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Fiamanya S, Cipolla L, Prieto M, Stelling J. Exploring the value of MALDI-TOF MS for the detection of clonal outbreaks of Burkholderia contaminans. J Microbiol Methods 2020; 181:106130. [PMID: 33383044 DOI: 10.1016/j.mimet.2020.106130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Molecular genetics has risen in both output and affordability to become the gold standard in diagnosis, however it is not yet available for most routine clinical microbiology due to cost and the level of skill it requires. Matrix assisted laser desorption/ionisation - time of flight mass spectrometry (MALDI-TOF MS) approaches may be useful in bridging the gap between low-resolution phenotypic methods and bulky genotypic methods in the goal of epidemiological source-typing of microbes. Burkholderia has been shown to be identifiable at the subspecies level using MALDI-TOF MS. There have not yet been studies assessing the ability of MALDI-TOF MS to source-type Burkholderia contaminans isolates into epidemiologically relevant outbreak clusters. METHODS 55 well-characterised B. contaminans isolates were used to create a panel for analysis of MALDI-TOF MS biomarker peaks and their relation to outbreak strains, location, source, patient, diagnosis and isolate genetics. Unsupervised clustering was performed and classification models were generated using biostatistical analysis software. RESULTS B. contaminans spectra derived from MALDI-TOF MS were of sufficiently high resolution to identify 100% of isolates. Unsupervised clustering methods showed poor evidence of spectra clustering by all characteristics measured. Classification algorithms were discriminatory, with Genetic Algorithm models showing 100% recognition capability for all outbreaks, the pulsed-field gel electrophoresis (PFGE) typeability model, and 96.63% recognition for the location model. A consistent peak at m/z of approximately 6943 was identified in all non-typeable strains but in none of the typeable strains. CONCLUSIONS MALDI-TOF MS successfully discriminates B. contaminans isolates into clonal, epidemiological clusters, and can recognise isolates non-typeable by PFGE. Further work should investigate this capability, and include peptide studies and genomic sequencing to identify individual proteins or genes responsible for this non-typeablity, particularly at the peak weight identified.
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Affiliation(s)
- Selali Fiamanya
- Oxford University Clinical Academic Graduate School, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - Lucía Cipolla
- Servicio Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas 'Dr. C. G. Malbrán', Av Velez Sarsfield 563, 1281 Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Prieto
- Servicio Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas 'Dr. C. G. Malbrán', Av Velez Sarsfield 563, 1281 Ciudad Autónoma de Buenos Aires, Argentina
| | - John Stelling
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School 25 Shattuck Street, Boston, MA 02115, USA
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Murugesan M, Ranjan J, Devanga Ragupathi NK, Michael JS, Viggeswarpu S, Wilson BP, Veeraraghavan B. Diagnostic methods and identification challenges experienced in a Burkholderia contaminans outbreak occurred in a tertiary care centre. Indian J Med Microbiol 2020; 39:192-195. [PMID: 33966861 DOI: 10.1016/j.ijmmb.2020.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Recently, a novel species contaminans belonging to the family Burkholderia cepacia complex (Bcc) is rising as a hospital pathogen. Detection of Burkholderia contaminans, a member of Bcc can be done only by MALDI TOF and sequencing techniques. We report the diagnostic challenges faced in an outbreak of bacteremia due to B. contaminans grown in diltiazem vials. METHOD The department of microbiology notified the infection control team about a cluster of eleven patients with B. contaminans isolated from blood culture. An outbreak investigation was initiated by performing environmental surveillance and sterility testing of solutions given for the patients. Routine phenotypical methods for identification of species followed by MALDI-TOF and sequencing was performed to identify the pathogen. RESULTS All the patients detected with B. contaminans were having cardiac disease and received diltiazem. Sterility testing of diltiazem vials given for the patient and an unopened vial of same batch has grown B. contaminans. Clonal typing has confirmed the sequence similarities between patient and solution isolates. CONCLUSION Due to diagnostic challenge in identifying the species of Bcc, MALDI TOF and clonal typing remains the key diagnostic tools available to detect Bcc species at an earliest especially in an outbreak.
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Affiliation(s)
- Malathi Murugesan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India; Hospital Infection Control Committee, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jai Ranjan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India; Hospital Infection Control Committee, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Joy Sarojini Michael
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India; Hospital Infection Control Committee, Christian Medical College, Vellore, Tamil Nadu, India
| | - Surekha Viggeswarpu
- Department of Geriatrics, Christian Medical College, Vellore, Tamil Nadu, India
| | - Benny Paul Wilson
- Department of Geriatrics, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India.
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Burkholderia cepacia complex: 11 years of surveillance in patients with Cystic Fibrosis in Posadas, Argentina. Rev Argent Microbiol 2020; 52:176-182. [DOI: 10.1016/j.ram.2019.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/20/2019] [Accepted: 08/27/2019] [Indexed: 11/23/2022] Open
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Jia Z, Gwynne L, Sedgwick AC, Müller M, Williams GT, Jenkins ATA, James TD, Schönherr H. Enhanced Colorimetric Differentiation between Staphylococcus aureus and Pseudomonas aeruginosa Using a Shape-Encoded Sensor Hydrogel. ACS APPLIED BIO MATERIALS 2020; 3:4398-4407. [DOI: 10.1021/acsabm.0c00403] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zhiyuan Jia
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany
| | - Lauren Gwynne
- Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Adam C. Sedgwick
- Department of Chemistry, The University of Texas at Austin, 105 E 24th street A5300, Austin, Texas 78712-1224, United States
| | - Mareike Müller
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany
| | | | | | - Tony D. James
- Department of Chemistry, University of Bath, Bath BA2 7AY, U.K
| | - Holger Schönherr
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ), Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Straße 2, 57076 Siegen, Germany
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Abdel Samad R, Al Disi Z, Mohammad Ashfaq MY, Wahib SM, Zouari N. The use of principle component analysis and MALDI-TOF MS for the differentiation of mineral forming Virgibacillus and Bacillus species isolated from sabkhas. RSC Adv 2020; 10:14606-14616. [PMID: 35497157 PMCID: PMC9051895 DOI: 10.1039/d0ra01229g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 04/01/2020] [Indexed: 01/23/2023] Open
Abstract
Occurrence of mineral forming and other bacteria in mats is well demonstrated. However, their high diversity shown by ribotyping has not been explained, although it could explain the diversity of formed minerals. Common biomarkers as well as phylogenic relationships are useful tools for clustering the isolates and the prediction of their potential role in the natural niche. In this study, a combination of MALDI-TOF MS with PCA was shown to be a powerful tool to categorize 35 mineral forming bacterial isolates isolated from Dohat Faishakh sabkha, northwest of Qatar (23 from decaying mats and 12 from living ones). The 23 strains from decaying mats belong to the Virgibacillus genus as identified by ribotyping and are shown to be highly involved in the formation of protodolomite and a diversity of minerals. They were used as internal references for the categorization of sabkha bacteria. Combination of the isolation of bacteria on selective mineral forming media, their MALDI TOF MS protein profiling and PCA analysis established their relationship in a phylloproteomic dendrogram based on protein biomarkers including m/z 4905, 3265, 5240, 6430, 7765, and 9815. PCA analysis clustered the studied isolates into 3 major clusters, showing strong correspondence to the 3 phylloproteomic groups that were established by the dendrogram. Both clustering analysis means have evidently demonstrated a relationship between known Virgibacillus strains and other related bacteria based on profiling of their synthesized proteins. Thus, larger populations of bacteria in mats can be easily screened for their potential to exhibit certain activities, which is of ecological, environmental and biotechnological significance. Occurrence of mineral forming and other bacteria in mats is well demonstrated.![]()
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Affiliation(s)
- Rim Abdel Samad
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
| | - Zulfa Al Disi
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
| | | | - Sara Mohiddin Wahib
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
| | - Nabil Zouari
- Department of Biological and Environmental Sciences
- College of Arts and Sciences
- Qatar University
- Doha
- Qatar
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6
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Váradi L, Luo JL, Hibbs DE, Perry JD, Anderson RJ, Orenga S, Groundwater PW. Methods for the detection and identification of pathogenic bacteria: past, present, and future. Chem Soc Rev 2018. [PMID: 28644499 DOI: 10.1039/c6cs00693k] [Citation(s) in RCA: 263] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In order to retard the rate of development of antibacterial resistance, the causative agent must be identified as rapidly as possible, so that directed patient treatment and/or contact precautions can be initiated. This review highlights the challenges associated with the detection and identification of pathogenic bacteria, by providing an introduction to the techniques currently used, as well as newer techniques that are in development. Focusing on the chemical basis for these techniques, the review also provides a comparison of their advantages and disadvantages.
