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Park JH, Kim TS, Park H, Kang CK. Delay in the diagnosis of Brucella abortus bacteremia in a nonendemic country: a case report. BMC Infect Dis 2024; 24:489. [PMID: 38741035 PMCID: PMC11089730 DOI: 10.1186/s12879-024-09377-y] [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: 12/22/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND It is challenging to diagnose brucellosis in nonendemic regions because it is a nonspecific febrile disease. The accurate identification of Brucella spp. in clinical microbiology laboratories (CMLs) continues to pose difficulties. Most reports of misidentification are for B. melitensis, and we report a rare case of misidentified B. abortus. CASE PRESENTATION A 67-year-old man visited an outpatient clinic complaining of fatigue, fever, and weight loss. The patient had a history of slaughtering cows with brucellosis one year prior, and his Brucella antibody tests were negative twice. After blood culture, the administration of doxycycline and rifampin was initiated. The patient was hospitalized due to a positive blood culture. Gram-negative coccobacilli were detected in aerobic blood culture bottles, but the CML's lack of experience with Brucella prevented appropriate further testing. Inaccurate identification results were obtained for a GN ID card of VITEK 2 (bioMérieux, USA) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using a MALDI Biotyper (Bruker, Germany). The strain showed 100.0% identity with Brucella spp. according to 16S rRNA sequencing. MALDI-TOF MS peaks were reanalyzed using the CDC MicrobeNet database to determine Brucella spp. (score value: 2.023). The patient was discharged after nine days of hospitalization and improved after maintaining only doxycycline for six weeks. The isolate was also identified as Brucella abortus by genomic evidence. CONCLUSION Automated identification instruments and MALDI-TOF MS are widely used to identify bacteria in CMLs, but there are limitations in accurately identifying Brucella spp. It is important for CMLs to be aware of the possibility of brucellosis through communication with clinicians. Performing an analysis with an additional well-curated MALDI-TOF MS database such as Bruker security-relevant (SR) database or CDC MicrobeNet database is helpful for quickly identifying the genus Brucella.
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Affiliation(s)
- Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, Republic of Korea.
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Elmaghrabi MM, Alharbi NS, Alobaidi AS, Abdulmanea AA, Kadaikunnan S, Ramadan AA, Khaled JM. Iron-tannic acid nano-coating: A promising treatment approach for enhancing Lactococcus lactis antibiotic resistance. Saudi Pharm J 2024; 32:102052. [PMID: 38590610 PMCID: PMC10999874 DOI: 10.1016/j.jsps.2024.102052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
The objective of this study was to explore a novel methodology for the synthesis of nanocoated probiotics following their collection and cultivation under optimized conditions, in light of their significant contribution to human health. Probiotics are instrumental in sustaining immune health by modulating the gastrointestinal microbiota and facilitating digestion. However, the equilibrium they maintain can be adversely affected by antibiotic treatments. It is critical to investigate the vulnerability of probiotics to antibiotics, considering the potential implications. This research aimed to assess whether nanoparticle coating could augment the probiotics' resistance to antibiotic influence. A strain of Lactococcus lactis (L. lactis) was isolated, cultured, and comprehensively characterized utilizing state-of-the-art methodologies, including the VITEK® 2 compact system, VITEK® MS, and 16S rRNA gene sequencing. The nanoparticle coating was performed using iron (III) chloride hexahydrate and tannic acid, followed by an evaluation of the probiotics' resistance to a range of antibiotics. The analysis through scanning electron microscopy (SEM) and atomic force microscopy (AFM) demonstrated a partial nanoparticle coating of the probiotics, which was further supported by UV/Vis spectroscopy findings, suggesting enhanced resistance to standard antibiotics. The results revealed that this strain possesses a unique protein profile and is genetically similar to strains identified in various other countries. Moreover, nano-encapsulation notably increased the strain's resistance to a spectrum of standard antibiotics, including Benzylpenicillin, Teicoplanin, Oxacillin, Vancomycin, Tetracycline, Rifampicin, Erythromycin, and Clindamycin. These findings imply that nanoparticle-coated probiotics may effectively counteract the detrimental effects of extended antibiotic therapy, thus preserving their viability and beneficial influence on gastrointestinal health.
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Affiliation(s)
- Marwa M. Elmaghrabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naiyf S. Alharbi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed S. Alobaidi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Adel A. Abdulmanea
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shine Kadaikunnan
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | | | - Jamal M. Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Celestino CA, Rocca MF, Ayala SM, Irazu L, Escobar GI. First Argentine database for the accurate identification of Brucella to species level by MALDI-TOF MS. Acta Trop 2023; 248:107036. [PMID: 37793493 DOI: 10.1016/j.actatropica.2023.107036] [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: 06/05/2023] [Revised: 09/04/2023] [Accepted: 10/01/2023] [Indexed: 10/06/2023]
Abstract
MALDI-TOF mass spectrometry (MS) has proven to be a fast and reliable method for the identification of a large number of taxonomic groups. It offers the advantage of being able to incorporate protein spectra of microorganisms that are absent or poorly represented in commercial databases, such as the genus Brucella. The aim of the study was to build the first database of protein spectra of local biological variants of Brucella in Argentina and of standard strains. First, the identification performance of a panel of 135 strains was evaluated with the Swedish database ¨Folkhälsomyndigheten¨ (containing protein spectra of several international standards of the genus Brucella) imported from the open access site https://spectra.folkhalsomyndigheten.se/spectra/. With this library 100 % of the strains were correctly identified by mass spectrometry to genus level, but not to species level. Due to the limitation found, an in-house database was designed with local Brucella isolates from Argentina and standard strains used in routine bacteriological diagnosis. For its validation, a panel of strains, different from those used to develop the extended local database (n: 177), was used to, simultaneously, challenge both libraries. The samples were processed by triplicate and the results obtained were: 177 strains correctly identified to genus and species level compared to the gold standard method (phenotypic typing), meeting the criteria accepted by the literature and the manufacturer as reliable identification. Only 2 of these isolates had score values lower than 2 (1.862) and were therefore not included in the calculation of results. According to these results, MALDI-TOF MS is a fast and reliable method for the routine identification of the different Brucella species, and even has the advantage of reducing the time of exposure to pathogenic microorganisms for laboratorians. It could be considered a valuable technique to replace, in the near future, the current conventional techniques due to the ease of transferring protein spectra, avoiding the use of reference strains that are difficult to find commercially available and commonly used in phenotypic typing.
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Affiliation(s)
- Celina Analía Celestino
- Laboratorio de Brucelosis, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina.
| | - María Florencia Rocca
- Servicio de Bacteriología Especial, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina; Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (ReNaEM Argentina), Argentina
| | - Sandra Marcela Ayala
- Laboratorio de Brucelosis, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Lucía Irazu
- Deparatamento de Parasitología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina
| | - Gabriela Ileana Escobar
- Laboratorio de Brucelosis, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas (INEI), Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) «Dr. Carlos G. Malbrán», Ciudad Autónoma de Buenos Aires, Argentina; Red Nacional de Espectrometría de Masas aplicada a la Microbiología Clínica (ReNaEM Argentina), Argentina.
