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Takei S, Teramoto K, Sekiguchi Y, Ihara H, Tohya M, Iwamoto S, Tanaka K, Khasawneh A, Horiuchi Y, Misawa S, Naito T, Kirikae T, Tada T, Tabe Y. Identification of Mycobacterium abscessus using the peaks of ribosomal protein L29, L30 and hemophore-related protein by MALDI-MS proteotyping. Sci Rep 2024; 14:11187. [PMID: 38755267 PMCID: PMC11099050 DOI: 10.1038/s41598-024-61549-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Mycobacteroides (Mycobacterium) abscessus, which causes a variety of infectious diseases in humans, is becoming detected more frequently in clinical specimens as cases are spreading worldwide. Taxonomically, M. abscessus is composed of three subspecies of M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense, with different susceptibilities to macrolides. In order to identify rapidly these three subspecies, we determined useful biomarker proteins, including ribosomal protein L29, L30, and hemophore-related protein, for distinguishing the subspecies of M. abscessus using the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) profiles. Thirty-three clinical strains of M. abscessus were correctly identified at the subspecies-level by the three biomarker protein peaks. This study ultimately demonstrates the potential of routine MALDI-MS-based laboratory methods for early identification and treatment for M. abscessus infections.
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Affiliation(s)
- Satomi Takei
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kanae Teramoto
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Analytical and Measurement Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Hiroaki Ihara
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mari Tohya
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Abdullah Khasawneh
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuki Horiuchi
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigeki Misawa
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Clinical Laboratory Technology, Faculty of Medical Science, Juntendo University, Tokyo, Japan
| | - Toshio Naito
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Teruo Kirikae
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiome Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Yoko Tabe
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Matsumoto M, Chien TBC, Machida Y, Matoyama H, Kishihara T, Sato S, Kawato S, Hirono I, Sano M, Kato G. Mycolicibacterium cyprinidarum sp. nov., a rapidly growing species isolated from diseased koi carp, Cyprinus carpio. Int J Syst Evol Microbiol 2024; 74. [PMID: 38809248 DOI: 10.1099/ijsem.0.006404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024] Open
Abstract
A rapidly growing nontuberculous mycobacterium was isolated from diseased koi carp in Niigata, Japan, which was identified as representing a novel Mycolicibacterium species through whole genome sequence analysis. The bacterial isolates (NGTWS0302, NGTWS1803T and NGTWSNA01) were found to belong to the genus Mycolicibacterium through phylogenetic analysis using whole genome sequences of mycobacteria species. The bacterial colony was smooth, moist and non-chromogenic on 1% Ogawa medium at 30 °C. In biochemical characteristic tests, the bacterial isolates showed positive reactions for catalase activity, Tween 80 hydrolysis and tellurite reduction. The isolates were sensitive to 2-4 µg ml-1 ampicillin, kanamycin and rifampicin. Based on these results, we propose a novel Mycolicibacterium species, Mycolicibacterium cyprinidarum sp. nov. The type strain is NGTWS1803T (=JCM 35117T=ATCC TSD-289T).
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Affiliation(s)
- Megumi Matsumoto
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Tang Belinda Chien Chien
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Yuichiro Machida
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Hisato Matoyama
- Niigata Prefectural Inland Water Fisheries Experiment Station, 2650 Okawahara, Nagaoka, Niigata, 940-1137, Japan
| | - Tatsuya Kishihara
- Niigata Prefectural Inland Water Fisheries Experiment Station, 2650 Okawahara, Nagaoka, Niigata, 940-1137, Japan
| | - Shoh Sato
- Niigata Prefectural Inland Water Fisheries Experiment Station, 2650 Okawahara, Nagaoka, Niigata, 940-1137, Japan
| | - Satoshi Kawato
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Ikuo Hirono
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Motohiko Sano
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Goshi Kato
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
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Sur S, Patra T, Karmakar M, Banerjee A. Mycobacterium abscessus: insights from a bioinformatic perspective. Crit Rev Microbiol 2022:1-16. [PMID: 35696783 DOI: 10.1080/1040841x.2022.2082268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mycobacterium abscessus is a nontuberculous mycobacterium, associated with broncho-pulmonary infections in individuals suffering from cystic fibrosis, bronchiectasis, and pulmonary diseases. The risk factors for transmission include biofilms, contaminated water resources, fomites, and infected individuals. M. abscessus is extensively resistant to antibiotics. To date, there is no vaccine and combination antibiotic therapy is followed. However, drug toxicities, low cure rates, and high cost of treatment make it imperfect. Over the last 20 years, bioinformatic studies on M. abscessus have advanced our understanding of the pathogen. This review integrates knowledge from the analysis of genomes, microbiomes, genomic variations, phylogeny, proteome, transcriptome, secretome, antibiotic resistance, and vaccine design to further our understanding. The utility of genome-based studies in comprehending disease progression, surveillance, tracing transmission routes, and epidemiological outbreaks on a global scale has been highlighted. Furthermore, this review underlined the importance of using computational methodologies for pinpointing factors responsible for pathogen survival and resistance. We reiterate the significance of interdisciplinary research to fight M. abscessus. In a nutshell, the outcome of computational studies can go a long way in creating novel therapeutic avenues to control M. abscessus mediated pulmonary infections.
