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Ioannou P, Baliou S, Kofteridis D. Robinsoniella peoriensis Infections in Humans-A Narrative Review. Antibiotics (Basel) 2024; 13:570. [PMID: 38927236 PMCID: PMC11200903 DOI: 10.3390/antibiotics13060570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
Robinsoniella peoriensis is a Gram-positive, strictly anaerobic, spore-forming, rod-shaped bacterium belonging to the phylum Firmicutes and the family Lachnospiraceae. Until now, R. peoriensis is the only species of its genus. It was first isolated in 2003 during a study into the flora of lagoons and manure pits. Given the rarity of this microorganism and the sparse information in the literature about its way of transmission, the way to diagnose its infections and identify it in the microbiology laboratory, and its public health relevance, the present study aimed to identify all the published cases of Robinsoniella, describe the epidemiological, clinical, and microbiological characteristics, and provide information about its antimicrobial resistance, treatment, and outcomes. A narrative review was performed based on a Pubmed/Medline and Scopus databases search. In total, 14 studies provided data on 17 patients with infections by Robinsoniella. The median age of patients was 63 years and 47% were male. The most common types of infection were bone and joint infections, bacteremia, infective endocarditis, and peritonitis. The only isolated species was R. peoriensis, and antimicrobial resistance to clindamycin was 50%, but was 0% to the combination of piperacillin with tazobactam, aminopenicillin with a beta-lactamase inhibitor, and metronidazole which were the most commonly used antimicrobials for the treatment of these infections. The overall mortality depends on the type of infection and is notable only for bacteremia, while all other infections had an optimal outcome. Future studies should better assess these infections' clinical and epidemiological characteristics and the mechanisms of the antimicrobial resistance of this microorganism from a mechanistic and genetic perspective.
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Affiliation(s)
- Petros Ioannou
- School of Medicine, University of Crete, 71003 Heraklion, Greece
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2
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Alves G, Ogurtsov AY, Porterfield H, Maity T, Jenkins LM, Sacks DB, Yu YK. Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1138-1155. [PMID: 38740383 PMCID: PMC11157548 DOI: 10.1021/jasms.3c00445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/16/2024]
Abstract
Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.
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Affiliation(s)
- Gelio Alves
- National
Center for Biotechnology Information, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Aleksey Y. Ogurtsov
- National
Center for Biotechnology Information, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland 20894, United States
| | - Harry Porterfield
- Department
of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Tapan Maity
- Laboratory
of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lisa M. Jenkins
- Laboratory
of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David B. Sacks
- Department
of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yi-Kuo Yu
- National
Center for Biotechnology Information, National Library of Medicine,
National Institutes of Health, Bethesda, Maryland 20894, United States
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3
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Alipourfard I, Darvishi M, Khalighfard A, Ghazi F, Mobed A. Nanomaterial-based methods for sepsis management. Enzyme Microb Technol 2024; 174:110380. [PMID: 38147783 DOI: 10.1016/j.enzmictec.2023.110380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/26/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Sepsis is a serious disease caused by an impaired host immune response to infection, resulting in organ dysfunction, tissue damage and is responsible for high in-hospital mortality (approximately 20%). Recently, WHO documented sepsis as a global health priority. Nevertheless, there is still no effective and specific therapy for clinically detecting sepsis. Nanomaterial-based approaches have appeared as promising tools for identifying bacterial infections. In this review, recent biosensors are introduced and summarized as nanomaterial-based platforms for sepsis management and severe complications. Biosensors can be used as tools for the diagnosis and treatment of sepsis and as nanocarriers for drug delivery. In general, diagnostic methods for sepsis-associated bacteria, biosensors developed for this purpose are presented in detail, and their strengths and weaknesses are discussed. In other words, readers of this article will gain a comprehensive understanding of biosensors and their applications in sepsis management.
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Affiliation(s)
- Iraj Alipourfard
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Mohammad Darvishi
- Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Arghavan Khalighfard
- Department of Nursing and Midwifery٫ Faculty of Midwifery٬ Zanjan University of Medical Sciences, Zanjan, Iran
| | - Farhood Ghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 5154853431, Iran
| | - Ahmad Mobed
- Infectious and Tropical Diseases Research Center, Clinical Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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4
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Jones Severino Vasconcelos QD, Silva Frederico MJ, Sousa Alves RD, Jesus Pinheiro Gomes Bandeira TD, Amaral de Moraes ME, Aragão GF. Effects of whey protein supplementation on gut microbiota of Wistar rats with valproic acid-induced autism symptoms. Future Microbiol 2024; 19:213-226. [PMID: 37934065 DOI: 10.2217/fmb-2023-0051] [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: 03/01/2023] [Accepted: 09/21/2023] [Indexed: 11/08/2023] Open
Abstract
Aim: To evaluate the effects of whey protein (WP) supplementation (1.24 mg/g, 24 days) in rats with autism spectrum disorder (ASD) induced by valproic acid (400 mg/kg, single dose). Materials & methods: Wistar rats (14 days old) were divided into four groups: control, ASD, ASD plus WP and WP. Results: WP increased bacterial diversity and the number of colonies. Bacteria from the Firmicutes phylum were predominantly found in the supplemented groups (p < 0.05). WP also improved the animals' memory in the Y-maze test and decreased the time that male animals spent in the 'solitary chamber' (p < 0.05). Conclusion: WP supplementation positively influenced gut microbiota, along with memory.
