451
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Rapid molecular detection of inducible macrolide resistance in Mycobacterium chelonae and M. abscessus strains: a replacement for 14-day susceptibility testing? J Clin Microbiol 2014; 52:1705-7. [PMID: 24554745 DOI: 10.1128/jcm.03464-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The erm(41) gene causes inducible macrolide resistance in Mycobacterium abscessus but not Mycobacterium chelonae. erm(41) sequencing of 285 M. abscessus and 45 M. chelonae isolates was compared to 14-day susceptibility; agreement percentages were 98.9% and 100%, respectively. Extended incubation may not be necessary for M. chelonae, and the erm(41) genotype is a useful adjunct for M. abscessus.
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452
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van der Werf MJ, Ködmön C, Katalinić-Janković V, Kummik T, Soini H, Richter E, Papaventsis D, Tortoli E, Perrin M, van Soolingen D, Zolnir-Dovč M, Ostergaard Thomsen V. Inventory study of non-tuberculous mycobacteria in the European Union. BMC Infect Dis 2014; 14:62. [PMID: 24502462 PMCID: PMC3922012 DOI: 10.1186/1471-2334-14-62] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/22/2013] [Indexed: 11/16/2022] Open
Abstract
Background Since non-tuberculous mycobacteria (NTM) disease is not notifiable in most European Union (EU) and European Economic Area (EEA) countries, the epidemiological situation of the >150 NTM species is largely unknown. We aimed to collect data on the frequency of NTM detection and NTM species types in EU/EEA countries. Methods Officially nominated national tuberculosis reference laboratories of all EU/EEA countries were asked to provide information on: laboratory routines for detection and identification of NTM, including drug sensitivity testing (DST) methods; data on the number and type of NTM species identified; coverage and completeness of the provided data on NTM; type and number of human specimens tested for NTM; and number of specimens tested for Mycobacterium tuberculosis complex and NTM. This information was summarized and the main results are described. Results In total, 99 different NTM species were identified with M. avium, M. gordonae, M. xenopi , M. intracellulare, and M. fortuitum identified most frequently. Seven percent of the NTM species could not be identified. NTM was cultured from between 0.4-2.0% of the specimens (data from four countries). The laboratories use culturing methods optimised for M. tuberculosis complex. Identification is mainly carried out by a commercial line probe assay supplemented with sequencing. Most laboratories carried out DST for rapid growers and only at the explicit clinical request for slow growers. Conclusion It is likely that the prevalence of NTM is underestimated because diagnostic procedures are not optimized specifically for NTM and isolates may not be referred to the national reference laboratory for identification. Due to the diagnostic challenges and the need to establish the clinical relevance of NTM, we recommend that countries should concentrate detection and identification in only few laboratories.
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453
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Sharma P, Gupta SK, Rolain JM. Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution. Expert Rev Anti Infect Ther 2014; 12:343-55. [PMID: 24502835 DOI: 10.1586/14787210.2014.887441] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cystic fibrosis (CF) airways harbor a wide variety of new and/or emerging multidrug resistant bacteria which impose a heavy burden on patients. These bacteria live in close proximity with one another, which increases the frequency of lateral gene transfer. The exchange and movement of mobile genetic elements and genomic islands facilitate the spread of genes between genetically diverse bacteria, which seem to be advantageous to the bacterium as it allows adaptation to the new niches of the CF lungs. Niche adaptation is one of the major evolutionary forces shaping bacterial genome composition and in CF the chronic strains adapt and become less virulent. The purpose of this review is to shed light on CF bacterial genome alterations. Next-generation sequencing technology is an exciting tool that may help us to decipher the genome architecture and the evolution of bacteria colonizing CF lungs.
