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Litterio M, Castello L, Venuta ME, Abel S, Fernández-Canigia L, Legaria MC, Rollet R, Vaustat D, Azula N, Fox B, Otero S, Maldonado ML, Mangieri NA, Rossetti MA, Predari SC, Cejas D, Barberis C. Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina. Rev Argent Microbiol 2024; 56:33-61. [PMID: 38368217 DOI: 10.1016/j.ram.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 02/19/2024] Open
Abstract
The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.
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Affiliation(s)
- Mirta Litterio
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Liliana Castello
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Elena Venuta
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Sofía Abel
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - María Cristina Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - Raquel Rollet
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Daniela Vaustat
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Buenos Aires, Argentina
| | | | - Silvina Otero
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - Natalia Alejandra Mangieri
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Adelaida Rossetti
- Hospital Interzonal de Agudos Presidente Perón, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Silvia Carla Predari
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Buenos Aires, Argentina
| | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina.
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2
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Coryell MP, Sava RL, Hastie JL, Carlson PE. Application of MALDI-TOF MS for enumerating bacterial constituents of defined consortia. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12558-5. [PMID: 37148337 DOI: 10.1007/s00253-023-12558-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/08/2023]
Abstract
Characterization of live biotherapeutic product (LBP) batches typically includes a measurement of viability, such as colony forming units (CFU). However, strain-specific CFU enumeration assays can be complicated by the presence of multiple organisms in a single product with similar growth requirements. To overcome specific challenges associated with obtaining strain-specific CFU values from multi-strain mixtures, we developed a method combining mass spectrometry-based colony identification with a traditional CFU assay. This method was assessed using defined consortia made from up to eight bacterial strains. Among four replicate batches of an eight-strain mixture, observed values differed from expected values by less than 0.4 log10 CFU among all strains measured (range of differences, -0.318 to + 0.267). The average difference between observed and expected values was + 0.0308 log10 CFU, with 95% limits of agreement from -0.347 to 0.408 (Bland-Altman analysis). To estimate precision, a single batch of eight-strain mixture was assayed in triplicate by three different users, for a total of nine measurements. Pooled standard deviation values ranged from 0.067 to 0.195 log10 CFU for the eight strains measured, and user averages did not differ significantly. Leveraging emerging mass-spectrometry-based colony identification tools, a novel method for simultaneous enumeration and identification of viable bacteria from mixed-strain consortia was developed and tested. This study demonstrates the potential for this approach to generate accurate and consistent measurements of up to eight bacterial strains simultaneously and may provide a flexible platform for future refinements and modifications. KEY POINTS: • Enumeration of live biotherapeutics is essential for product quality and safety. • Conventional CFU counting may not differentiate between strains in microbial products. • This approach was developed for direct enumeration of mixed bacterial strains simultaneously.
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Affiliation(s)
- Michael P Coryell
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Rosa L Sava
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Jessica L Hastie
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Paul E Carlson
- Division of Bacterial, Parasitic, and Allergenic Products; Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, USA.
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3
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Challenging the problematic detection of clostridial isolates causing late-blowing defect with MALDI-TOF MS. CZECH JOURNAL OF FOOD SCIENCES 2023. [DOI: 10.17221/199/2022-cjfs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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4
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Routine Use of Anaerobic Blood Culture Bottles for Specimens Collected from Adults and Children Enhances Microorganism Recovery and Improves Time to Positivity. J Clin Microbiol 2022; 60:e0050022. [PMID: 36040158 PMCID: PMC9491166 DOI: 10.1128/jcm.00500-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The utility of anaerobic blood culture bottles remains controversial, especially for specimens from children. Data are limited on the inclusion of an anaerobic bottle as part of a blood culture "set" when using contemporary blood culture instruments and media. Here, we evaluated the clinical utility of anaerobic blood culture bottles (FN Plus) and aerobic bottles (FA Plus) for the BacT/Alert Virtuo blood culture system (bioMérieux). A total of 158,710 bottles collected between November 2018 and October 2019 were evaluated. There were 6,652 positive anaerobic bottles, of which 384 (5.8%) contained 403 obligate anaerobes. In patients <19 years old, there were 389 positive anaerobic bottles, with 15 (1.8%) containing 16 obligate anaerobes. If not for anaerobic bottles, all but 8 obligate anaerobes would have gone undetected. Furthermore, anaerobic bottles were advantageous for some facultative anaerobes. Staphylococcus aureus from anaerobic bottles demonstrated statistically significant increased recovery (1,992 anaerobic versus 1,901 aerobic bottles, P = 0.009) and faster mean time to positivity (1,138 versus 1,174 min, P = 0.027). Only 25 microorganisms had statistically significant improved recovery and/or faster time to positivity from aerobic versus anaerobic bottles, suggesting anaerobic bottles offer comparable growth for most species. Finally, if only an aerobic bottle had been collected, 2,027 fewer positive cultures would have been detected and 7,452 fewer isolates would have been reported, including cultures with S. aureus (413 isolates, 10.6% less), Pseudomonas aeruginosa (9 isolates, 3.1% less) and Escherichia coli (193 isolates, 14.0% less). Taken together, these findings support the practice of routinely including an anaerobic bottle for blood culture collection.
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5
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Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group. J Clin Microbiol 2022; 60:e0236120. [PMID: 35700139 DOI: 10.1128/jcm.02361-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteroides fragilis group (BFG) species are common members of the human microbiota that provide several benefits to healthy hosts, yet BFG are also the most common anaerobes isolated from human infections, including intra-abdominal infections, abscesses, and bloodstream infection. Compared to many other anaerobes associated with disease, members of the BFG are more likely to be resistant to commonly used antimicrobials, including penicillin (>90% resistant), carbapenems (2 to 20% resistant), and metronidazole (0.2 to 4% resistant). As a result, infection with BFG bacteria can be associated with poor clinical outcomes. Here, we discuss the role of BFG in human health and disease, proposed taxonomic reclassifications within the BFG, and updates in methods for species-level identification. The increasing availability of whole-genome sequencing (WGS) supports recent proposals that the BFG now span two families (Bacteroidaceae and "Tannerellaceae") and multiple genera (Bacteroides, Parabacteroides, and Phocaeicola) within the phylum Bacteroidota. While members of the BFG are often reported to "group" rather than "species" level in many clinical settings, new reports of species-specific trends in antimicrobial resistance profiles and improved resolution of identification tools support routine species-level reporting in clinical practice. Empirical therapy may not be adequate for treatment of serious infections with BFG, warranting susceptibility testing for serious infections. We summarize methods for antimicrobial susceptibility testing and resistance prediction for BFG, including broth microdilution, agar dilution, WGS, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We examine global trends in BFG antimicrobial resistance and review genomics of BFG, revealing insights into rapid activation and dissemination of numerous antimicrobial resistance mechanisms.