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Affiliation(s)
| | | | - Renata de Sousa Alves
- Department of Clinical and Toxicological Analysis, Federal University of Ceara, 60430-160, Fortaleza, Brazil
| | | | | | - Gislei Frota Aragão
- Health Science Center, State University of Ceara, 60430-275, Fortaleza, Brazil
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5
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Malaluang P, Åkerholm T, Nyman G, Lindahl J, Hansson I, Morrell JM. Bacteria in the healthy equine vagina during the estrous cycle. Theriogenology 2024; 213:11-18. [PMID: 37793220 DOI: 10.1016/j.theriogenology.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023]
Abstract
An understanding of the normal bacterial microbiota of any organ is essential to provide the background to conditions and interventions that might cause the microbiota to change. In the vagina of the mare, a change of bacterial microbiota could be induced by introduction of semen, treatment with antibiotics, discharge from an unhealthy uterus etc. Previous studies on equine vaginal bacteria are not all conducted in the same way and results are not altogether consistent. Therefore, this study was designed to provide a deeper understanding of the bacterial microbiota of the mare vagina, and possible changes throughout the estrous cycle. The cranial portion of the vagina was sampled on day 0 (ovulation), day 3, day 7, and day 14 of the estrous cycle. The vaginal sampling was conducted with double-guarded occluded swabs from the cranial floor of the vagina. Ovulation was determined by rectal palpation and ultrasonic examination, and the day 0 samples were taken within ±24 h of ovulation. Swabs were brought to the laboratory in Amies medium within 2-3 h and were plated out immediately on both selective and non-selective agars. Results were registered as amount of growth (qualitatively), bacterial species and number of isolates. Bacterial growth was highest on day 3 and 7, representing the beginning and middle of diestrus. The dominant bacteria were Escherichia coli and Streptococcus zooepidemicus. Escherichia coli was especially dominant in maiden mares, compared to the mares that had foaled. An increase in bacterial diversity throughout the estrous cycle was observed, being highest on day 14. These results suggest that there are changes in the bacterial microbiota of the mare vagina throughout the normal estrous cycle.
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Affiliation(s)
- P Malaluang
- Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - T Åkerholm
- Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - G Nyman
- Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden; Lövsta Stud, Upplands Väsby, Sweden
| | - J Lindahl
- Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden; Current Affiliation Department of Animal Health and Antibiotic Strategies, National Veterinary Institute, Uppsala, Sweden
| | - I Hansson
- Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - J M Morrell
- Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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Litterio M, Castello L, Venuta ME, Abel S, Fernández-Canigia L, Legaria MC, Rollet R, Vaustat D, Azula N, Fox B, Otero S, Maldonado ML, Mangieri NA, Rossetti MA, Predari SC, Cejas D, Barberis C. Comparison of two MALDI-TOF MS systems for the identification of clinically relevant anaerobic bacteria in Argentina. Rev Argent Microbiol 2024; 56:33-61. [PMID: 38368217 DOI: 10.1016/j.ram.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 02/19/2024] Open
Abstract
The aim of this study was to compare the performance of two MALDI-TOF MS systems in the identification of clinically relevant strict anaerobic bacteria. The 16S rRNA gene sequencing was the gold standard method when discrepancies or inconsistencies were observed between platforms. A total of 333 isolates were recovered from clinical samples of different centers in Buenos Aires City between 2016 and 2021. The isolates were identified in duplicate using two MALDI-TOF MS systems, BD Bruker Biotyper (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMèrieux, Marcy-l'Etoile, France). Using the Vitek MS system, the identification of anaerobic isolates yielded the following percentages: 65.5% (n: 218) at the species or species-complex level, 71.2% (n: 237) at the genus level, 29.4% (n: 98) with no identification and 5.1% (n: 17) with misidentification. Using the Bruker Biotyper system, the identification rates were as follows: 85.3% (n: 284) at the species or species-complex level, 89.7% (n: 299) at the genus level, 14.1% (n: 47) with no identification and 0.6% (n: 2) with misidentification. Differences in the performance of both methods were statistically significant (p-values <0.0001). In conclusion, MALDI-TOF MS systems speed up microbial identification and are particularly effective for slow-growing microorganisms, such as anaerobic bacteria, which are difficult to identify by traditional methods. In this study, the Bruker system showed greater accuracy than the Vitek system. In order to be truly effective, it is essential to update the databases of both systems by increasing the number of each main spectrum profile within the platforms.