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Affiliation(s)
- Poonam Sharma
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergents, CNRS-IRD, UMR 7278, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, 27 Bd Jean-Moulin, Marseille Cedex 05 13385, France
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454
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Jeong BH, Kim SY, Jeon K, Huh HJ, Ki CS, Lee NY, Shin SJ, Koh WJ. The First Korean Case of Nontuberculous Mycobacterial Lung Disease Caused by Mycobacterium abscessus Subspecies bolletii in a Patient with Bronchiectasis. Tuberc Respir Dis (Seoul) 2014; 76:30-3. [PMID: 24523815 PMCID: PMC3919962 DOI: 10.4046/trd.2014.76.1.30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/04/2013] [Accepted: 09/16/2013] [Indexed: 11/24/2022] Open
Abstract
We report the first Korean case of lung diseases caused by Mycobacterium abscessus subsp. bolletii in a previously healthy male, except for a previous history of pulmonary tuberculosis and bronchiectasis. All serial isolates are identified as M. abscessus subsp. bolletii by multi-locus sequence analysis based on the hsp65, rpoB, and 16S rRNA fragments. At the genetic level, the isolate has the erm(41) gene with a T28 sequevar, associated with clarithromycin resistance, and no rrl mutation. The isolate is resistant to clarithromycin. Although the symptoms and radiographic findings have improved after combination of antibiotics, the follow-up sputum cultures are persistently positive.
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Affiliation(s)
- Byeong-Ho Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyeongman Jeon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Jae Shin
- Department of Microbiology, Yonsei University College of Medicine, Seoul, Korea
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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455
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Harris SR, Okoro CK. Whole-Genome Sequencing for Rapid and Accurate Identification of Bacterial Transmission Pathways. J Microbiol Methods 2014. [DOI: 10.1016/bs.mim.2014.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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456
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457
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Cody AJ, Bennett JS, Maiden MC. Multi-Locus Sequence Typing and the Gene-by-Gene Approach to Bacterial Classification and Analysis of Population Variation. J Microbiol Methods 2014. [DOI: 10.1016/bs.mim.2014.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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458
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Macheras E, Konjek J, Roux AL, Thiberge JM, Bastian S, Leão SC, Palaci M, Sivadon-Tardy V, Gutierrez C, Richter E, Rüsch-Gerdes S, Pfyffer GE, Bodmer T, Jarlier V, Cambau E, Brisse S, Caro V, Rastogi N, Gaillard JL, Heym B. Multilocus sequence typing scheme for the Mycobacterium abscessus complex. Res Microbiol 2013; 165:82-90. [PMID: 24384536 DOI: 10.1016/j.resmic.2013.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/19/2013] [Indexed: 11/29/2022]
Abstract
We developed a multilocus sequence typing (MLST) scheme for Mycobacterium abscessus sensu lato, based on the partial sequencing of seven housekeeping genes: argH, cya, glpK, gnd, murC, pta and purH. This scheme was used to characterize a collection of 227 isolates recovered between 1994 and 2010 in France, Germany, Switzerland and Brazil. We identified 100 different sequence types (STs), which were distributed into three groups on the tree obtained by concatenating the sequences of the seven housekeeping gene fragments (3576bp): the M. abscessus sensu stricto group (44 STs), the "M. massiliense" group (31 STs) and the "M. bolletii" group (25 STs). SplitTree analysis showed a degree of intergroup lateral transfers. There was also evidence of lateral transfer events involving rpoB. The most prevalent STs in our collection were ST1 (CC5; 20 isolates) and ST23 (CC3; 31 isolates). Both STs were found in Europe and Brazil, and the latter was implicated in a large post-surgical procedure outbreak in Brazil. Respiratory isolates from patients with cystic fibrosis belonged to a large variety of STs; however, ST2 was predominant in this group of patients. Our MLST scheme, publicly available at www.pasteur.fr/mlst, offers investigators a valuable typing tool for M. abscessus sensu lato in future epidemiological studies throughout the world.
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Affiliation(s)
- Edouard Macheras
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Julie Konjek
- EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Anne-Laure Roux
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Laboratoire de Microbiologie, Hôpital Raymond Poincaré, AP-HP, Garches, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Jean-Michel Thiberge
- Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Sylvaine Bastian
- Centre national de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 47-83 Boulevard de l'Hôpital, 75013 Paris, France; APHP, Groupe Hospitalier Pitié-Salpêtrière, Laboratoire de Bactériologie - Hygiène, 47-83 Boulevard de l'Hôpital, 75013 Paris, France.