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Otoo EA, Ocloo FC, Appiah V. Effect of gamma irradiation on shelf life of smoked guinea fowl (Numida meleagris) meat stored at refrigeration temperature. Radiat Phys Chem Oxf Engl 1993 2022. [DOI: 10.1016/j.radphyschem.2022.110041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Abstract
One of the most prevalent complications of diabetes mellitus are diabetic foot ulcers (DFU). Diabetic foot ulcers represent a complex condition placing individuals at-risk for major lower extremity amputations and are an independent predictor of patient mortality. DFU heal poorly when standard of care therapy is applied. In fact, wound healing occurs only approximately 30% within 12 weeks and only 45% regardless of time when standard of care is utilized. Similarly, diabetic foot infections occur in half of all DFU and conventional microbiologic cultures can take several days to process before a result is known. DFU represent a significant challenge in this regard because DFU often demonstrate polymicrobial growth, become resistant to preferred antibiotic therapy, and do not inform providers about long-term prognosis. In addition, conventional culture yields may be affected by the timing of antibiotic administration and collection of tissue for analysis. This may lead to suboptimal antibiotic administration or debilitating amputations. The microbiome of DFU is a new frontier to better understand the interactions between host organisms and pathogenic ones. Newer molecular techniques are readily available to assist in analyzing the constituency of the microbiome of DFU. These emerging techniques have already been used to study the microbiome of DFU and have clinical implications that may alter standard of care practice in the near future. Here emerging molecular techniques that can provide clinicians with rapid DFU-related-information and help prognosticate outcomes in this vulnerable patient population are presented.
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Affiliation(s)
- Brian M. Schmidt
- Michigan Medicine, Department of
Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, Ann Arbor,
MI, USA
- Brian M. Schmidt, DPM, Assistant Professor,
Department of Internal Medicine, Division of Metabolism, Endocrinology, and
Diabetes, University of Michigan Medical School, 24 Frank Lloyd Wright Drive,
Lobby C, Ann Arbor, MI 48106, USA.
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8
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Wolf EA, Rettig HC, Lupatsii M, Schlüter B, Schäfer K, Friedrich D, Graspeuntner S, Rupp J. Culturomics Approaches Expand the Diagnostic Accuracy for Sexually Transmitted Infections. Int J Mol Sci 2021; 22:ijms221910815. [PMID: 34639153 PMCID: PMC8509341 DOI: 10.3390/ijms221910815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
Sexually transmitted infections (STIs) are a major health concern with clinical manifestations being acknowledged to cause severe reproductive impairment. Research in infectious diseases has been centered around the known major pathogens for decades. However, we have just begun to understand that the microbiota of the female genital tract is of particular importance for disease initiation, infection progression, and pathological outcome. Thus, we are now aware that many poorly described, partially not yet known, or cultured bacteria may pave the way for an infection and/or contribute to disease severity. While sequencing-based methods are an important step in diagnosing STIs, culture-based methods are still the gold-standard method in diagnostic routine, providing the opportunity to distinguish phenotypic traits of bacteria. However, current diagnostic culture routines suffer from several limitations reducing the content of information about vaginal microbiota. A detailed characterization of microbiota-associated factors is needed to assess the impact of single-bacterial isolates from the vaginal community on vaginal health and the containment of STIs. Here we provide current concepts to enable modern culture routines and create new ideas to improve diagnostic approaches with a conjunct usage of bioinformatics. We aim to enable scientists and physicians alike to overcome long-accepted limitations in culturing bacteria of interest to the human health. Eventually, this may improve the quality of culture-based diagnostics, facilitate a research interface, and lead to a broader understanding of the role of vaginal microbiota in reproductive health and STIs.
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Affiliation(s)
- Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Britta Schlüter
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, 23538 Lübeck, Germany;
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Dirk Friedrich
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
- Correspondence:
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9
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İnal N, Karagöz A, Turhan E, Hazirolan G. First pediatric case of osteomyelitis caused by Robinsoniella peoriensis. Acta Microbiol Immunol Hung 2021. [PMID: 33950858 DOI: 10.1556/030.2020.01122] [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: 12/30/2019] [Accepted: 03/03/2020] [Indexed: 11/19/2022]
Abstract
Robinsoniella peoriensis is a gram-positive, spore-forming, anaerobic rod. In our study, we isolated R. peoriensis from an open fracture of the left distal tibia of a three-year-old male patient. Tissue anaerobic culture was positive for R. peoriensis. It was identified with both matrix-assisted laser desorption ionization time-of-flight mass spectrometry and confirmed via 16S rRNA gene sequencing. The patient responded to ampicillin-sulbactam and amikacin antibiotic therapy. Antimicrobial susceptibility testing should be performed to guide the choice of treatment. To the best of our knowledge, this is the first report of R. peoriensis osteomyelitis in a pediatric patient and first report from Turkey.
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Affiliation(s)
- Neşe İnal
- 1 Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Alper Karagöz
- 2 Department of Molecular Biology and Genetics, USA University, Turkey
| | - Egemen Turhan
- 3 Department of Orthopedics and Traumatology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Gülşen Hazirolan
- 1 Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
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Alcalá L, Marín M, Ruiz A, Quiroga L, Zamora-Cintas M, Fernández-Chico MA, Muñoz P, Rodríguez-Sánchez B. Identifying Anaerobic Bacteria Using MALDI-TOF Mass Spectrometry: A Four-Year Experience. Front Cell Infect Microbiol 2021; 11:521014. [PMID: 33968791 PMCID: PMC8101409 DOI: 10.3389/fcimb.2021.521014] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/26/2021] [Indexed: 12/23/2022] Open
Abstract
Because of the special culture requirements of anaerobic bacteria, their low growth-rate and the difficulties to isolate them, MALDI-TOF MS has become a reliable identification tool for these microorganisms due to the little amount of bacteria required and the accuracy of MALDI-TOF MS identifications. In this study, the performance of MALDI-TOF MS for the identification of anaerobic isolates during a 4-year period is described. Biomass from colonies grown on Brucella agar was directly smeared onto the MALDI-TOF target plate and submitted to on-plate protein extraction with 1μl of 100% formic acid. Sequencing analysis of the 16S rRNA gene was used as a reference method for the identification of isolates unreliably or not identified by MALDI-TOF MS. Overall, 95.7% of the isolates were identified to the species level using the updated V6 database vs 93.8% with previous databases lacking some anaerobic species; 68.5% of the total were reliably identified with high-confidence score values (≥2.0) and 95.0% with low-confidence values (score value ≥1.7). Besides, no differences between Gram-positive and Gram-negative isolates were detected beyond a slight decrease of correct species assignment for gram positive cocci (94.1% vs 95.7% globally). MALDI-TOF MS has demonstrated its usefulness for the identification of anaerobes, with high correlation with phenotypic and conventional methods. Over the study period, only 2.1% of the isolates could not be reliably identified and required molecular methods for a final identification. Therefore, MALDI-TOF MS provided reliable identification of anaerobic isolates, allowing clinicians to streamline the most appropriate antibiotic therapy and manage patients accordingly.
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Affiliation(s)
- Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
| | - Adrián Ruiz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Lidia Quiroga
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Maribel Zamora-Cintas
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Antonia Fernández-Chico
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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11
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Jussiaux F, Miot-Sertier C, Nguyen-Lopez D, Badet C, Samot J. Reliability of MALDI-TOF mass spectrometry to identify oral isolates of Streptococcus salivarius and Lactobacillus spp. Arch Oral Biol 2020; 121:104983. [PMID: 33242690 DOI: 10.1016/j.archoralbio.2020.104983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The aim of this study is to evaluate the performance of MALDI-TOF mass spectrometry in identifying bacteria isolated in the oral cavity known to be of probiotic interest. DESIGN We evaluated Bruker MALDI Biotyper for the identification of 92 clinical oral isolates of probiotic interest (31 Streptococcus salivarius and 61 Lactobacillus spp.) by comparing direct colony method with on-plate formic acid extraction. Isolates were previously identified by use of biochemical methods and molecular biology. RESULTS Using the manufacturer's suggested genus and species level cutoff scores, the direct colony method identified 42 (45.7%) isolates at the genus level and 35 (38%) at the species level while the on-plate extraction method correctly identified 90 (97.8%) isolates at the genus level and 82 (89.1%) at the species level. The difference between the two methods was statistically significant at the genus and species levels (P ≤ 0.0001). After dividing the isolates into two subgroups, the analysis was repeated. The direct colony method identified correctly all isolates of Streptococcus salivarius at the species level. In contrast, the direct colony method allowed the identification of only 11 (18%) lactobacilli at the genus level and 4 (6.6%) at the species level. The on-plate extraction method was statistically (P ≤ 0.0001) more efficient since 59 (96.7%) lactobacilli were identified at the genus level and 51 (83.6%) at the species level. CONCLUSIONS MALDI Biotyper can efficiently identify Streptococcus salivarius regardless of the preparative method but on-plate extraction is superior to direct colony method for the identification of lactobacilli.
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Affiliation(s)
| | - Cécile Miot-Sertier
- Univ. Bordeaux, ISVV, EA 4577, Unité de Recherche Œnologie, USC 1366 INRAE, F-33140 Villenave d'Ornon, France
| | - Darrène Nguyen-Lopez
- Centre Hospitalier Universitaire de Bordeaux, Pôle de Médecine et Chirurgie Bucco-Dentaire, Bordeaux, France
| | - Cécile Badet
- Univ. Bordeaux, UFR des Sciences Odontologiques, Bordeaux, France; Univ. Bordeaux, ISVV, EA 4577, Unité de Recherche Œnologie, USC 1366 INRAE, F-33140 Villenave d'Ornon, France; Centre Hospitalier Universitaire de Bordeaux, Pôle de Médecine et Chirurgie Bucco-Dentaire, Bordeaux, France
| | - Johan Samot
- Univ. Bordeaux, UFR des Sciences Odontologiques, Bordeaux, France; Univ. Bordeaux, ISVV, EA 4577, Unité de Recherche Œnologie, USC 1366 INRAE, F-33140 Villenave d'Ornon, France; Centre Hospitalier Universitaire de Bordeaux, Pôle de Médecine et Chirurgie Bucco-Dentaire, Bordeaux, France.
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Fredua-Agyeman M, Ofosu-Boateng M, Offei AO, Mehta M, Gaisford S, Limayem A. Study on the functional properties of potential indigenous probiotics isolated from human samples in West Africa. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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GAJDÁCS MÁRIÓ, URBÁN EDIT. Relevance of anaerobic bacteremia in adult patients: A never-ending story? Eur J Microbiol Immunol (Bp) 2020; 10:64-75. [PMID: 32590337 PMCID: PMC7391379 DOI: 10.1556/1886.2020.00009] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/19/2020] [Indexed: 11/30/2022] Open
Abstract
Obligate anaerobic bacteria are considered important constituents of the microbiota of humans; in addition, they are also important etiological agents in some focal or invasive infections and bacteremia with a high level of mortality. Conflicting data have accumulated over the last decades regarding the extent in which these pathogens play an intrinsic role in bloodstream infections. Clinical characteristics of anaerobic bloodstream infections do not differ from bacteremia caused by other pathogens, but due to their longer generation time and rigorous growth requirements, it usually takes longer to establish the etiological diagnosis. The introduction of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) has represented a technological revolution in microbiological diagnostics, which has allowed for the fast, accurate and reliable identification of anaerobic bacteria at a low sample cost. The purpose of this review article is to summarize the currently available literature data on the prevalence of anaerobic bacteremia in adults for physicians and clinical microbiologists and to shed some light on the complexity of this topic nowadays.
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Affiliation(s)
- MÁRIÓ GAJDÁCS
- Department of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös utca 6., Szeged, 6720, Hungary
| | - EDIT URBÁN
- Department of Public Health, Faculty of Medicine, University of Szeged, Dóm tér 10., Szeged, 6720, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, Szigeti út 12., Pécs, 7624, Hungary
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Propionibacterium/Cutibacterium species-related positive samples, identification, clinical and resistance features: a 10-year survey in a French hospital. Eur J Clin Microbiol Infect Dis 2020; 39:1357-1364. [PMID: 32125556 DOI: 10.1007/s10096-020-03852-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
A 10-year retrospective study of Propionibacterium/Cutibacterium-positive samples gathered from hospitalized patients was conducted at Nantes University hospital. A total of 2728 Propionibacterium/Cutibacterium-positive samples analyzed between 2007 and 2016 were included. Due to the implementation of MALDI-TOF identification in 2013, most non-Cutibacterium acnes isolates were identified a second time using this technology. Over that period, Cutibacterium acnes remained the most predominant species accounting for 91.5% (2497/2728) of the isolates, followed by Cutibacterium avidum (4.2%, 115/2728) and Cutibacterium granulosum (2.4%, 64/2728). Regarding the origin of samples, the orthopaedic department was the main Cutibacterium sample provider representing 51.9% (1415/2728) of all samples followed by the dermatology department (11.5%, 315/2728). Samples were recovered from various tissue locations: 31.5% (858/2728) from surgery-related samples such as shoulder, spine or hip replacement devices and 19.1% (520/2728) from skin samples. MALDI-TOF method revealed misidentification before 2013. Cutibacterium avidum was falsely identified as C. granulosum (n = 33). Consequently, MALDI-TOF technology using up-to-date databases should be preferred to biochemical identification in order to avoid biased species identification. Regarding antibiotic resistance, 14.7% (20/136) of C. acnes was resistant to erythromycin. 4.1% (41/1005) of C. acnes strains, 17.9% (12/67) of C. avidum strains and 3.6% (1/28) of C. granulosum strains were found resistant to clindamycin.
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Kim D, Ji S, Kim JR, Kim M, Byun JH, Yum JH, Yong D, Lee K. Performance evaluation of a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, ASTA MicroIDSys system, in bacterial identification against clinical isolates of anaerobic bacteria. Anaerobe 2019; 61:102131. [PMID: 31778809 DOI: 10.1016/j.anaerobe.2019.102131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 11/15/2019] [Accepted: 11/23/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been introduced for bacterial identification. The ASTA MicroIDSys system (ASTA, Suwon, Korea) is a new MALDI-TOF MS system developed for species identification of microorganisms. We evaluated the performance of MicroIDSys against clinical isolates of anaerobic bacteria. MATERIAL AND METHODS A total of 370 non-duplicated clinical isolates of anaerobic bacteria were tested in this study. Bacterial identification with MicroIDSys was performed with a direct smear method, and measured spectra were analyzed using respective software. The results of MicroIDSys were compared with the results of Bruker Biotyper and 16S rRNA sequencing. RESULTS The overall agreement rates for the 370 clinical isolates (34 genera and 99 species) were 95.4% (353/370) at the genus level and 91.6% (n = 340) at the species level. Only 17 isolates were incorrectly identified at the genus level: five misidentifications and 12 unidentifications. The MicroIDSys system exhibited excellent performance in the identification of clinically relevant bacterial species. Most of the Bacteroides isolates (98.0%, 99/101) and all of the Clostridium difficile (100%, n = 11), Clostridium perfringens (100%, n = 10), Finegoldia magna (100%, n = 11), and Parvimonas micra (100%, n = 10) isolates were correctly identified at the species level. CONCLUSION The MicroIDSys system proved useful in the identification of anaerobic bacteria, especially clinically relevant species. This system could be of use in clinical microbiology laboratories as a primary tool for identifying anaerobic bacteria.
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Affiliation(s)
- Dokyun Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Seungeun Ji
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jung Rim Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Myungsook Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Jong Hwa Yum
- Department of Clinical Laboratory Science, Dong-eui University, Busan, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University, College of Medicine, Seoul, South Korea.
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Li Y, Shan M, Zhu Z, Mao X, Yan M, Chen Y, Zhu Q, Li H, Gu B. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect Dis 2019; 19:941. [PMID: 31699042 PMCID: PMC6836477 DOI: 10.1186/s12879-019-4584-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification. OBJECTIVE To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes. METHODS Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0. RESULTS The identification accuracy of MALDI-TOF MS was 84% for species (I2 = 98.0%, P < 0.1), and 92% for genus (I2 = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system. CONCLUSIONS Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.
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Affiliation(s)
- Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Mingzhu Shan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, 214200, China
| | - Mingju Yan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiuju Zhu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hongchun Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Bing Gu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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18
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Savas S, Hazirolan G, Karagoz A, Parlak M. From days to hours: Can MALDI-TOF MS system replace both conventional and molecular typing methods with new cut off level for Vancomycin Resistant Enterococcus faecium. J Microbiol Methods 2018; 162:62-68. [PMID: 30605699 DOI: 10.1016/j.mimet.2018.12.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 01/21/2023]
Abstract
Vancomycin-Resistant E. faecium (VRE) strains from clinical specimens were identified by conventional methods before. Following the phenotype-based identification, all strains were also identified using both BD Phoenix and VITEK MS bioMérieux System. Strains were typed with the Bruker MALDI-TOF MS system, pulsed field gel electrophoresis (PFGE) and 16S rRNA gene sequencing analysis and then the sensitivity compared for each. A cut off value of 850 assigned with Bruker MALDI-TOF MS system was found to give equal sensitivity to that of PFGE. Results obtained were compared with those of molecular typing. The main advantage of MALDI-TOF MS technology over the others was the much shorter analysis time which lasted only a few hours rather than days or a whole week. Also, the Bruker MALDI-TOF MS system was used for typing and compared with the gold standard method and this study is first to report the determined cut off level for typing of VRE strains.