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Affiliation(s)
- Linda Váradi
- Faculty of Pharmacy, The University of Sydney, Sydney, NSW 2006, Australia.
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7
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Martina P, Leguizamon M, Prieto CI, Sousa SA, Montanaro P, Draghi WO, Stämmler M, Bettiol M, de Carvalho CCCR, Palau J, Figoli C, Alvarez F, Benetti S, Lejona S, Vescina C, Ferreras J, Lasch P, Lagares A, Zorreguieta A, Leitão JH, Yantorno OM, Bosch A. Burkholderia puraquae sp. nov., a novel species of the Burkholderia cepacia complex isolated from hospital settings and agricultural soils. Int J Syst Evol Microbiol 2017; 68:14-20. [PMID: 29095137 DOI: 10.1099/ijsem.0.002293] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteria from the Burkholderia cepacia complex (Bcc) are capable of causing severe infections in patients with cystic fibrosis (CF). These opportunistic pathogens are also widely distributed in natural and man-made environments. After a 12-year epidemiological surveillance involving Bcc bacteria from respiratory secretions of Argentinean patients with CF and from hospital settings, we found six isolates of the Bcc with a concatenated species-specific allele sequence that differed by more than 3 % from those of the Bcc with validly published names. According to the multilocus sequence analysis (MLSA), these isolates clustered with the agricultural soil strain, Burkholderia sp. PBP 78, which was already deposited in the PubMLST database. The isolates were examined using a polyphasic approach, which included 16S rRNA, recA, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), DNA base composition, average nucleotide identities (ANIs), fatty acid profiles, and biochemical characterizations. The results of the present study demonstrate that the seven isolates represent a single novel species within the Bcc, for which the name Burkholderia puraquae sp. nov. is proposed. Burkholderia puraquae sp. nov. CAMPA 1040T (=LMG 29660T=DSM 103137T) was designated the type strain of the novel species, which can be differentiated from other species of the Bcc mainly from recA gene sequence analysis, MLSA, ANIb, MALDI-TOF MS analysis, and some biochemical tests, including the ability to grow at 42 °C, aesculin hydrolysis, and lysine decarboxylase and β-galactosidase activities.
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Affiliation(s)
- Pablo Martina
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.,Present address: IBS, CONICET-CCT Nordeste, Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Mariana Leguizamon
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Claudia I Prieto
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Silvia A Sousa
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | | | - Walter O Draghi
- Fundación Instituto Leloir and IIBA-Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos aires, Argentina.,IBBM, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Maren Stämmler
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institut, Berlin, Germany
| | - Marisa Bettiol
- Sala de Microbiología, Hospital de Niños «Sor María Ludovica», La Plata, Buenos Aires, Argentina
| | - Carla C C R de Carvalho
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Juliana Palau
- Sala de Microbiología, Hospital de Niños «Sor María Ludovica», La Plata, Buenos Aires, Argentina
| | - Cecilia Figoli
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Florencia Alvarez
- IBBM, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Silvina Benetti
- Laboratorio Cemar D. S. L. A. C, Municipalidad de Rosario, Santa Fe, Argentina
| | - Sergio Lejona
- Laboratorio Cemar D. S. L. A. C, Municipalidad de Rosario, Santa Fe, Argentina
| | - Cecilia Vescina
- Sala de Microbiología, Hospital de Niños «Sor María Ludovica», La Plata, Buenos Aires, Argentina
| | - Julián Ferreras
- IBS, CONICET-CCT Nordeste, Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Peter Lasch
- Proteomics and Spectroscopy Unit (ZBS6) at the Centre for Biological Threats and Special Pathogens, Robert Koch-Institut, Berlin, Germany
| | - Antonio Lagares
- IBBM, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir and IIBA-Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos aires, Argentina
| | - Jorge H Leitão
- iBB-Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Osvaldo M Yantorno
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Alejandra Bosch
- CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
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8
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Martina PF, Martínez M, Frada G, Alvarez F, Leguizamón L, Prieto C, Barrias C, Bettiol M, Lagares A, Bosch A, Ferreras J, Von Specht M. First time identification of Pandoraea sputorum from a patient with cystic fibrosis in Argentina: a case report. BMC Pulm Med 2017; 17:33. [PMID: 28173787 PMCID: PMC5297019 DOI: 10.1186/s12890-017-0373-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background Pandoraea species are considered emerging pathogens in the context of cystic fibrosis (CF) and are difficult to identify by conventional biochemical methods. These multidrug resistant bacteria remain poorly understood particularly in terms of natural resistance, mechanisms of acquired resistance and impact on the prognosis of the disease and the lung function. Among them, Pandoraea sputorum has been previously described in few cases of CF patients from Spain, Australia, France and United States, underlining the need of more clinical data for a better knowledge of its pathogenicity. This is the first report relating to P. sputorum in a CF patient in Argentina. Case presentation Pandoraea sputorum was identified in a nine-year-old cystic fibrosis patient from Argentina, after treatment failure during an exacerbation. The isolates were successfully identified by combining molecular techniques based on 16S rRNA sequencing and mass spectrometry (MS) methods, after reassessing previous misidentified isolates by conventional methods. After first isolation of P. sputorum, patient’s clinical condition worsened but later improved after a change in the treatment. Although isolates showed susceptibility to trimethoprim–sulfamethoxazole and imipenem, in our case, the antibiotic treatment failed in the eradication of P. sputorum. Conclusions All combined data showed a chronic colonization with P. sputorum associated to a deterioration of lung function. We noted that the presence of P. sputorum can be underestimated in CF patients and MALDI-TOF MS appears to be a promising means of accurate identification of Pandoraea species.