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Affiliation(s)
- Saubashya Sur
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Tanushree Patra
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Mistu Karmakar
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Anindita Banerjee
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
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Akwani WC, van Vliet AH, Joel JO, Andres S, Diricks M, Maurer FP, Chambers MA, Hingley-Wilson SM. The Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for Mycobacterium abscessus. Front Cell Infect Microbiol 2022; 12:816615. [PMID: 35419298 PMCID: PMC8995789 DOI: 10.3389/fcimb.2022.816615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Mycobacterium abscessus complex (MABC) is an important pathogen of immunocompromised patients. Accurate and rapid determination of MABC at the subspecies level is vital for optimal antibiotic therapy. Here we have used comparative genomics to design MABC subspecies-specific PCR assays. Analysis of single nucleotide polymorphisms and core genome multilocus sequence typing showed clustering of genomes into three distinct clusters representing the MABC subspecies M. abscessus, M. bolletii and M. massiliense. Pangenome analysis of 318 MABC genomes from the three subspecies allowed for the identification of 15 MABC subspecies-specific genes. In silico testing of primer sets against 1,663 publicly available MABC genomes and 66 other closely related Mycobacterium genomes showed that all assays had >97% sensitivity and >98% specificity. Subsequent experimental validation of two subspecies-specific genes each showed the PCR assays worked well in individual and multiplex format with no false-positivity with 5 other mycobacteria of clinical importance. In conclusion, we have developed a rapid, accurate, multiplex PCR-assay for discriminating MABC subspecies that could improve their detection, diagnosis and inform correct treatment choice.
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Affiliation(s)
- Winifred C. Akwani
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Arnoud H.M. van Vliet
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Jordan O. Joel
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Sönke Andres
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Margo Diricks
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Florian P. Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark A. Chambers
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Suzanne M. Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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β-Lactam Combinations That Exhibit Synergy against Mycobacteroides abscessus Clinical Isolates. Antimicrob Agents Chemother 2021; 65:AAC.02545-20. [PMID: 33361310 DOI: 10.1128/aac.02545-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 12/19/2020] [Indexed: 01/01/2023] Open
Abstract
Mycobacteroides abscessus (Mab) is an opportunistic environmental pathogen that can cause chronic pulmonary disease in the setting of structural lung conditions such as bronchiectasis, chronic obstructive pulmonary disease, and cystic fibrosis. These infections are often incurable and associated with rapid lung function decline. Mab is naturally resistant to most of the antibiotics available today, and current treatment guidelines require at least 1 year of daily multidrug therapy, which is often ineffective and is associated with significant toxicities. β-Lactams are the most widely used class of antibiotics and have a demonstrated record of safety and tolerability. Here, using a panel of recent clinical isolates of Mab, we evaluated the in vitro activities of dual-β-lactam combinations to identify new treatments with the potential to treat infections arising from a wide range of Mab strains. The Mab clinical isolates were heterogeneous, as reflected by the diversity of their genomes and differences in their susceptibilities to various drugs. Cefoxitin and imipenem are currently the only two β-lactams included in the guidelines for treating Mab disease, yet they are not used concurrently in clinical practice. However, this dual-β-lactam combination exhibited synergy against 100% of the isolates examined (n = 21). Equally surprising is the finding that the combination of two carbapenems, doripenem and imipenem, exhibited synergy against the majority of Mab isolates. In the setting of multidrug-resistant Mab disease with few therapeutic options, these combinations may offer viable immediate treatment options with efficacy against the broad spectrum of Mab strains infecting patients today.