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Hernández-Mora G, Chacón-Díaz C, Moreira-Soto A, Barrantes-Granados O, Suárez-Esquivel M, Viquez-Ruiz E, Barquero-Calvo E, Ruiz-Villalobos N, Hidalgo-Montealegre D, González-Barrientos R, Demeter EA, Estrella-Morales J, Zúñiga-Pereira AM, Quesada-Gómez C, Chaves-Olarte E, Lomonte B, Guzmán-Verri C, Drexler JF, Moreno E. Virulent Brucella nosferati infecting Desmodus rotundus has emerging potential due to the broad foraging range of its bat host for humans and wild and domestic animals. mSphere 2023; 8:e0006123. [PMID: 37404031 PMCID: PMC10449500 DOI: 10.1128/msphere.00061-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/28/2023] [Indexed: 07/06/2023] Open
Abstract
Desmodus rotundus, vampire bats, transmit dangerous infections, and brucellosis is a hazardous zoonotic disease, two adversities that coexist in the subtropical and tropical areas of the American continent. Here, we report a 47.89% Brucella infection prevalence in a colony of vampire bats inhabiting the tropical rainforest of Costa Rica. The bacterium induced placentitis and fetal death in bats. Wide-range phenotypic and genotypic characterization placed the Brucella organisms as a new pathogenic species named Brucella nosferati sp. nov., isolated from bat tissues, including the salivary glands, suggesting feeding behavior might favor transmission to their prey. Overall analyses placed B. nosferati as the etiological agent of a reported canine brucellosis case, demonstrating its potential for infecting other hosts. To assess the putative prey hosts, we analyzed the intestinal contents of 14 infected and 23 non-infected bats by proteomics. A total of 54,508 peptides sorted into 7,203 unique peptides corresponding to 1,521 proteins were identified. Twenty-three wildlife and domestic taxa, including humans, were foraged by B. nosferati-infected D. rotundus, suggesting contact of this bacterium with a broad range of hosts. Our approach is appropriate for detecting, in a single study, the prey preferences of vampire bats in a diverse area, demonstrating its suitability for control strategies where vampire bats thrive. IMPORTANCE The discovery that a high proportion of vampire bats in a tropical area is infected with pathogenic Brucella nosferati and that bats forage on humans and many wild and domestic animals is relevant from the perspective of emerging disease prevention. Indeed, bats harboring B. nosferati in their salivary glands may transmit this pathogenic bacterium to other hosts. This potential is not trivial since, besides the demonstrated pathogenicity, this bacterium possesses all the required virulent arsenal of dangerous Brucella organisms, including those that are zoonotic for humans. Our work has settled the basis for future surveillance actions in brucellosis control programs where these infected bats thrive. Moreover, our strategy to identify the foraging range of bats may be adapted for exploring the feeding habits of diverse animals, including arthropod vectors of infectious diseases, and therefore of interest to a broader audience besides experts on Brucella and bats.
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Affiliation(s)
- Gabriela Hernández-Mora
- Unidad de Microbiología Médico Veterinaria, Servicio Nacional de Salud Animal (SENASA), Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Andres Moreira-Soto
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Osvaldo Barrantes-Granados
- Unidad de Microbiología Médico Veterinaria, Servicio Nacional de Salud Animal (SENASA), Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Eunice Viquez-Ruiz
- Unidad de Microbiología Médico Veterinaria, Servicio Nacional de Salud Animal (SENASA), Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Nazareth Ruiz-Villalobos
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Daniela Hidalgo-Montealegre
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Rocío González-Barrientos
- Section of Anatomic Pathology, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Elena A. Demeter
- Section of Anatomic Pathology, Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Josimar Estrella-Morales
- Unidad de Microbiología Médico Veterinaria, Servicio Nacional de Salud Animal (SENASA), Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Ana-Mariel Zúñiga-Pereira
- Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Quesada-Gómez
- Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales (CIET), Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Jan Felix Drexler
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales (PIET), Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
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The Development of Diagnostic and Vaccine Strategies for Early Detection and Control of Human Brucellosis, Particularly in Endemic Areas. Vaccines (Basel) 2023; 11:vaccines11030654. [PMID: 36992237 DOI: 10.3390/vaccines11030654] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Brucellosis is considered one of the most serious zoonotic diseases worldwide. This disease affects both human and animal health, in addition to being one of the most widespread zoonotic illnesses in the Middle East and Northern Africa. Human brucellosis generally presents in a diverse and non-specific manner, making laboratory confirmation of the diagnosis critical to the patient’s recovery. A coordinated strategy for diagnosing and controlling brucellosis throughout the Middle East is required, as this disease cannot be known to occur without reliable microbiological, molecular, and epidemiological evidence. Consequently, the current review focuses on the current and emerging microbiological diagnostic tools for the early detection and control of human brucellosis. Laboratory assays such as culturing, serology, and molecular analysis can frequently be used to diagnose brucellosis. Although serological markers and nucleic acid amplification techniques are extremely sensitive, and extensive experience has been gained with these techniques in the laboratory diagnosis of brucellosis, a culture is still considered to be the “gold standard” due to the importance of this aspect of public health and clinical care. In endemic regions, however, serological tests remain the primary method of diagnosis due to their low cost, user-friendliness, and strong ability to provide a negative prediction, so they are commonly used. A nucleic acid amplification assay, which is highly sensitive, specific, and safe, is capable of enabling rapid disease diagnosis. Patients who have reportedly fully healed may continue to have positive molecular test results for a long time. Therefore, cultures and serological methods will continue to be the main tools for diagnosing and following up on human brucellosis for as long as no commercial tests or studies demonstrate adequate interlaboratory reproducibility. As there is no approved vaccine that prevents human brucellosis, vaccination-based control of animal brucellosis has become an important part of the management of human brucellosis. Over the past few decades, several studies have been conducted to develop Brucella vaccines, but the problem of controlling brucellosis in both humans and animals remains challenging. Therefore, this review also aims to present an updated overview of the different types of brucellosis vaccines that are currently available.
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About F, Pastre T, Boutrou M, Martinez AY, Melzani A, Peugny S, Michaud C, Zouaoui S, Carage T, Rose VS, Demar M, Lavigne JP, Djossou F, O'Callaghan D, Epelboin L, Keriel A. Novel Species of Brucella Causing Human Brucellosis, French Guiana. Emerg Infect Dis 2023; 29:333-340. [PMID: 36692350 PMCID: PMC9881788 DOI: 10.3201/eid2902.220725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Human brucellosis is a zoonoses caused by bacteria of the genus Brucella. Infection results in subacute or chronic debilitating disease with nonspecific clinical manifestations and is often associated with consuming unpasteurized dairy products. We report 2 cases of brucellosis in male patients who were hospitalized in distinct towns of French Guiana, an overseas territory of France located on the northeastern shore of South America. Both men were citizens of Brazil working as clandestine goldminers in the deep Amazonian rainforest. Characterization of the 2 bacterial isolates revealed that they represent a potential new species of Brucella. Medical practitioners working in contact with wildlife in this region of the world should be aware of the existence of these pathogens and the potential for human infection.
