda T, Taniyama H. Systemic mycobacteriosis in an aborted thoroughbred fetus in Japan. J Vet Med Sci 2014; 76:1617-21. [PMID: 25649944 PMCID: PMC4300377 DOI: 10.1292/jvms.14-0276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A male Thoroughbred fetus was
aborted on day 251 of pregnancy. Gross and histological examinations detected systemic
granulomatous lesions in many superficial and visceral lymph nodes and organs including
the liver, tonsils, lungs, thymus, spleen, right thyroid gland and gastrointestinal tract,
and suppurative placentitis, pyogranulomatous amnionitis and intralesional acid-fast
bacilli were also detected. An examination of the DNA base sequence of the β subunit of
RNA polymerase demonstrated that Mycobacterium avium strain 104 had
infected several organs. To the best of our knowledge, this is the first report of equine
fetal mycobacterial infection in Japan.
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Affiliation(s)
- Yuto Sano
- Department of Veterinary Pathology, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido 069-8501, Japan
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95
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Zhao X, Wang Y, Pang Y. Antimicrobial susceptibility and molecular characterization of Mycobacterium intracellulare in China. INFECTION GENETICS AND EVOLUTION 2014; 27:332-8. [PMID: 25131955 DOI: 10.1016/j.meegid.2014.07.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/24/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
Mycobacterium avium complex (MAC) is the most common non-tuberculosis mycobacterial pathogen isolated from respiratory samples, mainly including two species, Mycobacterium avium (M. avium) and Mycobacterium intracellulare (M. intracellulare). Although these two species belong to the same group, M. avium and M. intracellulare reveal significantly differences in pathogenicity and biology. Nevertheless, little is known regarding the drug resistant details profile of M. avium or M. intracellulare instead of MAC. Here, we examined the antimicrobial susceptibility profiles of 52 clinical M. intracellulare isolates against fourteen antimicrobial agents, which are widely selected for the treatment of nontuberculous mycobacteria (NTM) infection. The drug susceptibility test revealed that clarithromycin (47/52, 90.4%), rifampicin (41/52, 78.8%) and capreomycin (40/52, 76.9%) revealed highly antimicrobial activities against M. intracellulare isolates in vitro. Furthermore, all clarithromycin resistant isolates harbored mutations in the 23S rRNA gene, and the percentage of amikacin resistant ones with mutation in the rrs gene is 62.5% (10/16). The Hunter-Gaston Discriminatory Index (HGDI) value for the 16-loci Variable Number of Tandem Repeat (VNTR) typing of M. intracellulare isolates was 0.994, and M. intracellulare resistance to moxifloxacin was significantly more commonly found in clustered strains than in nonclustered strains (χ(2)=5.551, P=0.040). In conclusion, our data demonstrated that clarithromycin and capreomycin revealed highly antimicrobial activities against M. intracellulare isolates, and clarithromycin and amikacin resistance could be detected more readily and rapidly using molecular scanning of corresponding drug target than conventional drug susceptibility testing. We also found that infection by clustered strains was significantly associated with resistance to moxifloxacin.
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Affiliation(s)
- Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Yufeng Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yu Pang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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96
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Aurin TH, Munshi SK, Kamal SMM, Rahman MM, Hossain MS, Marma T, Rahman F, Noor R. Molecular approaches for detection of the multi-drug resistant tuberculosis (MDR-TB) in Bangladesh. PLoS One 2014; 9:e99810. [PMID: 24932706 PMCID: PMC4059658 DOI: 10.1371/journal.pone.0099810] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/17/2014] [Indexed: 01/30/2023] Open
Abstract
The principal obstacles in the treatment of tuberculosis (TB) are delayed and inaccurate diagnosis which often leads to the onset of the drug resistant TB cases. To avail the appropriate treatment of the patients and to hinder the transmission of drug-resistant TB, accurate and rapid detection of resistant isolates is critical. Present study was designed to demonstrate the efficacy of molecular techniques inclusive of line probe assay (LPA) and GeneXpert MTB/RIF methods for the detection of multi-drug resistant (MDR) TB. Sputum samples from 300 different categories of treated and new TB cases were tested for the detection of possible mutation in the resistance specific genes (rpoB, inhA and katG) through Genotype MTBDRplus assay or LPA and GeneXpert MTB/RIF tests. Culture based conventional drug susceptibility test (DST) was also carried out to measure the efficacy of the molecular methods employed. Among 300 samples, 191 (63.7%) and 193 (64.3%) cases were found to be resistant against rifampicin in LPA and GeneXpert methods, respectively; while 189 (63%) cases of rifampicin resistance were detected by conventional DST methods. On the other hand, 196 (65.3%) and 191 (63.7%) isolates showed isoniazid resistance as detected by LPA and conventional drug susceptibility test (DST), respectively. Among the drug resistant isolates (collectively 198 in LPA and 193 in conventional DST), 189 (95.6%) and 187 (96.9%) were considered to be MDR as examined by LPA and conventional DST, respectively. Category-II and -IV patients encountered higher frequency of drug resistance compared to those from category-I and new cases. Considering the higher sensitivity, specificity and accuracy along with the required time to results significantly shorter, our study supports the adoption of LPA and GeneXpert assay as efficient tools in detecting drug resistant TB in Bangladesh.
