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Litterio M, Castello L, Venuta ME, Abel S, Fernández-Canigia L, Legaria MC, Rollet R, Vaustat D, Azula N, Fox B, Otero S, Maldonado ML, Mangieri NA, Rossetti MA, Predari SC, Cejas D, Barberis C. Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina. Rev Argent Microbiol 2024; 56:33-61. [PMID: 38368217 DOI: 10.1016/j.ram.2023.12.001] [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: 02/20/2023] [Revised: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 02/19/2024] Open
Abstract
The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.
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Affiliation(s)
- Mirta Litterio
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Liliana Castello
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Elena Venuta
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Sofía Abel
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - María Cristina Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - Raquel Rollet
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Daniela Vaustat
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Buenos Aires, Argentina
| | | | - Silvina Otero
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - Natalia Alejandra Mangieri
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Adelaida Rossetti
- Hospital Interzonal de Agudos Presidente Perón, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Silvia Carla Predari
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Buenos Aires, Argentina
| | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina.
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Cobo F, Pérez-Carrasco V, Martín-Hita L, García-Salcedo JA, Navarro-Marí JM. Comparative evaluation of MALDI-TOF MS and 16S rRNA gene sequencing for the identification of clinically relevant anaerobic bacteria: critical evaluation of discrepant results. Anaerobe 2023; 82:102754. [PMID: 37321445 DOI: 10.1016/j.anaerobe.2023.102754] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
OBJECTIVES The main study objective was to evaluate the correlation between matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing results for the identification of anaerobes. METHODS A retrospective study was conducted of all anaerobic bacteria isolated from clinically significant specimens. MALDI-TOF (Bruker Byotyper) and 16S rRNA gene sequencing were performed in all strains. Identifications were considered correct when the concordance with gene sequencing was ≥99%. RESULTS The study included 364 isolates of anaerobic bacteria: 201 (55.2%) Gram-negative and 163 (44.8%) Gram-positive, mostly belonging to the genus Bacteroides. Isolates were largely obtained from blood cultures (128/35.4%) and intra-abdominal samples (116/32.1%). Overall, 87.3% of isolates were identified at species level using the version 9 database (89.5% of Gram-negative and 84.6% of Gram-positive anaerobic bacteria). All isolates belonging to the species B. fragilis sensu stricto were correctly identified by MALDI-TOF MS, but five cases of Phocaeicola (Bacteroides) dorei were misidentified as Phocaeicola (Bacteroides) vulgatus; all Prevotella isolates were correctly identified at the genus level, and most were correctly identified at the species level. Among Gram-positive anaerobes, 12 Anaerococcus species were not identified by MALDI-TOF MS, while six cases identified as Peptoniphilus indolicus were found to belong to other genera/species. CONCLUSIONS MALDI-TOF is a reliable technique for identifying most anaerobic bacteria, although the database needs frequent updating to identify rare, infrequent, and newly discovered species.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain.
| | - Virginia Pérez-Carrasco
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - Lina Martín-Hita
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José Antonio García-Salcedo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves, Granada, Spain
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3
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Fernández Vecilla D, Roche Matheus MP, Iglesias Hidalgo G, Ugalde Zárraga E, Unzaga Barañano MJ, Díaz de Tuesta Del Arco JL. Two cases of Prevotella oris causing serious pleuropulmonary infections. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2023; 36:439-441. [PMID: 37184104 PMCID: PMC10336306 DOI: 10.37201/req/001.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/22/2023] [Accepted: 03/17/2023] [Indexed: 05/16/2023]
Affiliation(s)
- D Fernández Vecilla
- Domingo Fernández Vecilla, Clinical microbiology Service, Basurto University Hospital. Montevideo Avenue, 18, Gurtubay pavilion, 3rd floor. Postal code: 48013, Bilbao (Basque country). Spain.
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4
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Prevotella oris: A lesser KNOWN etiological agent of pleural effusion. Anaerobe 2022; 78:102644. [PMID: 36116686 DOI: 10.1016/j.anaerobe.2022.102644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/07/2022] [Accepted: 09/11/2022] [Indexed: 11/20/2022]
Abstract
Prevotella are gram negative, obligate anaerobes and includes pigmented and non-pigmented species. They are typically regarded as commensals, especially of the gastrointestinal tract and oral cavity, although opportunistic endogenous infections are known to be caused by a small number of strains. We report a case of a 51-year-old man with right-sided chest pain. Chest X-ray showed mild haziness in the right lung and he was diagnosed with right sided pleural effusion. Prevotella oris was isolated after pleural pus culture.