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Affiliation(s)
- Sumeyra Savas
- The Scientific and Technological Research Council of Turkey, Kocaeli, Turkey.
| | - Gulsen Hazirolan
- Department of Medical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | | | - Mehmet Parlak
- Department of Medical Microbiology, Yuzuncu Yil University School of Medicine, Ankara, Turkey
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Evaluation of the Vitek MS and the MALDI Biotyper systems for the identification of less commonly isolated but clinically relevant anaerobes and facultative anaerobes. Anaerobe 2018; 54:210-216. [DOI: 10.1016/j.anaerobe.2018.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022]
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20
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Zamora-Cintas M, Marín M, Quiroga L, Martínez A, Fernández-Chico MA, Bouza E, Rodríguez-Sánchez B, Alcalá L. Identification of Porphyromonas isolates from clinical origin using MALDI-TOF Mass Spectrometry. Anaerobe 2018; 54:197-200. [PMID: 30541687 DOI: 10.1016/j.anaerobe.2018.06.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/13/2018] [Accepted: 06/30/2018] [Indexed: 11/25/2022]
Abstract
Despite the wide implementation of MALDI-TOF MS for the rapid and reliable identification of most microorganisms, some taxonomic groups such as the Porphyromonas genus remain largely untested. In this study we evaluated the performance of MALDI-TOF MS on this genus using a collection of 39 isolates sent for routine identification to our institution over a 16-year period. All of them were identified by DNA-sequencing analysis of the 16S rRNA gene plus the hsp60 gene when the previous one did not yield species-level assignment. MALDI-TOF MS provided correct identification at least at the genus level of 21/39 isolates (53.9%). Twelve isolates were correctly identified at the species level with a score value ≥ 2.0 and 9 more with score values < 2.0 and ≥ 1.7. The species most represented in the database (P. gingivalis and P. somerae) lay within this category. However, the species poorly represented in this database (P. asaccharolytica and P. uenonis) were mostly identified with lower scores (1.35-1.67) or remained unidentified by MALDI-TOF MS. The addition of two P. asaccharolytica reference spectra to our in-house library allowed 72.9% of genus-level identifications with 17/37 isolates (45.9%) identified with score values ≥ 2.0. Our results showed a high level of correlation between MALDI-TOF MS and DNA-based identification for Porphyromonas spp. strains at the species level, even with score values < 2.0. The reliability provided by MALDI-TOF MS increased when the database was fed with spectra from the species poorly represented in the commercial database.
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Affiliation(s)
- Maribel Zamora-Cintas
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain; Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain.
| | - Lidia Quiroga
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Andrea Martínez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Antonia Fernández-Chico
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilio Bouza
- Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain.
| | - Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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21
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Bakhtiary F, Sayevand HR, Remely M, Hippe B, Indra A, Hosseini H, Haslberger AG. Identification of Clostridium spp. derived from a sheep and cattle slaughterhouse by matrix-assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing. Journal of Food Science and Technology 2018; 55:3232-3240. [PMID: 30065434 DOI: 10.1007/s13197-018-3255-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 11/30/2022]
Abstract
Clostridia are widespread and some of them are serious human pathogens. Identification of Clostridium spp. is important for managing microbiological risks in the food industry. Samples derived from sheep and cattle carcasses from a slaughterhouse in Iran were analyzed by MALDI-TOF MS using direct transfer and extended direct transfer sample preparation methods and 16S rDNA sequencing. MALDI-TOF MS could identify ten species in 224 out of 240 Clostridium isolates. In comparison to the 16S rDNA sequencing, correct identification rate of the Clostridium spp. at the species level by MALDI-TOF MS technique was 93.3%. 16 isolates were not identified by MALDI-TOF MS but 16s rDNA sequencing identified them as C. estertheticum, C. frigidicarnis, and C. gasigenes species. The most frequently identified Clostridium species were: C. sporogenes (13%), C. cadaveris (12.5%), C. cochlearium (12%) and C. perfringens (10%). Extended direct transfer method [2.26 ± 0.18 log (score)] in comparison to direct transfer method [2.15 ± 0.23 log (score)] improved Clostridium spp. IDENTIFICATION Using a cut-off score of 1.7 was sufficient for accurate identification of Clostridium species. MALDI-TOF MS identification scores for Clostridium spp. decreased with longer incubation time. Clostridium species predominantly were isolated from carcasses after skinning and evisceration steps in the slaughterhouse. MALDI-TOF MS could be an accurate way to identify Clostridium species. Moreover, continuous improvement of the database and MALDI-TOF MS instrument enhance its performance in food control laboratories.
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Affiliation(s)
- Farzaneh Bakhtiary
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | - Hamid Reza Sayevand
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | - Marlene Remely
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | - Berit Hippe
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | | | - Hedayat Hosseini
- 3Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alexander G Haslberger
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
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22
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Rams TE, Sautter JD, Hsiao CY, van Winkelhoff AJ. Phenotypic identification of periodontal Prevotella intermedia/nigrescens group isolates validated by MALDI-TOF mass spectrometry. Anaerobe 2018; 54:201-204. [PMID: 29913204 DOI: 10.1016/j.anaerobe.2018.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 12/18/2022]
Abstract
The accuracy of a phenotypic scheme to recognize periodontal Prevotella intermedia/nigrescens group clinical isolates on primary isolation culture plates was assessed with matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 84 fresh subgingival isolates from 23 chronic periodontitis patients were presumptively recognized on anaerobically-incubated enriched Brucella blood agar primary isolation plates as P. intermedia/nigrescens based on their dark-pigmented colony morphology, brick-red autofluorescence under long-wave ultraviolet light, and a negative fluorescence test for lactose production. The presumptive P. intermedia/nigrescens clinical isolates were subjected to MALDI-TOF MS analysis using Bruker MALDI Biotyper analytic software containing mass spectra for P. intermedia and Prevotella nigrescens in its reference library of bacterial protein profiles. Using a ≥1.7 log score agreement threshold, 60 (71.4%) of the presumptive P. intermedia/nigrescens clinical isolates were confirmed as either P. intermedia (25 isolates) or P. nigrescens (35 isolates). All isolates with a <1.7 log score were also identified as P. intermedia or P. nigrescens from the top choice designated on the MALDI Biotyper most likely species identification list. These MALDI-TOF MS findings document the ability of the phenotypic scheme to correctly recognize most periodontal P. intermedia/nigrescens group clinical isolates on primary isolation culture plates.
