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Sasiene ZJ, LeBrun ES, Velappan N, Anderson AR, Patterson NH, Dufresne M, Farrow MA, Norris JL, Caprioli RM, Mach PM, McBride EM, Glaros TG. Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers. Analyst 2024; 149:3564-3574. [PMID: 38717518 DOI: 10.1039/d4an00325j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.
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Affiliation(s)
- Zachary J Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Erick S LeBrun
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nileena Velappan
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Austin R Anderson
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nathan H Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Melissa A Farrow
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Phillip M Mach
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Ethan M McBride
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Trevor G Glaros
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Pilkington E, Goncalves R, Henze L, Grapes N, Volk H, De Decker S. Determining the prevalence and risk factors for positive bacterial culture in canine discospondylitis: 120 cases. Vet Rec 2023; 193:e3053. [PMID: 37211971 DOI: 10.1002/vetr.3053] [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: 08/01/2022] [Revised: 04/05/2023] [Accepted: 04/27/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Identification of the aetiologic agent in canine discospondylitis is infrequent; and risk factors for a positive bacterial culture have not previously been reported. METHODS Medical records at three institutions were searched to identify clinical features of dogs with discospondylitis diagnosed via radiography or cross-sectional imaging. Inclusion in this retrospective case-control study required culture of one or more samples. Multivariable binary logistic regression identified features associated with a positive culture. RESULTS Fifty (42%) of 120 dogs had one or more positive culture results obtained from either urine (28/115), blood (25/78), intervertebral disc aspiration (10/34) or cerebrospinal fluid (1/18). A positive culture was associated with higher bodyweight (p = 0.002, odds ratio [OR] = 1.054, 95% confidence interval [CI]: 1.019-1.089), more sample types cultured (p = 0.037, OR = 1.806, 95% CI: 1.037-3.147) and institution (p = 0.021). The presence of possibly associated preceding events (e.g., surgery), pyrexia, number of disc sites affected and serum C-reactive protein result, among other features, were not statistically significant. LIMITATIONS All isolates cultured were included since differentiation of true aetiologic agents from contaminants was not possible without histological confirmation and culture from surgical or postmortem biopsies. CONCLUSIONS Clinical features typically associated with infection were not identified as risk factors for positive culture in canine discospondylitis. The statistical significance of the institution suggests that standardisation of sampling protocols is necessary.
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Affiliation(s)
- Ed Pilkington
- Small Animal Teaching Hospital, Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - Rita Goncalves
- Small Animal Teaching Hospital, Institute of Veterinary Science, University of Liverpool, Liverpool, UK
| | - Lea Henze
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hanover, Hanover, Germany
| | - Nick Grapes
- Department of Clinical Science and Services, Royal Veterinary College, Hatfield, UK
| | - Holger Volk
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hanover, Hanover, Germany
| | - Steven De Decker
- Department of Clinical Science and Services, Royal Veterinary College, Hatfield, UK
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Ahlat M, Aydin C, Kaya S, Baysallar M. Identification of root canal microbiota profiles of periapical tissue diseases using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anaerobe 2023; 84:102791. [PMID: 37925063 DOI: 10.1016/j.anaerobe.2023.102791] [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: 05/08/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
OBJECTIVES The purpose of this study was to identify microorganisms isolated from various periapical tissue diseases using Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) and classify them via an unsupervised machine learning approach. METHODS A total of 150 patients with various apical conditions and teeth in need of endodontic retreatment were divided into five groups, including Retreatment, Acute Apical Abscess, Chronic Apical Abscess, Acute Apical Periodontitis, and Chronic Apical Periodontitis. Samples were collected from root canals using paper points after agitating with a #10 K file then microorganisms were identified using MALDI-TOF-MS. Data were analyzed using a hierarchical clustering method. Quadruple clusters and dendrograms were formed according to similarities and dissimilarities. RESULTS A total of 80 species were identified representative of six different phyla. The most similar microorganism species identified were: ''Enterococcus faecalis'' between 21 and 23-year-old female cases in Retreatment group; ''Lactobacillus rhamnosus'' between 20 and 18-year-old male cases in Symptomatic Apical Abscess cases; ''Lactobacillus paracasei'' between 26 and 40-year-old male cases in Asymptomatic Apical Abscess cases; ''Enterococcus faecalis'' between 48 and 50-year-old female cases in Symptomatic Apical Periodontitis cases; ''Lactobacillus rhamnosus'' between 48 and 60-year-old male cases in Asymptomatic Apical Periodontitis cases. CONCLUSIONS MALDI-TOF MS can be considered a fast and high-throughput screening technique for microbial species identification in endodontics. Thus, it will provide valuable data for future research designs regarding periapical tissue diseases. As the MALDI-TOF MS database expands and comprehensive data becomes available, the relationship between microbial profiles and disease progression will become increasingly apparent.
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Affiliation(s)
- Mete Ahlat
- University of Health Sciences, Gulhane Faculty of Dentistry, Department of Endodontics, Ankara, Turkey.
| | - Cumhur Aydin
- University of Health Sciences, Gulhane Faculty of Dentistry, Department of Endodontics, Ankara, Turkey.
| | - Sinem Kaya
- University of Health Sciences, Gulhane Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey.
| | - Mehmet Baysallar
- University of Health Sciences, Gulhane Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey.
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“Omic” Approaches to Bacteria and Antibiotic Resistance Identification. Int J Mol Sci 2022; 23:ijms23179601. [PMID: 36077000 PMCID: PMC9455953 DOI: 10.3390/ijms23179601] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/28/2022] Open
Abstract
The quick and accurate identification of microorganisms and the study of resistance to antibiotics is crucial in the economic and industrial fields along with medicine. One of the fastest-growing identification methods is the spectrometric approach consisting in the matrix-assisted laser ionization/desorption using a time-of-flight analyzer (MALDI-TOF MS), which has many advantages over conventional methods for the determination of microorganisms presented. Thanks to the use of a multiomic approach in the MALDI-TOF MS analysis, it is possible to obtain a broad spectrum of data allowing the identification of microorganisms, understanding their interactions and the analysis of antibiotic resistance mechanisms. In addition, the literature data indicate the possibility of a significant reduction in the time of the sample preparation and analysis time, which will enable a faster initiation of the treatment of patients. However, it is still necessary to improve the process of identifying and supplementing the existing databases along with creating new ones. This review summarizes the use of “-omics” approaches in the MALDI TOF MS analysis, including in bacterial identification and antibiotic resistance mechanisms analysis.
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Chen D, Bryden WA, Fenselau C, McLoughlin M, Haddaway CR, Devin AP, Caton ER, Bradrick SS, Miller JM, Tacheny EA, Lemmon MM, Bogan J. MALDI-TOF Mass Spectrometric Detection of SARS-CoV-2 Using Cellulose Sulfate Ester Enrichment and Hot Acid Treatment. J Proteome Res 2022; 21:2055-2062. [PMID: 35787094 PMCID: PMC9305670 DOI: 10.1021/acs.jproteome.2c00238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Indexed: 11/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the ongoing coronavirus disease 2019 (COVID-19) pandemic. Here we report a novel strategy for the rapid detection of SARS-CoV-2 based on an enrichment approach exploiting the affinity between the virus and cellulose sulfate ester functional groups, hot acid hydrolysis, and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS). Virus samples were enriched using cellulose sulfate ester microcolumns. Virus peptides were prepared using the hot acid aspartate-selective hydrolysis and characterized by MALDI-TOF MS. Collected spectra were processed with a peptide fingerprint algorithm, and searching parameters were optimized for the detection of SARS-CoV-2. These peptides provide high sequence coverage for nucleocapsid (N protein) and allow confident identification of SARS-CoV-2. Peptide markers contributing to the detection were rigorously identified using bottom-up proteomics. The approach demonstrated in this study holds the potential for developing a rapid assay for COVID-19 diagnosis and detecting virus variants from a variety of sources, such as sewage and nasal swabs.