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Affiliation(s)
- Pablo F Martina
- Instituto de Biología Subtropical (IBS), CONICET-UNaM, Misiones, Argentina.,Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI) - CONICET/UNLP, La Plata, Argentina.,Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina
| | - Mónica Martínez
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina
| | - Guillermo Frada
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina
| | - Florencia Alvarez
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET/UNLP, La Plata, Argentina
| | | | - Claudia Prieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI) - CONICET/UNLP, La Plata, Argentina
| | - Carolina Barrias
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina
| | - Marisa Bettiol
- Hospital de Niños Sor María Ludovica, La Plata, Argentina
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular (IBBM) - CONICET/UNLP, La Plata, Argentina
| | - Alejandra Bosch
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI) - CONICET/UNLP, La Plata, Argentina
| | - Julián Ferreras
- Instituto de Biología Subtropical (IBS), CONICET-UNaM, Misiones, Argentina. .,Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.
| | - Martha Von Specht
- Hospital Pediátrico Dr F. Barreyro, Posadas, Misiones, Argentina. .,Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Argentina.
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Edler C, Derschum H, Köhler M, Neubauer H, Frickmann H, Hagen RM. Comparison of Mast Burkholderia Cepacia, Ashdown + Gentamicin, and Burkholderia Pseudomallei Selective Agar for the Selective Growth of Burkholderia Spp. Eur J Microbiol Immunol (Bp) 2017; 7:15-36. [PMID: 28386468 PMCID: PMC5372478 DOI: 10.1556/1886.2016.00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/05/2016] [Indexed: 01/16/2023] Open
Abstract
Reliable identification of pathogenic Burkholderia spp. like Burkholderia mallei and Burkholderia pseudomallei in clinical samples is desirable. Three different selective media were assessed for reliability and selectivity with various Burkholderia spp. and nontarget organisms. Mast Burkholderia cepacia agar, Ashdown + gentamicin agar, and B. pseudomallei selective agar were compared. A panel of 116 reference strains and well-characterized clinical isolates, comprising 30 B. pseudomallei, 20 B. mallei, 18 other Burkholderia spp., and 48 nontarget organisms, was used for this assessment. While all B. pseudomallei strains grew on all three tested selective agars, the other Burkholderia spp. showed a diverse growth pattern. Nontarget organisms, i.e., nonfermentative rod-shaped bacteria, other species, and yeasts, grew on all selective agars. Colony morphology did not allow unambiguous discrimination. While the assessed selective media reliably allowed the growth of a wide range of B. pseudomallei strains, growth of other Burkholderia spp. is only partially ensured. Growth of various nontarget organisms has to be considered. Therefore, the assessed media can only be used in combination with other confirmative tests in the diagnostic procedure for the screening for melioidosis or glanders.
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Affiliation(s)
- Carola Edler
- Department of Dermatology, German Armed Forces Hospital of Hamburg , Hamburg, Germany
| | - Henri Derschum
- CBRN Defence, Safety and Environmental Protection School, Science Division
| | | | - Heinrich Neubauer
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health , Jena, Germany
| | - Hagen Frickmann
- Department of Tropical Medicine at the Bernhard Nocht Institute, German Armed Forces Hospital of Hamburg, Hamburg, Germany; Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Ralf Matthias Hagen
- Department of Preventive Medicine, Bundeswehr Medical Academy , Munich, Germany
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10
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Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of highly pathogenic bacteria. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.04.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Power RF, Linnane B, Martin R, Power N, Harnett P, Casserly B, O'Connell NH, Dunne CP. The first reported case of Burkholderia contaminans in patients with cystic fibrosis in Ireland: from the Sargasso Sea to Irish Children. BMC Pulm Med 2016; 16:57. [PMID: 27103163 PMCID: PMC4840893 DOI: 10.1186/s12890-016-0219-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/12/2016] [Indexed: 12/26/2022] Open
Abstract
Background Burkholderia contaminans is an emerging pathogen in the cystic fibrosis (CF) setting. Included in the Burkholderia cepacia complex (Bcc), B. contaminans is a Gram negative, motile, obligate aerobe previously classified as a pseudomonad. Previous reports have described B. contaminans isolation from patients in Portugal, Switzerland, Spain, Argentina and the USA. This, however, is the first report relating to B. contaminans affecting Irish patients with CF, initially detected in a paediatric setting. Case presentation Burkholderia contaminans was identified in the routine analysis of sputum from a fourteen year old boy, at his annual review and subsequently from the sputum from his 19 year old brother. RecA gene sequencing and pulsed field gel electrophoresis (PFGE) were unable to distinguish between the isolates, which demonstrated with susceptibility to ciprofloxacin, cotrimoxazole, meropenem, pipercillin/tazobactam and ceftazidime. Both isolates were resistant to aztreonam, with reduced susceptibility to tobramycin. Following treatment with intravenous meropenem and ceftazidime, oral ciprofloxacin and nebulised tobramycin for 6 weeks, sputum specimens from both patients were negative for B. contaminans. No other member of the local CF cohort proved positive. Conclusions Bcc bacteria are associated with poor prognosis in CF and decreased life expectancy, specifically leading to a more rapid decline in lung function and, in some cases, to a fatal necrotizing pneumonia known as the “cepacia syndrome”. Some species exhibit innate resistance to multiple antimicrobial agents and their transmission rate can be high in susceptible patients. In that context, we describe the first incidence of CF-related B. contaminans in Ireland and its successful eradication from two patients, one paediatric, using an aggressive antimicrobial regimen.
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Affiliation(s)
- Rachel F Power
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Barry Linnane
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Ruth Martin
- University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Noelle Power
- University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Peig Harnett
- University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Brian Casserly
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Nuala H O'Connell
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.,University Hospital Limerick, Dooradoyle, Limerick, Ireland
| | - Colum P Dunne
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland.
