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Castro-Rodriguez B, Franco-Sotomayor G, Rodriguez-Pazmiño ÁS, Cardenas-Franco GE, Orlando SA, Hermoso de Mendoza J, Parra-Vera H, García-Bereguiain MÁ. Rapid and accurate identification and differentiation of Mycobacterium tuberculosis and non-tuberculous mycobacteria using PCR kits available in a high-burden setting. Front Public Health 2024; 12:1358261. [PMID: 38628855 PMCID: PMC11018931 DOI: 10.3389/fpubh.2024.1358261] [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] [Received: 12/19/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
Infections caused by mycobacteria, including Mycobacterium tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), are a major public health issue worldwide. An accurate diagnosis of mycobacterial species is a challenge for surveillance and treatment, particularly in high-burden settings usually associated with low- and middle-income countries. In this study, we analyzed the clinical performance of two commercial PCR kits designed for the identification and differentiation of MTBC and NTM, available in a high-burden setting such as Ecuador. A total of 109 mycobacteria isolates were included in the study, 59 of which were previously characterized as M. tuberculosis and the other 59 as NTM. Both kits displayed great clinical performance for the identification of M. tuberculosis, with 100% sensitivity. On the other hand, for NTM, one of the kits displayed a good clinical performance with a sensitivity of 94.9% (CI 95%: 89-100%), while the second kit had a reduced sensitivity of 77.1% (CI 95%: 65-89%). In conclusion, one of the kits is a fast and reliable tool for the identification and discrimination of MTBC and NTM from clinical isolates.
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Affiliation(s)
| | - Greta Franco-Sotomayor
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
- Universidad Católica Santiago de Guayaquil, Guayaquil, Ecuador
| | | | | | - Solón Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública "Leopoldo Izquieta Pérez", Guayaquil, Ecuador
- Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - Henry Parra-Vera
- Centro de Investigación Microbiológica (CIM), Guayaquil, Ecuador
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2
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Ngo C, Suwimonteerabutr J, Apiwatsiri P, Saenkankam I, Prapasarakul N, Morrell JM, Tummaruk P. Boar Seminal Microbiota in Relation to Sperm Quality under Tropical Environments. Animals (Basel) 2023; 13:3837. [PMID: 38136874 PMCID: PMC10740666 DOI: 10.3390/ani13243837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The present study was carried out to determine the seminal microbiota of boars and their correlation with sperm quality. A total of 17 ejaculates were collected from 17 Duroc boars and were classified according to sperm quality into two groups: low-quality (n = 8) and high-quality (n = 9). Each ejaculate was subjected to (i) semen evaluation, (ii) bacterial culture and MALDI-TOF identification, and (iii) 16S rRNA gene sequencing and bioinformatic analyses. No difference in the total bacterial count, alpha diversity, and beta diversity between the high-quality group and the low-quality group was detected (p > 0.05). While Globicatella sanguinis was negatively correlated with sperm quality (p < 0.05), Delftia acidovorans was positively correlated with sperm quality (p < 0.05). Lactobacillales (25.2%; LB) and Enterobacterales (10.3%; EB) were the most dominant bacteria and negatively correlated: EB = 507.3 - 0.5 × LB, R2 = 0.24, p < 0.001. Moreover, the abundance of Escherichia-shigella was negatively correlated with LB (r = -0.754, p < 0.001) and positively correlated with Proteus (r = 0.533, p < 0.05). Alysiella was positively correlated with Lactobacillus (r = 0.485, p < 0.05), Prevotella (r = 0.622, p < 0.01), and Staphylococcus (r = 0.489, p < 0.05). In conclusion, seminal microbiota is significantly associated with boar semen qualities. The distributions of the most dominant bacterial genera, the differences in the abundance of small subset microbes, and their correlation appear to have far more impact than the overall seminal bacterial content (e.g., total bacterial count, alpha diversity, and beta diversity) on sperm quality.
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Affiliation(s)
- CongBang Ngo
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (C.N.); (J.S.)
| | - Junpen Suwimonteerabutr
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (C.N.); (J.S.)
- Center of Excellent in Swine Reproduction, Chulalongkorn University, Bangkok 10330, Thailand
| | - Prasert Apiwatsiri
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (P.A.); (I.S.); (N.P.)
| | - Imporn Saenkankam
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (P.A.); (I.S.); (N.P.)
| | - Nuvee Prapasarakul
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (P.A.); (I.S.); (N.P.)
- Center of Excellence in Diagnosis and Monitoring for Animal Pathogens, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jane M. Morrell
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden;
| | - Padet Tummaruk
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; (C.N.); (J.S.)
- Center of Excellent in Swine Reproduction, Chulalongkorn University, Bangkok 10330, Thailand
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3
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Li L, Wu J, Lyon CJ, Jiang L, Hu TY. Clinical Peptidomics: Advances in Instrumentation, Analyses, and Applications. BME FRONTIERS 2023; 4:0019. [PMID: 37849662 PMCID: PMC10521655 DOI: 10.34133/bmef.0019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/19/2023] [Indexed: 10/19/2023] Open
Abstract
Extensive effort has been devoted to the discovery, development, and validation of biomarkers for early disease diagnosis and prognosis as well as rapid evaluation of the response to therapeutic interventions. Genomic and transcriptomic profiling are well-established means to identify disease-associated biomarkers. However, analysis of disease-associated peptidomes can also identify novel peptide biomarkers or signatures that provide sensitive and specific diagnostic and prognostic information for specific malignant, chronic, and infectious diseases. Growing evidence also suggests that peptidomic changes in liquid biopsies may more effectively detect changes in disease pathophysiology than other molecular methods. Knowledge gained from peptide-based diagnostic, therapeutic, and imaging approaches has led to promising new theranostic applications that can increase their bioavailability in target tissues at reduced doses to decrease side effects and improve treatment responses. However, despite major advances, multiple factors can still affect the utility of peptidomic data. This review summarizes several remaining challenges that affect peptide biomarker discovery and their use as diagnostics, with a focus on technological advances that can improve the detection, identification, and monitoring of peptide biomarkers for personalized medicine.
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Affiliation(s)
- Lin Li
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Jing Wu
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Li Jiang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, China
| | - Tony Y. Hu
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, LA, USA
- Department of Biomedical Engineering, School of Science and Engineering, Tulane University, New Orleans, LA, USA
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4
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Fukushima K, Matsumoto Y, Matsuki T, Saito H, Motooka D, Komukai S, Fukui E, Yamuchi J, Nitta T, Niitsu T, Abe Y, Nabeshima H, Nagahama Y, Nii T, Tsujino K, Miki K, Kitada S, Kumanogoh A, Akira S, Nakamura S, Kida H. MGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study. J Clin Microbiol 2023; 61:e0162622. [PMID: 36946719 PMCID: PMC10117113 DOI: 10.1128/jcm.01626-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Because nontuberculous mycobacterial pulmonary disease is a considerable health burden, a simple and clinically applicable analytical protocol enabling the identification of subspecies and drug-resistant disease is required to determine the treatment strategy. We aimed to develop a simplified workflow consisting only of direct sequencing of mycobacterial growth indicator tube cultures (MGIT-seq). In total, 138 patients were prospectively enrolled between April 2021 and May 2022, and culture-positive MGIT broths were subjected to sequencing using MinION, a portable next-generation sequencer. Sequence analysis was conducted to identify species using core genome multilocus sequence typing and to predict macrolide and amikacin (AMK) resistance based on previously reported mutations in rrl, rrs, and erm(41). The results were compared to clinical tests for species identification and drug susceptibility. A total of 116 patients with positive MGIT cultures were included in the analysis. MGIT-seq yielded 99.1% accuracy in species-level identification and identified 98 isolates (84.5%) at the subspecies level. Macrolide and AMK resistance were detected in 19.4% and 1.9% of Mycobacterium avium complex (MAC) and Mycobacterium abscessus isolates. The predicted macrolide and AMK resistance was consistent with the results of conventional drug susceptibility tests, with specificities of 97.6% and 100.0%, respectively. Direct MGIT-seq has achieved comprehensive identification and drug resistance detection of nontuberculous mycobacteria, which could be applicable to determine the treatment strategy by a single test in clinical practice.
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Affiliation(s)
- Kiyoharu Fukushima
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
- Global Center for Medical Engineering and Informatics, Suita, Osaka, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takanori Matsuki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Haruko Saito
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Sho Komukai
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Department of Biomedical Statistics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Eriko Fukui
- Department of General Thoracic surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - June Yamuchi
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Tadayoshi Nitta
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Takayuki Niitsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuko Abe
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Hiroshi Nabeshima
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Yasuharu Nagahama
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Takuro Nii
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Kazuyuki Tsujino
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Keisuke Miki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | | | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Hiroshi Kida
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
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5
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Pastrone L, Curtoni A, Criscione G, Scaiola F, Bottino P, Guarrasi L, Iannaccone M, Timke M, Costa C, Cavallo R. Evaluation of Two Different Preparation Protocols for MALDI-TOF MS Nontuberculous Mycobacteria Identification from Liquid and Solid Media. Microorganisms 2023; 11:microorganisms11010120. [PMID: 36677412 PMCID: PMC9866535 DOI: 10.3390/microorganisms11010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) identification is essential for establishing the relevance of the isolate and for appropriate antimicrobial therapy. Traditionally, NTM identification is performed by using Line Probe Assays (LPA), a costly and time-consuming technique requiring trained personnel. MALDI-TOF MS is a promising tool for NTM identification, and its use is rapidly growing. We evaluated the newly introduced MBT Mycobacteria kit (MBT) and the MycoEx preparation protocol (Bruker Daltonics, Germany) for NTM MALDI-TOF MS identification using LPA results as a reference. Fifty NTM grown on 7H11 agar and MGIT broth were analyzed with both protocols using the Bruker Microflex® LT MALDI-TOF MS (Bruker Daltonics) instrument. MBT and MycoEx provided identification results in 97.0% and 95.0% of the cases, respectively. With both protocols, 100% of the provided results agreed with LPA with no registered mismatch. MBT achieved an elevated number of highly probable identifications (88.0% vs. 83.0%) and a higher reproducibility rate of correct results (86.6% vs. 75.8%) in comparison to MycoEx. This study provides results about MBT performance for liquid and solid media, underlining the strengths and weakness under different conditions. Our results suggest that MALDI-TOF MS could provide a great advantage for timely and cost-saving NTM identification with potential implications for patient outcome.
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Affiliation(s)
- Lisa Pastrone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Antonio Curtoni
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Correspondence: ; Tel.: +39-011-633-7005
| | - Giulia Criscione
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Francesca Scaiola
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Paolo Bottino
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Luisa Guarrasi
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Marco Iannaccone
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
| | - Markus Timke
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, 10126 Turin, Italy
- Department of Public Health and Paediatrics, University of Turin, 10126 Turin, Italy
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6
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Frantsuzova E, Bogun A, Vetrova A, Delegan Y. Methods of Identifying Gordonia Strains in Clinical Samples. Pathogens 2022; 11:pathogens11121496. [PMID: 36558832 PMCID: PMC9786905 DOI: 10.3390/pathogens11121496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/04/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.
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Affiliation(s)
- Ekaterina Frantsuzova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Alexander Bogun
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia
| | - Anna Vetrova
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
| | - Yanina Delegan
- Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center “Pushchino Scientific Center for Biological Research of Russian Academy of Sciences” (FRC PSCBR RAS), 142290 Pushchino, Moscow Region, Russia
- Correspondence:
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7
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Pan X, Li Z, Huang S, Huang Y, Wang Q, Tao Z, Hu W. Mycolicibacterium aurantiacum sp. nov. and Mycolicibacterium xanthum sp. nov., two novel actinobacteria isolated from mangrove sediments. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two novel actinobacteria with the ability to degrade kerosene, designated as B3033T and Y57T, were isolated from mangrove sediments in Tieshan Harbour, South China Sea. Both strains are Gram-staining-positive, non-spore forming, slow-growing, oxidase-positive, non-motile and aerobic. Their major cellular fatty acids were C16 : 0 and C18 : 1ω9c. Analysis of 16S rRNA gene sequences revealed the close relationship of strain B3033T to
Mycobacterium kyogaense
DSM 107316T (99.4 % nucleotide identity) and strain Y57T to
Mycolicibacterium chubuense
ATCC 27278T (98.7 %) and
Mycolicibacterium rufum
JS14T (98.7 %). Whole genome average nucleotide blast identity (ANI) and the digital DNA–DNA hybridization (dDDH) values between the two isolates and the type strains of species of the genus
Mycolicibacterium
were lower than 94 and 45 %, respectively, which were below the threshold values of 95 % (for ANI) and 70 % (for dDDH) recommended for bacterial species differentiation. The genome sequence of B3033T comprised a circular 11.0 Mb chromosome with a DNA G+C content of 68.1 mol%. Y57T had a genome size of 5.6 Mb and a DNA G+C content of 68.7 mol%. Genes involved in degradation of aromatic compounds and copper resistance were identified in the genomes of both strains that could improve their adaptive capacity to the mangrove environment. These results combined with those of chemotaxonomic analyses, MALDI-TOF MS profiles and phenotypic analyses support the affiliation of these strains to two novel species within the genus
Mycolicibacterium
, for which we propose the names Mycolicibacterium aurantiacum sp. nov. B3033T (=KCTC 49712T=MCCC 1K04526T) and Mycolicibacterium xanthum sp. nov. Y57T (=KCTC 49711T=MCCC 1K04875T) as type strains.
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Affiliation(s)
- Xinli Pan
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, PR China
| | - Zhe Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, PR China
| | - Shushi Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, PR China
| | - Yuanlin Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, PR China
| | - Qiaozhen Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, PR China
| | - Zhanhua Tao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, PR China
| | - Wenjin Hu
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, Nanning, 530007, PR China
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, PR China
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8
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Huang Y, Ai L, Wang X, Sun Z, Wang F. Review and Updates on the Diagnosis of Tuberculosis. J Clin Med 2022; 11:jcm11195826. [PMID: 36233689 PMCID: PMC9570811 DOI: 10.3390/jcm11195826] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Diagnosis of tuberculosis, and especially the diagnosis of extrapulmonary tuberculosis, still faces challenges in clinical practice. There are several reasons for this. Methods based on the detection of Mycobacterium tuberculosis (Mtb) are insufficiently sensitive, methods based on the detection of Mtb-specific immune responses cannot always differentiate active disease from latent infection, and some of the serological markers of infection with Mtb are insufficiently specific to differentiate tuberculosis from other inflammatory diseases. New tools based on technologies such as flow cytometry, mass spectrometry, high-throughput sequencing, and artificial intelligence have the potential to solve this dilemma. The aim of this review was to provide an updated overview of current efforts to optimize classical diagnostic methods, as well as new molecular and other methodologies, for accurate diagnosis of patients with Mtb infection.
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9
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Shu Q, Rajagopal M, Fan J, Zhan L, Kong X, He Y, Rotcheewaphan S, Lyon CJ, Sha W, Zelazny AM, Hu T. Peptidomic analysis of mycobacterial secreted proteins enables species identification. VIEW 2022. [DOI: 10.1002/viw.20210019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Qingbo Shu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Meena Rajagopal
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Lingpeng Zhan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Xiangxing Kong
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Yifan He
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Suwatchareeporn Rotcheewaphan
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
- Department of Microbiology, Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Wei Sha
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Adrian M. Zelazny
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
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10
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Surgical site infections by atypical mycobacteria: prevalence and species characterization using MALDI-TOF and molecular LCD chip array. Infection 2022; 50:1557-1563. [PMID: 35716342 PMCID: PMC9705499 DOI: 10.1007/s15010-022-01864-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/24/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Surgical site infection (SSI) is a post-operative complication of high concern with adverse impact on patient prognosis and public health systems. Recently, SSI pathogens have experienced a change in microbial profile with increasing reports of non-tuberculous mycobacteria (NTM) as important pathogens. AIM of the study The study aimed to detect the prevalence of NTM among cases with SSIs and describe their species using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and PCR-based microarray. METHODS The study was conducted with 192 pus samples collected from patients with SSI. Mycobacterial investigations were done in the form of Ziehl-Neelsen (ZN) smears for acid-fast bacilli, automated mycobacterial culture to isolate mycobacteria, followed by immunochromatography test to predict NTM. NTM-positive cultures were tested by MALDI -TOF MS and PCR-based microarray to reach species-level identification. RESULTS Mycobacterial growth was found in 11/192 samples (5.7%) and identified as 4 NTM and 7 M. tuberculosis isolates with prevalence of 2.1% and 3.64%, respectively. The NTM species were described by MALDI-TOF as M. abscessus, M. porcinum, M. bacteremicum, and M. gordonae. Microarray agreed with MALDI-TOF in identifying one isolate (M. abscessus), while two isolates were classified as belonging to broad groups and one isolate failed to be identified. CONCLUSIONS The prevalence of NTM among SSI was found to be low, yet have to be considered in the diagnosis of mycobacteria. Employing advanced technologies in diagnosis is recommended to guide for appropriate treatment.
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Mycobacterium chimaera Identification Using MALDI-TOF MS Technology: A Practical Approach for the Clinical Microbiology Laboratories. Microorganisms 2022; 10:microorganisms10061184. [PMID: 35744702 PMCID: PMC9228860 DOI: 10.3390/microorganisms10061184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Mycobacterium chimaera (MC) is an environmental, slowly growing, non-tuberculous mycobacterium (NTM) belonging to Mycobacterium avium complex (MAC), which recently has been linked to severe cardiovascular infections following open heart and vascular surgery. The majority of the diagnostic laboratory tests used in routine are not able to distinguish MC from M. intracellulare (MI), because of the great genetic similarity existing between these two species. The Genotype Mycobacterium NTM-DR™ represents a valid method to differentiate between these species, but it is expensive, requiring also specialized personnel. Recently, MALDI-TOF MS has been proposed to identify relevant NTM. However, a software implementation is required to distinguish between MC and MI, presenting the two microorganisms’ overlapping spectra. The present study evaluates the feasibility of applying a MALDI-TOF logarithmic-based analysis in the routine of a clinical microbiology laboratory, and proposes an easy-to-use template spreadsheet to make the results quickly interpretable. The protocol was previously validated through the identification of 87 strains of MC/MI collected from clinical and environmental samples, and it was identified using the GenoType Mycobacterium NTM-DR™ and/or WGS. The proposed protocol provides accurate identification for the isolates tested; moreover, it is less expensive and more rapid than sequencing methods and can be implemented with minimum effort.
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12
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Song J, Yoon S, In Y, Kim D, Lee H, Yong D, Lee K. Substantial Improvement in Nontuberculous Mycobacterial Identification Using ASTA MicroIDSys Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry with an Upgraded Database. Ann Lab Med 2022; 42:358-362. [PMID: 34907106 PMCID: PMC8677478 DOI: 10.3343/alm.2022.42.3.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/08/2021] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
Identifying Mycobacterium using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is challenging. We evaluated the performance of MALDI-TOF MS in identifying nontuberculous mycobacteria (NTM) using the ASTA MicroIDSys system (ASTA Inc., Suwon, Korea) with the MycoDB v1.95s and upgraded MycoDB v2.0-beta databases. We tested 124 NTM isolates collected from Ogawa medium at Severance Hospital, Seoul, Korea, between January and April 2019. MicroIDSys scores were categorized into three groups: ≥140, reliable identification; 130-139, ambiguous identification; and <130, invalid identification. To validate the results, we used the reverse blot hybridization assay (Molecutech REBA MycoID, YD Diagnostics Corp., Korea). Initial analysis using MycoDB v1.95s resulted in 26.6% (33/124) reliable, 43.5% (54/124) ambiguous, and 29.8% (37/124) invalid identifications. Re-analysis using the upgraded MycoDB v2.0-beta database resulted in 94.4% (117/124) reliable, 4.0% (5/124) ambiguous, and 1.6% invalid (2/124) identifications. The percentage of reliable identifications that matched with the reference increased from 26.6% (33/124) with MycoDB v1.95s to 93.5% (116/124) with MycoDB v2.0-beta. The upgraded databases enable substantially improved NTM identification through deep learning in the inference algorithm and by considering more axes in the correlation analysis. MALDI-TOF MS using the upgraded database unambiguously identified most NTM species. Our study lays a foundation for applying MALDI-TOF MS for the simple and rapid identification of NTM isolated from solid media.
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Affiliation(s)
- Junhyup Song
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Shinyoung Yoon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Yongha In
- Department of Database Control, Nosquest Inc., Gyeonggi-do, Korea
| | - Daewon Kim
- Department of Laboratory Medicine, Gil Medical Center, Gachon University College of Medicine, Incheon, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, Korea
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Kashihara E, Fujita K, Yamamoto H, Odagaki T. Mycobacterium farcinogenes infection after fracture repair of the tibia and fibula. IDCases 2022; 28:e01468. [PMID: 35308775 PMCID: PMC8924634 DOI: 10.1016/j.idcr.2022.e01468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium farcinogenes is the causative agent of bovine farcy. M. farcinogenes shares common properties with rapidly growing mycobacteria, and distinguishing between M. farcinogenes and M. fortuitum is reportedly complex and challenging. Moreover, few studies have isolated M. farcinogenes from human clinical samples. A previously healthy 37-year-old male construction worker presented to the emergency department after a severe injury and was diagnosed with a Gustilo-Anderson type ⅢA fracture. After an uneventful postoperative period of two months, he experienced pain and serous discharge from the upper shin and lower calf region. Frequent debridement provided no relief, and the pathology cultures of the tissue were negative. However, M. farcinogenes was isolated from the fluid of the wound. The patient’s symptoms gradually improved with anti-mycobacterial drug treatment. Nontuberculous mycobacterial infections, including those caused by M. farcinogenes, should be considered in patients developing soft tissue infections despite negative pyogenic bacterial cultures several months after sustaining an open fracture.
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Unusual Presentation of Disseminated Mycobacterium kansasii Infection in Renal Transplant Recipients and Rapid Diagnosis Using Plasma Microbial Cell-free DNA Next-generation Sequencing. Transplant Direct 2022; 8:e1291. [PMID: 35368989 PMCID: PMC8966957 DOI: 10.1097/txd.0000000000001291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 12/01/2021] [Accepted: 12/22/2021] [Indexed: 11/26/2022] Open
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Lorente-Leal V, Liandris E, Bezos J, Pérez-Sancho M, Romero B, de Juan L. MALDI-TOF Mass Spectrometry as a Rapid Screening Alternative for Non-tuberculous Mycobacterial Species Identification in the Veterinary Laboratory. Front Vet Sci 2022; 9:827702. [PMID: 35155660 PMCID: PMC8831857 DOI: 10.3389/fvets.2022.827702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are difficult to identify by biochemical and genetic methods due to their microbiological properties and complex taxonomy. The development of more efficient and rapid methods for species identification in the veterinary microbiological laboratory is, therefore, of great importance. Although MALDI-TOF Mass Spectrometry (MS) has become a promising tool for the identification of NTM species in human clinical practise, information regarding its performance on veterinary isolates is scarce. This study assesses the capacity of MALDI-TOF MS to identify NTM isolates (n = 75) obtained from different animal species. MALDI-TOF MS identified 76.0% (n = 57) and 4% (n = 3) of the isolates with high and low confidence, respectively, in agreement with the identification achieved by Sanger sequencing of housekeeping genes (16S rRNA, hsp65, and rpoB). Thirteen isolates (17.3%) were identified by Sanger sequencing to the complex level, indicating that these may belong to uncharacterised species. MALDI-TOF MS approximated low confidence identifications toward closely related mycobacterial groups, such as the M. avium or M. terrae complexes. Two isolates were misidentified due to a high similarity between species or due to the lack of spectra in the database. Our results suggest that MALDI-TOF MS can be used as an effective alternative for rapid screening of mycobacterial isolates in the veterinary laboratory and potentially for the detection of new NTM species. In turn, Sanger sequencing could be implemented as an additional method to improve identifications in species for which MALDI-TOF MS identification is limited or for further characterisation of NTM species.
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Affiliation(s)
- Víctor Lorente-Leal
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Emmanouil Liandris
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
| | - Javier Bezos
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Marta Pérez-Sancho
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Beatriz Romero
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Beatriz Romero
| | - Lucía de Juan
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
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Cole AL, Kirk NM, Wang L, Hung CC, Samuelson JP. Mycobacterium fortuitum abortion in a sow. J Vet Diagn Invest 2022; 34:116-120. [PMID: 34448422 PMCID: PMC8689021 DOI: 10.1177/10406387211042289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Two aborted Chester White pig fetuses were presented to a veterinary diagnostic laboratory in Illinois. Postmortem examination identified no gross abnormalities. Histologic evaluation revealed multifocal necrosis of chorionic epithelial cells, coalescing areas of mineralization in the placenta, and focal accumulations of viable and degenerate neutrophils in the lung. Intra- and extracellular acid-fast bacilli were identified in the lesions in both the placenta and lungs. Bacterial culture of stomach contents yielded heavy growth of Mycobacterium fortuitum, a rapidly growing nontuberculous mycobacterium (NTM), which was further confirmed through whole-genome sequencing. NTM are opportunistic pathogens commonly found in the soil and in contaminated water supplies. In animals, M. fortuitum is typically introduced through cutaneous wounds leading to infections limited to the skin, with systemic infection being uncommon. To our knowledge, abortion caused by M. fortuitum has not been reported previously.
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Affiliation(s)
- Allysa L. Cole
- College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Natalie M. Kirk
- Departments of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Current address: Department of Veterinary Population Medicine, University of Minnesota Twin Cities, St. Paul, MN, USA
| | - Leyi Wang
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chien-Che Hung
- Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan P. Samuelson
- Jonathan P. Samuelson, Veterinary Diagnostic Laboratory, University of Illinois at Urbana-Champaign, 2001 S Lincoln, M/C 002, Urbana, IL 61802, USA.
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SARS-CoV-2 Supply Shortages and Tuberculosis Diagnostics: Current Issues Requiring Immediate Solutions. J Clin Microbiol 2021; 59:e0077821. [PMID: 34586893 PMCID: PMC8601221 DOI: 10.1128/jcm.00778-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The SARS-CoV-2 pandemic has strained manufacturing capacity worldwide, resulting in significant shortages of laboratory supplies both directly and indirectly. Such shortages include probe-based kits for detection of the Mycobacterium tuberculosis complex from positive liquid broth cultures. These shortages and possible loss of this particular assay have consequences for laboratory testing algorithms and public health in the United States. As there are no FDA-approved, commercially available options that currently exist which could immediately fill this gap, laboratories must identify alternatives and plan for modifying current testing algorithms to accommodate this change.
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18
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Li H, Liu C, Liang M, Liu D, Zhao B, Shi J, Zhao Y, Ou X, Zhang G. Tuberculosis Outbreak in an Educational Institution in Henan Province, China. Front Public Health 2021; 9:737488. [PMID: 34712640 PMCID: PMC8545879 DOI: 10.3389/fpubh.2021.737488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
On June 17, 2018, a case of pulmonary tuberculosis (TB) was reported among students at a senior high school in Luoning, China. The outbreak encompassed a total of 23 cases along with TB screening in the whole school by means of PPD and chest X-ray. By the end of September 2018, the entire 9 cases cultured positive had epidemiological association. All of the 9 Mycobacterium tuberculosis (Mtb) isolates available were sensitive to all drugs tested and had similar spoligotyping and 15 loci mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) profile. Whole-genome sequencing (WGS) of the Mtb isolates revealed 20 variable nucleotide positions within 8 cases, indicating a clonal outbreak. The index case, which was first identified and diagnosed, is separated from the cluster by a minimum number of 95 distinct SNPs. Minimum distance spanning tree (MST) indicted that the 8 cases were indeed part of a single transmission chain. It was concluded that this is an epidemic situation of TB outbreak exposed by the aggrieved index case at school, which was caused by the veiled infectious case wherein a student was suffering from TB and attending school simultaneously.
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Affiliation(s)
- Hui Li
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Chunfa Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Minghui Liang
- Luoyang Center for Disease Control and Prevention, Luoyang, China
| | - Dongxin Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Shi
- Henan Center for Disease Control and Prevention, Zhengzhou, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guolong Zhang
- Henan Center for Disease Control and Prevention, Zhengzhou, China
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19
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Pinar-Méndez A, Fernández S, Baquero D, Vilaró C, Galofré B, González S, Rodrigo-Torres L, Arahal DR, Macián MC, Ruvira MA, Aznar R, Caudet-Segarra L, Sala-Comorera L, Lucena F, Blanch AR, Garcia-Aljaro C. Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database. WATER RESEARCH 2021; 203:117543. [PMID: 34433109 DOI: 10.1016/j.watres.2021.117543] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/23/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.
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Affiliation(s)
- Anna Pinar-Méndez
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain; Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
| | - Sonia Fernández
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - David Baquero
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Carles Vilaró
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Belén Galofré
- Aigües de Barcelona, Empresa Metropolitana de Gestió del Cicle Integral de l'Aigua, General Batet 1-7, Barcelona 08028, Spain
| | - Susana González
- Cetaqua, Water technology center, Cornellà de Llobregat, Spain
| | - Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - M Carmen Macián
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - María A Ruvira
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Rosa Aznar
- Departamento de Microbiología y Ecología and Colección Española de Cultivos Tipo (CECT), Universitat de València, Valencia, Spain
| | - Laia Caudet-Segarra
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Laura Sala-Comorera
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Francisco Lucena
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Anicet R Blanch
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain; The Water Research Institute, University of Barcelona, Barcelona, Spain.
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20
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Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, Huang JJ, Zhang JJ, Xu YC, Hsueh PR. Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review. Microorganisms 2021; 9:microorganisms9071536. [PMID: 34361971 PMCID: PMC8304613 DOI: 10.3390/microorganisms9071536] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xin Hou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Wei Cheng
- Center of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100053, China;
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
- Correspondence: (Y.-C.X.); (P.-R.H.)
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 40447, Taiwan;
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence: (Y.-C.X.); (P.-R.H.)
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López Medrano R, Burgos Asurmendi I, Rivero Lezcano OM. A rapid proteomic system (MALDI-TOF) for nontuberculous-mycobacteria identification. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00203-2. [PMID: 34266677 DOI: 10.1016/j.eimc.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/24/2022]
Abstract
Proteomic techniques relaying upon mass spectrometry (MALDI_TOF) applied to nontuberculous mycobacteria (NTM) identification, constitute a difficult goal. Cell wall structure features complicates the protein extraction procedure. A total of 106 isolates belonging to a variety of MNTs species isolated from clinical samples taken at the Complejo Asistencial Universitario de León for a two years period (2019-20) were identified following a simplified method (MALDI-TOF Biotyper Bruker®) developped in our laboratory. The resultant identification was compared to a parallel one ruled on the Centro de Referencia de Majadahonda. A total of 22 different MNTs species were tested, obtaining an agreement of 91,5%. Only 9 minor discrepancies between species belonging to the same taxonomic group of MNTs were detected. The score obtained in the 67.92% of the cases was higher than 1.8. A time-saving of 24 minutes compared to the manufacturer's proceeding was achieved.
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Affiliation(s)
- Ramiro López Medrano
- Servicio de Microbiología. Complejo Asistencial Universitario de León, León, España.
| | - Isabel Burgos Asurmendi
- Servicio de Anestesiología y Reanimación. Complejo Asistencial Universitario de León, León, España
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22
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Wang X, Xu F, Ning K, Shen L, Qi X, Wang J. Construction and Application of MALDI-TOF Mass Spectrometry for the Detection of Haemophilus parasuis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5588855. [PMID: 33937398 PMCID: PMC8062181 DOI: 10.1155/2021/5588855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 01/02/2023]
Abstract
To construct a protein fingerprint database of Haemophilus parasuis (H. parasuis), thus improving its clinical diagnosis efficiency. A total of 15 H. parasuis standard strains were collected to establish a protein fingerprint database of H. parasuis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and the effects of different culture media and culture time on the quality and identification results of the protein fingerprint were investigated. The results showed that tryptone soy agar (TSA) and tryptone soy broth (TSB) media and different incubation times had no significant effect on the characteristic peaks of the protein profiles. In addition, 18 clinical isolates were used to compare the identification results of the self-built protein fingerprint database, PCR detection, and basic database. Only one strain was identified in the original VITEK-MS system database, while the self-made protein fingerprint database of H. parasuis was 100% accurate for the detection of 18 clinical isolate strains. The protein fingerprint database of H. parasuis built by our laboratory is suitable for rapid clinical diagnosis of H. parasuis, due to its high accuracy, efficiency, and strong specificity.
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Affiliation(s)
- Xiaoxu Wang
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Feng Xu
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Kun Ning
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Liping Shen
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Xinyong Qi
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
| | - Jian Wang
- Shanghai Animal Disease Control Center, 855 Hongjin Road, Shanghai 201103, China
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23
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Yoo IY, Shim HJ, Yun SA, Kang OK, Chung YN, Kim TY, Lee H, Kim J, Park YJ, Huh HJ, Lee NY. Evaluation of the ASTA MicroIDSys matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures. Int J Infect Dis 2020; 102:172-177. [PMID: 33039611 DOI: 10.1016/j.ijid.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVES We evaluated the performance of the MicroIDSys Elite system, a newly developed matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry system for identification of mycobacteria directly from positive MGIT liquid cultures. METHODS Analytical specificity was evaluated with 63 reference strains grown in mycobacteria growth indicator tube media. Prospective performance evaluation was conducted with primary liquid cultures of sputum samples for identification of mycobacteria, and results were compared to multigenerational sequencing as the reference method. Liquid media subcultures were also analyzed. RESULTS The accuracy for the 63 reference strains was 98.4% (62/63). A total of 167 paired mycobacterial primary cultures and subcultures in liquid media, comprised of seven Mycobacterium tuberculosis isolates, 109 slowly growing nontuberculous mycobacterial isolates, and 51 rapidly growing nontuberculous mycobacterial isolates, was identified by the MicroIDSys Elite system. Using primary liquid cultures, the MicroIDSys Elite system correctly identified 143 (85.6%) isolates; 21 (12.6%) resulted in "no identification"; and three (1.8%) isolates were misidentified. Using liquid media subcultures with this system, 159 (95.2%) isolates were correctly identified; seven (4.2%) resulted in "no identification"; and one (0.6%) isolate was misidentified. CONCLUSION The MicroIDSys Elite system is a useful routine diagnostic tool for identification of mycobacterial species from liquid culture.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hyang Jin Shim
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Ae Yun
- Center for Clinical Medicine, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - On Kyun Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yoo Na Chung
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyeyoung Lee
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, The Catholic Kwandong University, Incheon, Republic of Korea
| | - Jayoung Kim
