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Murray KN, Polley TM, Whipps CM, Hurley KM, Miller JH, Kent ML. Acute mortality in laboratory medaka (Oryzias latipes). J Am Vet Med Assoc 2023; 261:1-4. [PMID: 37699544 PMCID: PMC10911073 DOI: 10.2460/javma.23.07.0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023]
Affiliation(s)
- Katrina N Murray
- 1Zebrafish International Resource Center, University of Oregon, Eugene, OR
| | - Tamsen M Polley
- 2Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR
| | - Christopher M Whipps
- 3Department of Environmental Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY
| | | | | | - Michael L Kent
- 1Zebrafish International Resource Center, University of Oregon, Eugene, OR
- 5Department of Microbiology, College of Science, Oregon State University, Corvallis, OR
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2
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Yang L, Ding F, Lin Q, Xie J, Fan W, Dai F, Cui P, Liu W. A tool to automatically design multiplex PCR primer pairs for specific targets using diverse templates. Sci Rep 2023; 13:16451. [PMID: 37777580 PMCID: PMC10542359 DOI: 10.1038/s41598-023-43825-0] [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: 07/21/2023] [Accepted: 09/28/2023] [Indexed: 10/02/2023] Open
Abstract
Multiplex PCR is an increasingly popular method for identifying species, investigating environmental diversity, and conducting phylogenetic analysis. The complexity and increasing availability of diverse templates necessitate a highly automated approach to design degenerate primer pairs for specific targets with multiple sequences. Existing tools for degenerate primer design suffer from poor maintenance, semi-automation, low adaptability, and low tolerance for gaps. We developed PMPrimer, a Python-based tool for automated design and evaluation of multiplex PCR primer pairs for specific targets using diverse templates. PMPrimer automatically designs optimal multiplex PCR primer pairs using a statistical-based template filter; performs multiple sequence alignment, conserved region identification, and primer design; and evaluates the primers based on template coverage, taxon specificity, and target specificity. PMPrimer identifies conserved regions using Shannon's entropy method, tolerates gaps using a haplotype-based method, and evaluates multiplex PCR primer pairs based on template coverage and taxon specificity. We tested PMPrimer using datasets with diverse levels of conservation, sizes, and applications, including tuf genes of Staphylococci, hsp65 genes of Mycobacteriaceae, and 16S ribosomal RNA genes of Archaea. PMPrimer showed outstanding performance compared with existing tools and experimental validated primers. PMPrimer is available as a Python package at https://github.com/AGIScuipeng/PMPrimer .
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Affiliation(s)
- Lin Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China
| | - Feng Ding
- Shenzhen National Clinical Research Center for Infectious Diseases, No. 29, Bulan Road, Longgang District, Shenzhen, 518112, China
| | - Qiang Lin
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Junhua Xie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Wei Fan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, 400715, China.
| | - Peng Cui
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Wanfei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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3
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Jouet A, Braet SM, Gaudin C, Bisch G, Vasconcellos S, Epaminondas Nicacio de Oliveira do Livramento RE, Prado Palacios YY, Fontes AB, Lucena N, Rosa P, Moraes M, La K, Badalato N, Lenoir E, Ferré A, Clément M, Hasker E, Grillone SH, Abdou W, Said A, Assoumani Y, Attoumani N, Laurent Y, Cambau E, de Jong BC, Suffys PN, Supply P. Hi-plex deep amplicon sequencing for identification, high-resolution genotyping and multidrug resistance prediction of Mycobacterium leprae directly from patient biopsies by using Deeplex Myc-Lep. EBioMedicine 2023; 93:104649. [PMID: 37327675 DOI: 10.1016/j.ebiom.2023.104649] [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: 02/08/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Expansion of antimicrobial resistance monitoring and epidemiological surveillance are key components of the WHO strategy towards zero leprosy. The inability to grow Mycobacterium leprae in vitro precludes routine phenotypic drug susceptibility testing, and only limited molecular tests are available. We evaluated a culture-free targeted deep sequencing assay, for mycobacterial identification, genotyping based on 18 canonical SNPs and 11 core variable-number tandem-repeat (VNTR) markers, and detection of rifampicin, dapsone and fluoroquinolone resistance-associated mutations in rpoB/ctpC/ctpI, folP1, gyrA/gyrB, respectively, and hypermutation-associated mutations in nth. METHODS The limit of detection (LOD) was determined using DNA of M. leprae reference strains and from 246 skin biopsies and 74 slit skin smears of leprosy patients, with genome copies quantified by RLEP qPCR. Sequencing results were evaluated versus whole genome sequencing (WGS) data of 14 strains, and versus VNTR-fragment length analysis (FLA) results of 89 clinical specimens. FINDINGS The LOD for sequencing success ranged between 80 and 3000 genome copies, depending on the sample type. The LOD for minority variants was 10%. All SNPs detected in targets by WGS were identified except in a clinical sample where WGS revealed two dapsone resistance-conferring mutations instead of one by Deeplex Myc-Lep, due to partial duplication of the sulfamide-binding domain in folP1. SNPs detected uniquely by Deeplex Myc-Lep were missed by WGS due to insufficient coverage. Concordance with VNTR-FLA results was 99.4% (926/932 alleles). INTERPRETATION Deeplex Myc-Lep may help improve the diagnosis and surveillance of leprosy. Gene domain duplication is an original putative drug resistance-related genetic adaptation in M. leprae. FUNDING EDCTP2 programme supported by the European Union (grant number RIA2017NIM-1847 -PEOPLE). EDCTP, R2Stop: Effect:Hope, The Mission To End Leprosy, the Flemish Fonds Wetenschappelijk Onderzoek.
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Affiliation(s)
| | - Sofie Marijke Braet
- Institute of Tropical Medicine, Antwerp, Belgium; Department of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium; Research Foundation Flanders, Brussels, Belgium
| | | | | | - Sidra Vasconcellos
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | - Yrneh Yadamis Prado Palacios
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | | | | | - Patricia Rosa
- Instituto Lauro de Souza Lima, Bauru, São Paulo, Brazil
| | | | - Kevin La
- APHP-GHU Paris Nord Hôpital Bichat, Service de mycobactériologie spécialisée et de référence, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France; Université Paris Cité, INSERM, IAME UMR1137, Paris, France
| | | | | | | | | | - Epco Hasker
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | | | - Younoussa Assoumani
- Damien Foundation, Comoros; National Tuberculosis and Leprosy Control Program, Moroni, Comoros
| | | | | | - Emmanuelle Cambau
- APHP-GHU Paris Nord Hôpital Bichat, Service de mycobactériologie spécialisée et de référence, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France; Université Paris Cité, INSERM, IAME UMR1137, Paris, France
| | | | - Philip Noël Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil
| | - Philip Supply
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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5
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NonTuberculous Mycobacteria Blood Stream Infection in Pediatric and Adult Patients: 15 Years Surveillance. Pediatr Infect Dis J 2022; 41:e216-e219. [PMID: 35093997 DOI: 10.1097/inf.0000000000003473] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Nontuberculous Mycobacteria (NTM) are rare causes of bloodstream infection (BSI). This study addresses the management and prognosis of NTM BSI and the differences between adult and pediatric patients. METHODS We retrospectively reviewed the medical charts of patients at any age with NTM BSI, from January 1, 2005, to June 30, 2020. Data on demographics, underlying conditions, clinical manifestations, NTM species, antibiotic treatments and outcomes were retrieved. RESULTS Positive blood cultures for NTM were detected in 43 patients, 30 children and 13 adults. Median age: 10.37 years (IQR 6.692-39.864). Thirty-seven (86%) patients had an active malignant disease. Fever was the chief sign in 23 (53.5%) patients and pulmonary manifestations in 14 (32.6%). Rapidly growing NTM comprised 39 (90.7%) of the isolates. Central venous catheter (CVC) was documented in 39 (90.7%) cases, 31 (79.5%) of which were removed as part of treatment. Antibiotic treatment directed against NTM was documented in 26 (60.5%) patients. CVC was removed in 7/17 patients who were not treated with antibiotics. Relapse occurred in 3 cases; no 30-days mortality was reported. Children and adults had similar clinical characteristics. However, children had a higher rate of CVC at the time of bacteremia and a higher chance to receive treatment. CONCLUSION NTM BSI was seen mainly in oncologic patients with CVC. Children and adults had a similar disease course and outcome. Relapse was rare and NTM-related mortality was not reported.
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6
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Bogaerts B, Delcourt T, Soetaert K, Boarbi S, Ceyssens PJ, Winand R, Van Braekel J, De Keersmaecker SCJ, Roosens NHC, Marchal K, Mathys V, Vanneste K. A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches. J Clin Microbiol 2021; 59:e00202-21. [PMID: 33789960 PMCID: PMC8316078 DOI: 10.1128/jcm.00202-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/27/2021] [Indexed: 01/18/2023] Open
Abstract
The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.
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Affiliation(s)
- Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Julien Van Braekel
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, Internet Technology and Data Science Lab (IDLab), Interuniversity Microelectronics Centre (IMEC), Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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Jouet A, Gaudin C, Badalato N, Allix-Béguec C, Duthoy S, Ferré A, Diels M, Laurent Y, Contreras S, Feuerriegel S, Niemann S, André E, Kaswa MK, Tagliani E, Cabibbe A, Mathys V, Cirillo D, de Jong BC, Rigouts L, Supply P. Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs. Eur Respir J 2021; 57:13993003.02338-2020. [PMID: 32943401 PMCID: PMC8174722 DOI: 10.1183/13993003.02338-2020] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023]
Abstract
Conventional molecular tests for detecting Mycobacterium tuberculosis complex (MTBC) drug resistance on clinical samples cover a limited set of mutations. Whole-genome sequencing (WGS) typically requires culture. Here, we evaluated the Deeplex Myc-TB targeted deep-sequencing assay for prediction of resistance to 13 anti-tuberculous drugs/drug classes, directly applicable on sputum. With MTBC DNA tests, the limit of detection was 100–1000 genome copies for fixed resistance mutations. Deeplex Myc-TB captured in silico 97.1–99.3% of resistance phenotypes correctly predicted by WGS from 3651 MTBC genomes. On 429 isolates, the assay predicted 92.2% of 2369 first- and second-line phenotypes, with a sensitivity of 95.3% and a specificity of 97.4%. 56 out of 69 (81.2%) residual discrepancies with phenotypic results involved pyrazinamide, ethambutol and ethionamide, and low-level rifampicin or isoniazid resistance mutations, all notoriously prone to phenotypic testing variability. Only two out of 91 (2.2%) resistance phenotypes undetected by Deeplex Myc-TB had known resistance-associated mutations by WGS analysis outside Deeplex Myc-TB targets. Phenotype predictions from Deeplex Myc-TB analysis directly on 109 sputa from a Djibouti survey matched those of MTBSeq/PhyResSE/Mykrobe, fed with WGS data from subsequent cultures, with a sensitivity of 93.5/98.5/93.1% and a specificity of 98.5/97.2/95.3%, respectively. Most residual discordances involved gene deletions/indels and 3–12% heteroresistant calls undetected by WGS analysis or natural pyrazinamide resistance of globally rare “Mycobacterium canettii” strains then unreported by Deeplex Myc-TB. On 1494 arduous sputa from a Democratic Republic of the Congo survey, 14 902 out of 19 422 (76.7%) possible susceptible or resistance phenotypes could be predicted culture-free. Deeplex Myc-TB may enable fast, tailored tuberculosis treatment. The novel Deeplex Myc-TB molecular assay shows a high degree of accuracy for extensive prediction of susceptibility and resistance to 13 anti-tuberculous drugs, directly achievable without culture, which may enable fast, tailored tuberculosis treatmenthttps://bit.ly/3bAvcAt
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Affiliation(s)
- Agathe Jouet
- GenoScreen, Lille, France.,These authors contributed equally to this work
| | - Cyril Gaudin
- GenoScreen, Lille, France.,These authors contributed equally to this work
| | | | | | | | | | - Maren Diels
- BCCM/ITM, Mycobacteria Collection, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel, Borstel, Germany
| | - Emmanuel André
- Laboratory of Clinical Bacteriology and Mycology, Dept of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Michel K Kaswa
- National Tuberculosis Program, Kinshasa, Democratic Republic of the Congo
| | - Elisa Tagliani
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Cabibbe
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Daniela Cirillo
- Emerging Bacterial Pathogens, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bouke C de Jong
- Mycobacteriology Unit, Dept of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Dept of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Dept of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Philip Supply
- Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL (Center for Infection and Immunity of Lille), Lille, France
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8
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Molecular identification of Mycobacterium spp. isolated from Brazilian wild boars. Mol Biol Rep 2021; 48:1025-1031. [PMID: 33394225 DOI: 10.1007/s11033-020-06118-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
Wild boars (Sus scrofa) are susceptible to mycobacterial infections, including tuberculous and non-tuberculous mycobacteria. Recently, Mycobacterium spp. infections were described in Brazilian wild boars, which can act as bacterial reservoirs. Here, we aim to characterize 15 Mycobacterium spp. isolates from Brazilian wild boars' tissues through partial sequencing of the heat shock protein 65 (hsp65) gene and phylogenetic analysis. The isolates were classified as M. tuberculosis (33.3%), M. colombiense (33.3%), M. avium subsp. hominissuis (13.3%), M. parmense (13.3%) and M. mantenii (6.66%). The isolates classified as M. tuberculosis were confirmed as variant bovis by PCR. At phylogenetic analysis some isolates formed separated clades, indicating genetic variability. Different Mycobacterium species were recovered from wild boars circulating in Brazil, including mycobacteria associated to zoonotic infections, such as M. tuberculosis. In addition, this is the first report in Brazilian wild boars on M. mantenii and M. parmense detection, two recently described pathogenic mycobacteria. However, the isolates' genetic diversity-i.e. identities lower than 100% when compared to reference sequences-suggests that other genotyping tools would allow a deeper characterization. Nonetheless, the reported data contributes to the knowledge on mycobacterial infections in wild boars from Brazil.
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Ghielmetti G, Rosato G, Trovato A, Friedel U, Kirchgaessner C, Perroulaz C, Pendl W, Schulthess B, Bloemberg GV, Keller PM, Stephan R, Tortoli E. Mycobacterium helveticum sp. nov., a novel slowly growing mycobacterial species associated with granulomatous lesions in adult swine. Int J Syst Evol Microbiol 2020; 71. [PMID: 33355527 PMCID: PMC7968739 DOI: 10.1099/ijsem.0.004615] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The occurrence of nontuberculous mycobacteria in different hosts and their implication as obligate or opportunistic pathogens remain mainly unclear. Mycobacteriosis in pigs is usually associated with members of the Mycobacterium avium complex and, in particular, with ‘Mycobacterium avium subsp. hominissuis’. Here we describe a novel slow-growing mycobacterial species isolated from lymph nodes obtained from two sows housed in different Swiss farms. The animals presented chronic inappetence and mild diarrhoea. Gross pathology revealed focal caseous lymphadenopathy of the mesenteric lymph nodes. Complete genome sequencing of the two isolates from the two sows was performed. The genomes comprised 5.76 Mb and an average nucleotide identity score of 99.97 %. Whole genome sequence, mycolic acid and matrix-assisted laser desorption ionization-time of flight mass spectrometry analyses revealed that the two isolates were not related to any previously described Mycobacterium species. The closest related species was Mycobacterium parmense, a slow-growing scotochromogenic mycobacterium first isolated from a cervical lymph node of a 3-year-old child. The name proposed for the new species is Mycobacterium helveticum sp. nov. and 16-83T (=DSM 109965T= LMG 2019-02457T) is the type strain.
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Affiliation(s)
- Giovanni Ghielmetti
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Giovanni Ghielmetti,
| | - Giuliana Rosato
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Alberto Trovato
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Ute Friedel
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Constanze Kirchgaessner
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Carmen Perroulaz
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Wolfgang Pendl
- Department for Farm Animals, Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Bettina Schulthess
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Guido V. Bloemberg
- Institute for Food Safety and Hygiene, Swiss National Centre for Enteropathogenic Bacteria and Listeria, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Peter M. Keller
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Section of Veterinary Bacteriology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
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10
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Identification and drug susceptibility testing for nontuberculous mycobacteria. J Formos Med Assoc 2020; 119 Suppl 1:S32-S41. [DOI: 10.1016/j.jfma.2020.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/23/2020] [Accepted: 05/04/2020] [Indexed: 11/17/2022] Open
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11
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Seasonal Variability in the Microbial Community and Pathogens in Wastewater Final Effluents. WATER 2019. [DOI: 10.3390/w11122586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Numerous bacteria, especially pathogens, exist in wastewater final effluents, which can lead to possible human health and ecological security risks when effluents are reused or discharged. However, the diversity, composition, and spatiotemporal dynamics of bacteria in wastewater final effluents remain poorly understood. In this study, a comprehensive analysis of the microbial community and pathogens in wastewater final effluents was performed using high-throughput sequencing. The results revealed that wastewater final effluents in autumn exhibited the highest bacterial community richness and diversity, while those in winter exhibited the lowest. Bacteria in wastewater final effluents predominantly belonged to five phyla, in the order of Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Firmicutes. At the species level, there were 8~15 dominant species in the wastewater final effluent in each season, and Dokdonella immobilis, Rhizobium gallicum, Candidatus Flaviluna lacus, and Planctomyces limnophilus were the most dominant species in spring, summer, autumn, and winter, respectively. The seasonal variability in bacteria suggested that the microbial diversity and community in wastewater final effluents were mainly influenced by temperature, salinity, disinfection methods, and flocculants. Notably, pathogenic bacteria in wastewater effluents had both the highest relative abundance and species abundance in summer. Arcobacter spp., Legionella spp., and Mycobacterium spp. were the dominant pathogenic bacteria, and all pathogenic bacteria were mainly associated with dermatosis, enteropathies, septicemia, and pneumonia.
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A Global Survey of Mycobacterial Diversity in Soil. Appl Environ Microbiol 2019; 85:AEM.01180-19. [PMID: 31253672 DOI: 10.1128/aem.01180-19] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/20/2019] [Indexed: 12/14/2022] Open
Abstract
Mycobacteria are a diverse bacterial group ubiquitous in many soil and aquatic environments. Members of this group have been associated with human and other animal diseases, including the nontuberculous mycobacteria (NTM), which are of growing relevance to public health worldwide. Although soils are often considered an important source of environmentally acquired NTM infections, the biodiversity and ecological preferences of soil mycobacteria remain largely unexplored across contrasting climates and ecosystem types. Using a culture-independent approach by combining 16S rRNA marker gene sequencing with mycobacterium-specific hsp65 gene sequencing, we analyzed the diversity, distributions, and environmental preferences of soil-dwelling mycobacteria in 143 soil samples collected from a broad range of ecosystem types. The surveyed soils harbored highly diverse mycobacterial communities that span the full extent of the known mycobacterial phylogeny, with most soil mycobacteria (97% of mycobacterial clades) belonging to previously undescribed lineages. While mycobacteria tended to have higher relative abundances in cool, wet, and acidic soil environments, several individual mycobacterial clades had contrasting environmental preferences. We identified the environmental preferences of many mycobacterial clades, including the clinically relevant Mycobacterium avium complex that was more commonly detected in wet and acidic soils. However, most of the soil mycobacteria detected were not closely related to known pathogens, calling into question previous assumptions about the general importance of soil as a source of NTM infections. Together, this work provides novel insights into the diversity, distributions, and ecological preferences of soil mycobacteria and lays the foundation for future efforts to link mycobacterial phenotypes to their distributions.IMPORTANCE Mycobacteria are common inhabitants of soil, and while most members of this bacterial group are innocuous, some mycobacteria can cause environmentally acquired infections of humans and other animals. Human infections from nontuberculous mycobacteria (NTM) are increasingly prevalent worldwide, and some areas appear to be "hotspots" for NTM disease. While exposure to soil is frequently implicated as an important mode of NTM transmission, the diversity, distributions, and ecological preferences of soil mycobacteria remain poorly understood. We analyzed 143 soils from a range of ecosystems and found that mycobacteria and lineages within the group often exhibited predictable preferences for specific environmental conditions. Soils harbor large amounts of previously undescribed mycobacterial diversity, and lineages that include known pathogens were rarely detected in soil. Together, these findings suggest that soil is an unlikely source of many mycobacterial infections. The biogeographical patterns we documented lend insight into the ecology of this important group of soil-dwelling bacteria.
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Abstract
Bacteria thrive in showerheads and throughout household water distribution systems. While most of these bacteria are innocuous, some are potential pathogens, including members of the genus Mycobacterium that can cause nontuberculous mycobacterial (NTM) lung infection, an increasing threat to public health. We found that showerheads in households across the United States and Europe often harbor abundant mycobacterial communities that vary in composition depending on geographic location, water chemistry, and water source, with households receiving water treated with chlorine disinfectants having particularly high abundances of certain mycobacteria. The regions in the United States where NTM lung infections are most common were the same regions where pathogenic mycobacteria were most prevalent in showerheads, highlighting the important role of showerheads in the transmission of NTM infections. Bacteria within the genus Mycobacterium can be abundant in showerheads, and the inhalation of aerosolized mycobacteria while showering has been implicated as a mode of transmission in nontuberculous mycobacterial (NTM) lung infections. Despite their importance, the diversity, distributions, and environmental predictors of showerhead-associated mycobacteria remain largely unresolved. To address these knowledge gaps, we worked with citizen scientists to collect showerhead biofilm samples and associated water chemistry data from 656 households located across the United States and Europe. Our cultivation-independent analyses revealed that the genus Mycobacterium was consistently the most abundant genus of bacteria detected in residential showerheads, and yet mycobacterial diversity and abundances were highly variable. Mycobacteria were far more abundant, on average, in showerheads receiving municipal water than in those receiving well water and in U.S. households than in European households, patterns that are likely driven by differences in the use of chlorine disinfectants. Moreover, we found that water source, water chemistry, and household location also influenced the prevalence of specific mycobacterial lineages detected in showerheads. We identified geographic regions within the United States where showerheads have particularly high abundances of potentially pathogenic lineages of mycobacteria, and these “hot spots” generally overlapped those regions where NTM lung disease is most prevalent. Together, these results emphasize the public health relevance of mycobacteria in showerhead biofilms. They further demonstrate that mycobacterial distributions in showerhead biofilms are often predictable from household location and water chemistry, knowledge that advances our understanding of NTM transmission dynamics and the development of strategies to reduce exposures to these emerging pathogens.
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A Geospatial Epidemiologic Analysis of Nontuberculous Mycobacterial Infection: An Ecological Study in Colorado. Ann Am Thorac Soc 2018; 14:1523-1532. [PMID: 28594574 DOI: 10.1513/annalsats.201701-081oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RATIONALE Nontuberculous mycobacteria (NTM) are ubiquitous environmental microorganisms. Infection is thought to result primarily from exposure to soil and/or water sources. NTM disease prevalence varies greatly by geographic region, but the geospatial factors influencing this variation remain unclear. OBJECTIVES To identify sociodemographic and environmental ecological risk factors associated with NTM infection and disease in Colorado. METHODS We conducted an ecological study, combining data from patients with a diagnosis of NTM disease from National Jewish Health's electronic medical record database and ZIP code-level sociodemographic and environmental exposure data obtained from the U.S. Geological Survey, the U.S. Department of Agriculture, and the U.S. Census Bureau. We used spatial scan methods to identify high-risk clusters of NTM disease in Colorado. Ecological risk factors for disease were assessed using Bayesian generalized linear models assuming Poisson-distributed discrete responses (case counts by ZIP code) with the log link function. RESULTS We identified two statistically significant high-risk clusters of disease. The primary cluster included ZIP codes in urban regions of Denver and Aurora, as well as regions south of Denver, on the east side of the Continental Divide. The secondary cluster was located on the west side of the Continental Divide in rural and mountainous regions. After adjustment for sociodemographic, drive time, and soil variables, we identified three watershed areas with relative risks of 12.2, 4.6, and 4.2 for slowly growing NTM infections compared with the mean disease risk for all watersheds in Colorado. This study population carries with it inherent limitations that may introduce bias. The lack of complete capture of NTM cases in Colorado may be related to factors such as disease severity, education and income levels, and insurance status. CONCLUSIONS Our findings provide evidence that water derived from particular watersheds may be an important source of NTM exposure in Colorado. The watershed with the greatest risk of NTM disease contains the Dillon Reservoir. This reservoir is also the main water supply for major cities located in the two watersheds with the second and third highest disease risk in the state, suggesting an important possible source of infection.
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Lecorche E, Haenn S, Mougari F, Kumanski S, Veziris N, Benmansour H, Raskine L, Moulin L, Cambau E, Aubry A, Brossier F, Chauffour A, Jaffre J, Jarlier V, Robert J, Sougakoff W. Comparison of methods available for identification of Mycobacterium chimaera. Clin Microbiol Infect 2018; 24:409-413. [DOI: 10.1016/j.cmi.2017.07.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 10/19/2022]
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Bao JR, Clark RB, Master RN, Shier KL, Eklund LL. Acid-fast bacterium detection and identification from paraffin-embedded tissues using a PCR-pyrosequencing method. J Clin Pathol 2017; 71:148-153. [DOI: 10.1136/jclinpath-2016-204128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 01/15/2023]
Abstract
AimsAcid-fast bacterium (AFB) identification from formalin-fixed paraffin-embedded (FFPE) tissues is challenging and may not be readily available to the clinical laboratory. A method to detect and identify AFB from FFPE tissues using PCR and pyrosequencing (PCR-Seq) was developed and evaluated.MethodsThe method was validated using spiked cell-clotted paraffin blocks before use with patients’ specimens. DNA was extracted from tissue sections, and a 16S rRNA gene fragment was amplified and a signature sequence was produced on a PyroMark ID system. Sequences were aligned to established databases for AFB identification. Additional tissue sections were stained and examined for AFB.ResultsBoth sensitivity and specificity were 100% on spiked cell-clotted blocks without cross-reactivity with non-AFB. Of 302 FFPE tissues from patients, 116 (38%) were AFB-stain positive; 83 (72%) of these had AFB identified. The 21 AFB identified included Mycobacterium tuberculosis complex (14 cases), Mycobacterium leprae (3), Mycobacterium genavense (2), Mycobacterium marinum-ulcerans group (3) and 17 other AFB (61). Thirteen cases were AFB-stain indeterminate and 4 were positive by the PCR-Seq method. Of the AFB stain-negative cases, 167 were negative and 6 were positive by PCR-Seq.ConclusionsThe PCR-Seq method provided specific identification of various AFB species or complexes from FFPE tissues.
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Mycobacterium arupense, Mycobacterium heraklionense, and a Newly Proposed Species, "Mycobacterium virginiense" sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis. J Clin Microbiol 2016; 54:1340-51. [PMID: 26962085 DOI: 10.1128/jcm.00198-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 03/01/2016] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium terrae complex has been recognized as a cause of tenosynovitis, with M. terrae and Mycobacterium nonchromogenicum reported as the primary etiologic pathogens. The molecular taxonomy of the M. terrae complex causing tenosynovitis has not been established despite approximately 50 previously reported cases. We evaluated 26 isolates of the M. terrae complex associated with tenosynovitis or osteomyelitis recovered between 1984 and 2014 from 13 states, including 5 isolates reported in 1991 as M. nonchromogenicum by nonmolecular methods. The isolates belonged to three validated species, one new proposed species, and two novel related strains. The majority of isolates (20/26, or 77%) belonged to two recently described species: Mycobacterium arupense (10 isolates, or 38%) and Mycobacterium heraklionense (10 isolates, or 38%). Three isolates (12%) had 100% sequence identity to each other by 16S rRNA and 99.3 to 100% identity by rpoB gene region V sequencing and represent a previously undescribed species within the M. terrae complex. There were no isolates of M. terrae or M. nonchromogenicum, including among the five isolates reported in 1991. The 26 isolates were susceptible to clarithromycin (100%), rifabutin (100%), ethambutol (92%), and sulfamethoxazole or trimethoprim-sulfamethoxazole (70%). The current study suggests that M. arupense, M. heraklionense, and a newly proposed species ("M. virginiense" sp. nov.; proposed type strain MO-233 [DSM 100883, CIP 110918]) within the M. terrae complex are the major causes of tenosynovitis and osteomyelitis in the United States, with little change over 20 years. Species identification within this complex requires sequencing methods.
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Guglielmetti L, Mougari F, Lopes A, Raskine L, Cambau E. Human infections due to nontuberculous mycobacteria: the infectious diseases and clinical microbiology specialists' point of view. Future Microbiol 2015; 10:1467-83. [PMID: 26344005 DOI: 10.2217/fmb.15.64] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Nontuberculous mycobacteria (>150 species such as Mycobacterium avium, Mycobacterium kansasii, Mycobacterium chelonae and Mycobacterium abscessus) are opportunistic pathogens causing lung and extrarespiratory infections, beside M. ulcerans and M. marinum that are pathogens causing specific skin and soft tissue infections. Disseminated infections occur only in severe immunosuppressed conditions such as AIDS. The diagnosis is based on repeated isolations of the same mycobacterium associated with clinical and radiological signs, and the absence of tuberculosis. Precise species identification is obtained by molecular biology. Therapeutic antibiotic regimens differ with regard to the mycobacterial species that are involved. Prevention of iatrogenic infections relies on using sterile water in all injections, healthcare and cosmetic occupations. Future perspectives are to set effective antibiotic regimens tested in randomized therapeutic trials.
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Affiliation(s)
- Lorenzo Guglielmetti
- AP-HP, Hôpital Lariboisière-Fernand Widal, Service de Bactériologie, F-75010 Paris, France.,Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), F-75010 Paris, France.,Service de Maladies Infectieuses, Hôpital de Verona, Italie
| | - Faiza Mougari
- AP-HP, Hôpital Lariboisière-Fernand Widal, Service de Bactériologie, F-75010 Paris, France.,Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), F-75010 Paris, France.,IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France
| | - Amanda Lopes
- AP-HP, Hôpital Lariboisière-Fernand Widal, Service de Médecine interne 1, F-75475 Paris, France
| | - Laurent Raskine
- AP-HP, Hôpital Lariboisière-Fernand Widal, Service de Bactériologie, F-75010 Paris, France.,Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), F-75010 Paris, France
| | - Emmanuelle Cambau
- AP-HP, Hôpital Lariboisière-Fernand Widal, Service de Bactériologie, F-75010 Paris, France.,Centre National de Référence des Mycobactéries et Résistance des Mycobactéries aux Antituberculeux (CNR-MyRMA), F-75010 Paris, France.,IAME, UMR 1137, INSERM, Univ Paris Diderot, Sorbonne Paris Cité, F-75018 Paris, France
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Evaluation of the Ribosomal Protein S1 Gene (rpsA) as a Novel Biomarker for Mycobacterium Species Identification. BIOMED RESEARCH INTERNATIONAL 2015; 2015:271728. [PMID: 25945329 PMCID: PMC4402190 DOI: 10.1155/2015/271728] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 11/07/2014] [Indexed: 11/17/2022]
Abstract
Objectives. To evaluate the resolution and reliability of the rpsA gene, encoding ribosomal protein S1, as a novel biomarker for mycobacteria species identification. Methods. A segment of the rpsA gene (565 bp) was amplified by PCR from 42 mycobacterial reference strains, 172 nontuberculosis mycobacteria clinical isolates, and 16 M. tuberculosis complex clinical isolates. The PCR products were sequenced and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method. Results. Comparative sequence analysis of the rpsA gene provided the basis for species differentiation within the genus Mycobacterium. Slow- and rapid-growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. The sequences discrepancy was obvious between M. kansasii and M. gastri, M. chelonae and M. abscessus, M. avium and M. intracellulare, and M. szulgai and M. malmoense, which cannot be achieved by 16S ribosomal DNA (rDNA) homologue genes comparison. 183 of the 188 (97.3%) clinical isolates, consisting of 8 mycobacterial species, were identified correctly by rpsA gene blast. Conclusions. Our study indicates that rpsA sequencing can be used effectively for mycobacteria species identification as a supplement to 16S rDNA sequence analysis.
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Ngeow YF, Wong YL, Tan JL, Hong KW, Ng HF, Ong BL, Chan KG. Identification of new genomospecies in the Mycobacterium terrae complex. PLoS One 2015; 10:e0120789. [PMID: 25830768 PMCID: PMC4382200 DOI: 10.1371/journal.pone.0120789] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/06/2015] [Indexed: 11/24/2022] Open
Abstract
Members of the Mycobacterium terrae complex are slow-growing, non-chromogenic acid-fast bacilli found in the natural environment and occasionally in clinical material. These genetically closely-related members are difficult to differentiate by conventional phenotypic and molecular tests. In this paper we describe the use of whole genome data for the identification of four strains genetically similar to Mycobacterium sp. JDM601, a newly identified member of the M. terrae complex. Phylogenetic information from the alignment of genome-wide orthologous genes and single nucleotide polymorphisms show consistent clustering of the four strains together with M. sp. JDM601 into a distinct clade separate from other rapid and slow growing mycobacterial species. More detailed inter-strain comparisons using average nucleotide identity, tetra-nucleotide frequencies and analysis of synteny indicate that our strains are closely related to but not of the same species as M. sp. JDM601. Besides the 16S rRNA signature described previously for the M. terrae complex, five more hypothetical proteins were found that are potentially useful for the rapid identification of mycobacterial species belonging to the M. terrae complex. This paper illustrates the versatile utilization of whole genome data for the delineation of new bacterial species and introduces four new genomospecies to add to current members in the M. terrae complex.
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Affiliation(s)
- Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
| | - Yan Ling Wong
- 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
| | - Kar Wai Hong
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Hien Fuh Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Bee Lee Ong
- Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
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Mycobacterium phocaicum bacteremia: an emerging infection in pediatric hematology-oncology patients. Pediatr Infect Dis J 2014; 33:1299-301. [PMID: 25037036 DOI: 10.1097/inf.0000000000000477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Nontuberculous mycobacteria may cause central venous catheter-associated bacteremia. Between March 2011 and October 2013, 6 cases of Mycobacterium phocaicum bacteremia were found in the pediatric hematology-oncology department. All patients recovered. No positive blood culture was documented after removal of the central venous catheter. All 4 patients with pulsed field gel electrophoresis had the same pattern, different from the water sample, suggesting a common water source.