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Botucatu, 862, Vila Clementino, São Paulo SP CEP 04023-062, Brazil.
| | - Moises Palaci
- Nucleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari, 514, Goiabeiras Vitória - ES, CEP 29075-910, Brazil.
| | - Valérie Sivadon-Tardy
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France.
| | - Cristina Gutierrez
- Caribbean Public Health Agency (CARPHA), 16-18 Jamaica Boulevard, Federation Park, Port of Spain, Trinidad and Tobago.
| | - Elvira Richter
- National Reference Center for Mycobacteria, Forschungszentrum Borstel, Parkalle 18, 23845 Borstel, Germany.
| | - Sabine Rüsch-Gerdes
- National Reference Center for Mycobacteria, Forschungszentrum Borstel, Parkalle 18, 23845 Borstel, Germany.
| | - Gaby E Pfyffer
- Institut für Medizinische Mikrobiologie, Zentrum für LaborMedizin, Luzerner Kantonsspital, Spitalstrasse, 6004 Luzern, Switzerland.
| | - Thomas Bodmer
- Institut für Infektionskrankheiten, Universität Bern, Hochschulstrasse 4, 3010 Bern, Switzerland.
| | - Vincent Jarlier
- Centre national de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 47-83 Boulevard de l'Hôpital, 75013 Paris, France; APHP, Groupe Hospitalier Pitié-Salpêtrière, Laboratoire de Bactériologie - Hygiène, 47-83 Boulevard de l'Hôpital, 75013 Paris, France.
| | - Emmanuelle Cambau
- APHP, Groupe hospitalier Lariboisière-Fernand Widal, Laboratoire de Microbiologie, 2 rue Ambroise Paré, 75010 Paris, France.
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Nalin Rastogi
- Institut Pasteur, Laboratoire de Recherche et de Référence sur la Tuberculose et les Mycobactéries, BP 484 Morne Jolivière, Les Abymes 97183 Cedex, Guadeloupe, France.
| | - Jean-Louis Gaillard
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Laboratoire de Microbiologie, Hôpital Raymond Poincaré, AP-HP, Garches, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Beate Heym
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
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459
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Draft Genome Sequence of Mycobacterium abscessus subsp.
bolletii
INCQS 00594. GENOME ANNOUNCEMENTS 2013; 1:1/6/e00896-13. [PMID: 24201191 PMCID: PMC3820772 DOI: 10.1128/genomea.00896-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An epidemic of surgical-site infections by a single strain of Mycobacterium abscessus subsp. bolletii affected >1,700 patients in Brazil from 2004 to 2008. The genome of the epidemic prototype strain M. abscessus subsp. bolletii INCQS 00594, deposited in the collection of the National Institute for Health Quality Control (INCQS), was sequenced.
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460
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Kim BJ, Kim BR, Lee SY, Kook YH, Kim BJ. Rough colony morphology of Mycobacterium massiliense Type II genotype is due to the deletion of glycopeptidolipid locus within its genome. BMC Genomics 2013; 14:890. [PMID: 24341808 PMCID: PMC3878547 DOI: 10.1186/1471-2164-14-890] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/10/2013] [Indexed: 01/15/2023] Open
Abstract
Background Recently, we introduced the complete genome sequence of Mycobacterium massiliense clinical isolates, Asan 50594 belonging to Type II genotype with rough colony morphology. Here, to address the issue of whether the rough colony morphotype of M. massiliense Type II genotype is genetically determined or not, we compared polymorphisms of the glycopeptidolipid (GPL) gene locus between M. massiliense Type II Asan 50594 and other rapidly growing mycobacteria (RGM) strains via analysis of genome databases. Results We found deletions of 10 genes (24.8 kb), in the GPL biosynthesis related gene cluster of Asan 50594 genome, but no deletions in those of other smooth RGMs. To check the presence of deletions of GPL biosynthesis related genes in Mycobacterium abscessus − complex strains, PCRs targeting 12 different GPL genes (10 genes deleted in Asan 50594 genome as well as 2 conserved genes) were applied into 76 clinical strains of the M. abscessus complex strains [54 strains (Type I: 33, and Type II: 21) of M. massiliense and 22 strains (rough morphoype: 11 and smooth morphotype: 11) of M. abscessus]. No strains of the Type II genotype produced PCR amplicons in a total of 10 deleted GPL genes, suggesting loss of GPL biosynthesis genes in the genome of M. massiliense type II genotype strains. Conclusions Our data suggested that the rough colony morphotype of the M. massiliense Type II genotype may be acquired via deletion events at the GPL gene locus for evolutionary adaptation between the host and pathogen.