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Affiliation(s)
- Mirta Litterio
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Liliana Castello
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Elena Venuta
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | - Sofía Abel
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - María Cristina Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - Raquel Rollet
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Daniela Vaustat
- Hospital de Enfermedades Infecciosas Dr. Francisco Javier Muñiz, Buenos Aires, Argentina
| | - Natalia Azula
- Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Buenos Aires, Argentina
| | | | - Silvina Otero
- Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Buenos Aires, Argentina
| | | | - Natalia Alejandra Mangieri
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - María Adelaida Rossetti
- Hospital Interzonal de Agudos Presidente Perón, Avellaneda, Provincia de Buenos Aires, Argentina
| | - Silvia Carla Predari
- Universidad de Buenos Aires, Instituto de Investigaciones Médicas Alfredo Lanari, Departamento de Microbiología, Buenos Aires, Argentina
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina; CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Buenos Aires, Argentina
| | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina.
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Fernández Vecilla D, Roche Matheus MP, Urrutikoetxea Gutiérrez M, Iglesias Hidalgo G, Aspichueta Vivanco C, Díaz de Tuesta Del Arco JL. Brain abscess caused by Porphyromonas gingivalis and Eubacterium nodatum mimicking acute stroke. Anaerobe 2023; 84:102801. [PMID: 38007215 DOI: 10.1016/j.anaerobe.2023.102801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/27/2023]
Abstract
We described a case of a 65-year-old man with a brain abscess caused by Porphyromonas gingivalis and Eubacterium nodatum. The patient presented right central facial nerve palsy, mutism and right hemiparesis at the examination. The patient underwent a left frontal craniotomy with evacuation of the brain abscess. Specimens were collected for microbiological analysis and intravenous treatment was started with levetiracetam, dexamethasone, meropenem (1 g/8 h) and linezolid (600 mg/12 h). After identification of anaerobic bacteria the antibiotic treatment was changed to piperacillin/tazobactam (4 g/0,5 g/8 h), fulfilling 8 weeks of antibiotic with good clinical and radiological evolution.
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Affiliation(s)
- Domingo Fernández Vecilla
- Clinical Microbiology Service, Laredo Regional Hospital, Av. Derechos Humanos, 40, 39770, Laredo, Cantabria, Spain.
| | - Mary Paz Roche Matheus
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain
| | - Mikel Urrutikoetxea Gutiérrez
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain
| | | | - Cristina Aspichueta Vivanco
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain
| | - José Luis Díaz de Tuesta Del Arco
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao, Biscay, Spain; Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Biscay, Spain
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8
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Zhang H, Yang Y, Jiang Y, Zhang M, Xu Z, Wang X, Jiang J. Mass Spectrometry Analysis for Clinical Applications: A Review. Crit Rev Anal Chem 2023:1-20. [PMID: 37910438 DOI: 10.1080/10408347.2023.2274039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Mass spectrometry (MS) has become an attractive analytical method in clinical analysis due to its comprehensive advantages of high sensitivity, high specificity and high throughput. Separation techniques coupled MS detection (e.g., LC-MS/MS) have shown unique advantages over immunoassay and have developed as golden criterion for many clinical applications. This review summarizes the characteristics and applications of MS, and emphasizes the high efficiency of MS in clinical research. In addition, this review also put forward further prospects for the future of mass spectrometry technology, including the introduction of miniature MS instruments, point-of-care detection and high-throughput analysis, to achieve better development of MS technology in various fields of clinical application. Moreover, as ambient ionization mass spectrometry (AIMS) requires little or no sample pretreatment and improves the flux of MS, this review also summarizes its potential applications in clinic.
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Affiliation(s)
- Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Yali Yang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Meng Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Zhilong Xu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, P. R. China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, P. R. China
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9
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Stewart CE, McCafferty A, Sherertz R. Tannerella forsythia, Fusobacterium nucleatum, and Suspected Actinomyces Causing Massive Empyema: A Case Report. Cureus 2023; 15:e48117. [PMID: 38046736 PMCID: PMC10691742 DOI: 10.7759/cureus.48117] [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] [Accepted: 11/01/2023] [Indexed: 12/05/2023] Open
Abstract
This report presents the case of a polymicrobial empyema due to Fusobacterium nucleatum, Tannerella forsythia, and suspected Actinomyces spp., presenting as several weeks of progressive shortness of breath and malaise. The patient had many risk factors for a lower respiratory tract infection, including chronic alcohol abuse, a flu-like illness months prior, and a recent invasive dental procedure. An admission CT scan showed a large right pleural effusion. Blood cultures were negative, but an aspirate from the pleural effusion showed abundant gram-positive rods that did not grow aerobically. Subsequent anaerobic cultures at a reference laboratory grew Tannerella forsythia and Fusobacterium nucleatum. This report will review the diagnostic difficulties associated with anaerobic causes of empyema in general and the specific organisms implicated in this case.
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Affiliation(s)
- Courtney E Stewart
- Department of Internal Medicine, Grand Strand Medical Center, Myrtle Beach, USA
| | - Allison McCafferty
- Internal Medicine, Edward Via College of Osteopathic Medicine-Carolinas Campus, Spartanburg, USA
| | - Robert Sherertz
- Department of Internal Medicine, