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Abril AG, Quintela-Baluja M, Villa TG, Calo-Mata P, Barros-Velázquez J, Carrera M. Proteomic Characterization of Virulence Factors and Related Proteins in Enterococcus Strains from Dairy and Fermented Food Products. Int J Mol Sci 2022; 23:ijms231810971. [PMID: 36142880 PMCID: PMC9503237 DOI: 10.3390/ijms231810971] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 01/23/2023] Open
Abstract
Enterococcus species are Gram-positive bacteria that are normal gastrointestinal tract inhabitants that play a beneficial role in the dairy and meat industry. However, Enterococcus species are also the causative agents of health care-associated infections that can be found in dairy and fermented food products. Enterococcal infections are led by strains of Enterococcus faecalis and Enterococcus faecium, which are often resistant to antibiotics and biofilm formation. Enterococci virulence factors attach to host cells and are also involved in immune evasion. LC-MS/MS-based methods offer several advantages compared with other approaches because one can directly identify microbial peptides without the necessity of inferring conclusions based on other approaches such as genomics tools. The present study describes the use of liquid chromatography−electrospray ionization tandem mass spectrometry (LC−ESI−MS/MS) to perform a global shotgun proteomics characterization for opportunistic pathogenic Enterococcus from different dairy and fermented food products. This method allowed the identification of a total of 1403 nonredundant peptides, representing 1327 proteins. Furthermore, 310 of those peptides corresponded to proteins playing a direct role as virulence factors for Enterococcus pathogenicity. Virulence factors, antibiotic sensitivity, and proper identification of the enterococcal strain are required to propose an effective therapy. Data are available via ProteomeXchange with identifier PXD036435. Label-free quantification (LFQ) demonstrated that the majority of the high-abundance proteins corresponded to E. faecalis species. Therefore, the global proteomic repository obtained here can be the basis for further research into pathogenic Enterococcus species, thus facilitating the development of novel therapeutics.
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Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
| | - Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council (CSIC), Marine Research Institute (IIM), 36208 Vigo, Spain
- Correspondence:
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Gerace E, Mancuso G, Midiri A, Poidomani S, Zummo S, Biondo C. Recent Advances in the Use of Molecular Methods for the Diagnosis of Bacterial Infections. Pathogens 2022; 11:pathogens11060663. [PMID: 35745518 PMCID: PMC9229729 DOI: 10.3390/pathogens11060663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/31/2022] [Accepted: 06/05/2022] [Indexed: 12/14/2022] Open
Abstract
Infections caused by bacteria have a major impact on public health-related morbidity and mortality. Despite major advances in the prevention and treatment of bacterial infections, the latter continue to represent a significant economic and social burden worldwide. The WHO compiled a list of six highly virulent multidrug-resistant bacteria named ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) responsible for life-threatening diseases. Taken together with Clostridioides difficile, Escherichia coli, Campylobacter spp., (C. jejuni and C. coli), Legionella spp., Salmonella spp., and Neisseria gonorrhoeae, all of these microorganisms are the leading causes of nosocomial infections. The rapid and accurate detection of these pathogens is not only important for the early initiation of appropriate antibiotic therapy, but also for resolving outbreaks and minimizing subsequent antimicrobial resistance. The need for ever-improving molecular diagnostic techniques is also of fundamental importance for improving epidemiological surveillance of bacterial infections. In this review, we aim to discuss the recent advances on the use of molecular techniques based on genomic and proteomic approaches for the diagnosis of bacterial infections. The advantages and limitations of each of the techniques considered are also discussed.
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Affiliation(s)
| | - Giuseppe Mancuso
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Angelina Midiri
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Stefano Poidomani
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Sebastiana Zummo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
| | - Carmelo Biondo
- Department of Human Pathology, University of Messina, 98125 Messina, Italy; (G.M.); (A.M.); (S.P.); (S.Z.)
- Correspondence: ; Tel.: +39-090-2213322
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Lin H, Hu Z, Wu J, Lu Y, Chen J, Wu W. Methodology Establishment and Application of VITEK Mass Spectrometry to Detect Carbapenemase-Producing Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:761328. [PMID: 35223536 PMCID: PMC8873529 DOI: 10.3389/fcimb.2022.761328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
The ability of VITEK mass spectrometry (MS) in detection of bacterial resistance is currently under exploration and evaluation. In this study, we developed and validated a VITEK MS method to rapidly test carbapenemase-producing Klebsiella pneumoniae (CPKP). Solvents, antibiotic concentrations, crystal conditions and times, centrifugation speeds, and other factors were optimized to design a rapid sample pretreatment process for CPKP detection by VITEK MS. The related parameters of the mass spectrum were adjusted on the instrument to establish an CPKP detection mode. 133 clinically isolated strains of CPKP in the microbiology laboratory at the Shenzhen People’s Hospital from 2004 to 2017 were selected for accuracy evaluation. The fresh suspected strains from the microbiology laboratory in 2020 were used to complete the clinical verification. Two antibiotics, meropenem (MEM) and imipenem (IPM), were used as substrates. These two substrates were incubated with suspected CPKP, and the results were obtained by VITEK MS detection. Using this method, different types of CPKP showed different detection results and all the CPKP strains producing KPC-2 and IMP-4 carbapenemase were detected by VITEK MS. Thus, VITEK MS can be used for rapid detection of CPKP, especially for some common types of CPKP. This method provides high accuracy and speed of detection. Combined with its cost advantages, it can be intensely valuable in clinical microbiology laboratories after the standard operating procedures are determined.