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Mase A, Yamaguchi F, Funaki T, Yamazaki Y, Shikama Y, Fukuchi K. PCR amplification of the erm(41) gene can be used to predict the sensitivity of Mycobacterium abscessus complex strains to clarithromycin. Exp Ther Med 2019; 19:945-955. [PMID: 32010256 PMCID: PMC6966227 DOI: 10.3892/etm.2019.8289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/08/2019] [Indexed: 11/06/2022] Open
Abstract
A worldwide increase in the Mycobacterium abscessus (M. abscessus) complex has been observed. Therefore, the aim of the present study was to investigate the diversity of the rrl and erm(41) genes, both of which are associated with macrolide sensitivity in the M. abscessus complex. The current study also examined the efficacy of mass spectrometry as an alternative to molecular testing to classify subspecies of the M. abscessus complex. A total of 14 strains of the M. abscessus complex were obtained, and based on conventional analyses using housekeeping genes, 57% were determined to be M. abscessus subsp. abscessus, 43% were M. abscessus subsp. massiliense, and none were identified as M. abscessus subsp. bolletii. However, depending on the strain, it was not always possible to distinguish between the subspecies by mass spectrometry. Consequently, PCR products for the rrl and erm(41) genes were directly sequenced. Overall, 7.1% of the strains were identified to have a rrl mutation, and 92.9% carried a T at position 28 of erm(41). Results presented here suggest that the principal cause of treatment failure for M. abscessus complex infections is inducible macrolide resistance encoded by the erm(41) gene. From a strictly pragmatic standpoint, the phenotypic function of a putative erm(41) gene is the most important piece of information required by clinicians in order to prescribe an effective treatment. Although PCR amplification of erm(41) is not sufficient to differentiate between the M. abscessus complex subspecies, PCR can be easily and efficiently used to predict the sensitivity of members of the M. abscessus complex to clarithromycin.
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Affiliation(s)
- Ayaka Mase
- Department of Clinical Pathology, Showa University School of Medicine, Tokyo 142-8666, Japan.,Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Fumihiro Yamaguchi
- Department of Clinical Pathology, Showa University School of Medicine, Tokyo 142-8666, Japan.,Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Toshitaka Funaki
- Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Yohei Yamazaki
- Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Yusuke Shikama
- Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Kunihiko Fukuchi
- Department of Clinical Pathology, Showa University School of Medicine, Tokyo 142-8666, Japan
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Yano H, Suzuki H, Maruyama F, Iwamoto T. The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium. BMC Genomics 2019; 20:752. [PMID: 31623552 PMCID: PMC6798384 DOI: 10.1186/s12864-019-6078-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 09/04/2019] [Indexed: 11/10/2022] Open
Abstract
Background The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacterium avium complex (MAC) lung disease, is often mosaic and is composed of chromosomal segments originating from different lineages. This makes it difficult to infer the MAH lineage in a simple experimental set-up. To overcome this difficulty, we sought to identify chromosomal marker genes containing lineage-specific alleles by genome data mining. Results We conducted genetic population structure analysis, phylogenetic analysis, and a survey of historical recombination using data from 125 global MAH isolates. Six MAH lineages (EA1, EA2, SC1, SC2, SC3, and SC4) were identified in the current dataset. One P-450 gene (locus_tag MAH_0788/MAV_0940) in the recombination-cold region was found to have multiple alleles that could discriminate five lineages. By combining the information about allele type from one additional gene, the six MAH lineages as well as other M. avium subspecies were distinguishable. A recombination-cold region of 116 kb contains an insertion hotspot and is flanked by a mammalian cell-entry protein operon where allelic variants have previously been reported to occur. Hence, we speculate that the acquisition of lineage- or strain-specific insertions has introduced homology breaks in the chromosome, thereby reducing the chance of interlineage recombination. Conclusions The allele types of the newly identified marker genes can be used to predict major lineages of M. avium. The single nucleotide polymorphism typing approach targeting multiallelic loci in recombination-cold regions will facilitate the epidemiological study of MAC, and may also be useful for equivalent studies of other nontuberculous mycobacteria potentially carrying mosaic genomes.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Japan.
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan.