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Affiliation(s)
- Dapeng Chen
- Zeteo Tech, Inc.,
Sykesville, Maryland 21784, United States
| | | | - Catherine Fenselau
- Department of Chemistry and Biochemistry,
University of Maryland, College Park, Maryland 20742,
United States
| | | | | | - Alese P. Devin
- Zeteo Tech, Inc.,
Sykesville, Maryland 21784, United States
| | - Emily R. Caton
- Zeteo Tech, Inc.,
Sykesville, Maryland 21784, United States
| | | | - Joy M. Miller
- MRIGlobal, Kansas City,
Missouri 64110, United States
| | | | | | - Joseph Bogan
- MRIGlobal, Gaithersburg,
Maryland 20878, United States
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6
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Ochi F, Tauchi H, Kagajo M, Murakami S, Miyamoto H, Hamada J, Eguchi-Ishimae M, Eguchi M. Properties of Staphylococcus lugdunensis in Children. Glob Pediatr Health 2021; 8:2333794X211044796. [PMID: 34514060 PMCID: PMC8424600 DOI: 10.1177/2333794x211044796] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background. Staphylococcus lugdunensis is one of the clinically important coagulase-negative staphylococci. The purpose of this study was to elucidate the microbiological features of S. lugdunensis in hospitalized children. Methods. From January 2012 to December 2019, all isolates were retrospectively screened for S. lugdunensis. Results. Twenty-five children were eligible for study. Nineteen and six children were classified into a critical care unit group (Group A) and a general medical ward group (Group B), respectively. The prevalence of methicillin-resistant S. lugdunensis was significantly higher in Group A than in Group B (68.4% vs 0%; P < .01). Eleven children (44%) had S. lugdunensis infections, while the remaining children were colonized. Six of the 11 infected children (55%) had healthcare-associated infections. Moreover, 3 isolates exhibited the methicillin resistance. Conclusions. The bacteriological characteristics of S. lugdunensis differ depending on patient background. Selection of antibiotic treatment should in part rely on patient background data.
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Affiliation(s)
- Fumihiro Ochi
- Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Hisamichi Tauchi
- Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | - Mari Kagajo
- Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | | | | | - Junpei Hamada
- Ehime University Graduate School of Medicine, Toon, Ehime, Japan
| | | | - Mariko Eguchi
- Ehime University Graduate School of Medicine, Toon, Ehime, Japan
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7
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Full pathogen characterisation: species identification including the detection of virulence factors and antibiotic resistance genes via multiplex DNA-assays. Sci Rep 2021; 11:6001. [PMID: 33727586 PMCID: PMC7966752 DOI: 10.1038/s41598-021-85438-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/19/2021] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistances progressively cause treatment failures, and their spreading dynamics reached an alarming level. Some strains have already been classified as highly critical, e.g. the ones summarised by the acronym ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.). To restrain this trend and enable effective medication, as much information as possible must be obtained in the least possible time. Here, we present a DNA microarray-based assay that screens for the most important sepsis-relevant 44 pathogenic species, 360 virulence factors (mediate pathogenicity in otherwise non-pathogenic strains), and 409 antibiotic resistance genes in parallel. The assay was evaluated with 14 multidrug resistant strains, including all ESKAPE pathogens, mainly obtained from clinical isolates. We used a cost-efficient ligation-based detection platform designed to emulate the highly specific multiplex detection of padlock probes. Results could be obtained within one day, requiring approximately 4 h for amplification, application to the microarray, and detection.
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8
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Cole K, Atkins B, Llewelyn M, Paul J. Genomic investigation of clinically significant coagulase-negative staphylococci. J Med Microbiol 2021; 70. [PMID: 33704043 DOI: 10.1099/jmm.0.001337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Introduction. Coagulase-negative staphylococci have been recognized both as emerging pathogens and contaminants of clinical samples. High-resolution genomic investigation may provide insights into their clinical significance.Aims. To review the literature regarding coagulase-negative staphylococcal infection and the utility of genomic methods to aid diagnosis and management, and to identify promising areas for future research.Methodology. We searched Google Scholar with the terms (Staphylococcus) AND (sequencing OR (infection)). We prioritized papers that addressed coagulase-negative staphylococci, genomic analysis, or infection.Results. A number of studies have investigated specimen-related, phenotypic and genetic factors associated with colonization, infection and virulence, but diagnosis remains problematic.Conclusion. Genomic investigation provides insights into the genetic diversity and natural history of colonization and infection. Such information allows the development of new methodologies to identify and compare relatedness and predict antimicrobial resistance. Future clinical studies that employ suitable sampling frames coupled with the application of high-resolution whole-genome sequencing may aid the development of more discriminatory diagnostic approaches to coagulase-staphylococcal infection.
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Affiliation(s)
- Kevin Cole
- Brighton and Sussex Medical School, Brighton, UK.,Public Health England Collaborating Centre, Royal Sussex County Hospital, Brighton, UK
| | | | - Martin Llewelyn
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK.,Brighton and Sussex Medical School, Brighton, UK
| | - John Paul
- Public Health England Collaborating Centre, Royal Sussex County Hospital, Brighton, UK.,Brighton and Sussex Medical School, Brighton, UK
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Yao S, Zhao C, Shang M, Li J, Wang J. Enzyme-free and label-free detection of Staphylococcus aureus based on target-inhibited fluorescence signal recovery. Food Chem Toxicol 2021; 150:112071. [PMID: 33609594 DOI: 10.1016/j.fct.2021.112071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/07/2021] [Accepted: 02/14/2021] [Indexed: 12/30/2022]
Abstract
In this work, a one-step fluorometric strategy based on nanometal surface energy transfer (NSET) between carbon dots (CDs) and gold nanoparticles (AuNPs) was developed for facile detection of Staphylococcus aureus (S. aureus). The fluorescence of CDs was quenched up to 63.5% by AuNPs due to nucleic acid hybridization in the presence of linker DNA, which contained the complementary sequences of S. aureus-specific aptamer, and the fluorescence signal was in the "off" state. Upon aptamer addition, the CDs was released from linker DNA through the strong competitiveness of aptamer, leading to the notable fluorescence recovered. Once S. aureus is introduced, aptamer preferentially bind to the bacterial surface and cannot hybridize with complementary sequences in the linker DNA, resulting in the fluorescence signal with "off" state. Based on these findings, the performance and reliability of the fluorescence-based assay were evaluated. Compared to direct hybridization of complementary DNA on the surface of CDs and AuNPs, our sensing strategy has enhanced detection limit (10 cfu⋅mL-1) and improved linear range (10 to 106 cfu⋅mL-1) for S. aureus. Therefore, our proposed enzyme-free and label-free strategy may become a promising method for ease of operation, sensitive and selective S. aureus detection.
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Affiliation(s)
- Shuo Yao
- School of Public Health, Jilin University, Changchun, 130021, China
| | - Chao Zhao
- School of Public Health, Jilin University, Changchun, 130021, China
| | - Mingyu Shang
- College of Earth Sciences, Jilin University, Changchun, 130021, China.
| | - Juan Li
- School of Public Health, Jilin University, Changchun, 130021, China.
| | - Juan Wang
- School of Public Health, Jilin University, Changchun, 130021, China.
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Thi MTT, Wibowo D, Rehm BH. Pseudomonas aeruginosa Biofilms. Int J Mol Sci 2020; 21:ijms21228671. [PMID: 33212950 PMCID: PMC7698413 DOI: 10.3390/ijms21228671] [Citation(s) in RCA: 301] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/13/2020] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen causing devastating acute and chronic infections in individuals with compromised immune systems. Its highly notorious persistence in clinical settings is attributed to its ability to form antibiotic-resistant biofilms. Biofilm is an architecture built mostly by autogenic extracellular polymeric substances which function as a scaffold to encase the bacteria together on surfaces, and to protect them from environmental stresses, impedes phagocytosis and thereby conferring the capacity for colonization and long-term persistence. Here we review the current knowledge on P. aeruginosa biofilms, its development stages, and molecular mechanisms of invasion and persistence conferred by biofilms. Explosive cell lysis within bacterial biofilm to produce essential communal materials, and interspecies biofilms of P. aeruginosa and commensal Streptococcus which impedes P. aeruginosa virulence and possibly improves disease conditions will also be discussed. Recent research on diagnostics of P. aeruginosa infections will be investigated. Finally, therapeutic strategies for the treatment of P. aeruginosa biofilms along with their advantages and limitations will be compiled.