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Pereira CR, de Jesus Sousa T, Lima da Silva A, Gonçalves Dos Santos R, Minharro S, Costa Custódio DA, Pickard DJ, O'Callaghan D, Foster JT, de Castro Soares S, Juca Ramos RT, Góes-Neto A, Matiuzzi da Costa M, Lage AP, Azevedo V, Seles Dorneles EM. First report and whole-genome sequencing of Pseudochrobactrum saccharolyticum in Latin America. Microbes Infect 2023; 25:105018. [PMID: 35940401 DOI: 10.1016/j.micinf.2022.105018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/24/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023]
Abstract
The Brucellaceae family comprises microorganisms similar both phenotypically and genotypically, making it difficult to identify the etiological agent of these infections. This study reports the first isolation, identification, and characterization of Pseudochrobactrum saccharolyticum (strain 115) from Latin America. Strain 115 was isolated in 2007 from a bovine in Brazil and was initially classified as Brucella spp. by classical microbiological tests and bcsp31 PCR. The antimicrobial susceptibility of strain 115 was tested against drugs used to treat human brucellosis by minimal inhibitory concentration test. Subsequently, the whole genome of the strain was sequenced, assembled, and characterized. Phylogenetic trees built from 16S rRNA and recA gene sequences enabled the classification of strain 115 as Pseudochrobactrum spp. Phylogenomic analysis using Single Nucleotide Polymorphisms and Average Nucleotide Identity allowed the classification of the strain as P. saccharolyticum. Additionally, a Tetra Correlation Search identified one related genome from the same species, which was compared with strain 115 by analyzing genomic islands. This is the first identification and whole-genome sequence of P. saccharolyticum in Latin America and highlights a challenge in the diagnosis of bovine brucellosis, which could be solved by including the sequencing of 16S rRNA and recA genes in routine diagnostics.
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Affiliation(s)
- Carine Rodrigues Pereira
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Thiago de Jesus Sousa
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alessandra Lima da Silva
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Roselane Gonçalves Dos Santos
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sílvia Minharro
- Centro de Ciência da Saúde - Medicina - Araguaína, Universidade Federal de Tocantins, Tocantins, Brazil
| | - Dirceia Aparecida Costa Custódio
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Derek J Pickard
- Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - David O'Callaghan
- IVBIC, INSERM, Universite de Montpellier, Nimes, France; CNR Brucella, Laboratoire de Microbiologie, CHU Nimes, Nimes, France
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Siomar de Castro Soares
- Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Biológicas e Ciências Naturais, Universidade Federal Do Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Rommel Thiago Juca Ramos
- Instituto de Ciências Biológicas, Centro de Genômica e Biologia de Sistemas, Universidade Federal Do Pará, Belém, Pará, Brazil
| | - Aristóteles Góes-Neto
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mateus Matiuzzi da Costa
- Universidade Federal Do Vale Do São Francisco, Departamento de Zootecnia, Petrolina, Pernambuco, Brazil
| | - Andrey Pereira Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Departamento de Genética, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil.
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Thompson JE. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry in veterinary medicine: Recent advances (2019-present). Vet World 2022; 15:2623-2657. [PMID: 36590115 PMCID: PMC9798047 DOI: 10.14202/vetworld.2022.2623-2657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/11/2022] [Indexed: 11/22/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) has become a valuable laboratory tool for rapid diagnostics, research, and exploration in veterinary medicine. While instrument acquisition costs are high for the technology, cost per sample is very low, the method requires minimal sample preparation, and analysis is easily conducted by end-users requiring minimal training. Matrix-assisted laser desorption ionization-time-of-flight MS has found widespread application for the rapid identification of microorganisms, diagnosis of dermatophytes and parasites, protein/lipid profiling, molecular diagnostics, and the technique demonstrates significant promise for 2D chemical mapping of tissue sections collected postmortem. In this review, an overview of the MALDI-TOF technique will be reported and manuscripts outlining current uses of the technology for veterinary science since 2019 will be summarized. The article concludes by discussing gaps in knowledge and areas of future growth.
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Affiliation(s)
- Jonathan E. Thompson
- School of Veterinary Medicine, Texas Tech University, Amarillo, Texas 79106, United States,Corresponding author: Jonathan E. Thompson, e-mail:
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9
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Copur B, Pasa O. The role of the serum tube agglutination test in the monitoring of human brucellosis: evaluation of post-treatment SAT titers. Rev Assoc Med Bras (1992) 2022; 68:1234-1239. [PMID: 36228254 PMCID: PMC9575016 DOI: 10.1590/1806-9282.20220269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE Positive results of the serum tube agglutination test that persist after treatment may be interpreted by clinicians as treatment failures. Therefore, our study examined the value of serum tube agglutination test in demonstrating treatment success. METHODS In this retrospective study conducted at a single center, the pre- and post-treatment serum tube agglutination test titers of patients diagnosed with brucellosis were compared. RESULTS The end-of-treatment serum tube agglutination test titer was negative in 24 (18%) of 139 patients diagnosed with brucellosis. The most common complaints of the patients were fever (78.4%), chills (88.5%), sweating (84.9%), anorexia (79.1%), and arthralgia (63.3%). The rate of positive blood culture before the treatment was 68.3%. The absence of fever (p=0.005) and arthralgia (p=0.024) and the pretreatment serum tube agglutination test titer of <1/160 (p=0.014) were significant markers of serological cure. CONCLUSION Although serum tube agglutination test is an effective and very successful test in the diagnosis of brucellosis, our study shows that serum tube agglutination test is not useful in demonstrating the treatment success of human brucellosis in the early post-treatment period.
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Affiliation(s)
- Betul Copur
- Haseki Training and Research Hospital, Department of Infectious Diseases and Clinical Microbiology – Istanbul, Turkey.,Corresponding author:
| | - Ozgur Pasa
- Bitlis Tatvan State Hospital, Department of Clinical Microbiology – Bitlis, Turkey
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10
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Machine Learning Algorithms for Classification of MALDI-TOF MS Spectra from Phylogenetically Closely Related Species Brucella melitensis, Brucella abortus and Brucella suis. Microorganisms 2022; 10:microorganisms10081658. [PMID: 36014076 PMCID: PMC9416640 DOI: 10.3390/microorganisms10081658] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
(1) Background: MALDI-TOF mass spectrometry (MS) is the gold standard for microbial fingerprinting, however, for phylogenetically closely related species, the resolution power drops down to the genus level. In this study, we analyzed MALDI-TOF spectra from 44 strains of B. melitensis, B. suis and B. abortus to identify the optimal classification method within popular supervised and unsupervised machine learning (ML) algorithms. (2) Methods: A consensus feature selection strategy was applied to pinpoint from among the 500 MS features those that yielded the best ML model and that may play a role in species differentiation. Unsupervised k-means and hierarchical agglomerative clustering were evaluated using the silhouette coefficient, while the supervised classifiers Random Forest, Support Vector Machine, Neural Network, and Multinomial Logistic Regression were explored in a fine-tuning manner using nested k-fold cross validation (CV) with a feature reduction step between the two CV loops. (3) Results: Sixteen differentially expressed peaks were identified and used to feed ML classifiers. Unsupervised and optimized supervised models displayed excellent predictive performances with 100% accuracy. The suitability of the consensus feature selection strategy for learning system accuracy was shown. (4) Conclusion: A meaningful ML approach is here introduced, to enhance Brucella spp. classification using MALDI-TOF MS data.