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12
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Prieto CI, Palau MJ, Martina P, Achiary C, Achiary A, Bettiol M, Montanaro P, Cazzola ML, Leguizamón M, Massillo C, Figoli C, Valeiras B, Perez S, Rentería F, Diez G, Yantorno OM, Bosch A. [Cystic Fibrosis Cloud database: An information system for storage and management of clinical and microbiological data of cystic fibrosis patients]. Rev Argent Microbiol 2016; 48:27-37. [PMID: 26895996 DOI: 10.1016/j.ram.2015.11.002] [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: 05/04/2015] [Revised: 11/03/2015] [Accepted: 11/22/2015] [Indexed: 11/29/2022] Open
Abstract
The epidemiological and clinical management of cystic fibrosis (CF) patients suffering from acute pulmonary exacerbations or chronic lung infections demands continuous updating of medical and microbiological processes associated with the constant evolution of pathogens during host colonization. In order to monitor the dynamics of these processes, it is essential to have expert systems capable of storing and subsequently extracting the information generated from different studies of the patients and microorganisms isolated from them. In this work we have designed and developed an on-line database based on an information system that allows to store, manage and visualize data from clinical studies and microbiological analysis of bacteria obtained from the respiratory tract of patients suffering from cystic fibrosis. The information system, named Cystic Fibrosis Cloud database is available on the http://servoy.infocomsa.com/cfc_database site and is composed of a main database and a web-based interface, which uses Servoy's product architecture based on Java technology. Although the CFC database system can be implemented as a local program for private use in CF centers, it can also be used, updated and shared by different users who can access the stored information in a systematic, practical and safe manner. The implementation of the CFC database could have a significant impact on the monitoring of respiratory infections, the prevention of exacerbations, the detection of emerging organisms, and the adequacy of control strategies for lung infections in CF patients.
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Affiliation(s)
- Claudia I Prieto
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - María J Palau
- Sala de Microbiología, Hospital de Niños «Sor María Ludovica», La Plata, Buenos Aires, Argentina
| | - Pablo Martina
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Carlos Achiary
- Infocom S.A., Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrés Achiary
- Infocom S.A., Ciudad Autónoma de Buenos Aires, Argentina
| | - Marisa Bettiol
- Sala de Microbiología, Hospital de Niños «Sor María Ludovica», La Plata, Buenos Aires, Argentina
| | | | - María L Cazzola
- Sala de Bacteriología, Hospital HIGA, La Plata, Buenos Aires, Argentina
| | - Mariana Leguizamón
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Cintia Massillo
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Cecilia Figoli
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Brenda Valeiras
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Silvia Perez
- Sala de Bacteriología, Hospital HIGA, La Plata, Buenos Aires, Argentina
| | - Fernando Rentería
- Servicio de Neumonología, Hospital de Niños «Sor María Ludovica», La Plata, Buenos Aires, Argentina
| | - Graciela Diez
- Servicio de Neumonología, Hospital de Niños «Sor María Ludovica», La Plata, Buenos Aires, Argentina
| | - Osvaldo M Yantorno
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Alejandra Bosch
- CINDEFI, CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
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MALDI-TOF mass spectrometry for rapid identification of clinical fungal isolates based on ribosomal protein biomarkers. J Microbiol Methods 2015; 109:93-105. [DOI: 10.1016/j.mimet.2014.12.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 12/23/2022]
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Martina P, Feliziani S, Juan C, Bettiol M, Gatti B, Yantorno O, Smania AM, Oliver A, Bosch A. Hypermutation in Burkholderia cepacia complex is mediated by DNA mismatch repair inactivation and is highly prevalent in cystic fibrosis chronic respiratory infection. Int J Med Microbiol 2014; 304:1182-91. [PMID: 25217078 DOI: 10.1016/j.ijmm.2014.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 08/15/2014] [Accepted: 08/18/2014] [Indexed: 11/25/2022] Open
Abstract
The Burkholderia cepacia complex (Bcc) represents an important group of pathogens involved in long-term lung infection in cystic fibrosis (CF) patients. A positive selection of hypermutators, linked to antimicrobial resistance development, has been previously reported for Pseudomonas aeruginosa in this chronic infection setting. Hypermutability, however, has not yet been systematically evaluated in Bcc species. A total of 125 well characterized Bcc isolates recovered from 48 CF patients, 10 non-CF patients and 15 environmental samples were analyzed. In order to determine the prevalence of mutators their spontaneous mutation rates to rifampicin resistance were determined. In addition, the genetic basis of the mutator phenotypes was investigated by sequencing the mutS and mutL genes, the main components of the mismatch repair system (MRS). The overall prevalence of hypermutators in the collection analyzed was 13.6%, with highest occurrence (40.7%) among the chronically infected CF patients, belonging mainly to B. cenocepacia, B. multivorans, B. cepacia, and B. contaminans -the most frequently recovered Bcc species from CF patients worldwide. Thirteen (76.5%) of the hypermutators were defective in mutS and/or mutL. Finally, searching for a possible association between antimicrobial resistance and hypermutability, the resistance-profiles to 17 antimicrobial agents was evaluated. High antimicrobial resistance rates were documented for all the Bcc species recovered from CF patients, but, except for ciprofloxacin, a significant association with hypermutation was not detected. In conclusion, in the present study we demonstrate for the first time that, MRS-deficient Bcc species mutators are highly prevalent and positively selected in CF chronic lung infections. Hypermutation therefore, might be playing a key role in increasing bacterial adaptability to the CF-airway environment, facilitating the persistence of chronic lung infections.
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Affiliation(s)
- Pablo Martina
- CINDEFI-CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - Sofía Feliziani
- CIQUIBIC-CONICET, Centro de Investigaciones en Química Biológica de Córdoba, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Carlos Juan
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), 07010 Palma de Mallorca, Spain
| | - Marisa Bettiol
- Sala de Microbiología, Hospital de Niños de La Plata "Sor María Ludovica", 1900 La Plata, Argentina
| | - Blanca Gatti
- Sala de Microbiología, Hospital de Niños de La Plata "Sor María Ludovica", 1900 La Plata, Argentina
| | - Osvaldo Yantorno
- CINDEFI-CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Argentina
| | - Andrea M Smania
- CIQUIBIC-CONICET, Centro de Investigaciones en Química Biológica de Córdoba, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
| | - Antonio Oliver
- Servicio de Microbiología y Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria de Palma (IdISPa), 07010 Palma de Mallorca, Spain.
| | - Alejandra Bosch
- CINDEFI-CONICET-CCT La Plata, Centro de Biotecnología Aplicada, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Argentina.
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Classification algorithm for subspecies identification within the Mycobacterium abscessus species, based on matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2014; 52:3362-9. [PMID: 25009048 DOI: 10.1128/jcm.00788-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus, as a species, has been increasingly implicated in respiratory infections, notably in cystic fibrosis patients. The species comprises 3 subspecies, which can be difficult to identify. Since they differ in antibiotic susceptibility and clinical relevance, developing a routine diagnostic tool discriminating Mycobacterium abscessus at the subspecies level is a real challenge. Forty-three Mycobacterium abscessus species isolates, previously identified by multilocus sequence typing, were analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). A subspecies identification algorithm, based on five discriminating peaks, was drawn up and validated by blind identification of a further 49 strains, 94% of which (n = 46) were correctly identified. Two M. abscessus subsp. massiliense strains were misidentified as M. abscessus subsp. abscessus, and for 1 other strain identification failed. Inter- and intralaboratory reproducibility tests were conclusive. This study presents, for the first time, a classification algorithm for MALDI-TOF MS identification of the 3 M. abscessus subspecies. MALDI-TOF MS proved effective in discriminating within the M. abscessus species and might be easily integrated into the workflow of microbiology labs.
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Frickmann H, Neubauer H, Loderstaedt U, Derschum H, Hagen RM. rpsU-based discrimination within the genus Burkholderia. Eur J Microbiol Immunol (Bp) 2014; 4:106-16. [PMID: 24883196 DOI: 10.1556/eujmi.4.2014.2.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022] Open
Abstract
Sequencing of the gene rpsU reliably delineates saprophytic Burkholderia (B.) thailandensis from highly pathogenic B. mallei and B. pseudomallei. We analyzed the suitability of this technique for the delineation of the B. pseudomallei complex from other Burkholderia species. Both newly recorded and previously deposited sequences of well-characterized or reference strains (n = 84) of Azoarcus spp., B. ambifaria, B. anthina, B. caledonica, B. caribensis, B. caryophylli, B. cenocepacia, B. cepacia, B. cocovenenans, B. dolosa, B. fungorum, B. gladioli, B. glathei, B. glumae, B. graminis, B. hospita, B. kururensis, B. mallei, B. multivorans, B. phenazinium, B. phenoliruptrix, B. phymatum, B. phytofirmans, B. plantarii, B. pseudomallei, B. pyrrocinia, B. stabilis, B. thailandensis, B. ubonensis, B. vietnamiensis, B. xenovorans, not further defined Burkholderia spp., and the outliers Cupriavidus metallidurans, Laribacter hongkongensis, Pandorea norimbergensis, and Ralstonia pickettii were included in a multiple sequence analysis. Multiple sequence alignments led to the delineation of four major clusters, rpsU-I to rpsU-IV, with a sequence homology >92%. The B. pseudomallei complex formed the complex rpsU-II. Several Burkholderia species showed 100% sequence homology. This procedure is useful for the molecular confirmation or exclusion of glanders or melioidosis from primary patient material. Further discrimination within the Burkholderia genus requires other molecular approaches.
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Helmel M, Marchetti-Deschmann M, Allmaier G. Improved sample preparation for intact cell mass spectrometry (biotyping) of mycelium samples taken from a batch fermentation process of Penicillium chrysogenum. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:957-964. [PMID: 24623701 DOI: 10.1002/rcm.6849] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 01/21/2014] [Accepted: 01/21/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE Penicillium chrysogenum is an important species in biotechnology and an improved production rate for penicillin drug variants is of utmost interest. Intact cell mass spectrometry (ICMS) or biotyping can be a novel and time-saving tool to monitor a fermentation process of Penicillium strains for fast intervention during penicillin production. METHODS Fermentation broth was collected directly from a fermenter at specific time points known to show significantly different penicillin production rates. The mycelium was purified by washing multiple times with water and recovered by centrifugation. The mycelium was further mixed with matrix-assisted laser desorption/ionization (MALDI) MS matrix and immediately spotted on different types of targets. ICMS spectra were obtained by MALDI time-of-flight (TOF) MS in the positive ion linear mode in the m/z range 3000 to 16 000. RESULTS An ICMS method for culture broth samples of P. chrysogenum was developed. It was shown that ferulic acid mixed with sinapinic acid (2.5 mg and 22.5 mg/mL) is the most appropriate matrix combination. The matrices were dissolved in acetonitrile/0.1% trifluoroacetic acid (70/30, v/v) and spotted together with the sample on various target types. Sample preparation was thoroughly studied for homogeneity and reproducibility. CONCLUSIONS Culture broth directly collected from a bioreactor could be analyzed applying the optimized approach. The ideal choice of matrix, the adequate preparation technique and the type of target were the focus of this work showing that samples collected at different times during fermentation exhibit a characteristic pattern using the developed method.
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Affiliation(s)
- Michaela Helmel
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9/164, A-1060, Vienna, Austria
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18
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 511] [Impact Index Per Article: 51.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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Malainine SM, Moussaoui W, Prévost G, Scheftel JM, Mimouni R. Rapid identification of Vibrio parahaemolyticus isolated from shellfish, sea water and sediments of the Khnifiss lagoon, Morocco, by MALDI-TOF mass spectrometry. Lett Appl Microbiol 2013; 56:379-86. [PMID: 23464928 DOI: 10.1111/lam.12060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/13/2013] [Accepted: 02/19/2013] [Indexed: 11/30/2022]
Abstract
We establish the presence of Vibrio parahaemolyticus and deepen the comparison of isolates using MALDI-TOF MS for the typing of isolates originating from the Khnifiss lagoon (Morocco). Amongst 48 samples from sea water, sediment and shellfish isolated from different sites of Khnifiss lagoon, Morocco, we obtained 22 isolates of V. parahaemolyticus identified by Vitek 2™ System (bioMérieux) and MALDI Biotyper™ (Bruker Daltonics). All isolates were highly resistant to ampicillin and ticarcillin, moderately resistant to cefalotin, but sensitive to 16 other antimicrobials tested. MALDI-TOF MS was used to discriminate between closely related environmental strains of V. parahaemolyticus. A clustering and distribution based on MALDI-TOF spectra were generated using the BioTyper 1.1™ software. Despite low diversity in regard to the biochemical characteristics and antimicrobial resistance, the isolates evoke a larger biodiversity when analysed through mass spectra of abundant proteins. Different evaluations of a cut-off value showed that, when placed at a 10% threshold of the whole diversity, isolates differed by at least three mass peaks.
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Affiliation(s)
- S M Malainine
- Faculty of Sciences, Laboratory of Biotechnology & Valorisation of Natural Resources, University Ibn Zohr, Agadir, Morocco.
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20
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Pattison SH, Rogers GB, Crockard M, Elborn JS, Tunney MM. Molecular detection of CF lung pathogens: current status and future potential. J Cyst Fibros 2013; 12:194-205. [PMID: 23402821 PMCID: PMC7105241 DOI: 10.1016/j.jcf.2013.01.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 01/08/2013] [Accepted: 01/11/2013] [Indexed: 12/24/2022]
Abstract
Molecular diagnostic tests, based on the detection and identification of nucleic acids in human biological samples, are increasingly employed in the diagnosis of infectious diseases and may be of future benefit to CF microbiology services. Our growing understanding of the complex polymicrobial nature of CF airway infection has highlighted current and likely future shortcomings in standard diagnostic practices. Failure to detect fastidious or slow growing microbes and misidentification of newly emerging pathogens could potentially be addressed using culture-independent molecular technologies with high target specificity. This review considers existing molecular diagnostic tests in the context of the key requirements for an envisaged CF microbiology focussed assay. The issues of assay speed, throughput, detection of multiple pathogens, data interpretation and antimicrobial susceptibility testing are discussed.