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Study on Molecular Profiles of Staphylococcus aureus Strains: Spectrometric Approach. Molecules 2020; 25:molecules25214894. [PMID: 33105903 PMCID: PMC7660162 DOI: 10.3390/molecules25214894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus remains a major health problem responsible for many epidemic outbreaks. Therefore, the development of efficient and rapid methods for studying molecular profiles of S. aureus strains for its further typing is in high demand. Among many techniques, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) represents a timely, cost-effective, and reliable strain typing approach, which is still rarely used due to insufficient knowledge about the impact of sample preparation and analysis conditions on the molecular profiles and strain classification efficiency of S. aureus. The aim of this study was to evaluate the effect of the culture conditions and matrix type on the differentiation of molecular profiles of various S. aureus strains via the MALDI TOF MS analysis and different computational methods. The analysis revealed that by changing the culture conditions, matrix type, as well as a statistical method, the differentiation of S. aureus strains can be significantly improved. Therefore, to accelerate the incorporation of the MALDI-based strain typing in routine laboratories, further studies on the standardization and searching of optimal conditions on a larger number of isolates and bacterial species are of great need.
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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Misidentification of Cutibacterium namnetense as Cutibacterium acnes among clinical isolates by MALDI-TOF VitekMS: usefulness of gyrB sequencing and new player in bone infections. Eur J Clin Microbiol Infect Dis 2020; 39:1605-1610. [PMID: 32382853 DOI: 10.1007/s10096-020-03873-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/20/2020] [Indexed: 01/03/2023]
Abstract
The taxonomy modification of Propionibacterium sp. with the description of new species, especially Cutibacterium namnetense, raises the question of species distribution in routine clinical samples. We performed a retrospective study during 3 years before the implementation of MALDI-TOF. Two hundred sixty-nine isolates were included in the study. MALDI-TOF identification, 16S rRNA, and new developed gyrB partial sequencings were performed. The most representative species was C. acnes in 88% of the cases, regardless of the origin of the clinical sample. Eventually, we identified three C. namnetense strains, representing a 1.1% prevalence over the period of time, including two bone infections. MALDI-TOF databases should be regularly updated to incorporate new species. gyrB sequencing constitutes a both easy and relevant method to identify Cutibacterium sp. especially C. namnetense, a new player in bone infections.
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Wei YS, Hsiao YC, Su GW, Chang YR, Lin HP, Wang YS, Tsai YT, Liao EC, Chen HY, Chou HC, Ko ML, Kuo WH, Chang SJ, Cheng WC, Chan HL. Identification of hyperglycemia-associated microbiota alterations in saliva and gingival sulcus. Arch Biochem Biophys 2020; 682:108278. [DOI: 10.1016/j.abb.2020.108278] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/27/2019] [Accepted: 01/20/2020] [Indexed: 01/15/2023]
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Staphylococcus lugdunensis Septic Arthritis following Arthroscopic Anterior Cruciate Ligament Reconstruction. Case Rep Orthop 2020; 2020:2813134. [PMID: 32082668 PMCID: PMC6995318 DOI: 10.1155/2020/2813134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 11/17/2022] Open
Abstract
Summary. We report two cases of Staphylococcus lugdunensis (S. lugdunensis) septic arthritis following arthroscopic anterior cruciate ligament (ACL) reconstruction. Both initial surgical procedures were ACL reconstruction along with simultaneous collateral ligament and meniscus procedures. Patients presented with septic arthritis three and ten weeks following the index procedure. Both patients successfully recovered with early arthroscopic irrigation, debridement, and synovial culture, in addition to long-term parenteral and oral antibiotics.Staphylococcus lugdunensis (S. lugdunensis) septic arthritis following arthroscopic anterior cruciate ligament (ACL) reconstruction. Both initial surgical procedures were ACL reconstruction along with simultaneous collateral ligament and meniscus procedures. Patients presented with septic arthritis three and ten weeks following the index procedure. Both patients successfully recovered with early arthroscopic irrigation, debridement, and synovial culture, in addition to long-term parenteral and oral antibiotics.S. lugdunensis) septic arthritis following arthroscopic anterior cruciate ligament (ACL) reconstruction. Both initial surgical procedures were ACL reconstruction along with simultaneous collateral ligament and meniscus procedures. Patients presented with septic arthritis three and ten weeks following the index procedure. Both patients successfully recovered with early arthroscopic irrigation, debridement, and synovial culture, in addition to long-term parenteral and oral antibiotics.
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Apoptosis of vaginal epithelial cells in clinical samples from women with diagnosed bacterial vaginosis. Sci Rep 2020; 10:1978. [PMID: 32029862 PMCID: PMC7005030 DOI: 10.1038/s41598-020-58862-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 01/22/2020] [Indexed: 01/10/2023] Open
Abstract
Bacterial vaginosis (BV) is one of the most common vaginal infections among women of childbearing age. Gardnerella vaginalis (G. vaginalis) is a keystone microorganism present in more than 95% of all BV cases. The first step of the infection process in BV is mediated by interaction of microorganisms with epithelial cells (ECs). However, the role of these cells in BV pathogenesis is largely unknown. The present study aimed to investigate the vaginal EC response during BV. Twenty healthy women and 34 women with BV were enrolled in this study. The number of ECs in the vaginal swab was counted and analyzed for intracellular signals and apoptosis by flow cytometry. Cell damage was evaluated by lactate dehydrogenase assay. Compared to that in healthy donors, the percentage of exfoliated vaginal ECs was increased in women with BV, and an absence of neutrophils was observed in both groups. Activation signals, such as p-IκBα and c-Fos were unmodulated in the vaginal ECs of women with BV. Moreover, EC damage and apoptosis were significantly increased in patients with BV. Apoptosis was related to caspase-3 activation and the presence of G. vaginalis. This study provides the first evidence of a direct involvement of G. vaginalis in the apoptotic process of vaginal ECs during BV. This effect was mediated by caspase-3 activation, and G. vaginalis appeared to be one of causes for inducing EC apoptosis in BV. Hence, our findings suggest a possible explanation for the increased exfoliation of ECs in the vagina during BV.
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Lina G. New insights into coagulase-negative staphylococci. Clin Microbiol Infect 2019; 25:1063. [PMID: 31212074 DOI: 10.1016/j.cmi.2019.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 10/26/2022]
Affiliation(s)
- G Lina
- CIRI, Centre International de Recherche en Infectiologie, Université Lyon 1, Ecole Normale Supérieure de Lyon, France; Centre National de Référence des Staphylocoques, Institut des Agent infectieux, Hôpital de la Croix Rousse, Hospices Civils de Lyon, Lyon, France.
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18
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Response to Questions Posed by the Food and Drug Administration Regarding Virulence Factors and Attributes that Define Foodborne Shiga Toxin-Producing Escherichia coli (STEC) as Severe Human Pathogens †. J Food Prot 2019; 82:724-767. [PMID: 30969806 DOI: 10.4315/0362-028x.jfp-18-479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
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- NACMCF Executive Secretariat, * U.S. Department of Agriculture, Food Safety and Inspection Service, Office of Public Health Science, PP3, 9-178, 1400 Independence Avenue S.W., Washington, D.C. 20250-3700, USA
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19
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Yeh HC, Lu JJ, Chang SC, Ge MC. Identification of microbiota in peri-implantitis pockets by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Sci Rep 2019; 9:774. [PMID: 30692557 PMCID: PMC6349886 DOI: 10.1038/s41598-018-37450-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 11/23/2018] [Indexed: 12/18/2022] Open
Abstract
The purpose of this study was to identify the microbial communities that colonize peri-implantitis pockets using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Subjects having at least one implant with peri-implantitis, no diabetes, and not taking antibiotics in the previous 3 months were selected. Peri-implantitis was defined when surrounding bone loss ≥0.5 mm and bleeding on probing was found. Microbial samples were collected from peri-implantitis pockets using paper points. After incubation and isolation, the colonies were analyzed by MALDI-TOF MS. A total of 126 isolates were cultivated and identified from 12 samples, in identification rates of 82.5% at the species level and 12.72% at the genus level. Although the compositions were highly variable, major habitants in different peri-implant pockets could be identified. Among them the most distinguished were Neisseria flavescens (87%), Streptococcus constellatus (56%), Slackia exigua (46%), Streptococcus intermedius (45%), Fusobacterium nucleatum (45%) and Gemella morbillorum (43%). This preliminary study provides comprehensive and reliable data for future study designs involving MALDI-TOF MS and peri-implantitis in a more specific, easy, rapid and economical way. MALDI-TOF MS could be a new clinical method to evaluate and monitor oral microbiota associated with the disease.