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5
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Webb KA, Olagoke O, Baird T, Neill J, Pham A, Wells TJ, Ramsay KA, Bell SC, Sarovich DS, Price EP. Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways. Microb Genom 2022; 8. [PMID: 35113778 PMCID: PMC8942031 DOI: 10.1099/mgen.0.000754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus Prevotella. Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of Prevotella species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid Prevotella species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of Prevotella and non-Prevotella species, followed by PCR screening of CF and COPD respiratory-derived cultures. Next, 35 PCR-positive isolates were subjected to whole-genome sequencing. Of eight identified Prevotella species, P. histicola, P. melaninogenica, P. nanceiensis, P. salivae and P. denticola overlapped between participant cohorts. Phylogenomic analysis revealed considerable interhost but limited intrahost diversity, suggesting patient-specific lineages in the lower airways, probably from oral cavity aspirations. Correlation of phenotypic AMR profiles with AMR genes identified excellent correlation between tetQ presence and decreased doxycycline susceptibility, and ermF presence and decreased azithromycin susceptibility and clindamycin resistance. AMR rates were higher in the CF isolates, reflecting greater antibiotic use in this cohort. All tested Prevotella isolates were tobramycin-resistant, providing a potential selection method to improve Prevotella culture retrieval rates. Our addition of 35 airway-derived Prevotella genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.
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Affiliation(s)
- Kasey A Webb
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Olusola Olagoke
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Timothy Baird
- Sunshine Coast Health Institute, Birtinya, Queensland, Australia.,Sunshine Coast Hospital and Health Service, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Jane Neill
- Sunshine Coast Hospital and Health Service, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Amy Pham
- University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Timothy J Wells
- University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Kay A Ramsay
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Present address: Child Health Research Centre, The University of Queensland, Centre for Children's Health Research, South Brisbane, Queensland, Australia
| | - Scott C Bell
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.,Adult Cystic Fibrosis Centre, The Prince Charles Hospital, Chermside, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Derek S Sarovich
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
| | - Erin P Price
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Sunshine Coast Health Institute, Birtinya, Queensland, Australia
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Prevotella in Pigs: The Positive and Negative Associations with Production and Health. Microorganisms 2020; 8:microorganisms8101584. [PMID: 33066697 PMCID: PMC7602465 DOI: 10.3390/microorganisms8101584] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/19/2022] Open
Abstract
A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.
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Toprak NU, Veloo ACM, Urban E, Wybo I, Jean-Pierre H, Morris T, Justesen US, Tripkovic V, Jeverica S, Soyletir G, Nagy E. Comparing identification of clinically relevant Prevotella species by VITEK MS and MALDI biotyper. Acta Microbiol Immunol Hung 2019; 67:6-13. [PMID: 31813262 DOI: 10.1556/030.66.2019.022] [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: 07/09/2019] [Accepted: 08/12/2019] [Indexed: 11/19/2022]
Abstract
In this multicenter study, we aimed to evaluate the performance of MALDI Biotyper and VITEK MS, for identification of Prevotella species. Three hundred and fourteen clinical isolates, collected in eight European countries between January 2014 and April 2016, were identified at the collecting sites by MALDI Biotyper (versions 3.0 and 3.1) and then reidentified by VITEK MS (version 3.0) in the central laboratory. 16S rRNA gene sequencing was used as a standard method. According to sequence analysis, the 314 Prevotella strains belonged to 19 species. MALDI Biotyper correctly identified 281 (89.5%) isolates to the species level and 33 (10.5%) only at the genus level. VITEK MS correctly identified 253 (80.6%) isolates at the species level and 276 (87.9%) isolates at the genus level. Thirty-three isolates belonging to P. bergensis, P. conceptionensis, P. corporis, P. histicola, and P. nanciensis, unavailable in the VITEK MS 3.0 database, were resulted in genus level or no identification. Six Prevotella strains, belonged to P. veroralis, P. timonensis, and P. conceptionensis not represented in the MALDI Biotyper system database, were misidentified at the genus level. In conclusion, both VITEK MS and MALDI Biotyper provided reliable and rapid identification. However, the permanent extension of the databases is needed.