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Affiliation(s)
- Thomas E Rams
- Department of Periodontology and Oral Implantology, and Oral Microbiology Testing Service Laboratory, Temple University School of Dentistry, 3223 North Broad Street, Philadelphia, PA 19140 USA; Department of Microbiology and Immunology, Temple University School of Medicine, 3500 North Broad Street, Philadelphia, PA 19140 USA.
| | - Jacqueline D Sautter
- Department of Periodontology and Oral Implantology, and Oral Microbiology Testing Service Laboratory, Temple University School of Dentistry, 3223 North Broad Street, Philadelphia, PA 19140 USA
| | - Chinhua Y Hsiao
- Department of Periodontology and Oral Implantology, and Oral Microbiology Testing Service Laboratory, Temple University School of Dentistry, 3223 North Broad Street, Philadelphia, PA 19140 USA
| | - Arie J van Winkelhoff
- Center for Dentistry and Oral Hygiene, Department of Oral Microbiology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands; Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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Sárvári KP, Sóki J, Iván M, Miszti C, Latkóczy K, Melegh SZ, Urbán E. MALDI-TOF MS versus 16S rRNA sequencing: Minor discrepancy between tools in identification of Bacteroides isolates. Acta Microbiol Immunol Hung 2018; 65:173-181. [PMID: 28889758 DOI: 10.1556/030.64.2017.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Members of the genus Bacteroides are important components of the normal microbiota of gastrointestinal tract; however, as opportunistic pathogens are also associated with severe or even life-threatening infections with significant mortality. Various species within Bacteroides fragilis group are phenotypically very similar; thus, their identifications with traditional-automated biochemical methods are frequently inaccurate. The identification of the newly discovered or reclassified bacteria can be doubtful because of the lack of biochemical profile in the database of these tests. The aim of this study was to determine the accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) method by testing of 400 Hungarian Bacteroides clinical isolates. Inaccurate identification results with MALDI-TOF MS were confirmed by 16S rRNA gene sequencing and findings were compared with traditional-automated biochemical test rapid ID 32A method as well.
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Affiliation(s)
| | - József Sóki
- 1 Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Miklós Iván
- 2 Institute of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Cecilia Miszti
- 3 Institute of Medical Microbiology, University of Debrecen, Debrecen, Hungary
| | | | - Szilvia Zsóka Melegh
- 5 Institute of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Edit Urbán
- 1 Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
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How to isolate, identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories. Clin Microbiol Infect 2018; 24:1139-1148. [PMID: 29458156 DOI: 10.1016/j.cmi.2018.02.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/09/2018] [Accepted: 02/11/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND There has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described using 16S rRNA gene sequencing of clinical isolates obtained from different infection sites with commercially available special culture media to support the growth of anaerobes. Several systems, such as anaerobic pouches, boxes, jars and chambers provide suitable anaerobic culture conditions to isolate even strict anaerobic bacteria successfully from clinical specimens. Beside the classical, time-consuming identification methods and automated biochemical tests, the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has revolutionized identification of even unusual and slow-growing anaerobes directly from culture plates, providing the possibility of providing timely information about anaerobic infections. AIMS The aim of this review article is to present methods for routine laboratories, which carry out anaerobic diagnostics on different levels. SOURCES Relevant data from the literature mostly published during the last 7 years are encompassed and discussed. CONTENT The review involves topics on the anaerobes that are members of the commensal microbiota and their role causing infection, the key requirements for collection and transport of specimens, processing of specimens in the laboratory, incubation techniques, identification and antimicrobial susceptibility testing of anaerobic bacteria. Advantages, drawbacks and specific benefits of the methods are highlighted. IMPLICATIONS The present review aims to update and improve anaerobic microbiology in laboratories with optimal conditions as well as encourage its routine implementation in laboratories with restricted resources.
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Stary L, Mezerova K, Skalicky P, Zboril P, Raclavsky V. Are we any closer to screening for colorectal cancer using microbial markers?A critical review. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2017; 161:333-338. [DOI: 10.5507/bp.2017.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 11/15/2017] [Indexed: 12/18/2022] Open
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26
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Veloo ACM, Jean-Pierre H, Justesen US, Morris T, Urban E, Wybo I, Shah HN, Friedrich AW, Morris T, Shah HN, Jean-Pierre H, Justesen US, Nagy E, Urban E, Kostrzewa M, Veloo A, Friedrich AW. A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS. Anaerobe 2017; 48:94-97. [PMID: 28797803 DOI: 10.1016/j.anaerobe.2017.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 11/15/2022]
Abstract
Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories.
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Affiliation(s)
- A C M Veloo
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands.
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue du Doyen Gaston Giraud, 34295 Montpellier Cedex 5, France; Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes Hydriques Santé Environnements, UMR 5569 Hydrosciences, UFR Pharmacie, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - U S Justesen
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - T Morris
- UK Anaerobe Reference Unit, Public Health Wales Microbiology, Cardiff, UK
| | - E Urban
- Institute of Clinical Microbiology, University of Szeged, Hungary
| | - I Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - H N Shah
- Department of Natural Sciences, Middlesex University, London NW4 4BT, UK
| | - A W Friedrich
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, The Netherlands
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27
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Rodríguez-Sánchez B, Alcalá L, Marín M, Ruiz A, Alonso E, Bouza E. Evaluation of MALDI-TOF MS (Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry) for routine identification of anaerobic bacteria. Anaerobe 2016; 42:101-107. [PMID: 27702604 DOI: 10.1016/j.anaerobe.2016.09.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 08/30/2016] [Accepted: 09/30/2016] [Indexed: 12/22/2022]
Abstract
Information regarding the use of MALDI-TOF MS as an alternative to conventional laboratory methods for the rapid and reliable identification of bacterial isolates is still limited. In this study, MALDI-TOF MS was evaluated on 295 anaerobic isolates previously identified by 16S rRNA gene sequencing and with biochemical tests (Rapid ID 32A system, BioMérieux). In total, 85.8% of the isolates were identified by MALDI-TOF MS at the species level vs 49.8% using the Rapid ID 32A system (p < 0.0001). None of the isolates was discordantly identified at the genus level using MALDI-TOF MS and only 9 of them could not be identified using the method. Thus, our results show that MALDI-TOF MS is a robust and reliable tool for the identification of anaerobic isolates in the microbiology laboratory. Its implementation will reduce the turnaround time for a final identification and the number of isolates that require 16S rRNA sequencing.