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Affiliation(s)
- Hwey-Chin Yeh
- Linyeh Dental Clinic, Taipei, Taiwan.,Department of Periodontics, Section of Dentistry, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan. .,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan.
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Mao-Cheng Ge
- Department of Laboratory Medicine, Chang Gung Memorial Hospital Linkou Medical Center, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
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20
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Abstract
A wide variety of microorganisms are potential respiratory pathogens, and the spectrum of known pathogens for each respiratory infection syndrome has not changed markers over recent years. Detection of likely etiologic agents of respiratory infections can help direct management and can also play an important role in disease surveillance. For this purpose, we are still reliant on many traditional diagnostic tools that have been used for decades in order to determine the microbial etiology of respiratory infections. However, these tools have been increasingly supplemented by newer methods, particular molecular diagnostic techniques, which have enabled the more rapid detection of many pathogens that were previously difficult to detect. These advances have particularly lead to improvements in the ability to detect respiratory viruses and also other microorganisms that do not normally colonize the respiratory tract. Recognition of the existence of the lung microbiome has challenged the traditional views of pneumonia pathogenesis and may provide the opportunity for new diagnostic tools that are focused on more than just detection of specific known pathogens. Continued liaison between clinicians and laboratory staff is vital in order to facilitate the most cost-effective use of laboratory diagnostics.
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21
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Mass Spectrometry Technology and qPCR for Detection of Enterococcus faecalis in Diabetic Foot Patients. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Di Gaudio F, Indelicato S, Indelicato S, Tricoli MR, Stampone G, Bongiorno D. Improvement of a rapid direct blood culture microbial identification protocol using MALDI-TOF MS and performance comparison with SepsiTyper kit. J Microbiol Methods 2018; 155:1-7. [DOI: 10.1016/j.mimet.2018.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022]
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23
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Martins KB, Ferreira AM, Mondelli AL, Rocchetti TT, Lr de S da Cunha MD. Evaluation of MALDI-TOF VITEK ®MS and VITEK ® 2 system for the identification of Staphylococcus saprophyticus. Future Microbiol 2018; 13:1603-1609. [PMID: 30421630 DOI: 10.2217/fmb-2018-0195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To compare two identification methods for coagulase-negative staphylococci (CoNS) isolated from patients with urinary tract infections, VITEK® 2 and MALDI-TOF VITEK®MS, with genotypic identification by internal transcribed spacer PCR (ITS-PCR). RESULTS A total of 217 CoNS isolates were studied. Agreement of the VITEK® 2 system with ITS-PCR was 84.8%, with 98% sensitivity and 100% specificity. Thirty-one of the 33 strains incorrectly identified by VITEK® 2 belonged to the species Staphylococcus saprophyticus. MALDI-TOF VITEK®MS showed an excellent correlation with ITS-PCR since it correctly identified all CoNS isolates. CONCLUSION MALDI-TOF VITEK®MS is more accurate than the automated VITEK® 2 system in identifying CoNS isolated from urinary tract infections to species level, particularly urinary isolates of S. saprophyticus.
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Affiliation(s)
- Katheryne B Martins
- Department of Microbiology & Immunology, Botucatu Biosciences Institute, UNESP - Univ. Estadual Paulista, Botucatu, SP, Brazil
| | - Adriano M Ferreira
- Laboratory of Microbiology, University Hospital of the Botucatu School of Medicine (HC-FMB), UNESP - Univ. Estadual Paulista, Botucatu, SP, Brasil
| | - Alessandro L Mondelli
- Department of Internal Medicine, Botucatu School of Medicine University Hospital, UNESP - Univ. Estadual Paulista, Botucatu, SP, Brazil
| | - Taisa T Rocchetti
- Department of Microbiology & Immunology, Botucatu Biosciences Institute, UNESP - Univ. Estadual Paulista, Botucatu, SP, Brazil
| | - Maria de Lr de S da Cunha
- Department of Microbiology & Immunology, Botucatu Biosciences Institute, UNESP - Univ. Estadual Paulista, Botucatu, SP, Brazil
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24
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Pérez-Sancho M, Vela AI, Horcajo P, Ugarte-Ruiz M, Domínguez L, Fernández-Garayzábal JF, de la Fuente R. Rapid differentiation of Staphylococcus aureus subspecies based on MALDI-TOF MS profiles. J Vet Diagn Invest 2018; 30:813-820. [PMID: 30280650 DOI: 10.1177/1040638718805537] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus encompasses 2 subspecies ( aureus and anaerobius) with significant differences in their epidemiology and pathogenicity. We evaluated the suitability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the rapid identification of both subspecies using a panel of 52 S. aureus isolates (30 subsp. anaerobius and 22 subsp. aureus) recovered from different origins, countries, and years. The on-board library identification system correctly identified 42 of 52 (81%) S. aureus isolates at the species level with score values >2.0. Limited performance was observed for differentiation of S. aureus subspecies (particularly subsp. anaerobius). Visual inspection of MALDI-TOF MS profiles identified 5 subspecies-specific mass peaks ( m/ z 3430 and 6861 in S. aureus subsp. anaerobius, and m/ z 4046, 6890, and 8093 in S. aureus subsp. aureus) with 100% sensitivity and specificity values, which is potentially useful for differentiating these subspecies. The suitability of 3 models, Genetic Analysis (GA), Quick Classifier (QC), and Supervised Neural Network, for automatic identification of both subspecies was evaluated using the Recognition Capability (RC) and Cross Validation (CV) values provided by the on-board ClinProTools software. The GA and QC models reached RC and CV values of 100%. Both models were externally validated using a panel of 26 S. aureus isolates of both subspecies, with both models correctly classifying all isolates of both subspecies. MALDI-TOF MS coupled with ClinProTools software represents a rapid and simple approach for S. aureus subspecies discrimination.
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Affiliation(s)
- Marta Pérez-Sancho
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Ana I Vela
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Pilar Horcajo
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Lucas Domínguez
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - José F Fernández-Garayzábal
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
| | - Ricardo de la Fuente
- VISAVET Health Surveillance Centre (Pérez-Sancho, Vela, Ugarte-Ruiz, Fernández-Garayzábal, Domínguez), Complutense University, Madrid, Spain.,Animal Health Department, Veterinary Faculty (Vela, Horcajo, Fernández-Garayzábal, Domínguez, de la Fuente), Complutense University, Madrid, Spain
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25
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Orfanos S, Gomez C, Baron S, Akkisetty R, Dufeu N, Coltey B, Thomas PA, Rolain JM, Reynaud-Gaubert M. Impact of gram negative bacteria airway recolonization on the occurrence of chronic lung allograft dysfunction after lung transplantation in a population of cystic fibrosis patients. BMC Microbiol 2018; 18:88. [PMID: 30126365 PMCID: PMC6102836 DOI: 10.1186/s12866-018-1231-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 08/10/2018] [Indexed: 12/15/2022] Open
Abstract
Background Chronic Lung Allograft Dysfunction (CLAD) is the main cause of morbidity and mortality after the first year following lung transplantation (LTx). Risk factors of CLAD have been extensively studied, but the association between gram-negative bacteria (GNB) bronchial colonization and the development of CLAD is controversial. The purpose of our study was to investigate the association between post-transplant recolonization with the same species or de-novo colonization with a new GNB species and CLAD. The same analysis was performed on a sub-group of patients at the strain level using Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry technique. Results Forty adult cystic fibrosis (CF) patients who underwent a first bilateral LTx in the University Hospital of Marseille, between January 2010 and December 2014, were included in the study. Patients with GNB de-novo colonization had a higher risk of developing CLAD (OR = 6.72, p = 0.04) and a lower rate of CLAD-free survival (p = 0.005) compared to patients with GNB recolonization. No conclusion could be drawn from the subgroup MALDI-TOF MS analysis at the strain level. Conclusion Post-LTx GNB airway recolonization seems to be a protective factor against CLAD, whereas de-novo colonization with a new species of GNB seems to be a risk factor for CLAD. Electronic supplementary material The online version of this article (10.1186/s12866-018-1231-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarah Orfanos
- Aix-Marseille University, Faculté de médecine, Marseille, France.