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11
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Hamidi H, Bagheri Nejad R, Es-Haghi A, Ghassempour A. A Combination of MALDI-TOF MS Proteomics and Species-Unique Biomarkers' Discovery for Rapid Screening of Brucellosis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1530-1540. [PMID: 35816556 DOI: 10.1021/jasms.2c00110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Brucellosis is considered to be a zoonotic infection with a predominant incidence in most parts of Iran that may even simply involve diagnostic laboratory personnel. In the present study, we apply matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for rapid and reliable discrimination of Brucella abortus and Brucella melitensis, based on proteomic mass patterns from chemically treated whole-cell analyses. Biomarkers of the low molecular weight proteome in the MALDI-TOF MS spectra were assigned to conserved ribosomal and structural protein families that were found in genome assemblies of B. abortus and B. melitensis in the NCBI database. Significant protein mass signals successfully mapped to ribosomal proteins and structural proteins, such as integration host factor subunit alpha, cold-shock proteins, HU family DNA-binding protein, ATP synthase subunit C, and GNAT family N-acetyltransferase, with specific biomarker peaks that have been identified for each virulent and vaccine strain. Web-accessible bioinformatics algorithms, with a robust data analysis workflow, followed by ribosomal and structural protein mapping, significantly enhanced the reliable assignment of key proteins and accurate identification of Brucella species. Furthermore, clinical samples were analyzed to confirm the most dominant protein biomarker candidates and their relevance for the identifications of B. melitensis and B. abortus. With proper optimization, we envision that the presented MALDI-TOF MS proteomics analyses, coupled with special usage of bioinformatics, could be used as a cost-efficient strategy for the diagnostics of brucellosis and introduce a reliable identification protocol for species of dangerous bacteria.
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Affiliation(s)
- Hamideh Hamidi
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, 19839-69411 Tehran, Iran
| | - Ramin Bagheri Nejad
- Department of Physico Chemistry, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), 31975/148 Karaj, Iran
| | - Ali Es-Haghi
- Department of Physico Chemistry, Razi Vaccine & Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), 31975/148 Karaj, Iran
| | - Alireza Ghassempour
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, 19839-69411 Tehran, Iran
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12
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Inal N, Hazırolan G. Misidentification of Brucella melitensis as Octrobactrum deajoenense with MALDI-TOF MS: A report of three cases. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:210-212. [PMID: 35473994 DOI: 10.1016/j.eimce.2021.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/05/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Neşe Inal
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey.
| | - Gülşen Hazırolan
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey
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13
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High-Resolution Melting PCR as Rapid Genotyping Tool for Brucella Species. Microorganisms 2022; 10:microorganisms10020336. [PMID: 35208791 PMCID: PMC8876322 DOI: 10.3390/microorganisms10020336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 02/06/2023] Open
Abstract
Brucella sp. are the causative agents of brucellosis. One of the main characteristics of the Brucella genus concerns its very high genetic homogeneity. To date, classical bacteriology typing is still considered as the gold standard assay for direct diagnosis of Brucella. Molecular approaches are routinely used for the identification of Brucella at the genus level. However, genotyping is more complex, and to date, no method exists to quickly assign a strain into species and biovar levels, and new approaches are required. Next generation sequencing (NGS) opened a new era into the diagnosis of bacterial diseases. In this study, we designed a high-resolution melting (HRM) method for the rapid screening of DNA and direct assignment into one of the 12 species of the Brucella genus. This method is based on 17 relevant single nucleotide polymorphisms (SNPs), identified and selected from a whole genome SNP (wgSNP) analysis based on 988 genomes (complete and drafts). These markers were tested against the collection of the European Reference Laboratory (EU-RL) for brucellosis (1440 DNAs extracted from Brucella strains). The results confirmed the reliability of the panel of 17 SNP markers, allowing the differentiation of each species of Brucella together with biovars 1, 2, and 3 of B. suis and vaccine strain Rev1 (B. melitensis) within 3 h, which is a considerable gain of time for brucellosis diagnosis. Therefore, this genotyping tool provides a new and quick alternative for Brucella identification based on SNPs with the HRM-PCR assay.
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14
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Microbiological Laboratory Diagnosis of Human Brucellosis: An Overview. Pathogens 2021; 10:pathogens10121623. [PMID: 34959578 PMCID: PMC8709366 DOI: 10.3390/pathogens10121623] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Brucella spp. are Gram-negative, non-motile, non-spore-forming, slow-growing, facultative intracellular bacteria causing brucellosis. Brucellosis is an endemic of specific geographic areas and, although underreported, represents the most common zoonotic infection, with an annual global incidence of 500,000 cases among humans. Humans represent an occasional host where the infection is mainly caused by B. melitensis, which is the most virulent; B. abortus; B. suis; and B. canis. A microbiological analysis is crucial to identifying human cases because clinical symptoms of human brucellosis are variable and aspecific. The laboratory diagnosis is based on three different microbiological approaches: (i) direct diagnosis by culture, (ii) indirect diagnosis by serological tests, and (iii) direct rapid diagnosis by molecular PCR-based methods. Despite the established experience with serological tests and highly sensitive nucleic acid amplification tests (NAATs), a culture is still considered the “gold standard” in the laboratory diagnosis of brucellosis due to its clinical and epidemiological relevance. Moreover, the automated BC systems now available have increased the sensitivity of BCs and shortened the time to detection of Brucella species. The main limitations of serological tests are the lack of common interpretative criteria, the suboptimal specificity due to interspecies cross-reactivity, and the low sensitivity during the early stage of disease. Despite that, serological tests remain the main diagnostic tool, especially in endemic areas because they are inexpensive, user friendly, and have high negative predictive value. Promising serological tests based on new synthetic antigens have been recently developed together with novel point-of-care tests without the need for dedicated equipment and expertise. NAATs are rapid tests that can help diagnose brucellosis in a few hours with high sensitivity and specificity. Nevertheless, the interpretation of NAAT-positive results requires attention because it may not necessarily indicate an active infection but rather a low bacterial inoculum, DNA from dead bacteria, or a patient that has recovered. Refined NAATs should be developed, and their performances should be compared with those of commercial and home-made molecular tests before being commercialized for the diagnosis of brucellosis. Here, we review and report the most common and updated microbiological diagnostic methods currently available for the laboratory diagnosis of brucellosis.
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15
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Yu X, Jiang W, Huang X, Lin J, Ye H, Liu B. rRNA Analysis Based on Long-Read High-Throughput Sequencing Reveals a More Accurate Diagnostic for the Bacterial Infection of Ascites. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6287280. [PMID: 34869767 PMCID: PMC8642000 DOI: 10.1155/2021/6287280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022]
Abstract
Traditional pathogenic diagnosis presents defects such as a low positivity rate, inability to identify uncultured microorganisms, and time-consuming nature. Clinical metagenomics next-generation sequencing can be used to detect any pathogen, compensating for the shortcomings of traditional pathogenic diagnosis. We report third-generation long-read sequencing results and second-generation short-read sequencing results for ascitic fluid from a patient with liver ascites and compared the two types of sequencing results with the results of traditional clinical microbial culture. The distribution of pathogenic microbial species revealed by the two types of sequencing results was quite different, and the third-generation sequencing results were consistent with the results of traditional microbial culture, which can effectively guide subsequent treatment. Short reads, the lack of amplification, and enrichment to amplify signals from trace pathogens, and host background noise may be the reasons for the high error in the second-generation short-read sequencing results. Therefore, we propose that long-read-based rRNA analysis technology is superior to the short-read shotgun-based metagenomics method in the identification of pathogenic bacteria.
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Affiliation(s)
- Xiaoling Yu
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Wenqian Jiang
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xinhui Huang
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Jun Lin
- Institute of Applied Genomics, Fuzhou University, Fuzhou 350108, China
| | - Hanhui Ye
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Baorong Liu
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
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16
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Kornspan D, Brendebach H, Hofreuter D, Mathur S, Blum SE, Fleker M, Bardenstein S, Al Dahouk S. Protein Biomarker Identification for the Discrimination of Brucella melitensis Field Isolates From the Brucella melitensis Rev.1 Vaccine Strain by MALDI-TOF MS. Front Microbiol 2021; 12:712601. [PMID: 34745025 PMCID: PMC8569450 DOI: 10.3389/fmicb.2021.712601] [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: 05/20/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Brucella melitensis Rev.1 is a live attenuated vaccine strain that is widely used to control brucellosis in small ruminants. For successful surveillance and control programs, rapid identification and characterization of Brucella isolates and reliable differentiation of vaccinated and naturally infected animals are essential prerequisites. Although MALDI-TOF MS is increasingly applied in clinical microbiology laboratories for the diagnosis of brucellosis, species or even strain differentiation by this method remains a challenge. To detect biomarkers, which enable to distinguish the B. melitensis Rev.1 vaccine strain from B. melitensis field isolates, we initially searched for unique marker proteins by in silico comparison of the B. melitensis Rev.1 and 16M proteomes. We found 113 protein sequences of B. melitensis 16M that revealed a homologous sequence in the B. melitensis Rev.1 annotation and 17 of these sequences yielded potential biomarker pairs. MALDI-TOF MS spectra of 18 B. melitensis Rev.1 vaccine and 183 Israeli B. melitensis field isolates were subsequently analyzed to validate the identified marker candidates. This approach detected two genus-wide unique biomarkers with properties most similar to the ribosomal proteins L24 and S12. These two proteins clearly discriminated B. melitensis Rev.1 from the closely related B. melitensis 16M and the Israeli B. melitensis field isolates. In addition, we verified their discriminatory power using a set of B. melitensis strains from various origins and of different MLVA types. Based on our results, we propose MALDI-TOF MS profiling as a rapid, cost-effective alternative to the traditional, time-consuming approach to differentiate certain B. melitensis isolates on strain level.
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Affiliation(s)
- David Kornspan
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Holger Brendebach
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Dirk Hofreuter
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Shubham Mathur
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Shlomo Eduardo Blum
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | - Marcelo Fleker
- Department of Bacteriology, Kimron Veterinary Institute (KVI), Bet Dagan, Israel
| | | | - Sascha Al Dahouk
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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17
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Guo P, Wu Z, Liu P, Chen Y, Liao K, Peng Y, He Y. Identification and Antifungal Susceptibility Analysis of Stephanoascus ciferrii Complex Species Isolated From Patients With Chronic Suppurative Otitis Media. Front Microbiol 2021; 12:680060. [PMID: 34367086 PMCID: PMC8334361 DOI: 10.3389/fmicb.2021.680060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Background Stephanoascus ciferrii is a heterothallic ascomycetous yeast-like fungus. Recently, the concept of S. ciferrii complex has been proposed and it consists of S. ciferrii, Candida allociferrii, and Candida mucifera. We aimed to identify 32 strains of S. ciferrii complex isolated from patients with chronic suppurative otitis media (CSOM) at the species level and analyze the morphology and antifungal susceptibility profiles of the three species. Method The sequencing of the internal transcribed spacer (ITS) region and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) were used to identify S. ciferrii complex species. The SARAMIS software was used for cluster analysis of the mass spectra. All the strains were cultured on Sabouraud dextrose agar (SDA) and CHROM plates for 7 days. In the meantime, colonies of the 32 strains went through Gram staining. The Sensititre YeastOne YO10 colorimetric panel was used for the antifungal susceptibility analysis. Results There were 10 strains of C. allociferrii (31.25%), six strains of C. mucifera (18.75%), and 16 strains of S. ciferrii (50%) in the 32 strains of S. ciferrii complex according to the sequencing of the ITS region. MALDI-TOF MS could identify S. ciferrii but showed no results for C. allociferrii and C. mucifera. The cluster analysis of the mass spectra by SARAMIS indicated that the MALDI-TOF MS could distinguish the three species. The morphology characteristics of the three species were similar. As for antifungal susceptibility, S. ciferrii and C. mucifera tended to have high fluconazole MICs compared with C. allociferrii. C. mucifera and C. allociferrii had relatively low flucytosine MICs while S. ciferrii owned high flucytosine MICs. Besides, C. mucifera tended to have a higher MIC value than S. ciferrii for amphotericin B and C. allociferrii for anidulafungin, micafungin, and caspofungin. Conclusion The antifungal susceptibility profiles of the three species of S. ciferrii complex had their own characteristics. Besides, more mass spectra of C. allociferrii and C. mucifera are needed to construct the reference database for S. ciferrii complex species, enabling MALDI-TOF MS to identify S. ciferrii complex at species level.
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Affiliation(s)
- Penghao Guo
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhongwen Wu
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Pingjuan Liu
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yili Chen
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kang Liao
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yaqin Peng
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuting He
- Department of Clinical Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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18
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Rouzic N, Desmier L, Cariou ME, Gay E, Foster JT, Williamson CHD, Schmitt F, Le Henaff M, Le Coz A, Lorléac'h A, Lavigne JP, O'Callaghan D, Keriel A. First Case of Brucellosis Caused by an Amphibian-type Brucella. Clin Infect Dis 2021; 72:e404-e407. [PMID: 32719850 DOI: 10.1093/cid/ciaa1082] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/24/2020] [Indexed: 11/12/2022] Open
Abstract
We report the first case of brucellosis caused by an isolate whose genome is identical that of a frog isolate from Texas, demonstrating the zoonotic potential of amphibian-type Brucella. Importantly, with such atypical Brucella, correct diagnosis cannot be performed using routine serological tests or identification methods.