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Affiliation(s)
| | | | | | | | - Bum-Joon Kim
- Department of Microbiology and Immunology, Biomedical Sciences, Liver Research Institute, Cancer Research Institute and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul 110-799, Republic of Korea.
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461
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Tan JL, Khang TF, Ngeow YF, Choo SW. A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus. BMC Genomics 2013; 14:879. [PMID: 24330254 PMCID: PMC3878664 DOI: 10.1186/1471-2164-14-879] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/10/2013] [Indexed: 11/22/2022] Open
Abstract
Background Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12 M. abscessus strains and used phylogenomic analysis to perform subspecies classification. Results A data mining approach was used to rank and select informative genes based on the relative entropy metric for the construction of a phylogenetic tree. The resulting tree topology was similar to that generated using the concatenation of five classical housekeeping genes: rpoB, hsp65, secA, recA and sodA. Additional support for the reliability of the subspecies classification came from the analysis of erm41 and ITS gene sequences, single nucleotide polymorphisms (SNPs)-based classification and strain clustering demonstrated by a variable number tandem repeat (VNTR) assay and a multilocus sequence analysis (MLSA). We subsequently found that the concatenation of a minimal set of three median-ranked genes: DNA polymerase III subunit alpha (polC), 4-hydroxy-2-ketovalerate aldolase (Hoa) and cell division protein FtsZ (ftsZ), is sufficient to recover the same tree topology. PCR assays designed specifically for these genes showed that all three genes could be amplified in the reference strain of M. abscessus ATCC 19977T. Conclusion This study provides proof of concept that whole-genome sequence-based data mining approach can provide confirmatory evidence of the phylogenetic informativeness of existing markers, as well as lead to the discovery of a more economical and informative set of markers that produces similar subspecies classification in M. abscessus. The systematic procedure used in this study to choose the informative minimal set of gene markers can potentially be applied to species or subspecies classification of other bacteria.
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Affiliation(s)
| | - Tsung Fei Khang
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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462
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Cho YJ, Yi H, Chun J, Cho SN, Daley CL, Koh WJ, Jae Shin S. The genome sequence of 'Mycobacterium massiliense' strain CIP 108297 suggests the independent taxonomic status of the Mycobacterium abscessus complex at the subspecies level. PLoS One 2013; 8:e81560. [PMID: 24312320 PMCID: PMC3842311 DOI: 10.1371/journal.pone.0081560] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
Members of the Mycobacterium abscessus complex are rapidly growing mycobacteria that are emerging as human pathogens. The M. abscessus complex was previously composed of three species, namely M. abscessus sensu stricto, 'M. massiliense', and 'M. bolletii'. In 2011, 'M. massiliense' and 'M. bolletii' were united and reclassified as a single subspecies within M. abscessus: M. abscessus subsp. bolletii. However, the placement of 'M. massiliense' within the boundary of M. abscessus subsp. bolletii remains highly controversial with regard to clinical aspects. In this study, we revisited the taxonomic status of members of the M. abscessus complex based on comparative analysis of the whole-genome sequences of 53 strains. The genome sequence of the previous type strain of 'Mycobacterium massiliense' (CIP 108297) was determined using next-generation sequencing. The genome tree based on average nucleotide identity (ANI) values supported the differentiation of 'M. bolletii' and 'M. massiliense' at the subspecies level. The genome tree also clearly illustrated that 'M. bolletii' and 'M. massiliense' form a distinct phylogenetic clade within the radiation of the M. abscessus complex. The genomic distances observed in this study suggest that the current M. abscessus subsp. bolletii taxon should be divided into two subspecies, M. abscessus subsp. massiliense subsp. nov. and M. abscessus subsp. bolletii, to correspondingly accommodate the previously known 'M. massiliense' and 'M. bolletii' strains.