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Gato E, Anantharajah A, Arroyo MJ, Artacho MJ, Caballero JDD, Candela A, Chudějová K, Constanso IP, Elías C, Fernández J, Jiménez J, Lumbreras P, Méndez G, Mulet X, Pérez-Palacios P, Rodríguez-Sánchez B, Cantón R, Hrabák J, Mancera L, Martínez-Martínez L, Oliver A, Pascual Á, Verroken A, Bou G, Oviaño M. Multicenter Performance Evaluation of MALDI-TOF MS for Rapid Detection of Carbapenemase Activity in Enterobacterales: The Future of Networking Data Analysis With Online Software. Front Microbiol 2022; 12:789731. [PMID: 35154029 PMCID: PMC8834885 DOI: 10.3389/fmicb.2021.789731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid detection of carbapenemase activity in Enterobacterales in clinical microbiology laboratories during a multicenter networking validation study. The study was divided into three different stages: “software design,” “intercenter evaluation,” and “clinical validation.” First, a standardized procedure with an online software for data analysis was designed. Carbapenem resistance was detected by measuring imipenem hydrolysis and the results were automatically interpreted using the Clover MS data analysis software (Clover BioSoft, Spain). Second, a series of 74 genotypically characterized Enterobacterales (46 carbapenemase-producers and 28 non carbapenemase-producers) were analyzed in 8 international centers to ensure the reproducibility of the method. Finally, the methodology was evaluated independently in all centers during a 2-month period and results were compared with the reference standard for carbapenemase detection used in each center. The overall agreement rate relative to the reference method for carbapenemase resistance detection in clinical samples was 92.5%. The sensitivity was 93.9% and the specificity, 100%. Results were obtained within 60 min and accuracy ranged from 83.3 to 100% among the different centers. Further, our results demonstrate that MALDI-TOF MS is an outstanding tool for rapid detection of carbapenemase activity in Enterobacterales in clinical microbiology laboratories. The use of a simple in-house procedure with online software allows routine screening of carbapenemases in diagnostics, thereby facilitating early and appropriate antimicrobial therapy.
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Affiliation(s)
- Eva Gato
- Servicio de Microbiología, Red Española de Investigación en Patología Infecciosa, Instituto de Investigación Biomédica da Coruña, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
| | | | | | - María José Artacho
- Unidad de Gestión Clínica de Microbiología, Red Española de Investigación en Patología Infecciosa, Hospital Universitario Reina Sofía, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Córdoba, Spain
| | - Juan de Dios Caballero
- Servicio de Microbiología, Red Española de Investigación en Patología Infecciosa, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Candela
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Kateřina Chudějová
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | - Ignacio Pedro Constanso
- Servicio de Análisis Clínicos, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Cristina Elías
- Unidad de Gestión Clínica de Microbiología, Red Española de Investigación en Patología Infecciosa, Hospital Universitario Reina Sofía, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | | | - Pilar Lumbreras
- Servicio de Microbiología, Hospital Universitario Central de Asturias, Instituto de Investigación Sanitaria del Principado de Asturias, Oviedo, Spain
| | | | - Xavier Mulet
- Servicio de Microbiología, Hospital Universitario Son Espases, Red Española de Investigación en Patología Infecciosa, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Palma, Spain
| | - Patricia Pérez-Palacios
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, CSIC, Red Española de Investigación en Patología Infecciosa, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Universidad de Sevilla, Seville, Spain
| | | | - Rafael Cantón
- Servicio de Microbiología, Red Española de Investigación en Patología Infecciosa, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jaroslav Hrabák
- Department of Microbiology, Faculty of Medicine, University Hospital in Pilsen, Charles University, Pilsen, Czechia
| | | | - Luis Martínez-Martínez
- Unidad de Gestión Clínica de Microbiología, Red Española de Investigación en Patología Infecciosa, Hospital Universitario Reina Sofía, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba, Córdoba, Spain
- Departamento de Química Agrícola, Edafología y Microbiología, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Oliver
- Servicio de Microbiología, Hospital Universitario Son Espases, Red Española de Investigación en Patología Infecciosa, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Palma, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología Clínica, CSIC, Red Española de Investigación en Patología Infecciosa, Hospital Universitario Virgen Macarena, Instituto de Biomedicina de Sevilla, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Universidad de Sevilla, Seville, Spain