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Affiliation(s)
- Nicolas Rouzic
- Unité de Médecine Interne-Maladies Infectieuses, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Ludovic Desmier
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
| | - Marie-Estelle Cariou
- Laboratoire de biologie médicale, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Eugénie Gay
- Laboratoire de biologie médicale, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Jeffrey T Foster
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, USA
| | - Charles H D Williamson
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, USA
| | - François Schmitt
- Laboratoire de biologie médicale, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Mikael Le Henaff
- Service de Pneumologie, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Alain Le Coz
- Service de Pneumologie, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Aurélien Lorléac'h
- Unité de Médecine Interne-Maladies Infectieuses, Groupe Hospitalier Bretagne Sud, Lorient, France
| | - Jean-Philippe Lavigne
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
| | - David O'Callaghan
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
| | - Anne Keriel
- Centre National de Référence (CNR) des Brucella, CHU de Nîmes, Nîmes, France.,VBMI, U1047, INSERM, Université de Montpellier, Nîmes, France
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19
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Inal N, Hazırolan G. Misidentification of Brucella melitensis as Octrobactrum deajoenense with MALDI-TOF MS: A report of three cases. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00069-0. [PMID: 33836909 DOI: 10.1016/j.eimc.2021.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 11/03/2022]
Affiliation(s)
- Neşe Inal
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey.
| | - Gülşen Hazırolan
- Faculty of Medicine, Department of Medical Microbiology, Hacettepe University, Ankara, Turkey
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20
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Zhou X, Xuan D, Hu S, Du J, Pu J, Jin D, Zhao F, Yin F, Cui X, Huang Y, Wang G, Wu Q, Lu G, Niu L. Pelistega ratti sp. nov. from Rattus norvegicus of Hainan island. Int J Syst Evol Microbiol 2021; 71. [PMID: 33688803 DOI: 10.1099/ijsem.0.004733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (NLN63T and NLN82) of Gram-stain-negative, oxidase- and catalase-positive, bacilli-shaped organisms were isolated from the faecal samples of two separate Rattus norvegicus in Baisha county of Hainan Province, Southern PR China. Phylogenetic analysis based on the near full-length 16S rRNA sequences revealed that strain NLN63T belongs to the genus Pelistega, having maximum similarity to Pelistega suis CCUG 64465T (97.1 %), Pelistega europaea CCUG 39967T (96.2 %) and Pelistega indica DSM 27484T (96.2 %), respectively. The phylogenomic tree built on 553 core genes from genomes of 20 species in the genus Pelistega and other adjacent genera further confirmed that strains NLN63T and NLN82 form a distinct subline and exhibit specific phylogenetic affinity with P. europaea CCUG 39967T. In digital DNA-DNA hybridization analyses, strain NLN63T showed low estimated DNA reassociation values (21.4-22.6 %) with the type strains of the species in the genus Pelistega. The DNA G+C contents of strains NLN63T and NLN82 were 37.3 and 37.1 mol%, respectively. Strain NLN63T had a unique MALDI-TOF MS profile, contained Q-8 as the major quinone and C16 : 0, summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c or both) and summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c or both) as the dominant fatty acids. Based upon these polyphasic characterization data obtained from the present study, a novel species of the genus Pelistega, Pelistega ratti sp. nov., is proposed with NLN63T (=GDMCC 1.1697T=JCM 33788T) as the type strain.
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Affiliation(s)
- Xiaojun Zhou
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Clinical laboratory department of Hainan General Hospital, Haikou, 570311, PR China
| | - Duanduan Xuan
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China
| | - Shoukui Hu
- Peking University shougang hospital, Beijing, 100144, PR China
| | - Jiang Du
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China
| | - Ji Pu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Dong Jin
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Fan Zhao
- Peking University shougang hospital, Beijing, 100144, PR China
| | - Feifei Yin
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Xiuji Cui
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Yi Huang
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Gaoyu Wang
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Qiang Wu
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Gang Lu
- Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China
| | - Lina Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, 571199, PR China.,Department of Pathogen Biology, Hainan Medical University, Haikou, Hainan, PR China.,Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, Hainan Medical University, Haikou, Hainan, PR China
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21
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Blake KS, Choi J, Dantas G. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cell Mol Life Sci 2021; 78:2585-2606. [PMID: 33582841 PMCID: PMC8005480 DOI: 10.1007/s00018-020-03717-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/26/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022]
Abstract
Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.
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Affiliation(s)
- Kevin S Blake
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - JooHee Choi
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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22
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Ling J, Li G, Shao H, Wang H, Yin H, Zhou H, Song Y, Chen G. Helix Matrix Transformation Combined With Convolutional Neural Network Algorithm for Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry-Based Bacterial Identification. Front Microbiol 2020; 11:565434. [PMID: 33304324 PMCID: PMC7693542 DOI: 10.3389/fmicb.2020.565434] [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: 05/25/2020] [Accepted: 10/26/2020] [Indexed: 01/27/2023] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis is a rapid and reliable method for bacterial identification. Classification algorithms, as a critical part of the MALDI-TOF MS analysis approach, have been developed using both traditional algorithms and machine learning algorithms. In this study, a method that combined helix matrix transformation with a convolutional neural network (CNN) algorithm was presented for bacterial identification. A total of 14 bacterial species including 58 strains were selected to create an in-house MALDI-TOF MS spectrum dataset. The 1D array-type MALDI-TOF MS spectrum data were transformed through a helix matrix transformation into matrix-type data, which was fitted during the CNN training. Through the parameter optimization, the threshold for binarization was set as 16 and the final size of a matrix-type data was set as 25 × 25 to obtain a clean dataset with a small size. A CNN model with three convolutional layers was well trained using the dataset to predict bacterial species. The filter sizes for the three convolutional layers were 4, 8, and 16. The kernel size was three and the activation function was the rectified linear unit (ReLU). A back propagation neural network (BPNN) model was created without helix matrix transformation and a convolution layer to demonstrate whether the helix matrix transformation combined with CNN algorithm works better. The areas under the receiver operating characteristic (ROC) curve of the CNN and BPNN models were 0.98 and 0.87, respectively. The accuracies of the CNN and BPNN models were 97.78 ± 0.08 and 86.50 ± 0.01, respectively, with a significant statistical difference (p < 0.001). The results suggested that helix matrix transformation combined with the CNN algorithm enabled the feature extraction of the bacterial MALDI-TOF MS spectrum, which might be a proposed solution to identify bacterial species.
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Affiliation(s)
- Jin Ling
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China.,Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Gaomin Li
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China.,Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Hong Shao
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China.,Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Hong Wang
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China.,Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Hongrui Yin
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China.,Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Hu Zhou
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yufei Song
- Department of Gastroenterology, Lihuili Hospital of Ningbo Medical Center, Ningbo, China
| | - Gang Chen
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China.,Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
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23
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MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks. Sci Rep 2020; 10:19246. [PMID: 33159111 PMCID: PMC7648634 DOI: 10.1038/s41598-020-75960-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
Brucellosis is one of the most common bacterial zoonoses worldwide affecting not only livestock and wildlife but also pets. Canine brucellosis is characterized by reproductive failure in dogs. Human Brucella canis infections are rarely reported but probably underestimated due to insufficient diagnostic surveillance. To improve diagnostics, we investigated dogs in a breeding kennel that showed clinical manifestations of brucellosis and revealed positive blood cultures. As an alternative to the time-consuming and hazardous classical identification procedures, a newly developed species-specific intact-cell matrix-assisted laser desorption/ionization–time of flight mass spectrometry analysis was applied, which allowed for rapid identification of B. canis and differentiation from closely related B. suis biovar 1. High-throughput sequencing and comparative genomics using single nucleotide polymorphism analysis clustered our isolates together with canine and human strains from various Central and South American countries in a distinct sub-lineage. Hence, molecular epidemiology clearly defined the outbreak cluster and demonstrated the endemic situation in South America. Our study illustrates that MALDI-TOF MS analysis using a validated in-house reference database facilitates rapid B. canis identification at species level. Additional whole genome sequencing provides more detailed outbreak information and leads to a deeper understanding of the epidemiology of canine brucellosis.