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Affiliation(s)
- Tafsina Haque Aurin
- Department of Microbiology, Stamford University Bangladesh, Dhaka, Bangladesh
| | | | - S. M. Mostofa Kamal
- National Tuberculosis Reference Laboratory (NTRL), NIDCH, Mohakhali, Dhaka, Bangladesh
| | | | - Md. Shamim Hossain
- National Tuberculosis Reference Laboratory (NTRL), NIDCH, Mohakhali, Dhaka, Bangladesh
| | - Thaythayhla Marma
- National Tuberculosis Reference Laboratory (NTRL), NIDCH, Mohakhali, Dhaka, Bangladesh
| | - Farjana Rahman
- Department of Microbiology, Stamford University Bangladesh, Dhaka, Bangladesh
| | - Rashed Noor
- Department of Microbiology, Stamford University Bangladesh, Dhaka, Bangladesh
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97
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Tseng SP, Teng SH, Lee PS, Wang CF, Yu JS, Lu PL. Rapid identification of M. abscessus and M. massiliense by MALDI-TOF mass spectrometry with a comparison to sequencing methods and antimicrobial susceptibility patterns. Future Microbiol 2014; 8:1381-9. [PMID: 24199798 DOI: 10.2217/fmb.13.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Development of the matrix-assisted laser desorption ionization-TOF (MALDI-TOF) mass spectrometry method to rapidly identify Mycobacteria abscessus and Mycobacteria massiliense from M. abscessus complex in clinical microbiology laboratories. MATERIALS & METHODS Of 128 M. abscessus complex clinical isolates, sequence analysis identified 64 as M. massiliense and 64 as M. abscessus. MALDI-TOF mass spectrometry with clustering analysis created a model to differentiate these two species. Multilocus sequence typing was used to confirm our model. RESULTS Using a model containing five signals, 100% species recognition was achieved for 50 strains of each species. The sequence type (ST) cluster of M. abscessus was distinct from the cluster of M. massiliense. ST1 was prevalent (59%) among M. abscessus isolates, and ST117 was common (41%) among M. massiliense isolates. CONCLUSION Molecular methods are more costly and time-consuming and may not be available in the clinical microbial laboratory. Subsequently, MALDI-TOF analysis could be a rapid identification method in the future.
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Affiliation(s)
- Sung-Pin Tseng
- Department of Medical Laboratory Science & Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
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99
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Tran AC, Halse TA, Escuyer VE, Musser KA. Detection of Mycobacterium avium complex DNA directly in clinical respiratory specimens: opportunities for improved turn-around time and cost savings. Diagn Microbiol Infect Dis 2014; 79:43-8. [DOI: 10.1016/j.diagmicrobio.2014.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 01/15/2023]
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Chisti MJ, Graham SM, Duke T, Ahmed T, Ashraf H, Faruque ASG, La Vincente S, Banu S, Raqib R, Salam MA. A prospective study of the prevalence of tuberculosis and bacteraemia in Bangladeshi children with severe malnutrition and pneumonia including an evaluation of Xpert MTB/RIF assay. PLoS One 2014; 9:e93776. [PMID: 24695758 PMCID: PMC3973596 DOI: 10.1371/journal.pone.0093776] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 03/10/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Severe malnutrition is a risk factor for pneumonia due to a wide range of pathogens but aetiological data are limited and the role of Mycobacterium tuberculosis is uncertain. METHODS We prospectively investigated severely malnourished young children (<5 years) with radiological pneumonia admitted over a 15-month period. Investigations included blood culture, sputa for microscopy and mycobacterial culture. Xpert MTB/RIF assay was introduced during the study. Study children were followed for 12 weeks following their discharge from the hospital. RESULTS 405 eligible children were enrolled, with a median age of 10 months. Bacterial pathogens were isolated from blood culture in 18 (4.4%) children, of which 72% were Gram negatives. Tuberculosis was confirmed microbiologically in 7% (27/396) of children that provided sputum - 10 by culture, 21 by Xpert MTB/RIF assay, and 4 by both tests. The diagnostic yield from induced sputum was 6% compared to 3.5% from gastric aspirate. Sixty (16%) additional children had tuberculosis diagnosed clinically that was not microbiologically confirmed. Most confirmed tuberculosis cases did not have a positive contact history or positive tuberculin test. The sensitivity and specificity of Xpert MTB/RIF assay compared to culture was 67% (95% CI: 24-94) and 92% (95% CI: 87-95) respectively. Overall case-fatality rate was 17% and half of the deaths occurred in home following discharge from the hospital. CONCLUSION AND SIGNIFICANCE TB was common in severely malnourished Bangladeshi children with pneumonia. X-pert MTB/RIF assay provided higher case detection rate compared to sputum microscopy and culture. The high mortality among the study children underscores the need for further research aimed at improved case detection and management for better outcomes.
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Affiliation(s)
- Mohammod Jobayer Chisti
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
- Centre for International Child Health, The University of Melbourne Department of Paediatrics and Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Stephen M. Graham
- Centre for International Child Health, The University of Melbourne Department of Paediatrics and Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, Australia
- International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Trevor Duke
- Centre for International Child Health, The University of Melbourne Department of Paediatrics and Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Hasan Ashraf
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | - Sophie La Vincente
- Centre for International Child Health, The University of Melbourne Department of Paediatrics and Murdoch Childrens Research Institute, Royal Children’s Hospital, Melbourne, Australia
| | - Sayera Banu
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Rubhana Raqib
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mohammed Abdus Salam
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
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