| | - Alexia Verroken
- Service de Microbiologie, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Germán Bou
- Servicio de Microbiología, Red Española de Investigación en Patología Infecciosa, Instituto de Investigación Biomédica da Coruña, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Marina Oviaño
- Servicio de Microbiología, Red Española de Investigación en Patología Infecciosa, Instituto de Investigación Biomédica da Coruña, CIBER de Enfermedades Infecciosas (CIBERIFEC), Instituto de Salud Carlos III, Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
- *Correspondence: Marina Oviaño,
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Occurrence of the p019 Gene in the blaKPC-Harboring Plasmids: Adverse Clinical Impact for Direct Tracking of KPC-Producing Klebsiella pneumoniae by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2021; 59:e0023821. [PMID: 33980650 DOI: 10.1128/jcm.00238-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently been used for the direct detection of KPC-producing isolates by analysis of the 11,109 Da mass peak representing the P019 protein. In this study, we evaluate the presence of the 11,109 Da mass peak in a collection of 435 unduplicated Klebsiella pneumoniae clinical isolates. The prevalence of the P019 peak in the blaKPC K. pneumoniae isolates was 49.2% (32/65). The 11,109 Da mass peak was not observed in any of the other carbapenemase (319) or noncarbapenemase producers (116). Computational analysis of the presence of the p019 gene was performed in the aforementioned carbapenemase-producing K. pneumoniae isolates fully characterized by whole-genome sequencing (WGS) and in a further collection of 1,649 K. pneumoniae genomes included in EuSCAPE. Herein, we have demonstrated that the p019 gene is not exclusively linked to the pKpQil plasmid but that it is present in the following plasmids: IncFIB(K)/IncFII(K)/ColRNAI, IncFIB(pQil), IncFIB(pQil)/ColRNAI, IncFIB(pQil)/IncFII(K), IncFIB(K)/IncFII(K), and IncX3. In addition, we have proven the independent movement of the Tn4401 and the ISKpn31, of which the p019 gene is a component. The absence of the p019 gene was obvious in Col440I, Col(pHAD28), IncFIB(K)/IncX3/IncFII(K), and IncFIB(K)/IncFII(K) plasmids. In addition, we also observed another plasmid in which neither Tn4401 nor ISKpn31 was found, IncP6. In the EuSCAPE, the occurrence of p019 varied from 0% to 100% among the different geographical locations. The adverse clinical impact of the diminished prevalence of the p019 gene within the plasmid encoding KPC-producing Klebsiella pneumoniae puts forward the need for reconsideration when applying this technique in a clinical setting.
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Pawlak Z, Andrusiów S, Pajączkowska M, Janczura A. Identification of Fungi Isolated from Oral Cavity of Patients with HIV Using MALDI-TOF MS. J Clin Med 2021; 10:jcm10081570. [PMID: 33917925 PMCID: PMC8068364 DOI: 10.3390/jcm10081570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/06/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND A growing incidence of invasive fungal infections, especially among immunocompromised patients, has given increased significance to microbiological diagnostics of yeast-like fungi. More accurate and faster fungi identification methods that can compete with classical methods are being searched for. In this paper, classical microbiological methods are compared to MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry). METHODS The diagnostic material was collected from buccal mucosa from 98 adults, including 69 with HIV. Only positive cultures were included in the study. RESULTS Matching results were obtained in 45 samples, and there were nonmatching results in 35 samples, with the majority of these in the study group, constituting 50% of identifications within this group. A particularly common mistake resulting from the use of classical methods is the false identification of C. dubliniensis as C. albicans. Additionally, C. tropicalis proves to be difficult to identify. CONCLUSIONS Our results and literature data suggest that MALDI-TOF MS should be considered an effective alternative to classical methods in terms of fungi identification, especially among HIV-positive patients, due to the different morphology of fungal colonies.
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Affiliation(s)
- Zuzanna Pawlak
- Students Scientific Society of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Faculty of Medicine, Wroclaw Medical University, 51-149 Wroclaw, Poland; (Z.P.); (S.A.)
| | - Szymon Andrusiów
- Students Scientific Society of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Faculty of Medicine, Wroclaw Medical University, 51-149 Wroclaw, Poland; (Z.P.); (S.A.)
| | - Magdalena Pajączkowska
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Adriana Janczura
- Department of Microbiology, Faculty of Medicine, Wroclaw Medical University, 50-368 Wroclaw, Poland;
- Correspondence:
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