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Barrera-Galicia GC, Peniche-Pavía HA, Peña-Cabriales JJ, Covarrubias SA, Vera-Núñez JA, Délano-Frier JP. Metabolic Footprints of Burkholderia Sensu Lato Rhizosphere Bacteria Active against Maize Fusarium Pathogens. Microorganisms 2021; 9:microorganisms9102061. [PMID: 34683382 PMCID: PMC8538949 DOI: 10.3390/microorganisms9102061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Consistent with their reported abundance in soils, several Burkholderia sensu lato strains were isolated from the rhizosphere of maize plants cultivated at different sites in central México. Comparative analysis of their 16S rRNA gene sequences permitted their separation into three distinctive clades, which were further subdivided into six other clusters by their close resemblance to (1) Trinickia dinghuensis; (2) Paraburkholderia kirstenboschensis, P. graminis, P. dilworthii and P. rhynchosiae; (3) B. gladioli; (4) B. arboris; (5) B. contaminans, or (6) B. metallica representative species. Direct confrontation assays revealed that these strains inhibited the growth of pathogenic Fusarium oxysporum f. sp. radicis-lycopersici, and F. verticillioides within a roughly 3-55% inhibition range. The use of a DIESI-based non-targeted mass spectroscopy experimental strategy further indicated that this method is an option for rapid determination of the pathogen inhibitory capacity of Burkholderia sensu lato strains based solely on the analysis of their exometabolome. Furthermore, it showed that the highest anti-fungal activity observed in B. contaminans and B. arboris was associated with a distinctive abundance of certain m/z ions, some of which were identified as components of the ornbactin and pyochelin siderophores. These results highlight the chemical diversity of Burkholderia sensu lato bacteria and suggest that their capacity to inhibit the Fusarium-related infection of maize in suppressive soils is associated with siderophore synthesis.
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Affiliation(s)
- Guadalupe C. Barrera-Galicia
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Héctor A. Peniche-Pavía
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Juan José Peña-Cabriales
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
| | - Sergio A. Covarrubias
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - José A. Vera-Núñez
- Área de Ciencias de la Salud, Ciudad Universitaria Campus Siglo XXI, Universidad Autónoma de Zacatecas, Zacatecas 98160, Zacatecas, Mexico; (S.A.C.); (J.A.V.-N.)
| | - John P. Délano-Frier
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato 36824, Guanajuato, Mexico; (G.C.B.-G.); (H.A.P.-P.); (J.J.P.-C.)
- Correspondence: ; Tel.: +52-462-623-9600
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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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Rocca MF, Zintgraff JC, Dattero ME, Santos LS, Ledesma M, Vay C, Prieto M, Benedetti E, Avaro M, Russo M, Nachtigall FM, Baumeister E. A combined approach of MALDI-TOF mass spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs. J Virol Methods 2020; 286:113991. [PMID: 33045283 PMCID: PMC7546642 DOI: 10.1016/j.jviromet.2020.113991] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023]
Abstract
This study with MALDI-TOF comprises, as far as we know, the first report describing the performance of this technology with COVID-19 diagnosis. This work would encourage researchers to explore the potential of MALDI-TOF MS to assess the feasibility of this technology, as a rapid and reproducible screening tool for diagnosis of SARS-CoV-2. According to our preliminary results, mass spectrometry-based methods combined with multivariate analysis showed potential as a complementary diagnostic tool.
Coronavirus disease 2019, known as COVID-19, is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The early, sensitive and specific detection of SARS-CoV-2 virus is widely recognized as the critical point in responding to the ongoing outbreak. Currently, the diagnosis is based on molecular real time RT-PCR techniques, although their implementation is being threatened due to the extraordinary demand for supplies worldwide. That is why the development of alternative and / or complementary tests becomes so relevant. Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms, for the detection of COVID-19 positive and negative protein profiles directly from nasopharyngeal swabs samples. According to the preliminary results obtained, accuracy = 67.66 %, sensitivity = 61.76 %, specificity = 71.72 %, and although these parameters still need to be improved to be used as a screening technique, mass spectrometry-based methods coupled with multivariate analysis showed that it is an interesting tool that deserves to be explored as a complementary diagnostic approach due to the low cost and fast performance. However, further steps, such as the analysis of a large number of samples, should be taken in consideration to determine the applicability of the method developed.
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Affiliation(s)
- María Florencia Rocca
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina; Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (ReNaEM Argentina), Argentina.
| | - Jonathan Cristian Zintgraff
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina; Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (ReNaEM Argentina), Argentina
| | - María Elena Dattero
- Servicio de Virosis respiratorias, Centro Nacional de Influenza de OMS, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales del Ministerio de Salud, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas (INEI) -Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonardo Silva Santos
- Instituto de Química de Recursos Naturales, Universidad de Talca, Talca 3460000, Chile
| | - Martín Ledesma
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (ReNaEM Argentina), Argentina; Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina; CONICET, Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina
| | - Carlos Vay
- Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (ReNaEM Argentina), Argentina; Laboratorio de Bacteriología, Departamento de Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Prieto
- Instituto Nacional de Enfermedades Infecciosas (INEI) - Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina; Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (ReNaEM Argentina), Argentina
| | - Estefanía Benedetti
- Servicio de Virosis respiratorias, Centro Nacional de Influenza de OMS, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales del Ministerio de Salud, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas (INEI) -Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Martín Avaro
- Servicio de Virosis respiratorias, Centro Nacional de Influenza de OMS, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales del Ministerio de Salud, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas (INEI) -Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Mara Russo
- Servicio de Virosis respiratorias, Centro Nacional de Influenza de OMS, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales del Ministerio de Salud, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas (INEI) -Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | | | - Elsa Baumeister
- Servicio de Virosis respiratorias, Centro Nacional de Influenza de OMS, Laboratorio Nacional de Referencia de Enfermedades Respiratorias Virales del Ministerio de Salud, Departamento de Virología, Instituto Nacional de Enfermedades Infecciosas (INEI) -Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
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Rocca MF, Barrios R, Zintgraff J, Martínez C, Irazu L, Vay C, Prieto M. Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification. PLoS One 2019; 14:e0218077. [PMID: 31269022 PMCID: PMC6608940 DOI: 10.1371/journal.pone.0218077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/09/2019] [Indexed: 01/21/2023] Open
Abstract
Mass spectrometry has revolutionized the clinical microbiology field in America’s and Europe’s industrialized countries, for being a fast, reliable and inexpensive technique. Our study is based on the comparison of the performance of two commercial platforms, Microflex LT (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMérieux, Marcy l´Etoile, France) for the identification of unusual and hard-to-diagnose microorganisms in a Reference Laboratory in Argentina. During a four-month period (February–May 2018) the diagnostic efficiency and the concordance between both systems were assessed, and the results were compared with the polyphasic taxonomic identification of all isolates. The study included 265 isolates: 77 Gram-Negative Bacilli, 33 Gram-Positive Cocci, 40 Anaerobes, 35 Actinomycetales, 19 Fastidious Microorganisms and 61 Gram-Positive Bacilli. All procedures were practiced according to the manufacturer’s recommendations in each case by duplicate, and strictly in parallel. Other relevant factors, such as the utility of the recommended extraction protocols, reagent stability and connectivity were also evaluated. Both systems correctly identified the majority of the isolates to species and complex level (82%, 217/265). Vitex MS achieved a higher number of correct species-level identifications between the gram-positive microorganisms; however, it presented greater difficulty in the identification of non-fermenting bacilli and a higher number of incorrect identifications when the profile of the microorganism was not represented in the commercial database. Both platforms showed an excellent performance on the identification of anaerobic bacteria and fastidious species. Both systems enabled the fast and reliable identification of most of the tested isolates and were shown to be very practical for the user.
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Affiliation(s)
- María Florencia Rocca
- Laboratorio Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI)–Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
- * E-mail:
| | - Rubén Barrios
- Laboratorio de Bacteriología, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Jonathan Zintgraff
- Laboratorio Bacteriología Clínica, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI)–Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Claudia Martínez
- Laboratorio Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI)–Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía Irazu
- Instituto Nacional de Enfermedades Infecciosas (INEI)–Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carlos Vay
- Instituto de Fisiopatología y Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Prieto
- Laboratorio Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI)–Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) “Dr. Carlos G. Malbrán”, Ciudad Autónoma de Buenos Aires, Argentina
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