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Joao I, Cristovao P, Antunes L, Nunes B, Jordao L. Identification of nontuberculous mycobacteria by partial gene sequencing and public databases. Int J Mycobacteriol 2014; 3:144-51. [DOI: 10.1016/j.ijmyco.2014.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 04/07/2014] [Indexed: 11/26/2022] Open
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Mirsaeidi M, Farshidpour M, Ebrahimi G, Aliberti S, Falkinham JO. Management of nontuberculous mycobacterial infection in the elderly. Eur J Intern Med 2014; 25:356-63. [PMID: 24685313 PMCID: PMC4067452 DOI: 10.1016/j.ejim.2014.03.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 03/04/2014] [Accepted: 03/10/2014] [Indexed: 01/15/2023]
Abstract
The incidence of nontuberculous mycobacteria (NTM) has increased over the last decades. Elderly people are more susceptible to NTM and experience increased morbidities. NTM incidence is expected to rise due to an increasing elderly population at least up to 2050. Given the importance of NTM infection in the elderly, an increasing interest exists in studying NTM characteristics in the aged population. In this review, we summarize the characteristics of NTM infection among elderly patients. We focus on epidemiology, clinical presentation, and treatment options of NTM in this age group. We highlight the differences in the diagnosis and treatment between rapid and slow growing mycobacterial infections. The current recommendation for treatment of NTM is discussed. We debate if in vitro susceptibility testing has a role in the treatment of NTM. Drug-drug interaction between antibiotics used to treat NTM and other medications, particularly warfarin, is another important issue that we discuss. Finally, we review the prognosis of NTM disease in elderly patients.
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Affiliation(s)
- Mehdi Mirsaeidi
- Section of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine M/C 719, University of IL at Chicago, USA.
| | - Maham Farshidpour
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Golnaz Ebrahimi
- Section of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine M/C 719, University of IL at Chicago, USA
| | - Stefano Aliberti
- Department of Health Science, University of Milan Bicocca, Clinica Pneumologica, AO San Gerardo, Via Pergolesi 33, Monza, Italy
| | - Joseph O Falkinham
- Department of Biological Science, University of Virginia Tech, Blacksburg, VA, USA
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Distribution of nontuberculous mycobacteria by multigene sequence-based typing and clinical significance of isolated strains. J Clin Microbiol 2014; 52:1207-12. [PMID: 24501029 DOI: 10.1128/jcm.03053-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Species identification of nontuberculous mycobacteria (NTM) is challenging due to the increasing number of identified NTM species and the lack of standardized testing strategies. The objectives of this study were to investigate the distribution of NTM species recovered from respiratory specimens by multigene sequence-based typing and to evaluate the clinical significance of identified species. Two hundred thirty-two consecutive clinical NTM isolates were subjected to sequencing of multiple genes, including hsp65, rpoB, and 16S-23S rRNA internal transcribed spacer (ITS) sequence. In addition, clinical data from all patients whose specimens had NTM isolates were analyzed to examine clinical virulence and treatment history. Eighteen strains from 227 isolates from 169 patients were successfully identified at the species level by multigene sequence-based typing. Mycobacterium avium complex and M. abscessus complex made up the majority of isolated NTM (88%; 199/227), followed by M. fortuitum complex (4%; 10/227). The pathogenic potential of NTM differs enormously by species, and M. avium complex and M. abscessus complex revealed especially high levels of virulence compared with findings for other NTM species. The results from our work support M. avium complex and M. abscessus complex being the most common NTM species with highly pathogenic potential isolated from clinical respiratory specimens and could be a good resource for molecular epidemiology of NTM species in South Korea.
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Tan JL, Khang TF, Ngeow YF, Choo SW. A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus. BMC Genomics 2013; 14:879. [PMID: 24330254 PMCID: PMC3878664 DOI: 10.1186/1471-2164-14-879] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/10/2013] [Indexed: 11/22/2022] Open
Abstract
Background Mycobacterium abscessus is a rapidly growing mycobacterium that is often associated with human infections. The taxonomy of this species has undergone several revisions and is still being debated. In this study, we sequenced the genomes of 12 M. abscessus strains and used phylogenomic analysis to perform subspecies classification. Results A data mining approach was used to rank and select informative genes based on the relative entropy metric for the construction of a phylogenetic tree. The resulting tree topology was similar to that generated using the concatenation of five classical housekeeping genes: rpoB, hsp65, secA, recA and sodA. Additional support for the reliability of the subspecies classification came from the analysis of erm41 and ITS gene sequences, single nucleotide polymorphisms (SNPs)-based classification and strain clustering demonstrated by a variable number tandem repeat (VNTR) assay and a multilocus sequence analysis (MLSA). We subsequently found that the concatenation of a minimal set of three median-ranked genes: DNA polymerase III subunit alpha (polC), 4-hydroxy-2-ketovalerate aldolase (Hoa) and cell division protein FtsZ (ftsZ), is sufficient to recover the same tree topology. PCR assays designed specifically for these genes showed that all three genes could be amplified in the reference strain of M. abscessus ATCC 19977T. Conclusion This study provides proof of concept that whole-genome sequence-based data mining approach can provide confirmatory evidence of the phylogenetic informativeness of existing markers, as well as lead to the discovery of a more economical and informative set of markers that produces similar subspecies classification in M. abscessus. The systematic procedure used in this study to choose the informative minimal set of gene markers can potentially be applied to species or subspecies classification of other bacteria.
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Affiliation(s)
| | - Tsung Fei Khang
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Escobar-Escamilla N, Ramírez-González JE, González-Villa M, Torres-Mazadiego P, Mandujano-Martínez A, Barrón-Rivera C, Bäcker CE, Fragoso-Fonseca DE, Olivera-Díaz H, Alcántara-Pérez P, Hernández-Solís A, Cícero-Sabido R, Cortés-Ortíz IA. Hsp65 phylogenetic assay for molecular diagnosis of nontuberculous mycobacteria isolated in Mexico. Arch Med Res 2013; 45:90-7. [PMID: 24333253 DOI: 10.1016/j.arcmed.2013.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 10/22/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND AND AIMS Nontuberculous mycobacteria (NTM) are mainly distributed as important emerging pathogens in patients with chronic or immunosuppressive diseases. Accurate identification of causative species is crucial for proper treatment and patient follow-up. However, several difficulties are associated with phenotypic and molecular diagnostic methods for precise identification at the species level due to shared metabolic and genetic characteristics. We undertook this study to evaluate the application of the phylogenetic method based on hsp65 gene into Telenti's PCR-restriction enzyme analysis (PRA) for molecular identification of NTM. METHODS The study population was comprised of 1646 Mycobacterium clinical isolates (AFB positive) collected from 2008-2011, of which 537 (32.6%) were MNT identified by PRA analysis. DNA sequencing of hsp65 in 53 isolates (10%) was performed. Sequence identification through NCBI-Basic Local Alignment Search Tool (BLAST) achieved correct identification in 23 isolates. Phylogenetic trees including hsp65 available GenBank sequences for all described genres of NTM and hsp65 obtained sequences were constructed using Mega 5.05 software. We compared sequence identification based on phylogenetic clustering and BLAST similarity search. RESULTS Phylogenetic clustering allowed more specific differentiation of closely related species and clearer identification in comparison with BLAST; 30 Mycobacterium species (this is the first report of isolation of some of these from clinical samples in Mexico) were identified in this way. CONCLUSIONS The proposed 440 bp hsp65 phylogenetic method allows a better identification tool to differentiate Mycobacterium species and is useful to complement diagnosis and epidemiological surveillance of NTM.
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Affiliation(s)
- Noé Escobar-Escamilla
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - José Ernesto Ramírez-González
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Maribel González-Villa
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Pilar Torres-Mazadiego
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - América Mandujano-Martínez
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | | | | | - David Esaú Fragoso-Fonseca
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Hiram Olivera-Díaz
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Patricia Alcántara-Pérez
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico
| | - Alejandro Hernández-Solís
- Servicio de Neumología, Hospital General de México "Eduardo Liceaga", Secretaría de Salud, México, D.F., Mexico
| | - Raúl Cícero-Sabido
- Facultad de Medicina, Universidad Nacional Autónoma de México, México, D.F., Mexico
| | - Iliana Alejandra Cortés-Ortíz
- Departamento de Biología Molecular y Validación de Técnicas, Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Secretaría de Salud, México, D.F., Mexico.
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Daniels JB. Molecular diagnostics for infectious disease in small animal medicine: an overview from the laboratory. Vet Clin North Am Small Anim Pract 2013; 43:1373-84, vii. [PMID: 24144096 DOI: 10.1016/j.cvsm.2013.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular diagnostic tests have augmented the way in which veterinary practitioners approach the diagnosis of infectious disease. The technical bases of these tests are explained in addition to the general clinical applications for which they are most aptly suited, as individual assays are best discussed in the context of their respective diseases. In this article, an emphasis is placed on validation of molecular tests so that practitioners can be educated consumers of molecular diagnostics. The relationships between disease prevalence and positive and negative predictive values are discussed. Finally, examples of the pitfalls of multiplex polymerase chain reaction testing are illustrated.
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Affiliation(s)
- Joshua B Daniels
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, 601 Vernon Tharp Drive, Columbus, OH 43210, USA.
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Shukla S, Sharma R, Shukla SK. Detection and identification of globally distributed mycobacterial fish pathogens in some ornamental fish in India. Folia Microbiol (Praha) 2013; 58:429-36. [DOI: 10.1007/s12223-013-0225-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/17/2013] [Indexed: 10/27/2022]
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Enhancement of Conventional Phenotypic Methods with Molecular-Based Methods for the More Definitive Identification of Nontuberculous Mycobacteria. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.clinmicnews.2012.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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First report of disseminated Mycobacterium skin infections in two liver transplant recipients and rapid diagnosis by hsp65 gene sequencing. J Clin Microbiol 2011; 49:3733-8. [PMID: 21880973 DOI: 10.1128/jcm.05088-11] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We present here the first report of disseminated skin Mycobacterium infections in two liver transplant recipients, in which hsp65 gene sequencing was used for rapid species identification. Both patients had hepatitis B virus-related cirrhosis and diabetes mellitus and presented with progressive generalized, nodular skin lesions. In one patient, a 50-year-old woman who had frequent contact with marine fish, an acid-fast bacillus was isolated from skin biopsy tissue after 2 months of culture. While awaiting phenotypic identification results, hsp65 gene sequencing showed that it was most closely related to that of Mycobacterium marinum with 100% nucleotide identity. The patient was treated with oral rifampin, ethambutol, and moxifloxacin. In the other patient, a 59-year-old woman, direct PCR for Mycobacterium using hsp65 gene from skin biopsy tissue was positive, with the sequence most closely related to that of M. haemophilum with 100% nucleotide identity. Based on PCR results, the patient was treated with clarithromycin, ethambutol, moxifloxacin, and amikacin. A strain of M. haemophilum was only isolated after 3 months. Skin lesions of both patients resolved after 1 year of antimycobacterial therapy. Nontuberculous Mycobacterium infections should be considered in liver transplant recipients presenting with chronic, nodular skin lesions. This report highlights the crucial role of hsp65 gene PCR and sequencing on both cultured isolates and direct clinical specimens for rapid diagnosis of slow-growing Mycobacterium infection.
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