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Affiliation(s)
- Nurver Ulger Toprak
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Alida C. M. Veloo
- Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Edit Urban
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Helene Jean-Pierre
- Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Centre Hospitalier Régional Universitaire de Montpellier, Montpellier, France
| | - Trefor Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - Ulrik Stenz Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Vesna Tripkovic
- Department of Clinical and Molecular Microbiology, University Hospital Center, Zagreb, Croatia
| | - Samo Jeverica
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Guner Soyletir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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8
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Mörtelmaier C, Panda S, Robertson I, Krell M, Christodoulou M, Reichardt N, Mulder I. Identification performance of MALDI-ToF-MS upon mono- and bi-microbial cultures is cell number and culture proportion dependent. Anal Bioanal Chem 2019; 411:7027-7038. [PMID: 31486868 PMCID: PMC6834929 DOI: 10.1007/s00216-019-02080-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/31/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023]
Abstract
Biotyping using matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) mass spectroscopy (MS) has revolutionized microbiology by allowing clinicians and scientists to rapidly identify microbes at genus and species levels. The present study extensively assesses the suitability and reliability of MALDI-ToF biotyping of 14 different aerobic and anaerobic bacterial species as pure and mixed cultures. Reliable identification at species level was possible from biomaterial of older colonies and even frozen biomaterial, although this was species dependent. Using standard instrument settings and direct application of biomaterial onto the MALDI-ToF target plates, it was determined that the cell densities necessary for completely reliable identification of pure cultures varied between 2.40 × 108 and 1.10 × 1010 viable cell counts (VCCs) per mL, depending on the species. Evaluation of the mixed culture algorithm of the Bruker Biotyper® software showed that the performance of the algorithm depends greatly on the targeted species, on their phylogenetic distance, and on their ratio of VCC per mL in the mixed culture. Hence, the use of MALDI-ToF-MS with incorporation of the mixed culture algorithm of the software is a useful pre-screening tool for early identification of contaminants, but due to the great variability in performance between different species and the usually unknown percentage of the possible contaminant in the mixture, it is advisable to combine this method with other microbiology methods.
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Affiliation(s)
| | - Suchita Panda
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
| | - Iain Robertson
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
| | - Mareike Krell
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
| | | | | | - Imke Mulder
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
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9
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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10
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Validation of MALDI-TOF MS Biotyper database optimized for anaerobic bacteria: The ENRIA project. Anaerobe 2018; 54:224-230. [DOI: 10.1016/j.anaerobe.2018.03.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/06/2018] [Accepted: 03/09/2018] [Indexed: 12/25/2022]
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11
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Schaumann R, Dallacker-Losensky K, Rosenkranz C, Genzel GH, Stîngu CS, Schellenberger W, Schulz-Stübner S, Rodloff AC, Eschrich K. Discrimination of Human Pathogen Clostridium Species Especially of the Heterogeneous C. sporogenes and C. botulinum by MALDI-TOF Mass Spectrometry. Curr Microbiol 2018; 75:1506-1515. [PMID: 30120528 DOI: 10.1007/s00284-018-1552-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022]
Abstract
Clostridium species cause several local and systemic diseases. Conventional identification of these microorganisms is in part laborious, not always reliable, time consuming or does not always distinguish different species, i.e., C. botulinum and C. sporogenes. All in, there is a high interest to find out a reliable, powerful and rapid method to identify Clostridium spp. not only on genus but also on species level. The aim of the present study was to identify Clostridium spp. strains and also to find differences and metabolic groups of C. botulinum by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS). A total of 123 strains of Clostridium spp. (C. botulinum, n = 40, C. difficile, n = 11, C. tetani, n = 11, C. sordellii, n = 20, C. sporogenes, n = 18, C. innocuum, n = 10, C. perfringens, n = 13) were analyzed by MALDI-TOF MS in combination with methods of multivariate statistical analysis. MALDI-TOF MS analysis in combination with methods of multivariate statistical analysis was able to discriminate between the different tested Clostridium spp., even between species which are closely related and difficult to differentiate by traditional methods, i.e., C. sporogenes and C. botulinum. Furthermore, the method was able to separate the different metabolic groups of C. botulinum. Especially, E gene-positive C. botulinum strains are clearly distinguishable from the other species but also from those producing other toxin types. Thus, MALDI-TOF MS represents a reliable and above all quick method for identification of cultivated Clostridium species.
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Affiliation(s)
- Reiner Schaumann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | - Kevin Dallacker-Losensky
- Department of Trauma Surgery and Orthopedics, Reconstructive and Septic Surgery, and Sports Traumatology, German Armed Forces Hospital Ulm, Ulm, Germany.
| | - Christiane Rosenkranz
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | | | - Catalina S Stîngu
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | | | | | - Arne C Rodloff
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | - Klaus Eschrich
- Institute of Biochemistry, University Hospital of Leipzig, Leipzig, Germany
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12
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Ulger Toprak N, Alida C M V, Urban E, Wybo I, Justesen US, Jean-Pierre H, Morris T, Akgul O, Kulekci G, Soyletir G, Nagy E. Performance of mass spectrometric identification of clinical Prevotella species using the VITEK MS system: A prospective multi-center study. Anaerobe 2018; 54:205-209. [PMID: 29880448 DOI: 10.1016/j.anaerobe.2018.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/15/2018] [Accepted: 05/29/2018] [Indexed: 12/12/2022]
Abstract
Prevotella species, members of the human microbiota, can cause opportunistic infections. Rapid and accurate identification of Prevotella isolates plays a critical role in successful treatment, especially since the antibiotic susceptibility profile differs between species. Studies, mostly carried out using the Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Biotyper system, showed that MALDI-TOF MS is an accurate, rapid and satisfactory method for the identification of clinically important anaerobes. In this multi-center study, we assessed the performance of the MALDI-TOF MS VITEK MS system for the identification of clinical Prevotella isolates. A total of 508 Prevotella isolates, representing 19 different species, collected from 11 European countries, Kuwait and Turkey between January 2014 and April 2016, were identified using VITEK MS (v3.0). The reliability of the identification was assessed by 16S rRNA gene sequencing. Using VITEK MS, 422 (83.1%) of the 508 isolates were identified on the species level, 459 (90.4%) on the genus level. A total of 49 (9.6%) isolates were not identified correctly. 16S rRNA gene sequencing results showed that this was partly due to the fact that several species were not represented in the database. However, some species that were represented in the database were also not identified. Five Prevotella strains were misidentified at the genus level, 2 of these strains belonged to a species not represented in the database. In general, the VITEK MS offers a reliable and rapid identification of Prevotella species, however the databases needs to be expanded.
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Affiliation(s)
- Nurver Ulger Toprak
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey.
| | - Veloo Alida C M
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, the Netherlands
| | - Edit Urban
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Ulrik S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Helene Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Laboratoire de Bactériologie, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Trefor Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - Oncu Akgul
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey
| | - Guven Kulekci
- Istanbul University, Faculty of Dentistry, Department of Microbiology, Istanbul, Turkey
| | - Guner Soyletir
- Marmara University School of Medicine, Department of Microbiology, Istanbul, Turkey
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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Aberkane S, Pradel B, Dumont Y, Veloo AC, Laurens C, Bonzon L, Godreuil S, Marchandin H, Jean-Pierre H. Clinical sources and antimicrobial susceptibility of Prevotella timonensis at the university hospital of Montpellier, France. Anaerobe 2018; 50:19-21. [DOI: 10.1016/j.anaerobe.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022]
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Boiten KE, Jean-Pierre H, Veloo ACM. Assessing the clinical relevance of Fenollaria massiliensis in human infections, using MALDI-TOF MS. Anaerobe 2018; 54:240-245. [PMID: 29559332 DOI: 10.1016/j.anaerobe.2018.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 12/09/2022]
Abstract
Within the European Network for the Rapid Identification of Anaerobes (ENRIA) project eight clinical isolates of Fenollaria massiliensis were encountered. In this study a more extensive description of this species is given and the MALDI-TOF MS database is optimized for its identification. F. massiliensis is an anaerobic Gram positive rod with the tendency to decolorize quickly. It is mostly encountered in clinical samples from the groin region. Less common and non-valid species are not represented in the MALDI-TOF MS database. Therefore, F. massiliensis can only be identified by laboratories performing 16S rDNA gene sequencing. The addition of less common and non-valid species to the database will give insight in their clinical relevance.
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Affiliation(s)
- K E Boiten
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands.
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôspital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France
| | - A C M Veloo
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
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How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories. Clin Microbiol Infect 2018; 24:1139-1148. [PMID: 29458156 DOI: 10.1016/j.cmi.2018.02.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/09/2018] [Accepted: 02/11/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND There has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described using 16S rRNA gene sequencing of clinical isolates obtained from different infection sites with commercially available special culture media to support the growth of anaerobes. Several systems, such as anaerobic pouches, boxes, jars and chambers provide suitable anaerobic culture conditions to isolate even strict anaerobic bacteria successfully from clinical specimens. Beside the classical, time-consuming identification methods and automated biochemical tests, the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has revolutionized identification of even unusual and slow-growing anaerobes directly from culture plates, providing the possibility of providing timely information about anaerobic infections. AIMS The aim of this review article is to present methods for routine laboratories, which carry out anaerobic diagnostics on different levels. SOURCES Relevant data from the literature mostly published during the last 7 years are encompassed and discussed. CONTENT The review involves topics on the anaerobes that are members of the commensal microbiota and their role causing infection, the key requirements for collection and transport of specimens, processing of specimens in the laboratory, incubation techniques, identification and antimicrobial susceptibility testing of anaerobic bacteria. Advantages, drawbacks and specific benefits of the methods are highlighted. IMPLICATIONS The present review aims to update and improve anaerobic microbiology in laboratories with optimal conditions as well as encourage its routine implementation in laboratories with restricted resources.
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Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of human oral Capnocytophaga species. Anaerobe 2017; 48:89-93. [DOI: 10.1016/j.anaerobe.2017.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/13/2017] [Accepted: 07/20/2017] [Indexed: 11/23/2022]
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17
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Performance of MALDI-TOF MS for identification of oral Prevotella species. Anaerobe 2017; 47:89-93. [DOI: 10.1016/j.anaerobe.2017.04.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/17/2017] [Accepted: 04/20/2017] [Indexed: 01/26/2023]
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18
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Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Shah HN, Friedrich AW, Morris T, Shah HN, Jean-Pierre H, Justesen US, Nagy E, Urban E, Kostrzewa M, Veloo A, Friedrich AW. A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS. Anaerobe 2017; 48:94-97. [PMID: 28797803 DOI: 10.1016/j.anaerobe.2017.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 11/15/2022]
Abstract
Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories.
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Affiliation(s)
- A C M Veloo
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France; Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - U S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - T Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - E Urban
- Institute of Clinical Microbiology, University of Szeged, Hungary
| | - I Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - H N Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - A W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
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ESCMID postgraduate education course: applications of MALDI-TOF mass spectrometry in clinical microbiology. Microbes Infect 2017; 19:433-442. [PMID: 28669790 DOI: 10.1016/j.micinf.2017.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 06/16/2017] [Indexed: 02/04/2023]
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Balakrishnan B, Luckey D, Marietta E, Karau M, Patel R, Murray J, Taneja V. Development of a real-time PCR method for quantification of Prevotella histicola from the gut. Anaerobe 2017; 48:37-41. [PMID: 28684342 DOI: 10.1016/j.anaerobe.2017.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 01/19/2023]
Abstract
We designed species-specific primers and developed a qPCR method for enumerating P. histicola from intestinal samples. The two designed primer sets showed specificity for the target 16S rRNA gene of P. histicola. The absolute qPCR method was sensitive to quantify as few as 103 colony-forming units (CFU) in the gut.
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Affiliation(s)
| | - David Luckey
- Department of Immunology, Mayo Clinic, Rochester, MN55905, USA
| | - Eric Marietta
- Department of Gastroenterology, Mayo Clinic, Rochester, MN55905, USA
| | - Melissa Karau
- Department of Clinical Microbiology, Mayo Clinic, Rochester, MN55905, USA
| | - Robin Patel
- Department of Clinical Microbiology, Mayo Clinic, Rochester, MN55905, USA
| | - Joseph Murray
- Department of Gastroenterology, Mayo Clinic, Rochester, MN55905, USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, MN55905, USA.
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Rahi P, Prakash O, Shouche YS. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists. Front Microbiol 2016; 7:1359. [PMID: 27625644 PMCID: PMC5003876 DOI: 10.3389/fmicb.2016.01359] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 08/17/2016] [Indexed: 12/29/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies.
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Affiliation(s)
- Praveen Rahi
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Om Prakash
- Microbial Culture Collection, National Centre for Cell Science Pune, India
| | - Yogesh S Shouche
- Microbial Culture Collection, National Centre for Cell Science Pune, India
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Veloo ACM, de Vries ED, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, van Winkelhoff AJ. The optimization and validation of the Biotyper MALDI-TOF MS database for the identification of Gram-positive anaerobic cocci. Clin Microbiol Infect 2016; 22:793-798. [PMID: 27404365 DOI: 10.1016/j.cmi.2016.06.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/13/2016] [Accepted: 06/22/2016] [Indexed: 11/29/2022]
Abstract
Gram-positive anaerobic cocci (GPAC) account for 24%-31% of the anaerobic bacteria isolated from human clinical specimens. At present, GPAC are under-represented in the Biotyper MALDI-TOF MS database. Profiles of new species have yet to be added. We present the optimization of the matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) database for the identification of GPAC. Main spectral profiles (MSPs) were created for 108 clinical GPAC isolates. Identity was confirmed using 16S rRNA gene sequencing. Species identification was considered to be reliable if the sequence similarity with its closest relative was ≥98.7%. The optimized database was validated using 140 clinical isolates. The 16S rRNA sequencing identity was compared with the MALDI-TOF MS result. MSPs were added from 17 species that were not yet represented in the MALDI-TOF MS database or were under-represented (fewer than five MSPs). This resulted in an increase from 53.6% (75/140) to 82.1% (115/140) of GPAC isolates that could be identified at the species level using MALDI-TOF MS. An improved log score was obtained for 51.4% (72/140) of the strains. For strains with a sequence similarity <98.7% with their closest relative (n = 5) or with an inconclusive sequence identity (n = 4), no identification was obtained by MALDI-TOF MS or in the latter case an identity with one of its relatives. For some species the MSP of the type strain was not part of the confined cluster of the corresponding clinical isolates. Also, not all species formed a homogeneous cluster. It emphasizes the necessity of adding sufficient MSPs of human clinical isolates.
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Affiliation(s)
- A C M Veloo
- Department of Medical Microbiology, University of Groningen, University Medical Centre Groningen, The Netherlands.
| | - E D de Vries
- Department of Medical Microbiology, University of Groningen, University Medical Centre Groningen, The Netherlands
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, Montpellier, France; Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, Montpellier, France
| | - U S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - T Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - E Urban
- Institute of Clinical Microbiology, University of Szeged, Hungary
| | - I Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - A J van Winkelhoff
- Department of Medical Microbiology, University of Groningen, University Medical Centre Groningen, The Netherlands; Department of Dentistry and Oral Hygiene, University of Groningen, University Medical Centre Groningen, The Netherlands
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Bacterial Infections. MOLECULAR PATHOLOGY IN CLINICAL PRACTICE 2016. [PMCID: PMC7123846 DOI: 10.1007/978-3-319-19674-9_49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular techniques have revolutionized the detection and identification of microorganisms. Real-time PCR has allowed for the rapid and accurate detection of MRSA, VRE, and group B Streptococcus. The identification of difficult and slow-growing organisms has been expedited by sequence-based methods such as 16S rRNA gene sequencing. Rapid identification of organisms and detection of resistance markers directly from positive blood culture bottles has become a reality. Finally, a transformation is taking place with the introduction of MALDI-TOF into clinical laboratories that promises to improve the accuracy and speed of bacterial and fungal identifications by days. The advantages of these methodologies and their associated clinical applications, along with their inherent pitfalls and problems, are elucidated in this chapter.
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Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses. PLoS One 2015; 10:e0130265. [PMID: 26103050 PMCID: PMC4477887 DOI: 10.1371/journal.pone.0130265] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 05/18/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported. METHODS The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains. RESULTS Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed. CONCLUSION Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3-100%. However, the inter-species similarities were relatively low, ranging from 68.7-97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.
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25
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Shilnikova II, Dmitrieva NV. Evaluation of antibiotic susceptibility of Bacteroides, Prevotella and Fusobacterium species isolated from patients of the N. N. Blokhin Cancer Research Center, Moscow, Russia. Anaerobe 2015; 31:15-8. [DOI: 10.1016/j.anaerobe.2014.08.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/31/2014] [Accepted: 08/01/2014] [Indexed: 12/01/2022]
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26
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Nagy E, Ábrók M, Bartha N, Bereczki L, Juhász E, Kardos G, Kristóf K, Miszti C, Urbán E. Special application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry in clinical microbiological diagnostics. Orv Hetil 2014; 155:1495-503. [DOI: 10.1556/oh.2014.29985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry as a new possibility for rapid identification of bacteria and fungi revolutionized the clinical microbiological diagnostics. It has an extreme importance in the routine microbiological laboratories, as identification of the pathogenic species rapidly will influence antibiotic selection before the final determination of antibiotic resistance of the isolate. The classical methods for identification of bacteria or fungi, based on biochemical tests, are influenced by many environmental factors. The matrix-assisted laser desorption ionization time-of-flight mass spectrometry is a rapid method which is able to identify a great variety of the isolated bacteria and fungi based on the composition of conserved ribosomal proteins. Recently several other applications of the method have also been investigated such as direct identification of pathogens from the positive blood cultures. There are possibilities to identify bacteria from the urine samples in urinary tract infection or from other sterile body fluids. Using selective enrichment broth Salmonella sp from the stool samples can be identified more rapidly, too. The extended spectrum beta-lactamase or carbapenemase production of the isolated bacteria can be also detected by this method helping the antibiotic selection in some cases. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry based methods are suitable to investigate changes in deoxyribonucleic acid or ribonucleic acid, to carry out rapid antibiotic resistance determination or other proteomic analysis. The aim of this paper is to give an overview about present possibilities of using this technique in the clinical microbiological routine procedures. Orv. Hetil., 2014, 155(38), 1495–1503.
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Affiliation(s)
- Erzsébet Nagy
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Marianna Ábrók
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Noémi Bartha
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - László Bereczki
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
| | - Emese Juhász
- Semmelweis Egyetem, Általános Orvostudományi Kar Laboratóriumi Medicina Intézet, Klinikai Mikrobiológiai Diagnosztikai Laboratórium Budapest
| | - Gábor Kardos
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Mikrobiológiai Intézet Debrecen
| | - Katalin Kristóf
- Semmelweis Egyetem, Általános Orvostudományi Kar Laboratóriumi Medicina Intézet, Klinikai Mikrobiológiai Diagnosztikai Laboratórium Budapest
| | - Cecilia Miszti
- Debreceni Egyetem, Általános Orvostudományi Kar Orvosi Mikrobiológiai Intézet Debrecen
| | - Edit Urbán
- Szegedi Tudományegyetem, Általános Orvostudományi Kar Klinikai Mikrobiológiai Diagnosztikai Intézet Szeged Pf. 427 6701
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Nagy E. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new possibility for the identification and typing of anaerobic bacteria. Future Microbiol 2014; 9:217-33. [DOI: 10.2217/fmb.13.150] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
ABSTRACT: Anaerobic bacteria predominate in the normal flora of humans and are important, often life-threatening pathogens in mixed infections originating from the indigenous microbiota. The isolation and identification of anaerobes by phenotypic and DNA-based molecular methods at a species level is time-consuming and laborious. Following the successful adaptation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the routine laboratory identification of bacteria, the extensive development of a database has been initiated to use this method for the identification of anaerobic bacteria. Not only frequently isolated anaerobic species, but also newly recognized and taxonomically rearranged genera and species can be identified using direct smear samples or whole-cell protein extraction, and even phylogenetically closely related species can be identified correctly by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Typing of anaerobic bacteria on a subspecies level, determination of antibiotic resistance and direct identification of blood culture isolates will revolutionize anaerobe bacteriology in the near future.
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Affiliation(s)
- Elizabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, 6701 Szeged, PO Box 427, Hungary
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28
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Empyema caused by Prevotella bivia complicating an unusual case of spontaneous chylothorax. J Clin Microbiol 2014; 52:1284-6. [PMID: 24452170 DOI: 10.1128/jcm.03282-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spontaneous chylothorax is rare in adults. We present an unusual case that was complicated by Prevotella bivia empyema. Full recovery was achieved with chest tube drainage and prompt treatment with intravenous clindamycin.
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Lau SKP, Tang BSF, Teng JLL, Chan TM, Curreem SOT, Fan RYY, Ng RHY, Chan JFW, Yuen KY, Woo PCY. Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories. J Clin Pathol 2013; 67:361-6. [PMID: 24143023 DOI: 10.1136/jclinpath-2013-201818] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIMS Although the revolutionary matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are 'difficult-to-identify' by phenotypic tests has been less well studied. We aim to evaluate the usefulness of MALDI-TOF MS for identification of 'difficult-to-identify' bacterial isolates. METHODS We evaluated the performance of the Bruker MALDI-TOF MS system for a collection of 67 diverse clinically important bacterial isolates that were less commonly encountered, possessed ambiguous biochemical profiles or belonged to newly discovered species. The results were compared with 16S rRNA gene sequencing as a reference method for species identification. RESULTS Using 16S rRNA gene sequencing as the reference method, 30 (45%) isolates were identified correctly to species level (score ≥2.0), 20 (30%) were only identified to genus level (score ≥1.7), four (6%) were misidentified (incorrect species with score ≥2.0 or incorrect genus with score ≥1.7) and 13 (19%) showed 'no identification' (score <1.7). Aerobic Gram-positive bacteria showed the highest percentage of correct species identification, followed by aerobic Gram-negative, anaerobic Gram-positive and anaerobic Gram-negative bacteria. Sixteen isolates identified to genus level actually showed the correct species but with scores below the threshold for species identification. Most isolates which showed 'no identification' were due to the absence of the corresponding species in the Bruker database. CONCLUSIONS Expansion of commercial databases to include reference spectra of less commonly encountered and newly discovered species and to increase available spectra for each species is required to improve the accuracy of MALDI-TOF MS for identifying 'difficult-to-identify' bacteria.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, , Hong Kong, China
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Wybo I, Van den Bossche D, Soetens O, Vekens E, Vandoorslaer K, Claeys G, Glupczynski Y, Ieven M, Melin P, Nonhoff C, Rodriguez-Villalobos H, Verhaegen J, Piérard D. Fourth Belgian multicentre survey of antibiotic susceptibility of anaerobic bacteria. J Antimicrob Chemother 2013; 69:155-61. [PMID: 24008826 PMCID: PMC3861333 DOI: 10.1093/jac/dkt344] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Objectives To collect recent data on the susceptibility of anaerobes to antimicrobial agents with known activity against anaerobes, and to compare them with results from previous Belgian multicentre studies. Methods Four hundred and three strict anaerobic clinical isolates were prospectively collected from February 2011 to April 2012 in eight Belgian university hospitals. MICs were determined by one central laboratory for 11 antimicrobial agents using Etest methodology. Results According to EUCAST breakpoints, >90% of isolates were susceptible to amoxicillin/clavulanate (94%), piperacillin/tazobactam (91%), meropenem (96%), metronidazole (92%) and chloramphenicol (98%), but only 70% and 40% to clindamycin and penicillin, respectively. At CLSI recommended breakpoints, only 71% were susceptible to moxifloxacin and 79% to cefoxitin. MIC50/MIC90 values for linezolid and for tigecycline were 1/4 and 0.5/4 mg/L, respectively. When compared with survey data from 2004, no major differences in susceptibility profiles were noticed. However, the susceptibility of Prevotella spp. and other Gram-negative bacilli to clindamycin decreased from 91% in 1993–94 and 82% in 2004 to 69% in this survey. Furthermore, the susceptibility of clostridia to moxifloxacin decreased from 88% in 2004 to 66% in 2011–12 and that of fusobacteria from 90% to 71%. Conclusions Compared with previous surveys, little evolution was seen in susceptibility, except a decline in activity of clindamycin against Prevotella spp. and other Gram-negative bacteria, and of moxifloxacin against clostridia. Since resistance was detected to all antibiotics, susceptibility testing of anaerobic isolates is indicated in severe infections to confirm appropriateness of antimicrobial therapy.