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Gan HM, Lee MVL, Savka MA. Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4. PeerJ 2019; 7:e6366. [PMID: 30775173 PMCID: PMC6369824 DOI: 10.7717/peerj.6366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 12/20/2018] [Indexed: 12/21/2022] Open
Abstract
The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
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Affiliation(s)
- Han Ming Gan
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.,School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Melvin V L Lee
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Michael A Savka
- College of Science, The Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
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Ng HF, Tan JL, Zin T, Yap SF, Ngeow YF. A mutation in anti-sigma factor MAB_3542c may be responsible for tigecycline resistance in Mycobacterium abscessus. J Med Microbiol 2018; 67:1676-1681. [DOI: 10.1099/jmm.0.000857] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hien Fuh Ng
- 1Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Malaysia
| | - Joon Liang Tan
- 2Faculty of Information Science and Technology, Multimedia University, Malaysia
| | - Thaw Zin
- 1Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Malaysia
| | - Sook Fan Yap
- 1Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Malaysia
| | - Yun Fong Ngeow
- 1Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Malaysia
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Costa-Alcalde JJ, Barbeito-Castiñeiras G, González-Alba JM, Aguilera A, Galán JC, Pérez-Del-Molino ML. Comparative evaluation of the identification of rapidly growing non-tuberculous mycobacteria by mass spectrometry (MALDI-TOF MS), GenoType Mycobacterium CM/AS assay and partial sequencing of the rpoβ gene with phylogenetic analysis as a reference method. Enferm Infecc Microbiol Clin 2018; 37:160-166. [PMID: 29871765 DOI: 10.1016/j.eimc.2018.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/10/2018] [Accepted: 04/13/2018] [Indexed: 11/25/2022]
Abstract
INTRODUCTION The American Thoracic Society and the Infectious Diseases Society of America recommend that clinically significant non-tuberculous mycobacteria (NTM) should be identified to the species level in order to determine their clinical significance. The aim of this study was to evaluate identification of rapidly growing NTM (RGM) isolated from clinical samples by using MALDI-TOF MS and a commercial molecular system. The results were compared with identification using a reference method. METHODS We included 46 clinical isolates of RGM and identified them using the commercial molecular system GenoType® CM/AS (Hain, Lifescience, Germany), MALDI-TOF MS (Bruker) and, as reference method, partial rpoβ gene sequencing followed by BLAST and phylogenetic analysis with the 1093 sequences available in the GeneBank. RESULTS The degree of agreement between GenoType® and MALDI-TOF MS and the reference method, partial rpoβ sequencing, was 27/43 (62.8%) and 38/43 cases (88.3%) respectively. For all the samples correctly classified by GenoType®, we obtained the same result with MALDI-TOF MS (27/27). However, MALDI-TOF MS also correctly identified 68.75% (11/16) of the samples that GenoType® had misclassified (p=0.005). CONCLUSIONS MALDI-TOF MS classified significantly better than GenoType®. When a MALDI-TOF MS score >1.85 was achieved, MALDI-TOF MS and partial rpoβ gene sequencing were equivalent. GenoType® was not able to distinguish between species belonging to the M. fortuitum complex. MALDI-TOF MS methodology is simple, rapid and associated with lower consumable costs than GenoType®. The partial rpoβ sequencing methods with BLAST and phylogenetic analysis were not able to identify some RGM unequivocally. Therefore, sequencing of additional regions would be indicated in these cases.
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Affiliation(s)
- José Javier Costa-Alcalde
- Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain.
| | - Gema Barbeito-Castiñeiras
- Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela - Universidade de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
| | - José María González-Alba
- Servicio de Microbiología Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - Antonio Aguilera
- Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain; Departamento de Microbioloxía, Universidad de Santiago de Compostela, A Coruña, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
| | - María Luisa Pérez-Del-Molino
- Servicio de Microbioloxía, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, A Coruña, Spain
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Tan JL, Ng KP, Ong CS, Ngeow YF. Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies. Front Microbiol 2017; 8:2042. [PMID: 29109707 PMCID: PMC5660101 DOI: 10.3389/fmicb.2017.02042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/06/2017] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear. We compared genome data from 243 M. abscessus strains downloaded from the NCBI ftp Refseq database to understand how the microevolutionary processes of homologous recombination and positive selection influenced the diversification of the M. abscessus complex at the subspecies level. The three subspecies are clearly separated in the Minimum Spanning Tree. Their MUMi-based genomic distances support the separation of M. massiliense and M. bolletii into two subspecies. Maximum Likelihood analysis through dN/dS (the ratio of number of non-synonymous substitutions per non-synonymous site, to the number of synonymous substitutions per synonymous site) identified distinct genes in each subspecies that could have been affected by positive selection during evolution. The results of genome-wide alignment based on concatenated locally-collinear blocks suggest that (a) recombination has affected the M. abscessus complex more than mutation and positive selection; (b) recombination occurred more frequently in M. massiliense than in the other two subspecies; and (c) the recombined segments in the three subspecies have come from different intra-species and inter-species origins. The results lead to the identification of possible gene sets that could have been responsible for the subspecies-specific features and suggest independent evolution among the three subspecies, with recombination playing a more significant role than positive selection in the diversification among members in this complex.