| | - Carine Gomez
- Aix-Marseille University, Faculté de médecine, Marseille, France.,Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
| | - Sophie Baron
- Aix-Marseille University, Faculté de médecine, Marseille, France.,URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Ritesh Akkisetty
- Department of Biology, Drexel University College of Art and Sciences, Philadelphia, USA
| | - Nadine Dufeu
- Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
| | - Bérengère Coltey
- Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
| | - Pascal Alexandre Thomas
- Aix-Marseille University, Faculté de médecine, Marseille, France.,Department of Thoracic Surgery, Lung Transplant Team APHM, University Hospital of Marseille, Marseille, France
| | - Jean Marc Rolain
- Aix-Marseille University, Faculté de médecine, Marseille, France.,URMITE CNRS IRD UMR 6236, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Martine Reynaud-Gaubert
- Aix-Marseille University, Faculté de médecine, Marseille, France.,Department of Respiratory Diseases, Lung Transplant Team, University Hospital of Marseille, Marseille, France
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Bronzato GF, Oliva MS, Alvin MG, Pribul BR, Rodrigues DP, Coelho SM, Coelho IS, Souza MM. MALDI-TOF MS as a tool for the identification of Vibrio alginolyticus from Perna perna mussels (Linnaeus, 1758). PESQUISA VETERINARIA BRASILEIRA 2018. [DOI: 10.1590/1678-5150-pvb-5233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
ABSTRACT: Vibrio species are ubiquitous in aquatic environments, including coastal and marine habitats. Vibrio alginolyticus is an opportunistic pathogen for fish, crustaceans and mussels and their identification by biochemical tests may be impaired due their nutritional requirements. The study used Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to identify 49 Vibrio spp. isolates associated with mussels (Perna perna) from different locations along the Rio de Janeiro coast. The rpoA gene was used as a genus-specific marker of Vibrio spp. and was positive in all 209 isolates. MALDI-TOF MS confirmed 87.8% of V. alginolyticus when compared to the results of the biochemical tests. Four isolates were identified as Shewanella putrefaciens (8.16%) and one was identified as V. parahaemolyticus (2.0%). Just one isolate was not identified by this technique (2.0%). The pyrH sequencing confirmed 75% of the proteomic technique results. MALDI-TOF MS is an excellent option for characterization of bacterial species, as it is efficient, fast and easy to apply. In addition, our study confirms its high specificity and sensitivity in these marine bacteria identification.
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Corvec S. Clinical and Biological Features of Cutibacterium (Formerly Propionibacterium) avidum, an Underrecognized Microorganism. Clin Microbiol Rev 2018; 31:e00064-17. [PMID: 29848774 PMCID: PMC6056840 DOI: 10.1128/cmr.00064-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The recent description of the genus Cutibacterium has altered the taxonomy of Propionibacterium species. These organisms still belong to the genera of the skin coryneform group, and the most-studied species remains Cutibacterium acnes. Cutibacterium avidum is also a known skin commensal. This underrecognized microorganism can, however, act as a pathogen after bacterial seeding and can be considered opportunistic, causing either superficial or deep/invasive infections. It can cause numerous infections, including but not limited to breast infections, skin abscesses, infective endocarditis, and device-related infections. The ecological niche of C. avidum is clearly different from that of other members of the genus: it is found in the axillary region or at wet sites rather than in dry, exposed areas, and the number of microorganisms increases during puberty. Historically, it has been used for its ability to modulate the immune response and for its antitumor properties. Conventional microbial culture methods and identification processes allow for its accurate identification and characterization. Thanks to the modern omics tools used for phylogenomic approaches, understanding C. avidum pathogenesis (including host-bacterium interactions and virulence factor characterization) is becoming easier, allowing for more thorough molecular characterization. These analyses have revealed that C. avidum causes diverse diseases mediated by multiple virulence factors. The recent genome approach has revealed specific genomic regions within this species that are involved in adherence and biofilm formation as well as fitness, survival, and defense functions. Numerous regions show the presence of phages and horizontal gene transfer. C. avidum remains highly sensitive to a broad spectrum of antibiotics, such as β-lactams, fluoroquinolones, macrolides, and rifampin, although erythromycin and clindamycin resistance has been described. A long-term treatment regimen with a combination of antibiotics is required to successfully eliminate the remaining adherent bacteria, particularly in the case of deep infections after debridement surgery.
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Affiliation(s)
- Stéphane Corvec
- CHU Nantes, Service de Bactériologie-Hygiène Hospitalière, Nantes, France
- CRCINA, INSERM, U1232, Université de Nantes, Nantes, France
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Abstract
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.
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Harris LG, El-Bouri K, Johnston S, Rees E, Frommelt L, Siemssen N, Christner M, Davies AP, Rohde H, Mack D. Rapid Identification of Staphylococci from Prosthetic Joint Infections Using MALDI-TOF Mass-Spectrometry. Int J Artif Organs 2018; 33:568-74. [DOI: 10.1177/039139881003300902] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2010] [Indexed: 11/15/2022]
Abstract
Hospital-acquired infections associated with implanted medical devices are most commonly caused by staphylococci. Current methods of species identification are slow, costly, and sometimes unreliable. We evaluated the ability of a Bruker Daltonics Microflex MALDI-TOF/MS in conjunction with MALDI Biotyper software to identify 158 characterized staphylococcal isolates from prosthetic joint infections, including 36 Staphylococcus aureus, 100 Staphylococcus epidermidis, 10 Staphylococcus capitis, 8 Staphylococcus lugdunensis, 2 Staphylococcus warneri, and 2 Staphylococcus haemolyticus isolates using the extraction method recommended by Bruker Daltonics. The suggested species identification by the MALDI Biotyper software was correct for all isolates, indicating reliable differentiation between S. aureus and coagulase-negative staphylococci. Applying the recommended criteria of the MALDI Biotyper software all 158 isolates gave scores ≥2.0, implying secure genus and probable species identification for all isolates. 34/36 S. aureus, 36/100 S. epidermidis, 5/10 S. capitis, 6/8 S. lugdunensis, 2/2 S. haemolyticus, 0/2 S. warneri displayed scores ≥2.3 implying highly probable species identification. For S. epidermidis 25/100 additional isolates had a score close to 2.3. It appears that additional clinically relevant staphylococcal isolates in the data base might aid in identification at scores implying highly probable species identification. The ability of the MALDI Biotyper software to recognize clonally-related strains within a species group (i.e. sub-typing) was investigated, and showed great potential. In conclusion, the MALDI-TOF/MS MALDI Biotyper system provides a promising rapid and reliable method of identifying clinical isolates from prosthetic joint infections to the species level, and has potential for sub-typing.