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Affiliation(s)
- Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
| | - Luis Alcalá
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain
| | - Adrián Ruiz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Elena Alonso
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058), Madrid, Spain; Medicine Department, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
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28
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Peeters B, Magerman K, Waumans L, Cartuyvels R. Laboratory survey and literature review of anaerobic bacteriology: foundations of a clinically orientated and evidence-based workup for anaerobic cultures. Diagn Microbiol Infect Dis 2016; 86:15-22. [DOI: 10.1016/j.diagmicrobio.2016.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/02/2016] [Accepted: 06/05/2016] [Indexed: 12/22/2022]
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29
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Abstract
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
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Affiliation(s)
- Deirdre L Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada T2N 1N4
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30
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Rams TE, Sautter JD, Getreu A, van Winkelhoff AJ. Phenotypic identification of Porphyromonas gingivalis validated with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Microb Pathog 2016; 94:112-6. [DOI: 10.1016/j.micpath.2016.01.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/27/2016] [Accepted: 01/27/2016] [Indexed: 12/12/2022]
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31
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Gonzalez MD, Weber CJ, Burnham CAD. Rapid identification of microorganisms from positive blood cultures by testing early growth on solid media using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Diagn Microbiol Infect Dis 2016; 85:133-5. [PMID: 27117518 DOI: 10.1016/j.diagmicrobio.2016.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 02/22/2016] [Accepted: 02/22/2016] [Indexed: 12/27/2022]
Abstract
We performed a retrospective analysis of a simple modification to MALDI-TOF MS for microorganism identification to accurately improve the turnaround time (TAT) for identification of Enterobacteriaceae recovered in blood cultures. Relative to standard MALDI-TOF MS procedures, we reduced TAT from 28.3 (n=90) to 21.2h (n=107).
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Affiliation(s)
- Mark D Gonzalez
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Carol J Weber
- Department of Laboratories, Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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32
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Hrdlickova Kuckova S, Rambouskova G, Hynek R, Cejnar P, Oltrogge D, Fuchs R. Evaluation of mass spectrometric data using principal component analysis for determination of the effects of organic lakes on protein binder identification. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:1270-1278. [PMID: 26505772 DOI: 10.1002/jms.3699] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 07/26/2015] [Accepted: 08/24/2015] [Indexed: 06/05/2023]
Abstract
Matrix-assisted laser desorption/ionisation-time of flight (MALDI-TOF) mass spectrometry is commonly used for the identification of proteinaceous binders and their mixtures in artworks. The determination of protein binders is based on a comparison between the m/z values of tryptic peptides in the unknown sample and a reference one (egg, casein, animal glues etc.), but this method has greater potential to study changes due to ageing and the influence of organic/inorganic components on protein identification. However, it is necessary to then carry out statistical evaluation on the obtained data. Before now, it has been complicated to routinely convert the mass spectrometric data into a statistical programme, to extract and match the appropriate peaks. Only several 'homemade' computer programmes without user-friendly interfaces are available for these purposes. In this paper, we would like to present our completely new, publically available, non-commercial software, ms-alone and multiMS-toolbox, for principal component analyses of MALDI-TOF MS data for R software, and their application to the study of the influence of heterogeneous matrices (organic lakes) for protein identification. Using this new software, we determined the main factors that influence the protein analyses of artificially aged model mixtures of organic lakes and fish glue, prepared according to historical recipes that were used for book illumination, using MALDI-TOF peptide mass mapping.
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Affiliation(s)
- Stepanka Hrdlickova Kuckova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Prague, Czech Republic
| | - Gabriela Rambouskova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Prague, Czech Republic
| | - Radovan Hynek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Prague, Czech Republic
| | - Pavel Cejnar
- Department of Computing and Control Engineering, University of Chemistry and Technology, Technická 3, 166 28 Prague 6, Prague, Czech Republic
| | - Doris Oltrogge
- Cologne Institute of Conservation Sciences, Ubierring 40, D-50678, Köln, Germany
| | - Robert Fuchs
- Cologne Institute of Conservation Sciences, Ubierring 40, D-50678, Köln, Germany
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33
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Charles PGP, Uçkay I, Kressmann B, Emonet S, Lipsky BA. The role of anaerobes in diabetic foot infections. Anaerobe 2015; 34:8-13. [PMID: 25841893 DOI: 10.1016/j.anaerobe.2015.03.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/24/2015] [Indexed: 12/25/2022]
Abstract
Diabetic foot infections (DFI) are a common cause of morbidity and, on occasion, even mortality. Infection can be either mono- or polymicrobial, with a wide variety of potential pathogens. Anaerobes may be involved, particularly in wounds that are deeper or more chronic, and are more frequently identified when using modern molecular techniques, such as 16s PCR and pyrosequencing. It remains unclear whether the presence of anaerobes in DFI leads to more severe manifestations, or if these organisms are largely colonizers associated with the presence of greater degrees of tissue ischemia and necrosis. Commonly used empiric antibiotic therapy for diabetic foot infections is generally broad-spectrum and usually has activity against the most frequently identified anaerobes, such as Peptostreptococcus and Bacteroides species. Adequate surgical debridement and, when needed, foot revascularization may be at least as important as the choice of antibiotic to achieve a successful treatment outcome.