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Affiliation(s)
- Joon L Tan
- Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Kee P Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chia S Ong
- Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Yun F Ngeow
- Department of Pre-clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Petaling Jaya, Malaysia
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12
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Llanes A, Restrepo CM, Rajeev S. Whole Genome Sequencing Allows Better Understanding of the Evolutionary History of Leptospira interrogans Serovar Hardjo. PLoS One 2016; 11:e0159387. [PMID: 27442015 PMCID: PMC4956267 DOI: 10.1371/journal.pone.0159387] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/02/2016] [Indexed: 11/19/2022] Open
Abstract
The genome of a laboratory-adapted strain of Leptospira interrogans serovar Hardjo was sequenced and analyzed. Comparison of the sequenced genome with that recently published for a field isolate of the same serovar revealed relatively high sequence conservation at the nucleotide level, despite the different biological background of both samples. Conversely, comparison of both serovar Hardjo genomes with those of L. borgpetersenii serovar Hardjo showed extensive differences between the corresponding chromosomes, except for the region occupied by their rfb loci. Additionally, comparison of the serovar Hardjo genomes with those of different L. interrogans serovars allowed us to detect several genomic features that may confer an adaptive advantage to L. interrogans serovar Hardjo, including a possible integrated plasmid and an additional copy of a cluster encoding a membrane transport system known to be involved in drug resistance. A phylogenomic strategy was used to better understand the evolutionary position of the Hardjo serovar among L. interrogans serovars and other Leptospira species. The proposed phylogeny supports the hypothesis that the presence of similar rfb loci in two different species may be the result of a lateral gene transfer event.
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Affiliation(s)
- Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Panamá, Panamá
- * E-mail:
| | - Carlos Mario Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Ciudad del Saber, Panamá, Panamá
| | - Sreekumari Rajeev
- Ross University School of Veterinary Medicine, Basseterre, St. Kitts & Nevis
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13
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Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, Dumas E, Brosch R, Bouchier C, Brisse S, Vandenbogaert M, Thiberge JM, Caro V, Ngeow YF, Tan JL, Herrmann JL, Gaillard JL, Heym B, Wirth T. Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications. BMC Genomics 2016; 17:118. [PMID: 26884275 PMCID: PMC4756508 DOI: 10.1186/s12864-016-2448-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/08/2016] [Indexed: 11/16/2022] Open
Abstract
Background In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB). Results Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal ‘patchwork’ architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains. Conclusion Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2448-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guillaume Sapriel
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,Laboratoire des Sciences du Climat et de l'Environnement, LSCE, UMR8212, Université de Versailles St. Quentin - CEA - CNRS, Saint-Aubin, France. .,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France.
| | - Julie Konjek
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Mickael Orgeur
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | - Laurent Bouri
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Lise Frézal
- Institut of Biology of the Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris, Cedex 05, France.
| | | | - Emilie Dumas
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | | | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | | | | | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Joon Liang Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Jean-Louis Herrmann
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Raymond Poincaré, Service de Microbiologie et Hygiène, Garches, France.
| | - Jean-Louis Gaillard
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Beate Heym
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Thierry Wirth
- Laboratoire de Biologie intégrative des populations, Evolution moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 16 rue Buffon, F-75231, Paris, Cedex 05, France.