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Affiliation(s)
- Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
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García-Sánchez JE, García-Sánchez E, Martín-Del-Rey Á, García-Merino E. [Anaerobic bacteria 150 years after their discovery by Pasteur]. Enferm Infecc Microbiol Clin 2013; 33:119-28. [PMID: 23648369 DOI: 10.1016/j.eimc.2013.03.012] [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] [Received: 01/14/2013] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 01/05/2023]
Abstract
In 2011 we celebrated the 150th anniversary of the discovery of anaerobic bacteria by Louis Pasteur. The interest of the biomedical community on such bacteria is still maintained, and is particularly focused on Clostridium difficile. In the past few years important advances in taxonomy have been made due to the genetic, technological and computing developments. Thus, a significant number of new species related to human infections have been characterised, and some already known have been reclassified. At pathogenic level some specimens of anaerobic microflora, that had not been isolated from human infections, have been now isolated in some clinical conditions. There was emergence (or re-emergence) of some species and clinical conditions. Certain anaerobic bacteria have been associated with established infectious syndromes. The virulence of certain strains has increased, and some hypotheses on their participation in certain diseases have been given. In terms of diagnosis, the routine use of MALDI-TOF has led to a shortening of time and a cost reduction in the identification, with an improvement directly related to the improvement of data bases. The application of real-time PCR has been another major progress, and the sequencing of 16srRNA gene and others is currently a reality for several laboratories. Anaerobes have increased their resistance to antimicrobial agents, and the emergence of resistance to carbapenems and metronidazole, and multi-resistance is a current reality. In this situation, linezolid could be an effective alternative for Bacteroides. Fidaxomicin is the only anti-anaerobic agent introduced in the recent years, specifically for the diarrhoea caused by C.difficile. Moreover, some mathematical models have also been proposed in relation with this species.
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Affiliation(s)
- José Elías García-Sánchez
- Departamento de Medicina Preventiva, Salud Pública y Microbiología Médica, Facultad de Medicina, Universidad de Salamanca, Salamanca, España.
| | - Enrique García-Sánchez
- Departamento de Medicina Preventiva, Salud Pública y Microbiología Médica, Facultad de Medicina, Universidad de Salamanca, Salamanca, España
| | - Ángel Martín-Del-Rey
- Departamento de Matemática Aplicada, Escuela Politécnica Superior de Ávila, Universidad de Salamanca, Ávila, España
| | - Enrique García-Merino
- Departamento de Salud, Instituto de Educación Secundaria Ramón y Cajal, Valladolid, España
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Patel R. Matrix-assisted laser desorption ionization-time of flight mass spectrometry in clinical microbiology. Clin Infect Dis 2013; 57:564-72. [PMID: 23595835 DOI: 10.1093/cid/cit247] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite widespread application of nucleic acid diagnostics, cultures remain integral in modern laboratories. Because cultures detect a large number of organism types, it is unlikely that they will disappear from clinical practice in the near future. Their downside is slow turn-around time, impacted by time to growth and identification of that growth. The latter is expedited using a new proteomic technology, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).
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Affiliation(s)
- Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology and Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.
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Nagy E, Becker S, Kostrzewa M, Barta N, Urbán E. The value of MALDI-TOF MS for the identification of clinically relevant anaerobic bacteria in routine laboratories. J Med Microbiol 2012; 61:1393-1400. [PMID: 22700545 DOI: 10.1099/jmm.0.043927-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between 2010 and 2011, 283 clinically relevant non-duplicate anaerobic isolates were analysed by MALDI-TOF MS and the results were compared with conventional identification. Immediately after isolation, an ethanol precipitation was carried out on isolated colonies and the stabilized samples were anonymized and sent to the laboratory of Bruker Daltonik, Bremen, Germany, where the identification was done using the standard protocol for micro-organism identification on a Microflex LT mass spectrometer equipped with the MALDI Biotyper 3.0 software. Of 283 isolates, 218 (77 %) were identified at species level [log(score) ≥2.0], 31 isolates (10.95 %) were identified at genus level [log(score) 1.7-2.0] and 34 (12 %) gave non-reliable identification [log(score) <1.7]. Out of the 31 isolates with log(score) 1.7-2.0, in the case of 24 isolates the species name given by the MALDI Biotyper was accepted if it was the same as for the classical identification. Of 218 isolates identified at species level, 40 results were discordant with phenotypic identification, and of the 31 isolates identified at genus level according to the manufacturer's score cut-off, four gave results discordant with the phenotypic method. For the 44 discordant results, 16S rRNA gene sequencing confirmed MALDI-TOF MS identification in 41 cases, leaving three isolates (0.7 %) that had been misidentified by MALDI-TOF MS.
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Affiliation(s)
- Elisabeth Nagy
- National Anaerobic Reference Laboratory, Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | | | | | - Noémi Barta
- National Anaerobic Reference Laboratory, Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Edit Urbán
- National Anaerobic Reference Laboratory, Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Szeged, Hungary
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