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Affiliation(s)
- Llinos G. Harris
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea - United Kingdom
| | - Khalid El-Bouri
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea - United Kingdom
| | - Stuart Johnston
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea - United Kingdom
| | - Eugene Rees
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea - United Kingdom
| | | | - Nicolaus Siemssen
- ENDO-Klinik Hamburg GmbH, Hamburg - Germany
- Endoprothetik und Gelenkchirurgie, Krankenhaus Tabea GmbH & Co. KG, Hamburg - Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Hospital, Eppendorf-Hamburg, Hamburg - Germany
| | - Angharad P. Davies
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea - United Kingdom
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea - United Kingdom
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Hospital, Eppendorf-Hamburg, Hamburg - Germany
| | - Dietrich Mack
- Medical Microbiology and Infectious Diseases, Institute of Life Science, School of Medicine, Swansea University, Swansea - United Kingdom
- Public Health Wales Microbiology ABM Swansea, Singleton Hospital, Abertawe-Bro Morgannwg University Health Board, Swansea - United Kingdom
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Fernández-Álvarez C, Torres-Corral Y, Santos Y. Use of ribosomal proteins as biomarkers for identification of Flavobacterium psychrophilum by MALDI-TOF mass spectrometry. J Proteomics 2018; 170:59-69. [DOI: 10.1016/j.jprot.2017.09.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/08/2017] [Accepted: 09/14/2017] [Indexed: 10/18/2022]
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31
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Weisener CG, Reid T. Combined imaging and molecular techniques for evaluating microbial function and composition: A review. SURF INTERFACE ANAL 2017. [DOI: 10.1002/sia.6317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christopher G. Weisener
- The University of Windsor Ontario-Great Lakes Institute for Environmental Research; 401 Sunset Avenue N9B3P4 Windsor ON Canada
| | - Thomas Reid
- The University of Windsor Ontario-Great Lakes Institute for Environmental Research; 401 Sunset Avenue N9B3P4 Windsor ON Canada
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Leke A, Goudjil S, Mullie C, Grognet S, Biendo M. PCR detection of staphylococcal enterotoxin genes and exfoliative toxin genes in methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains from raw human breast milk. CLINICAL NUTRITION EXPERIMENTAL 2017. [DOI: 10.1016/j.yclnex.2017.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Fernández-Álvarez C, Torres-Corral Y, Saltos-Rosero N, Santos Y. MALDI-TOF mass spectrometry for rapid differentiation of Tenacibaculum species pathogenic for fish. Appl Microbiol Biotechnol 2017; 101:5377-5390. [DOI: 10.1007/s00253-017-8324-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/29/2017] [Accepted: 04/29/2017] [Indexed: 11/24/2022]
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Höll L, Behr J, Vogel RF. Identification and growth dynamics of meat spoilage microorganisms in modified atmosphere packaged poultry meat by MALDI-TOF MS. Food Microbiol 2016; 60:84-91. [DOI: 10.1016/j.fm.2016.07.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 07/04/2016] [Accepted: 07/04/2016] [Indexed: 11/28/2022]
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Joly Condette C, Elion Dzon B, Hamdad F, Biendo M, Bach V, Khorsi-Cauet H. Use of molecular typing to investigate bacterial translocation from the intestinal tract of chlorpyrifos-exposed rats. Gut Pathog 2016; 8:50. [PMID: 27826358 PMCID: PMC5097847 DOI: 10.1186/s13099-016-0129-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/12/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Human are confronted on a daily basis with contaminant pesticide residues in food, water and other components of the environment. Although the digestive system is the first organ to come into contact with food contaminants, very few data are available on the impact of low-dose pesticide exposure during the in utero and postnatal periods on intestinal bacterial translocation (BT). Previous studies have revealed that chlorpyrifos (CPF) exposure is associated with intestinal dysbiosis and the contamination of sterile organs. Here, molecular typing was used to investigate intestinal bacterial translocation in rats exposed to chlorpyrifos in utero and during lactation. The translocated bacteria were profiled, and CPF tolerance and antibiotic resistance traits were determined. METHODS A total of 72 intestinal segments and extra-intestinal organs were obtained from 14 CPF-exposed rats. The samples were cultured to isolate bacterial strains that had tolerated treatment with 1 or 5 mg CPF/kg bodyweight/day in vivo. Strains were identified using matrix-assisted laser desorption/ionization (MALDI) Biotyper. The disk diffusion method was used to determine the antibiotic susceptibility. The isolates were genotyped with PCR assays for the enterobacterial repetitive intergenic consensus sequence and random amplification polymorphic DNA. RESULTS Bacterial translocation was confirmed for 7 of the 31 strains (22.6 %) isolated from extra-intestinal sites. Overall, the most prevalent bacteria were Staphylococcus aureus (55.5 % of the 72 intestinal and extra-intestinal isolates), Enterococcus faecalis (27.7 %) and Bacillus cereus (9.8 %). 5 % of the S. aureus isolates displayed methicillin resistance. Seventy two strains were identified phenotypically, and seven translocated strains (mainly S. aureus) were identified by genotyping. Genotypically confirmed translocation was mainly observed found in pesticide-exposed groups (6 out of 7). CONCLUSION BT from the intestinal tract colonized normally sterile extra-intestinal organs in CPF-exposed rats. Our findings validate the use of molecular typing for the assessment of intestinal BT in CPF-exposed rats during critical periods of development.
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Affiliation(s)
- Claire Joly Condette
- Laboratoire PeriTox UMR I 01, Faculty of Medicine, Centre Universitaire de Recherche Scientifique, Université de Picardie Jules Verne, Avenue René Laёnnec, 80054 Amiens cedex 1, France
- Laboratoire LNPC EA4666, Faculty of Medicine, Centre Universitaire de Recherche Scientifique, Université de Picardie Jules Verne, Avenue René Laёnnec, 80054 Amiens cedex 1, France
| | - Bertin Elion Dzon
- Laboratoire PeriTox UMR I 01, Faculty of Medicine, Centre Universitaire de Recherche Scientifique, Université de Picardie Jules Verne, Avenue René Laёnnec, 80054 Amiens cedex 1, France
| | - Farida Hamdad
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire Amiens Picardie, Avenue René Laёnnec, Salouёl, 80054 Amiens cedex 1, France
| | - Maurice Biendo
- Laboratoire PeriTox UMR I 01, Faculty of Medicine, Centre Universitaire de Recherche Scientifique, Université de Picardie Jules Verne, Avenue René Laёnnec, 80054 Amiens cedex 1, France
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire Amiens Picardie, Avenue René Laёnnec, Salouёl, 80054 Amiens cedex 1, France
| | - Véronique Bach
- Laboratoire PeriTox UMR I 01, Faculty of Medicine, Centre Universitaire de Recherche Scientifique, Université de Picardie Jules Verne, Avenue René Laёnnec, 80054 Amiens cedex 1, France
| | - Hafida Khorsi-Cauet
- Laboratoire PeriTox UMR I 01, Faculty of Medicine, Centre Universitaire de Recherche Scientifique, Université de Picardie Jules Verne, Avenue René Laёnnec, 80054 Amiens cedex 1, France
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L'Ollivier C, Ranque S. MALDI-TOF-Based Dermatophyte Identification. Mycopathologia 2016; 182:183-192. [PMID: 27734185 DOI: 10.1007/s11046-016-0080-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/06/2016] [Indexed: 01/09/2023]
Abstract
MALDI-TOF MS has become increasingly popular for microorganism identification in the routine laboratory. Compared with conventional morphology-based techniques, MALDI-TOF is relatively inexpensive (per-unit identification), involves a rapid result turnaround time and yields more accurate results without the need for highly qualified staff. However, this technology has been technically difficult to implement for filamentous fungi identification. Identification of dermatophytes, a type of filamentous fungi, remains particularly challenging, partly due to the lack of clear species definition for some taxa or within some species complexes. Review of the ten studies published between 2008 and 2015 shows that the accuracy of MALDI-TOF MS-based identification varied between 13.5 and 100 % for dermatophytes. This variability was partly due to inconsistencies concerning critical steps of the routine clinical laboratory process. Use of both a complete formic acid-acetonitrile protein extraction step and a manufacturer library supplemented with homemade reference spectra is essential for an accurate species identification. This technique is conversely unaffected by variations in other routine clinical laboratory conditions such as culture medium type, incubation time and type of mass spectrometry instrument. Provided that a reference spectra library is adequate for dermatophyte identification, MALDI-TOF MS identification is more economical and offers an accuracy comparable to that of DNA sequencing. The technique also represents an advantageous alternative to the protracted and labor-intensive dermatophyte identification via macroscopic and microscopic morphology in the routine clinical laboratory.
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Affiliation(s)
- Coralie L'Ollivier
- Aix-Marseille University, IP-TPT UMR MD3, 13885, Marseille, France.,Laboratory of Parasitology-Mycology, APHM CHU Timone, 13005, Marseille, France
| | - Stéphane Ranque
- Aix-Marseille University, IP-TPT UMR MD3, 13885, Marseille, France. .,Laboratory of Parasitology-Mycology, APHM CHU Timone, 13005, Marseille, France. .,Laboratoire de Parasitologie-Mycologie, AP-HM, CHU Timone, 264 rue Saint Pierre, 13385, Marseille, France.