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Affiliation(s)
- Sally H Pattison
- CF and Airways Microbiology Research Group, Queen's University Belfast, United Kingdom.
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Braga PAC, Tata A, Gonçalves dos Santos V, Barreiro JR, Schwab NV, Veiga dos Santos M, Eberlin MN, Ferreira CR. Bacterial identification: from the agar plate to the mass spectrometer. RSC Adv 2013. [DOI: 10.1039/c2ra22063f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Lambiase A, Del Pezzo M, Cerbone D, Raia V, Rossano F, Catania MR. Rapid identification of Burkholderia cepacia complex species recovered from cystic fibrosis patients using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Microbiol Methods 2012. [PMID: 23201483 DOI: 10.1016/j.mimet.2012.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aim of this study was to establish the identification ability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for bacteria of Burkholderia cepacia complex (Bcc) and to compare these results with those obtained by a molecular method (PCR-RFLP). A total of 57 isolates was used in the study. Isolates were collected from 31 patients attending the Regional Cystic Fibrosis Unit from January 2001 to December 2005. For phenotypic identification, both automated and manual systems were used. Using mass spectrometry, we identified all 57 isolates, previously identified by molecular method. Of these, 28 isolates were identified as B. cenocepacia, although not differentiated further into lineages. Moreover, other isolates were identified as B. cepacia (12 isolates), B. stabilis (12 isolates), and B. vietnamiensis (5 isolates). Our data indicate a good correlation between the two approaches.
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Affiliation(s)
- Antonietta Lambiase
- Department of Cellular and Molecular Biology and Pathology Luigi Califano, Medicine School, University Federico II, Naples, Italy.
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Genetic diversity of Burkholderia contaminans isolates from cystic fibrosis patients in Argentina. J Clin Microbiol 2012; 51:339-44. [PMID: 23135937 DOI: 10.1128/jcm.02500-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A total of 120 Burkholderia cepacia complex isolates collected during 2004-2010 from 66 patients in two cystic fibrosis reference centers in Argentina were analyzed. Burkholderia contaminans was the species most frequently recovered (57.6%), followed by Burkholderia cenocepacia (15%), a species distribution not reported so far. The recA-PCR-based techniques applied to the B. contaminans isolates revealed that 85% of the population carried the recA-ST-71 allele. Our results showed the utility of BOX-PCR genotyping in analyzing B. contaminans diversity. This approach allowed us to address clonal transmission during an outbreak and the genetic changes occurring in infecting bacteria over the course of chronic infection.
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Karger A, Stock R, Ziller M, Elschner MC, Bettin B, Melzer F, Maier T, Kostrzewa M, Scholz HC, Neubauer H, Tomaso H. Rapid identification of Burkholderia mallei and Burkholderia pseudomallei by intact cell Matrix-assisted Laser Desorption/Ionisation mass spectrometric typing. BMC Microbiol 2012; 12:229. [PMID: 23046611 PMCID: PMC3534143 DOI: 10.1186/1471-2180-12-229] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 09/25/2012] [Indexed: 11/17/2022] Open
Abstract
Background Burkholderia (B.) pseudomallei and B. mallei are genetically closely related species. B. pseudomallei causes melioidosis in humans and animals, whereas B. mallei is the causative agent of glanders in equines and rarely also in humans. Both agents have been classified by the CDC as priority category B biological agents. Rapid identification is crucial, because both agents are intrinsically resistant to many antibiotics. Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) has the potential of rapid and reliable identification of pathogens, but is limited by the availability of a database containing validated reference spectra. The aim of this study was to evaluate the use of MALDI-TOF MS for the rapid and reliable identification and differentiation of B. pseudomallei and B. mallei and to build up a reliable reference database for both organisms. Results A collection of ten B. pseudomallei and seventeen B. mallei strains was used to generate a library of reference spectra. Samples of both species could be identified by MALDI-TOF MS, if a dedicated subset of the reference spectra library was used. In comparison with samples representing B. mallei, higher genetic diversity among B. pseudomallei was reflected in the higher average Eucledian distances between the mass spectra and a broader range of identification score values obtained with commercial software for the identification of microorganisms. The type strain of B. pseudomallei (ATCC 23343) was isolated decades ago and is outstanding in the spectrum-based dendrograms probably due to massive methylations as indicated by two intensive series of mass increments of 14 Da specifically and reproducibly found in the spectra of this strain. Conclusions Handling of pathogens under BSL 3 conditions is dangerous and cumbersome but can be minimized by inactivation of bacteria with ethanol, subsequent protein extraction under BSL 1 conditions and MALDI-TOF MS analysis being faster than nucleic amplification methods. Our spectra demonstrated a higher homogeneity in B. mallei than in B. pseudomallei isolates. As expected for closely related species, the identification process with MALDI Biotyper software (Bruker Daltonik GmbH, Bremen, Germany) requires the careful selection of spectra from reference strains. When a dedicated reference set is used and spectra of high quality are acquired, it is possible to distinguish both species unambiguously. The need for a careful curation of reference spectra databases is stressed.
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Affiliation(s)
- Axel Karger
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Molecular Biology, Südufer 10, Greifswald-Insel Riems D-17493, Germany
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Gillanders LJ, Elborn JS, Gilpin DF, Schneiders T, Tunney MM. The airway microbiome in cystic fibrosis: challenges for therapy. ACTA ACUST UNITED AC 2011. [DOI: 10.2217/thy.11.81] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ahrholdt J, Murugaiyan J, Straubinger RK, Jagielski T, Roesler U. Epidemiological analysis of worldwide bovine, canine and human clinical Prototheca isolates by PCR genotyping and MALDI-TOF mass spectrometry proteomic phenotyping. Med Mycol 2011; 50:234-43. [PMID: 21905948 DOI: 10.3109/13693786.2011.597445] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study presents information on the phenotypic and genotypic characterization of clinical Prototheca spp. isolates obtained from different geographic regions. Of 350 isolates studied, 342 came from cattle, six from canines and two from humans. Phenotypic characterization was carried out by a matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) proteomic analysis. The peptide extraction that was used for this analysis included the additional steps of washing and sonication to increase the yield of peptide. Genotypic analysis was conducted using species- and genotype-specific primers. The study revealed that among the cattle isolates, 310 (90.6%) belonged to Prototheca zopfii genotype 2, 30 (8.8%) to P. blaschkeae, and two (0.6%) to P. zopfii genotype 1. P. zopfii genotype 2 is the principal etiological agent of protothecal mastitis in cattle regardless of the geographic region. Similarly, all canine and human isolates also belonged to the P. zopfii genotype 2, suggesting that this is probably the most virulent species of the genus. The role of P. blaschkeae needs further epidemiologic studies to ascertain its etiologic role in bovine mastitis. To the best of our knowledge, this is the first comprehensive study on phenotypic and genotypic characterization of P. zopfii and P. blaschkeae isolates originating from diverse clinical specimens from different countries.