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Affiliation(s)
- Patrick G P Charles
- Infectious Diseases Service, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Department of Infectious Diseases, Austin Health, Heidelberg, Australia; Department of Medicine, University of Melbourne, Parkville, Australia.
| | - Ilker Uçkay
- Infectious Diseases Service, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Orthopaedic Surgery Service, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Infection Control Program, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Benjamin Kressmann
- Infectious Diseases Service, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Orthopaedic Surgery Service, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Stéphane Emonet
- Infectious Diseases Service, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Laboratory of Bacteriology, Geneva University Hospitals, Geneva, Switzerland
| | - Benjamin A Lipsky
- Infectious Diseases Service, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland; Division of Medical Sciences (Infectious Diseases), University of Oxford, Oxford, UK
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34
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Hu JW, Cao MJ, Guo SC, Zhang LJ, Su WJ, Liu GM. Identification and inhibition of histamine-forming bacteria in blue scad (Decapterus maruadsi) and chub mackerel (Scomber japonicus). J Food Prot 2015; 78:383-9. [PMID: 25710155 DOI: 10.4315/0362-028x.jfp-14-296] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study, we investigated the differences in histamine accumulation between blue scad and chub mackerel and methods of inhibiting histamine-forming bacteria and controlling histamine accumulation in fish. The free histidine contents in blue scad and chub mackerel were 1.45 and 2.75 mg/g, respectively. The histamine-forming bacteria isolated from them were identified as Citrobacter freundii, Citrobacter braakii, and Enterobacter aerogenes using 16S rDNA sequence analysis, the VITEK 2 Compact system, and MALDI-TOF MS. The histamine-producing capacities of C. freundii, C. braakii, and E. aerogenes were 470, 1,057, and 4,213 mg/liter, respectively, after culture at 37°C for 48 h. Among the different antimicrobials and preservatives tested, potassium sorbate and sodium diacetate effectively inhibited the histamine-forming bacteria and their histamine production. After chub mackerel was dipped into 0.5% potassium sorbate or sodium diacetate, its histamine content increased more slowly at room temperature. Therefore, a potassium sorbate or sodium diacetate dipping treatment could effectively control histamine accumulation in fish.
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Affiliation(s)
- Jia-Wei Hu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, 361021, People's Republic of China
| | - Min-Jie Cao
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, 361021, People's Republic of China
| | - Shun-Cai Guo
- Jimei District Agricultural Technology Extension Training Center, Xiamen, Fujian, 361021, People's Republic of China
| | - Ling-Jing Zhang
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, 361021, People's Republic of China
| | - Wen-Jin Su
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, 361021, People's Republic of China
| | - Guang-Ming Liu
- College of Food and Biological Engineering, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, 361021, People's Republic of China.
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35
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Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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36
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Abstract
Abstract
BACKGROUND
First introduced into clinical microbiology laboratories in Europe, MALDI-TOF MS is being rapidly embraced by laboratories around the globe. Although it has multiple applications, its widespread adoption in clinical microbiology relates to its use as an inexpensive, easy, fast, and accurate method for identification of grown bacteria and fungi based on automated analysis of the mass distribution of bacterial proteins.
CONTENT
This review provides a historical perspective on this new technology. Modern applications in the clinical microbiology laboratory are reviewed with a focus on the most recent publications in the field. Identification of aerobic and anaerobic bacteria, mycobacteria, and fungi are discussed, as are applications for testing urine and positive blood culture bottles. The strengths and limitations of MALDI-TOF MS applications in clinical microbiology are also addressed.
SUMMARY
MALDI-TOF MS is a tool for rapid, accurate, and cost-effective identification of cultured bacteria and fungi in clinical microbiology. The technology is automated, high throughput, and applicable to a broad range of common as well as esoteric bacteria and fungi. MALDI-TOF MS is an incontrovertibly beneficial technology for the clinical microbiology laboratory.
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Affiliation(s)
- Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, MN
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37
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McElvania TeKippe E, Burnham CAD. Evaluation of the Bruker Biotyper and VITEK MS MALDI-TOF MS systems for the identification of unusual and/or difficult-to-identify microorganisms isolated from clinical specimens. Eur J Clin Microbiol Infect Dis 2014; 33:2163-71. [PMID: 24962194 DOI: 10.1007/s10096-014-2183-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 06/09/2014] [Indexed: 10/25/2022]
Abstract
The purpose of this investigation was to evaluate the analytical performance characteristics of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of unusual organisms. We evaluated the accuracy of two MALDI-TOF MS systems, bioMérieux VITEK MS (database v2.0) and Bruker Biotyper (software version 3.0), for the identification of the most difficult and/or unusual microorganisms isolated from clinical specimens. Our study included 174 bacterial isolates recovered from clinical cultures at Barnes-Jewish Hospital, St. Louis, MO, from 2009 to 2013, representing 50 genera and 52 species. MS identifications were compared to the identification reported by the reference laboratory. Discrepancies were resolved using molecular methods, including 16S rRNA gene sequencing and additional molecular methods. When performed, molecular methods were considered the gold standard. Of the 168 isolates resolved to the genus level, VITEK MS identified 145 (86.3 %), and of the 114 isolates resolved to the species level, 97 (85.1 %) were correctly identified. Bruker Biotyper identified 155 (92.3 %) of 168 isolates to the genus level and 97 (85.1 %) of 114 isolates to the species level. VITEK MS and Bruker Biotyper provided no identification for 17 (10.1 %) and 12 (7.1 %) organisms, respectively, and misidentified six (3.6 %) and one (0.6 %) isolate, respectively. Six isolates (3.6 %) were not resolvable to the genus level and were excluded from data analysis due to the lack of a gold standard for comparison. There was no significant difference in the number of organisms identified to the genus level, species level, unidentified, or misidentified by the two MALDI-TOF MS systems (p = 0.11, 1.0, 0.44, and 0.12, respectively).
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Affiliation(s)
- E McElvania TeKippe
- Department of Pathology & Immunology, Washington University School of Medicine, 660 South Euclid Avenue, Campus Box 8118, St. Louis, MO, 63110, USA
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