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Cassagne C, Normand AC, L'Ollivier C, Ranque S, Piarroux R. Performance of MALDI-TOF MS platforms for fungal identification. Mycoses 2016; 59:678-690. [DOI: 10.1111/myc.12506] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/04/2016] [Accepted: 03/12/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Carole Cassagne
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Anne-Cécile Normand
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
| | - Coralie L'Ollivier
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Stéphane Ranque
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
| | - Renaud Piarroux
- Parasitology and Mycology; Assistance Publique-Hôpitaux de Marseille; CHU Timone-Adultes; Marseilles CEDEX 5 France
- Aix-Marseille University; UMR MD3 IP-TPT; Marseilles France
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Angeletti S. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol Methods 2016; 138:20-29. [PMID: 27613479 DOI: 10.1016/j.mimet.2016.09.003] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 10/21/2022]
Abstract
The microbiological management of patients with suspected bacterial infection includes the identification of the pathogen and the determination of the antibiotic susceptibility. These traditional approaches, based on the pure culture of the microorganism, require at least 36-48h. A new method, Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS), has been recently developed to profile bacterial proteins from whole cell extracts and obtain a bacterial fingerprint able to discriminate microorganisms from different genera and species. By whole cell-mass spectrometry, microbial identification can be achieved within minutes from cultured isolate, rather than traditional phenotypic or genotypic characterizations. From the year 2009 an explosion of applications of this technology has been observed with promising results. Several studies have been performed and showed that MALDI-TOF represents a reliable alternative method for rapid bacteria and fungi identification in clinical setting. A future area of expansion is represented by the application of MALDI-TOF technology to the antibiotic susceptibility test. In conclusion, the revision of the literature available up to date demonstrated that MALDI-TOF MS represents an innovative technology for the rapid and accurate identification of bacterial and fungal isolates in clinical settings. By an earlier microbiological diagnosis, MALDI-TOF MS contributes to a reduced mortality and hospitalization time of the patients and consequently has a significant impact on cost savings and public health.
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Affiliation(s)
- Silvia Angeletti
- Clinical Pathology and Microbiology Unit, University Campus Bio-Medico of Rome, Italy.
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Abstract
PURPOSE OF REVIEW To highlight the importance of escalating pathogen resistance in ventilator-associated pneumonia (VAP) along with diagnostic and treatment implications. RECENT FINDINGS In a period of rising bacterial resistance, VAP remains an important infection occurring in critically ill patients. Risk factors for multidrug-resistant pathogens depend on both local epidemiology and host factors. New diagnostic techniques and antimicrobials can help with rapid bacterial identification and timely and appropriate treatment while avoiding emergence of bacterial resistance. SUMMARY Clinicians should be aware of risk factors for multidrug-resistant pathogens causing VAP and also of particularities of diagnosis and treatment of this important clinical entity.
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Elbehiry A, Al-Dubaib M, Marzouk E, Osman S, Edrees H. Performance of MALDI biotyper compared with Vitek ™ 2 compact system for fast identification and discrimination of Staphylococcus species isolated from bovine mastitis. Microbiologyopen 2016; 5:1061-1070. [PMID: 27364641 PMCID: PMC5221440 DOI: 10.1002/mbo3.389] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/23/2016] [Accepted: 05/28/2016] [Indexed: 12/19/2022] Open
Abstract
This study was designed to evaluate the ability of MALDI Biotyper (MBT) compared with Vitek™ 2 compact system for accurate identification of Staphylococcus aureus (S. aureus) and coagulase‐negative staphylococci (CNS) strains and discriminate methicillin‐sensitive S. aureus (MSSA) from methicillin‐resistant S. aureus (MRSA). Throughout Al‐Qassim region, Saudi Arabia, a total of 198 isolates of S. aureus (132 MSSA and 66 MRSA) and 44 CNS were collected from five dairy farms where the prevalence of staphylococcal mastitis was reported. The results produced by Vitek™ 2 compact system demonstrated that 123/132 MSSA isolates (93.18%), 61/66 MRSA (92.42%), and 37/44 CNS species (84.09%) were correctly identified. However; 130/132 MSSA (98.48%), 64/66 MRSA (96.96%), and 44/44 CNS (100%) were correctly identified by MBT with score ≥2. 00. The principal component analysis (PCA) dendrogram generated by MBT illustrated that the tested isolates were classified into two groups of Staphylococcus species at the distance level of 600. S. aureus isolates were found to be closely related with higher peak intensities in the mass of 3,993 Da, 4,121 Da and 5,845 Da were detected in MRSA, whereas, that were lost in MSSA. Conclusion: This study verified that MBT is an alternative powerful tool for precise identification and discrimination of Staphylococcus species.
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Affiliation(s)
- Ayman Elbehiry
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Sadat City University, Sadat, Egypt.,Department of Public Health, Microbiology Unit, College of Public Health and Health Informatics, Qassim University, Buraidah, Saudi Arabia
| | - Musaad Al-Dubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Eman Marzouk
- Department of Medical laboratories, College of Applied Medical Science, Qassim University, Buraidah, Saudi Arabia
| | - Salama Osman
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia.,Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelsheikh University, Buraidah, Egypt
| | - Husam Edrees
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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41
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Dilger T, Melzl H, Gessner A. Rapid and reliable identification of waterborne Legionella species by MALDI-TOF mass spectrometry. J Microbiol Methods 2016; 127:154-159. [PMID: 27260989 DOI: 10.1016/j.mimet.2016.05.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/29/2016] [Accepted: 05/30/2016] [Indexed: 10/21/2022]
Abstract
Detection and enumeration of Legionella bacteria in drinking water is regulated in Germany by ISO 11731-2. The mandatory method for species identification employs parallel subculturing of suspicious colonies on selective media requiring the handling of a large number of cultivation plates. After changes to the drinking water quality regulation in Germany in 2012 the demand for Legionella contamination testing increased drastically. A more reliable, faster and less laborious method for species identification is therefore desirable. Matrix-assisted laser desorption ionization followed by time of flight detection mass spectrometry (MALDI-TOF MS) promises an accelerated identification of bacteria with high reliability and reduced expenditure. Our study shows that MS-based species identification results are in full concordance with cultural and biochemical detection and differentiation and that valuable additional information can be gained, even though the ISO regulation demands an extended incubation period for primary bacterial cultures that is actually in contrast to the prerequisites of the MALDI Biotyper system. In addition, the established identification algorithm is very economical and improves time-to-result. Based on our findings, the amendment of MALID-TOF MS identification to ISO11731-2 as an alternative identification method should be taken into consideration.
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Affiliation(s)
| | - Holger Melzl
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Germany
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42
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Clinical Features, Outcomes, and Molecular Characteristics of Community- and Health Care-Associated Staphylococcus lugdunensis Infections. J Clin Microbiol 2016; 54:2051-7. [PMID: 27225402 DOI: 10.1128/jcm.00847-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus lugdunensis is a major cause of aggressive endocarditis, but it is also responsible for a broad spectrum of infections. The differences in clinical and molecular characteristics between community-associated (CA) and health care-associated (HA) S. lugdunensis infections have remained unclear. We performed a retrospective study of S. lugdunensis infections between 2003 and 2014 to compare the clinical and molecular characteristics of CA and HA isolates. We collected 129 S. lugdunensis isolates in total: 81 (62.8%) HA isolates and 48 (37.2%) CA isolates. HA infections were more frequent than CA infections in children (16.0% versus 4.2%, respectively; P = 0.041) and the elderly (38.3% versus 14.6%, respectively; P = 0.004). The CA isolates were more likely to cause skin and soft tissue infections (85.4% versus 19.8%, respectively; P < 0.001). HA isolates were more frequently responsible for bacteremia of unknown origin (34.6% versus 4.2%, respectively; P < 0.001) and for catheter-related bacteremia (12.3% versus 0%, respectively; P = 0.011) than CA isolates. Fourteen-day mortality was higher for HA infections than for CA infections (11.1% versus 0%, respectively). A higher proportion of the HA isolates than of the CA isolates were resistant to penicillin (76.5% versus 52.1%, respectively; P = 0.004) and oxacillin (32.1% versus 2.1%, respectively; P < 0.001). Two major clonal complexes (CC1 and CC3) were identified. Sequence type 41 (ST41) was the most common sequence type identified (29.5%). The proportion of ST38 isolates was higher for HA than for CA infections (33.3% versus 12.5%, respectively; P = 0.009). These isolates were of staphylococcal cassette chromosome mec element (SCCmec)type IV, V, or Vt. HA and CA S. lugdunensis infections differ in terms of their clinical features, outcome, antibiotic susceptibilities, and molecular characteristics.
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Nori P, Szymczak W, Park C, Gialanella P, Munjal I, Chung P, Guo Y, Williamson J, Ostrowsky B, Levi M. Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry as a First-Line Diagnostic Modality in Bacterial Meningitis and Septicemia: a Report of Five Cases. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.clinmicnews.2016.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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44
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Identification of Bacillus strains by MALDI TOF MS using geometric approach. Sci Rep 2015; 5:16989. [PMID: 26592761 PMCID: PMC4655313 DOI: 10.1038/srep16989] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 10/22/2015] [Indexed: 11/08/2022] Open
Abstract
Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to the Bacillus pumilus group. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species, Bacillus pumilus and Bacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available at http://www.bionet.nsc.ru/mbl/database/database.html.