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Affiliation(s)
- Jennifer Ahrholdt
- Institute for Animal Hygiene and Environmental Health, Free University of Berlin, Berlin.
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De Bel A, Wybo I, Vandoorslaer K, Rosseel P, Lauwers S, Piérard D. Acceptance criteria for identification results of Gram-negative rods by mass spectrometry. J Med Microbiol 2011; 60:684-686. [DOI: 10.1099/jmm.0.023184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Annelies De Bel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Paul Rosseel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Sabine Lauwers
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
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28
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Jacquier H, Carbonnelle E, Corvec S, Illiaquer M, Monnier A, Bille E, Zahar JR, Beretti JL, Jauréguy F, Fihman V, Tankovic J, Cattoir V. Revisited distribution of nonfermenting Gram-negative bacilli clinical isolates. Eur J Clin Microbiol Infect Dis 2011; 30:1579-86. [DOI: 10.1007/s10096-011-1263-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/28/2011] [Indexed: 12/01/2022]
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29
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Buskirk AD, Hettick JM, Chipinda I, Law BF, Siegel PD, Slaven JE, Green BJ, Beezhold DH. Fungal pigments inhibit the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of darkly pigmented fungi. Anal Biochem 2011; 411:122-8. [DOI: 10.1016/j.ab.2010.11.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 11/10/2010] [Accepted: 11/11/2010] [Indexed: 10/18/2022]
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30
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Bittar F, Rolain JM. Detection and accurate identification of new or emerging bacteria in cystic fibrosis patients. Clin Microbiol Infect 2011; 16:809-20. [PMID: 20880410 DOI: 10.1111/j.1469-0691.2010.03236.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Respiratory infections remain a major threat to cystic fibrosis (CF) patients. The detection and correct identification of the bacteria implicated in these infections is critical for the therapeutic management of patients. The traditional methods of culture and phenotypic identification of bacteria lack both sensitivity and specificity because many bacteria can be missed and/or misidentified. Molecular analyses have recently emerged as useful means to resolve these problems, including molecular methods for accurate identification or detection of bacteria and molecular methods for evaluation of microbial diversity. These recent molecular technologies have increased the list of new and/or emerging pathogens and epidemic strains associated with CF patients. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry of intact cells has also emerged recently as a powerful and rapid method for the routine identification of bacteria in clinical microbiology laboratories and will certainly represent the method of choice also for the routine identification of bacteria in the context of CF. Finally, recent data derived from molecular culture-independent analyses indicate the presence of a previously underestimated, complex microbial community in sputa from CF patients. Interestingly, full genome sequencing of some bacteria frequently recovered from CF patients has highlighted the fact that the lungs of CF patients are hotspots for lateral gene transfer and the adaptation of these ecosystems to a specific chronic condition.
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Affiliation(s)
- F Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS-IRD, UMR 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille Cedex 05, France
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31
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Bittar F, Cassagne C, Bosdure E, Stremler N, Dubus JC, Sarles J, Reynaud-Gaubert M, Raoult D, Rolain JM. Outbreak of Corynebacterium pseudodiphtheriticum infection in cystic fibrosis patients, France. Emerg Infect Dis 2010; 16:1231-6. [PMID: 20678316 PMCID: PMC3298292 DOI: 10.3201/eid1608.100193] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
An increasing body of evidence indicates that nondiphtheria corynebacteria may be responsible for respiratory tract infections. We report an outbreak of Corynebacterium pseudodiphtheriticum infection in children with cystic fibrosis (CF). To identify 18 C. pseudodiphtheriticum strains isolated from 13 French children with CF, we used molecular methods (partial rpoB gene sequencing) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Clinical symptoms were exhibited by 10 children (76.9%), including cough, rhinitis, and lung exacerbations. The results of MALDI-TOF identification matched perfectly with those obtained from molecular identification. Retrospective analysis of sputum specimens by using specific real-time PCR showed that approximately 20% of children with CF were colonized with these bacteria, whereas children who did not have CF had negative test results. Our study reemphasizes the conclusion that correctly identifying bacteria at the species level facilitates detection of an outbreak of new or emerging infections in humans.
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Affiliation(s)
- Fadi Bittar
- Universite de la Mediterranée, Marseille, France
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32
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Lasch P, Drevinek M, Nattermann H, Grunow R, Stämmler M, Dieckmann R, Schwecke T, Naumann D. Characterization of Yersinia Using MALDI-TOF Mass Spectrometry and Chemometrics. Anal Chem 2010; 82:8464-75. [DOI: 10.1021/ac101036s] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Lasch
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Michal Drevinek
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Herbert Nattermann
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Roland Grunow
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Maren Stämmler
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Ralf Dieckmann
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Torsten Schwecke
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
| | - Dieter Naumann
- Biomedical Spectroscopy (P 25) and Centre for Biological Security (ZBS 2), Robert-Koch-Institut, Nordufer 20, D-13353 Berlin, Germany, National Institute for Nuclear, Biological and Chemical Protection, Kamenna 71, CZ-26231 Milin, Czech Republic, and Department of Biological Safety, Antibiotic Resistance and Resistance Determinants, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, D-12277 Berlin, Germany
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33
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Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level. J Clin Microbiol 2010; 48:1169-75. [PMID: 20164271 DOI: 10.1128/jcm.01881-09] [Citation(s) in RCA: 380] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial identification relies primarily on culture-based methodologies requiring 24 h for isolation and an additional 24 to 48 h for species identification. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is an emerging technology newly applied to the problem of bacterial species identification. We evaluated two MALDI-TOF MS systems with 720 consecutively isolated bacterial colonies under routine clinical laboratory conditions. Isolates were analyzed in parallel on both devices, using the manufacturers' default recommendations. We compared MS with conventional biochemical test system identifications. Discordant results were resolved with "gold standard" 16S rRNA gene sequencing. The first MS system (Bruker) gave high-confidence identifications for 680 isolates, of which 674 (99.1%) were correct; the second MS system (Shimadzu) gave high-confidence identifications for 639 isolates, of which 635 (99.4%) were correct. Had MS been used for initial testing and biochemical identification used only in the absence of high-confidence MS identifications, the laboratory would have saved approximately US$5 per isolate in marginal costs and reduced average turnaround time by more than an 8-h shift, with no loss in accuracy. Our data suggest that implementation of MS as a first test strategy for one-step species identification would improve timeliness and reduce isolate identification costs in clinical bacteriology laboratories now.