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24
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O'Callaghan D. Human brucellosis: recent advances and future challenges. Infect Dis Poverty 2020; 9:101. [PMID: 32703319 PMCID: PMC7376320 DOI: 10.1186/s40249-020-00715-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/03/2020] [Indexed: 11/10/2022] Open
Affiliation(s)
- David O'Callaghan
- Bacterial Virulence and Infectious Disease, University of Montpellier, INSERM, Nimes, France. .,Brucellosis National Reference Centre (CNR), Microbiology Laboratory, Caremeau University Hospital, Nimes, France.
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25
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Jiang H, Feng L, Lu J. Updated Guidelines for the Diagnosis of Human Brucellosis - China, 2019. China CDC Wkly 2020; 2:487-489. [PMID: 34594685 PMCID: PMC8393123 DOI: 10.46234/ccdcw2020.129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/27/2020] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hai Jiang
- 1 State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lan Feng
- 1 State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jinxing Lu
- 1 State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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26
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Jiang H, O'Callaghan D, Ding JB. Brucellosis in China: history, progress and challenge. Infect Dis Poverty 2020; 9:55. [PMID: 32448394 PMCID: PMC7247241 DOI: 10.1186/s40249-020-00673-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022] Open
Abstract
Brucellosis is a neglected zoonosis. It causes acute febrile illness and a potentially debilitating chronic infection in humans, and livestock infection has substantial socioeconomic impact. Over the past two decades, improvements have been made to better understand the various aspects of human and animal brucellosis. Meanwhile, especially in the developing world, immense challenges that remain in controlling and eradicating brucellosis are novel diagnostics tools and efficacious vaccines. Here, we will focus on the remarkable issues on epidemiological survey, as well as the priority and challenge of brucellosis in China. Brucellosis will be controlled with meaningful collaboration between local and public partnerships effectively applying a One Health framework.
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Affiliation(s)
- Hai Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - David O'Callaghan
- VBMI, Universite de Montpellier, INSERM, UFR Medecine, 186, Chemin du Carreau de Lanes, 30908, Nimes Cedex 2, France.,Centre National de Reference Brucella, CHU de Nimes, Nimes, France
| | - Jia-Bo Ding
- Department of Diagnostic Technology, China Institute of Veterinary Drug Control, Beijing, China
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27
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Wareth G, Pletz MW, Neubauer H, Murugaiyan J. Proteomics of Brucella: Technologies and Their Applications for Basic Research and Medical Microbiology. Microorganisms 2020; 8:microorganisms8050766. [PMID: 32443785 PMCID: PMC7285364 DOI: 10.3390/microorganisms8050766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/26/2022] Open
Abstract
Brucellosis is a global zoonosis caused by Gram-negative, facultative intracellular bacteria of the genus Brucella (B.). Proteomics has been used to investigate a few B. melitensis and B. abortus strains, but data for other species and biovars are limited. Hence, a comprehensive analysis of proteomes will significantly contribute to understanding the enigmatic biology of brucellae. For direct identification and typing of Brucella, matrix-assisted laser desorption ionization - time of flight mass spectrometry (MALDI - TOF MS) has become a reliable tool for routine diagnosis due to its ease of handling, price and sensitivity highlighting the potential of proteome-based techniques. Proteome analysis will also help to overcome the historic but still notorious Brucella obstacles of infection medicine, the lack of safe and protective vaccines and sensitive serologic diagnostic tools by identifying the most efficient protein antigens. This perspective summarizes past and recent developments in Brucella proteomics with a focus on species identification and serodiagnosis. Future applications of proteomics in these fields are discussed.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt
- Correspondence: ; Tel.: +49-364-1804-2296
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany;
| | - Jayaseelan Murugaiyan
- Institute of Animal Hygiene and Environmental Health, Centre for Infectious Medicine, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany;
- Department of Biotechnology, SRM University AP, Neerukonda, Mangalagiri, Andhra Pradesh 522502, India
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28
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Khaliulina Ushakova T, Perera Lerin AI, Sahagún Pareja J, Dolz Aspas R, Puyal Barcelona M, Sancho García A, Jiménez Moraleda B, Matovelle Ochoa C, Salvo Gonzalo S. [Identification of Brucella melitensis as Ochrobactrum anthropi by MALDI-TOF MS]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2020; 33:223-224. [PMID: 32312029 PMCID: PMC7262385 DOI: 10.37201/req/009.2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- T Khaliulina Ushakova
- Tatiana Khaliulina Ushakova, Servicio de Microbiología. Hospital Clínico Universitario Lozano Blesa, Avenida San Juan Bosco, 15, 50009, Zaragoza, Spain.
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29
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Cen YK, Lin JG, Wang YL, Wang JY, Liu ZQ, Zheng YG. The Gibberellin Producer Fusarium fujikuroi: Methods and Technologies in the Current Toolkit. Front Bioeng Biotechnol 2020; 8:232. [PMID: 32292777 PMCID: PMC7118215 DOI: 10.3389/fbioe.2020.00232] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
In recent years, there has been a noticeable increase in research interests on the Fusarium species, which includes prevalent plant pathogens and human pathogens, common microbial food contaminants and industrial microbes. Taken the advantage of gibberellin synthesis, Fusarium fujikuroi succeed in being a prevalent plant pathogen. At the meanwhile, F. fujikuroi was utilized for industrial production of gibberellins, a group of extensively applied phytohormone. F. fujikuroi has been known for its outstanding performance in gibberellin production for almost 100 years. Research activities relate to this species has lasted for a very long period. The slow development in biological investigation of F. fujikuroi is largely due to the lack of efficient research technologies and molecular tools. During the past decade, technologies to analyze the molecular basis of host-pathogen interactions and metabolic regulations have been developed rapidly, especially on the aspects of genetic manipulation. At the meanwhile, the industrial fermentation technologies kept sustained development. In this article, we reviewed the currently available research tools/methods for F. fujikuroi research, focusing on the topics about genetic engineering and gibberellin production.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jian-Guang Lin
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - You-Liang Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Jun-You Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, China
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30
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Identification of Brucella spp. isolates and discrimination from the vaccine strain Rev.1 by MALDI-TOF mass spectrometry. Mol Cell Probes 2020; 51:101533. [PMID: 32068074 DOI: 10.1016/j.mcp.2020.101533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/21/2020] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
Brucellosis' surveillance and control programs require robust laboratory techniques that can reliably identify and biotype Brucella strains and discriminate between vaccine and field infection. In the recent years, Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) has revolutionized the routine identification of several microorganisms in clinical microbiology laboratories. Nevertheless, its application on Brucella spp. identification is limited since there are no reference spectra in the commercial databases, due to the microorganism's potential bioterrorist use. In this study, a custom MALDI-TOF MS reference library was constructed and its performance on identification at species level was evaluated using 75 Brucella spp. isolates. Furthermore, distinct peak biomarkers were detected for biovar assignment and discrimination from vaccine strain Rev.1. Analysis of mass peak profiles allowed Brucella accurate identification at genus and species level (100%) with no misidentifications. Despite the high intrageneric similarity, MALDI-TOF MS database succeeded in classifying at biovar level, 47 out of 62 B. melitensis bv. 3 isolates (75.81%), whereas all B. melitensis strains, except for one, were correctly discriminated from vaccine strain Rev.1. MALDI-TOF MS appeared to be a rapid, cost-effective and reliable method for the routine identification of brucellae which reduces time consumption in pathogen identification and could replace in the near future the current conventional and molecular techniques. Its ability to differentiate vaccine from field infection could facilitate brucellosis' monitoring systems contributing in the effective control of the disease.
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Brucella Exposure Risk Events in 10 Clinical Laboratories, New York City, USA, 2015 to 2017. J Clin Microbiol 2020; 58:JCM.01096-19. [PMID: 31694974 DOI: 10.1128/jcm.01096-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/22/2019] [Indexed: 12/18/2022] Open
Abstract
From 2015 to 2017, 11 confirmed brucellosis cases were reported in New York City, leading to 10 Brucella exposure risk events (Brucella events) in 7 clinical laboratories (CLs). Most patients had traveled to countries where brucellosis is endemic and presented with histories and findings consistent with brucellosis. CLs were not notified that specimens might yield a hazardous organism, as the clinicians did not consider brucellosis until they were notified that bacteremia with Brucella was suspected. In 3 Brucella events, the CLs did not suspect that slow-growing, small Gram-negative bacteria might be harmful. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), which has a limited capacity to identify biological threat agents (BTAs), was used during 4 Brucella events, which accounted for 84% of exposures. In 3 of these incidents, initial staining of liquid media showed Gram-positive rods or cocci, including some cocci in chains, suggesting streptococci. Over 200 occupational exposures occurred when the unknown isolates were manipulated and/or tested on open benches, including by procedures that could generate infectious aerosols. During 3 Brucella events, the CLs examined and/or manipulated isolates in a biological safety cabinet (BSC); in each CL, the CL had previously isolated Brucella Centers for Disease Control and Prevention recommendations to prevent laboratory-acquired brucellosis (LAB) were followed; no seroconversions or LAB cases occurred. Laboratory assessments were conducted after the Brucella events to identify facility-specific risks and mitigations. With increasing MALDI-TOF MS use, CLs are well-advised to adhere strictly to safe work practices, such as handling and manipulating all slow-growing organisms in BSCs and not using MALDI-TOF MS for identification until BTAs have been ruled out.
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32
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Keyburn AL, Buller N. Brucella: not your ‘typical’ intracellular pathogen. MICROBIOLOGY AUSTRALIA 2020. [DOI: 10.1071/ma20010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Currently the genus Brucella consists of a group of bacteria that are genetically monospecific yet phenotypically diverse, and a recent genetic and phenotypic divergent group known as ‘atypical' Brucellae. The host range is extremely varied and includes mammals, including humans, terrestrial animals and marine mammals, but now extends to reptiles and amphibians. Almost all Brucella species are zoonotic. The disease collectively termed Brucellosis leads to abortion and reproductive disease in animals, whereas human infection presents as a non-specific undulating fever accompanied by general malaise, chills, joint pain, muscle aches, genitourinary disease and adverse pregnancy outcomes. These Gram-negative coccobacilli invade and replicate in the host macrophages where they can limit the effects of the host immune system and antibiotic treatment. Due to the phenotypic and genotypic diversity and close relationship with Ochrobactrum species, the genus Brucella presents challenges for accurate identification and recognition of new species.
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Abstract
The clinical presentation of brucellosis in humans is variable and unspecific, and thus, laboratory corroboration of the diagnosis is essential for the patient's proper treatment. The diagnosis of brucellar infections can be made by culture, serological tests, and nucleic acid amplification assays. Modern automated blood culture systems enable detection of acute cases of brucellosis within the routine 5- to 7-day incubation protocol employed in clinical microbiology laboratories, although a longer incubation and performance of blind subcultures may be needed for protracted cases. Serological tests, though they lack specificity and provide results that may be difficult to interpret in individuals repeatedly exposed to Brucella organisms, nevertheless remain a diagnostic cornerstone in resource-poor countries. Nucleic acid amplification assays combine exquisite sensitivity, specificity, and safety and enable rapid diagnosis of the disease. However, long-term persistence of positive molecular test results in patients that have apparently fully recovered is common and has unclear clinical significance and therapeutic implications. Therefore, as long as there are no sufficiently validated commercial tests or studies that demonstrate an adequate interlaboratory reproducibility of the different homemade PCR assays, cultures and serological methods will remain the primary tools for the diagnosis and posttherapeutic follow-up of human brucellosis.
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Affiliation(s)
- Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Pilar Morata
- Biochemistry and Molecular Biology Department, Faculty of Medicine, University of Málaga, Málaga, Spain
- IBIMA, Málaga, Spain
| | - Juan D Colmenero
- Infectious Diseases Service, University Regional Hospital, Málaga, Spain
- IBIMA, Málaga, Spain
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34
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Rapid Detection of Microbial Mass Spectra VITEK-MS for Campylobacter jejuni and Listeria monocytogenes. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01663-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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35
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Grenga L, Pible O, Armengaud J. Pathogen proteotyping: A rapidly developing application of mass spectrometry to address clinical concerns. CLINICAL MASS SPECTROMETRY 2019; 14 Pt A:9-17. [DOI: 10.1016/j.clinms.2019.04.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 04/25/2019] [Accepted: 04/27/2019] [Indexed: 12/13/2022]
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36
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Kostrzewa M, Nagy E, Schröttner P, Pranada AB. How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria - the rare and the unknown. Expert Rev Mol Diagn 2019; 19:667-682. [PMID: 31303071 DOI: 10.1080/14737159.2019.1643238] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: Ten years after its introduction into clinical microbiology, MALDI-TOF mass spectrometry has become the standard routine identification tool for bacteria in most laboratories. The technology has accelerated analyses and improved the quality of results. The greatest significance has been observed for bacteria that were challenging to be identified by traditional methods. Areas covered: We searched in existing literature (Pubmed) for reports how MALDI-TOF MS has contributed to identification of rare and unknown bacteria from different groups. We describe how this has improved the diagnostics in different groups of bacteria. Reference patterns for strains which yet cannot be assigned to a known species even enable the search for related bacteria in studies as well as in routine diagnostics. MALDI-TOF MS can help to discover and investigate new species and their clinical relevance. It is a powerful tool in the elucidation of the bacterial composition of complex microbiota in culturomics studies. Expert opinion: MALDI-TOF MS has improved the diagnosis of bacterial infections. It also enables knowledge generation for prospective diagnostics. The term 'hard-to-identify' might only be rarely attributed to bacteria in the future. Novel applications are being developed, e.g. subspecies differentiation, typing, and antibiotic resistance testing which may further contribute to improved microbial diagnostics.
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Affiliation(s)
- Markus Kostrzewa
- Bioanalytical Development, Bruker Daltonik GmbH , Bremen , Germany
| | - Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged , Szeged , Hungary
| | - Percy Schröttner
- Institut für Medizinische Mikrobiologie und Hygiene, Technische Universität Dresden , Dresden , Germany
| | - Arthur B Pranada
- Department of Medical Microbiology, MVZ Dr. Eberhard & Partner Dortmund (ÜBAG) , Dortmund , Germany
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