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Camoez M, Sierra JM, Dominguez MA, Ferrer-Navarro M, Vila J, Roca I. Automated categorization of methicillin-resistant Staphylococcus aureus clinical isolates into different clonal complexes by MALDI-TOF mass spectrometry. Clin Microbiol Infect 2015; 22:161.e1-161.e7. [PMID: 26482268 DOI: 10.1016/j.cmi.2015.10.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 11/28/2022]
Abstract
Early identification of methicillin-resistant Staphylococcus aureus (MRSA) dominant clones involved in infection and initiation of adequate infection control measures are essential to limit MRSA spread and understand MRSA population dynamics. In this study we evaluated the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) for the automated discrimination of the major MRSA lineages (clonal complexes, CC) identified in our hospital during a 20-year period (1990-2009). A collection of 82 well-characterized MRSA isolates belonging to the four main CCs (CC5, CC8, CC22 and CC398) was split into a reference set (n = 36) and a validation set (n = 46) to generate pattern recognition models using the ClinProTools software for the identification of MALDI-TOF/MS biomarker peaks. The supervised neural network (SNN) model showed the best performance compared with two other models, with sensitivity and specificity values of 100% and 99.11%, respectively. Eleven peaks (m/z range: 3278-6592) with the highest separation power were identified and used to differentiate all four CCs. Validation of the SNN model using ClinProTools resulted in a positive predictive value (PPV) of 99.6%. The specific contribution of each peak to the model was used to generate subtyping reference signatures for automated subtyping using the BioTyper software, which successfully classified MRSA isolates into their corresponding CCs with a PPV of 98.9%. In conclusion, we find this novel automated MALDI-TOF/MS approach to be a promising, powerful and reliable tool for S. aureus typing.
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Affiliation(s)
- M Camoez
- Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge, Universidad de Barcelona, Barcelona, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain
| | - J M Sierra
- Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge, Universidad de Barcelona, Barcelona, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain
| | - M A Dominguez
- Department of Microbiology, Hospital Universitari de Bellvitge, Instituto de Investigación Biomédica de Bellvitge, Universidad de Barcelona, Barcelona, Spain; Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain.
| | - M Ferrer-Navarro
- Department of Clinical Microbiology, ISGlobal, Barcelona CRESIB, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - J Vila
- Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain; Department of Clinical Microbiology, ISGlobal, Barcelona CRESIB, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - I Roca
- Spanish Network for Research in Infectious Diseases (REIPI), Barcelona, Spain; Department of Clinical Microbiology, ISGlobal, Barcelona CRESIB, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
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Munier AL, de Lastours V, Barbier F, Chau F, Fantin B, Ruimy R. Comparative dynamics of the emergence of fluoroquinolone resistance in staphylococci from the nasal microbiota of patients treated with fluoroquinolones according to their environment. Int J Antimicrob Agents 2015; 46:653-9. [PMID: 26508586 DOI: 10.1016/j.ijantimicag.2015.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 09/03/2015] [Accepted: 09/08/2015] [Indexed: 11/25/2022]
Abstract
Fluoroquinolone-resistant staphylococci (FQRS) are primarily selected in the nasal microbiota during fluoroquinolone (FQ) treatment. To gain insight into the dynamics of the emergence of FQRS, 49 hospitalised patients (HPs) and 62 community patients (CPs) treated with FQs were studied. Nasal swabs were collected before (T0), at the end of (T1) and 1 month after (T2) FQ treatment. FQRS were identified by mass spectrometry. Antibiotic resistance was determined. Pre- and post-exposure staphylococci populations were compared phenotypically and by MLST to determine the origin of FQRS. At T0, 33/49 HPs (67%) and 24/62 CPs (39%) carried FQRS (OR=3.3, 95% CI: 1.4-7.9; P<0.001). Among patients with no FQRS at T0, 15/16 HPs (94%) and 16/38 CPs (42%) had FQRS detected at T1 and/or T2 (OR=19.6, 95% CI: 2.5-902; P<0.001). Among FQRS having emerged, co-resistance to meticillin was detected in 87% and 82% of HPs and CPs, respectively. No selection of resistance emerging from the initial microbiota was evidenced. FQRS showed decreased species diversity in favour of Staphylococcus haemolyticus and Staphylococcus epidermidis. As a consequence of FQ treatment, acquisition of FQRS in the nasal microbiota is frequent in the community and almost inevitable in hospitals. Acquisition from extranasal sites prevails. A restriction in species diversity in favour of more pathogenic and resistant species occurs. This highlights the major impact of FQ treatment on nasal microbiota, the role of the ecological environment in the emergence of FQRS, and the high-risk of dissemination of resistant staphylococci.
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Affiliation(s)
- Anne-Lise Munier
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France; INSERM, IAME, UMR 1137, F-75018 Paris, France
| | - Victoire de Lastours
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France; INSERM, IAME, UMR 1137, F-75018 Paris, France; Assistance Publique-Hôpitaux de Paris, Hôpital Beaujon, Service de Médecine Interne, F-92110 Clichy, France
| | - François Barbier
- Medical Intensive Care Unit (ICU), La Source Hospital, F-45100 Orléans, France
| | - Françoise Chau
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France; INSERM, IAME, UMR 1137, F-75018 Paris, France
| | - Bruno Fantin
- Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France; INSERM, IAME, UMR 1137, F-75018 Paris, France; Assistance Publique-Hôpitaux de Paris, Hôpital Beaujon, Service de Médecine Interne, F-92110 Clichy, France
| | - Raymond Ruimy
- Department of Microbiology, Nice Academic Hospital, F-06200 Nice, France; Université Nice-Sophia Antipolis, F-06200 Nice, France.
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Singhal N, Kumar M, Kanaujia PK, Virdi JS. MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 2015; 6:791. [PMID: 26300860 PMCID: PMC4525378 DOI: 10.3389/fmicb.2015.00791] [Citation(s) in RCA: 795] [Impact Index Per Article: 88.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 07/21/2015] [Indexed: 01/13/2023] Open
Abstract
Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.
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Affiliation(s)
- Neelja Singhal
- Department of Microbiology, University of Delhi New Delhi, India
| | - Manish Kumar
- Department of Biophysics, University of Delhi New Delhi, India
| | - Pawan K Kanaujia
- Department of Microbiology, University of Delhi New Delhi, India
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Lin JF, Cheng CW, Kuo AJ, Liu TP, Yang CC, Huang CT, Lee MH, Lu JJ. Clinical experience and microbiologic characteristics of invasive Staphylococcus lugdunensis infection in a tertiary center in northern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 48:406-12. [DOI: 10.1016/j.jmii.2013.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 11/27/2022]
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Abstract
PURPOSE OF REVIEW To highlight the clinical importance of ventilator-associated pneumonia (VAP) in an era of escalating antimicrobial resistance. RECENT FINDINGS VAP continues to be an important infection in the critically ill. The development of rapid microbiologic diagnostics and new antimicrobial agents offer opportunities for improved treatment strategies for VAP balancing the need to treat effectively in a timely manner and antimicrobial stewardship. Additionally, the new surveillance definitions for assessing the quality of care in critically ill patients (ventilator-associated events, ventilator-associated conditions, and infection-related ventilator-associated conditions) do not appear to be adequate surrogates for the identification of VAP. SUMMARY Clinicians caring for critically ill patients should be aware of the importance of correctly treating VAP. As new diagnostic technologies and antimicrobials become available for VAP, their incorporation into routine patient management should occur in a way that optimizes patient outcomes wherein minimizing further emergence of antimicrobial resistance.
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Mupirocin Resistance in Isolates of Staphylococcus spp. from Nasal Swabs in a Tertiary Hospital in France. J Clin Microbiol 2015; 53:2713-5. [PMID: 26019208 DOI: 10.1128/jcm.00274-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/16/2015] [Indexed: 11/20/2022] Open
Abstract
Mupirocin is a topical antibiotic largely used to eradicate staphylococcal nasal carriage. Here, we investigated the prevalence of mupirocin-resistant Staphylococcus aureus and coagulase-negative staphylococcal isolates recovered from patients in different wards in a hospital (Lyon, France), which were determined both phenotypically with an Epsilometer test (Etest) and genetically by PCR for mupA and mupB.
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