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34
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High-throughput identification of bacteria and yeast by matrix-assisted laser desorption ionization-time of flight mass spectrometry in conventional medical microbiology laboratories. J Clin Microbiol 2010; 48:900-7. [PMID: 20053859 DOI: 10.1128/jcm.02071-09] [Citation(s) in RCA: 443] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is suitable for high-throughput and rapid diagnostics at low costs and can be considered an alternative for conventional biochemical and molecular identification systems in a conventional microbiological laboratory. First, we evaluated MALDI-TOF MS using 327 clinical isolates previously cultured from patient materials and identified by conventional techniques (Vitek-II, API, and biochemical tests). Discrepancies were analyzed by molecular analysis of the 16S genes. Of 327 isolates, 95.1% were identified correctly to genus level, and 85.6% were identified to species level by MALDI-TOF MS. Second, we performed a prospective validation study, including 980 clinical isolates of bacteria and yeasts. Overall performance of MALDI-TOF MS was significantly better than conventional biochemical systems for correct species identification (92.2% and 83.1%, respectively) and produced fewer incorrect genus identifications (0.1% and 1.6%, respectively). Correct species identification by MALDI-TOF MS was observed in 97.7% of Enterobacteriaceae, 92% of nonfermentative Gram-negative bacteria, 94.3% of staphylococci, 84.8% of streptococci, 84% of a miscellaneous group (mainly Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella [HACEK]), and 85.2% of yeasts. MALDI-TOF MS had significantly better performance than conventional methods for species identification of staphylococci and genus identification of bacteria belonging to HACEK group. Misidentifications by MALDI-TOF MS were clearly associated with an absence of sufficient spectra from suitable reference strains in the MALDI-TOF MS database. We conclude that MALDI-TOF MS can be implemented easily for routine identification of bacteria (except for pneumococci and viridans streptococci) and yeasts in a medical microbiological laboratory.
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35
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Dieckmann R, Strauch E, Alter T. Rapid identification and characterization of Vibrio species using whole-cell MALDI-TOF mass spectrometry. J Appl Microbiol 2009; 109:199-211. [PMID: 20059616 DOI: 10.1111/j.1365-2672.2009.04647.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIMS Vibrio identification by means of traditional microbiological methods is time consuming because of the many biochemical tests that have to be performed to distinguish closely related species. This work aimed at evaluating the use of MALDI-TOF mass spectrometry for the rapid identification of Vibrio (V.) spp. as an advantageous application to rapidly discriminate the most important Vibrio spp. and distinguish Vibrio spp. from closely related bacterial species like Photobacterium damselae and Grimontia hollisae and other aquatic bacteria like Aeromonas spp. METHODS AND RESULTS Starting from sub-colony amounts of pure cultures grown on agar plates, a very simple sample preparation procedure was established and combined with a rapid and automated measurement protocol that allowed species identification within minutes. Closely related species like Vibrio alginolyticus and Vibrio parahaemolyticus or Vibrio cholerae and Vibrio mimicus could thus be differentiated by defining signatures of species-identifying biomarker ions (SIBIs). As a reference method for species designation and for determination of relationships between strains with molecular markers, partial rpoB gene sequencing was applied. CONCLUSIONS The MALDI-TOF MS-based method as well as the rpoB sequence-based approach for Vibrio identification described in this study produced comparable classification results. The construction of phylogenetic trees from MALDI-TOF MS and rpoB sequences revealed a very good congruence of both methods. SIGNIFICANCE AND IMPACT OF THE STUDY Our results suggest that whole-cell MALDI-TOF MS-based proteometric characterization represents a powerful tool for rapid and accurate classification and identification of Vibrio spp. and related species.
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Affiliation(s)
- R Dieckmann
- Department of Biological Safety, Federal Institute for Risk Assessment, Berlin, Germany.
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36
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Moliner C, Ginevra C, Jarraud S, Flaudrops C, Bedotto M, Couderc C, Etienne J, Fournier PE. Rapid identification of Legionella species by mass spectrometry. J Med Microbiol 2009; 59:273-284. [PMID: 19926729 DOI: 10.1099/jmm.0.014100-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Legionella species are facultative, intracellular bacteria that infect macrophages and protozoa, with the latter acting as transmission vectors to humans. These fastidious bacteria mostly cause pulmonary tract infections and are routinely identified by various molecular methods, mainly PCR targeting the mip gene and sequencing, which are expensive and time-consuming. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has emerged as a rapid and inexpensive method for identification of bacterial species. This study evaluated the use of MALDI-TOF-MS for rapid species and serogroup identification of 21 Legionella species recognized as human pathogens. To this end, a reference MS database was developed including 59 Legionella type strains, and a blind test was performed using 237 strains from various species. Two hundred and twenty-three of the 237 strains (94.1 %) were correctly identified at the species level, although ten (4.2 %) were identified with a score lower than 2.0. Fourteen strains (5.9 %) from eight species were misidentified at the species level, including seven (3.0 %) with a significant score, suggesting an intraspecific variability of protein profiles within some species. MALDI-TOF-MS was reproducible but could not identify Legionella strains at the serogroup level. When compared with mip gene sequencing, MALDI-TOF-MS exhibited a sensitivity of 99.2 and 89.9 % for the identification of Legionella strains at the genus and species level, respectively. This study demonstrated that MALDI-TOF-MS is a reliable tool for the rapid identification of Legionella strains at the species level.
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Affiliation(s)
- Claire Moliner
- URMITE CNRS-IRD UMR 6236, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Christophe Ginevra
- Hospices Civils de Lyon, Faculté de Médecine Lyon Est Claude Bernard, Lyon, France.,Université de Lyon, Lyon, France.,INSERM, U851, 21 avenue Tony Garnier, 69007 Lyon, France.,Université Lyon 1, IFR128, Lyon, France
| | - Sophie Jarraud
- Université Lyon 1, IFR128, Lyon, France.,Hospices Civils de Lyon, Faculté de Médecine Lyon Est Claude Bernard, Lyon, France.,Université de Lyon, Lyon, France.,INSERM, U851, 21 avenue Tony Garnier, 69007 Lyon, France
| | - Christophe Flaudrops
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Marielle Bedotto
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Carine Couderc
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Jerome Etienne
- Université Lyon 1, IFR128, Lyon, France.,INSERM, U851, 21 avenue Tony Garnier, 69007 Lyon, France.,Université de Lyon, Lyon, France.,Hospices Civils de Lyon, Faculté de Médecine Lyon Est Claude Bernard, Lyon, France
| | - Pierre-Edouard Fournier
- Fédération de Microbiologie Clinique, Hôpital de la Timone, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France.,URMITE CNRS-IRD UMR 6236, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France
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