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Affiliation(s)
- Yong-Joon Cho
- Chunlab, Inc., Seoul National University, Seoul, Korea
| | - Hana Yi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Korea
- Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Jongsik Chun
- Chunlab, Inc., Seoul National University, Seoul, Korea
| | - Sang-Nae Cho
- Department of Microbiology and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Korea
| | - Charles L. Daley
- Division of Mycobacterial and Respiratory Infections, Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, Korea
- * E-mail: (WJK); (SJS)
| | - Sung Jae Shin
- Department of Microbiology and Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul, Korea
- * E-mail: (WJK); (SJS)
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463
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Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA. Nat Protoc 2013; 8:2404-12. [PMID: 24202554 DOI: 10.1038/nprot.2013.147] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The study of bacterial populations using whole-genome sequencing is of considerable scientific and clinical interest. However, obtaining bacterial genomic information is not always trivial: the target bacteria may be difficult to culture or uncultured, and they may be found within samples containing complex mixtures of other contaminating microbes and/or host cells, from which it is very difficult to derive robust sequencing data. Here we describe our procedure to generate sufficient DNA for whole-genome sequencing from clinical samples and without the need for culture, as successfully used on the difficult-to-culture, obligate intracellular pathogen Chlamydia trachomatis. Our protocol combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification (WGA), which is followed by high-throughput sequencing. Compared with other techniques that might be used to generate such data, IMS-MDA is an inexpensive, low-technology and highly transferable process that provides amplified genomic DNA for sequencing from target bacteria in under 5 h, with little hands-on time.
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464
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Discrimination of Mycobacterium abscessus subsp. massiliense from Mycobacterium abscessus subsp. abscessus in clinical isolates by multiplex PCR. J Clin Microbiol 2013; 52:251-9. [PMID: 24197885 DOI: 10.1128/jcm.01327-13] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapidly growing mycobacterium M. abscessus sensu lato is the causative agent of emerging pulmonary and skin diseases and of infections following cosmetic surgery and postsurgical procedures. M. abscessus sensu lato can be divided into at least three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. Clinical isolates of rapidly growing mycobacteria were previously identified as M. abscessus by DNA-DNA hybridization. More than 30% of these 117 clinical isolates were differentiated as M. abscessus subsp. massiliense using combinations of multilocus genotyping analyses. A much more cost-effective technique to distinguish M. abscessus subsp. massiliense from M. abscessus subsp. abscessus, a multiplex PCR assay, was developed using the whole-genome sequence of M. abscessus subsp. massiliense JCM15300 as a reference. Several primer sets were designed for single PCR to discriminate between the strains based on amplicons of different sizes. Two of these single-PCR target sites were chosen for development of the multiplex PCR assay. Multiplex PCR was successful in distinguishing clinical isolates of M. abscessus subsp. massiliense from samples previously identified as M. abscessus. This approach, which spans whole-genome sequencing and clinical diagnosis, will facilitate the acquisition of more-precise information about bacterial genomes, aid in the choice of more relevant therapies, and promote the advancement of novel discrimination and differential diagnostic assays.
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465
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Maiden MCJ, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 2013; 11:728-36. [PMID: 23979428 PMCID: PMC3980634 DOI: 10.1038/nrmicro3093] [Citation(s) in RCA: 462] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.