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14
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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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15
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Suzuki H, Yoshida S, Yoshida A, Okuzumi K, Fukusima A, Hishinuma A. A novel cluster of Mycobacterium abscessus complex revealed by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). Diagn Microbiol Infect Dis 2015; 83:365-70. [DOI: 10.1016/j.diagmicrobio.2015.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/16/2015] [Accepted: 08/21/2015] [Indexed: 10/23/2022]
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16
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Inducible and Acquired Clarithromycin Resistance in the Mycobacterium abscessus Complex. PLoS One 2015; 10:e0140166. [PMID: 26448181 PMCID: PMC4598034 DOI: 10.1371/journal.pone.0140166] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Clarithromycin was considered the cornerstone for the treatment of Mycobacterium abscessus complex infections. Genetic resistance mechanisms have been described and many experts propose amikacin as an alternative. Nevertheless, clarithromycin has several advantages; therefore, it is necessary to identify the non-functional erm(41) allele to determine the most suitable treatment. The aims of this study were to characterize the molecular mechanisms of clarithromycin resistance in a collection of Mycobacterium abscessus complex isolates and to verify the relationship between these mechanisms and the antibiogram. MATERIALS AND METHODS Clinical isolates of M. abscessus complex (n = 22) from 16 patients were identified using four housekeeping genes (rpoB, secA1, sodA and hsp65), and their genetic resistance was characterized by studying erm(41) and rrl genes. Nine strains were recovered from the clinical isolates and subjected to E-test and microdilution clarithromycin susceptibility tests, with readings at 3, 7 and 14 days. RESULTS We classified 11/16 (68.8%) M. abscessus subsp. abscessus, 4/16 (25.0%) M. abscessus subsp. bolletii, and 1/16 (6.3%) M. abscessus subsp. massiliense. T28 erm(41) allele was observed in 8 Mycobacterium abscessus subps. abscessus and 3 Mycobacterium abscessus subsp. bolletii. One strain of M. abscessus subsp. bolletii had an erm(41) gene truncated and was susceptible to clarithromycin. No mutations were observed in rrl gene first isolates. In three patients, follow-up of initial rrl wild-type strains showed acquired resistance. CONCLUSIONS Most clinical isolates of M. abscessus complex had inducible resistance to clarithromycin and total absence of constitutive resistance. Our findings showed that the acquisition of resistance mutations in rrl gene was associated with functional and non-functional erm(41) gene. Caution is needed when using erm(41) sequencing alone to identify M. abscessus subspecies. This study reports an acquired mutation at position 2057 of rrl gene, conferring medium-low clarithromycin constitutive resistance.
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Support from Phylogenomic Networks and Subspecies Signatures for Separation of Mycobacterium massiliense from Mycobacterium bolletii. J Clin Microbiol 2015; 53:3042-6. [PMID: 26157149 DOI: 10.1128/jcm.00541-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/09/2015] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus subspecies classification has important clinical implications. We used phylogenomic network and amino acid analyses to provide evidence for the separation of Mycobacterium bolletii and Mycobacterium massiliense into two distinct subspecies which can potentially be differentiated rapidly by their protein signatures.
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18
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Isolation and characterization of a native avirulent strain of Streptococcus suis serotype 2: a perspective for vaccine development. Sci Rep 2015; 5:9835. [PMID: 25891917 PMCID: PMC4402706 DOI: 10.1038/srep09835] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 03/19/2015] [Indexed: 01/05/2023] Open
Abstract
Streptococcus suis, an emerging infectious pathogen, is the cause of two large-scale outbreaks of human streptococcal toxic shock syndrome in China, and has attracted much attention from the scientific community. The genetic basis of its pathogenesis remains enigmatic, and no effective prevention measures have been established. To better understand the virulence differentiation of S. suis and develop a promising vaccine, we isolated and sequenced a native avirulent S. suis strain (05HAS68). Animal experiments revealed that 05HAS68 is an avirulent strain and could protect piglets from the attack of virulent strains. Comparative genomics analyses demonstrated the genetic basis for the lack of virulence in 05HAS68, which is characterized by the absence of some important virulence-associated factors and the intact 89K pathogenicity island. Lack of virulence was also illustrated by reduced survival of 05HAS68 compared to a virulent strain in pig whole blood. Further investigations revealed a large-scale genomic rearrangement in 05HAS68, which was proposed to be mediated by transposase genes and/or prophages. This genomic rearrangement may have caused the genomic diversity of S. suis, and resulted in biological discrepancies between 05HAS68 and highly virulent S. suis strains.
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