- Department of Laboratory Medicine, International St. Mary's Hospital, College of Medicine, The Catholic Kwandong University, Incheon, Republic of Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - Nam Yong Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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24
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Pereira AC, Ramos B, Reis AC, Cunha MV. Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches. Microorganisms 2020; 8:microorganisms8091380. [PMID: 32916931 PMCID: PMC7563442 DOI: 10.3390/microorganisms8091380] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-500-000 (ext. 22461)
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Kalaiarasan E, Thangavelu K, Krishnapriya K, Muthuraj M, Jose M, Joseph NM. Diagnostic performance of real time PCR and MALDI-TOF in the detection of nontuberculous mycobacteria from clinical isolates. Tuberculosis (Edinb) 2020; 125:101988. [PMID: 32916384 DOI: 10.1016/j.tube.2020.101988] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 02/07/2023]
Abstract
This study aimed to evaluate the performance of real-time PCR (qPCR) and MALDI-TOF for accurate and timely detection of nontuberculous mycobacterium (NTM) from clinical isolates. We collected fifty NTM suspected Mycobacteria Growth Indicator Tube (MGIT) cultures and analysed the diagnostic performance of qPCR and VITEK MS using Line Probe Assay (LPA) GenoType CM (Common Mycobacteria) as gold standard. The qPCR assays targeting 16S rRNA, ITS and IS6110 genes were developed for the identification of NTM and Mycobacterium tuberculosis complex (MTBC). LPA GenoType CM, a PCR technique targeting 23S rRNA gene, followed by reverse hybridization and line probe technology identified 90% of Mycobacterium species including M. fortuitum (16%,n = 8), M. intracellulare (10%,n = 5), M. gordonae (10%,n = 5), M. xenopi (4%,n = 2), M. scrofulaceum (4%,n = 2), Mycobacterium additional species (AS) (32%,n = 16) and MTBC (14%,n = 7), qPCR detected 80% of Mycobacterium species (NTM, 66% (n = 33) and MTBC, 14% (n = 7)) and MALDI-TOF, 52% (M. fortuitum (12%,n = 6), M. intracellulare (10%, n = 5), M. simiae (8%,n = 4), M. gordonae (8%,n = 4), and MTBC (14%,n = 7)). Sensitivity of qPCR and MALDI-TOF was 88.9% and 57.8%, respectively with 100% specificity. The combination of qPCR and MALDI-TOF remains an appropriate test for timely diagnosis of Mycobacterium species. This may eventually assist to detect the cases that may have been missed by phenotypic tests and enhance the NTM diagnosis capability to improve effective patient management.
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Affiliation(s)
- Ellappan Kalaiarasan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Kalpana Thangavelu
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Krishnakumariamma Krishnapriya
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
| | - Muthaiah Muthuraj
- Intermediate Reference Laboratory, Government Hospital for Chest Diseases, Pondicherry, India
| | - Maria Jose
- Intermediate Reference Laboratory, Government Hospital for Chest Diseases, Pondicherry, India
| | - Noyal Mariya Joseph
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India.
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26
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Ghielmetti G, Hilbe M, Friedel U, Menegatti C, Bacciarini L, Stephan R, Bloemberg G. Mycobacterial infections in wild boars (Sus scrofa) from Southern Switzerland: Diagnostic improvements, epidemiological situation and zoonotic potential. Transbound Emerg Dis 2020; 68:573-586. [PMID: 32640107 PMCID: PMC8247353 DOI: 10.1111/tbed.13717] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
The occurrence of mycobacterial infections in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. In addition to the well-known pathogenic members of the Mycobacterium tuberculosis - complex (MTBC), over 180 non-tuberculous mycobacteria (NTM) species have been described. Although the large majority of the NTM is assumed to be non-pathogenic to most individuals, an increasing trend in NTM infections has been observed over the last decades. The reasons of such augmentation are probably more than one: improved laboratory diagnostics, an increasing number of immunocompromised patients and individuals with lung damage are some of the possible aspects. Mandibular lymph nodes of 176 hunted wild boars from the pre-Alpine region of Canton Ticino, Switzerland, were collected. Following gross inspection, each lymph node was subjected to culture and to an IS6110 based real-time PCR specific for MTBC members. Histology was performed of a selection of lymph nodes (n = 14) presenting gross visible lesions. Moreover, accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) species identification was compared with sequence analysis of a combination of housekeeping genes. Mycobacteria of the MTBC were detected in 2.8% of the wild boars (n = 5; CI95% 1.2-6.5) and were all confirmed to be Mycobacterium microti by molecular methods. In addition, based on the examined lymph nodes, NTM were detected in 57.4% (n = 101; CI95% 50.0-64.5) of the wild boars originating from the study area. The 111 isolates belonged to 24 known species and three potentially undescribed Mycobacterium species. M. avium subsp. hominissuis thereby predominated (22.5%) and was found in lymph nodes with and without macroscopic changes. Overall, the present findings show that, with the exception of undescribed Mycobacterium species where identification was not possible (3.6%; 4/111), MALDI-TOF MS had a high concordance rate (90.1%; 100/111 isolates) to the sequence-based reference method.
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Affiliation(s)
- Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Monika Hilbe
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | - Ute Friedel
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Guido Bloemberg
- Institute for Food Safety and Hygiene, National Reference Center for Enteropathogenic Bacteria and Listeria, University of Zurich, Zurich, Switzerland
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