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Affiliation(s)
- Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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466
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Davidson RM, Hasan NA, de Moura VCN, Duarte RS, Jackson M, Strong M. Phylogenomics of Brazilian epidemic isolates of Mycobacterium abscessus subsp. bolletii reveals relationships of global outbreak strains. INFECTION GENETICS AND EVOLUTION 2013; 20:292-7. [PMID: 24055961 DOI: 10.1016/j.meegid.2013.09.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
Abstract
Rapidly growing, non-tuberculous mycobacteria (NTM) in the Mycobacterium abscessus (MAB) species are emerging pathogens that cause various diseases including skin and respiratory infections. The species has undergone recent taxonomic nomenclature refinement, and is currently recognized as two subspecies, M. abscessus subsp. abscessus (MAB-A) and M. abscessus subsp. bolletii (MAB-B). The recently reported outbreaks of MAB-B in surgical patients in Brazil from 2004 to 2009 and in cystic fibrosis patients in the United Kingdom (UK) in 2006 to 2012 underscore the need to investigate the genetic diversity of clinical MAB strains. To this end, we sequenced the genomes of two Brazilian MAB-B epidemic isolates (CRM-0019 and CRM-0020) derived from an outbreak of skin infections in Rio de Janeiro, two unrelated MAB strains from patients with pulmonary infections in the United States (US) (NJH8 and NJH11) and one type MAB-B strain (CCUG 48898) and compared them to 25 publically available genomes of globally diverse MAB strains. Genome-wide analyses of 27,598 core genome single nucleotide polymorphisms (SNPs) revealed that the two Brazilian derived CRM strains are nearly indistinguishable from one another and are more closely related to UK outbreak isolates infecting CF patients than to strains from the US, Malaysia or France. Comparative genomic analyses of six closely related outbreak strains revealed geographic-specific large-scale insertion/deletion variation that corresponds to bacteriophage insertions and recombination hotspots. Our study integrates new genome sequence data with existing genomic information to explore the global diversity of infectious M. abscessus isolates and to compare clinically relevant outbreak strains from different continents.
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Affiliation(s)
- Rebecca M Davidson
- Integrated Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
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467
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Pawlik A, Garnier G, Orgeur M, Tong P, Lohan A, Le Chevalier F, Sapriel G, Roux AL, Conlon K, Honoré N, Dillies MA, Ma L, Bouchier C, Coppée JY, Gaillard JL, Gordon SV, Loftus B, Brosch R, Herrmann JL. Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus. Mol Microbiol 2013; 90:612-29. [PMID: 23998761 DOI: 10.1111/mmi.12387] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2013] [Indexed: 12/13/2022]
Abstract
Mycobacterium abscessus is an emerging pathogen that is increasingly recognized as a relevant cause of human lung infection in cystic fibrosis patients. This highly antibiotic-resistant mycobacterium is an exception within the rapidly growing mycobacteria, which are mainly saprophytic and non-pathogenic organisms. M. abscessus manifests as either a smooth (S) or a rough (R) colony morphotype, which is of clinical importance as R morphotypes are associated with more severe and persistent infections. To better understand the molecular mechanisms behind the S/R alterations, we analysed S and R variants of three isogenic M. abscessus S/R pairs using an unbiased approach involving genome and transcriptome analyses, transcriptional fusions and integrating constructs. This revealed different small insertions, deletions (indels) or single nucleotide polymorphisms within the non-ribosomal peptide synthase gene cluster mps1-mps2-gap or mmpl4b in the three R variants, consistent with the transcriptional differences identified within this genomic locus that is implicated in the synthesis and transport of Glyco-Peptido-Lipids (GPL). In contrast to previous reports, the identification of clearly defined genetic lesions responsible for the loss of GPL-production or transport makes a frequent switching back-and-forth between smooth and rough morphologies in M. abscessus highly unlikely, which is important for our understanding of persistent M. abscessus infections.
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Affiliation(s)
- Alexandre Pawlik
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France; EA 3647, University Versailles St Quentin in Yvelines, Garches, France; Microbiology Laboratory, Assistance Publique - Hôpitaux de Paris, Raymond Poincaré Hospital, Garches, France
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468
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Lobo LJ, Noone PG. Respiratory infections in patients with cystic fibrosis undergoing lung transplantation. THE LANCET RESPIRATORY MEDICINE 2013; 2:73-82. [PMID: 24461904 DOI: 10.1016/s2213-2600(13)70162-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cystic fibrosis is an inherited disease characterised by chronic respiratory infections associated with bronchiectasis. Lung transplantation has helped to extend the lives of patients with cystic fibrosis who have advanced lung disease. However, persistent, recurrent, and newly acquired infections can be problematic. Classic cystic fibrosis-associated organisms, such as Staphylococcus aureus and Pseudomonas aeruginosa, are generally manageable post-transplantation, and are associated with favourable outcomes. Burkholderia cenocepacia poses particular challenges, although other Burkholderia species are less problematic. Despite concerns about non-tuberculous mycobacteria, especially Mycobacterium abscessus, post-transplantation survival has not been definitively shown to be less than average in patients with these infections. Fungal species can be prevalent before and after transplantation and are associated with high morbidity, so should be treated aggressively. Appropriate viral screening and antiviral prophylaxis are necessary to prevent infection with and reactivation of Epstein-Barr virus and cytomegalovirus and their associated complications. Awareness of drug pharmacokinetics and interactions in cystic fibrosis is crucial to prevent toxic effects and subtherapeutic or supratherapeutic drug dosing. With the large range of potential infectious organisms in patients with cystic fibrosis, infection control in hospital and outpatient settings is important. Despite its complexity, lung transplantation in the cystic fibrosis population is safe, with good outcomes if the clinician is aware of all the potential pathogens and remains vigilant by means of surveillance and proactive treatment.
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Affiliation(s)
- Leonard J Lobo
- Division of Pulmonary and Critical Care Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Peadar G Noone
- Pulmonary Division, Department of Medicine, University of North Carolina, Chapel Hill, NC, USA.
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470
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Bryant JM, Grogono DM, Parkhill J, Floto RA. Transmission of M abscessus in patients with cystic fibrosis - Authors' reply. Lancet 2013; 382:504. [PMID: 23931921 DOI: 10.1016/s0140-6736(13)61709-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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471
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New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance. J Clin Microbiol 2013; 51:2943-9. [PMID: 23804391 DOI: 10.1128/jcm.01132-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus (M. abscessus sensu lato, or the M. abscessus group) comprises three closely related taxa whose taxonomic statuses are under revision, i.e., M. abscessus sensu stricto, Mycobacterium bolletii, and Mycobacterium massiliense. We describe here a simple, robust, and cost-effective PCR-based method for distinguishing among M. abscessus, M. massiliense, and M. bolletii. Based on the M. abscessus ATCC 19977(T) genome, regions that discriminated between M. abscessus and M. massiliense were identified through array-based comparative genomic hybridization. A typing scheme using PCR primers designed for four of these locations was applied to 46 well-characterized clinical isolates comprising 29 M. abscessus, 15 M. massiliense, and 2 M. bolletii isolates previously identified by multitarget sequencing. Interestingly, 2 isolates unequivocally identified as M. massiliense were shown to have a full-length erm(41) gene instead of the expected gene deletion and showed inducible clarithromycin resistance after 14 days. We propose using this PCR-based typing scheme combined with erm(41) PCR for straightforward identification of M. abscessus, M. massiliense, and M. bolletii and the assessment of inducible clarithromycin resistance. This method can be easily integrated into a routine workflow to provide subspecies-level identification within 24 h after isolation of the M. abscessus group.
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472
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Current Approaches to the Management of Infection in Cystic Fibrosis. CURRENT PEDIATRICS REPORTS 2013. [DOI: 10.1007/s40124-013-0024-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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473
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Affiliation(s)
- Brian P O'Sullivan
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA.
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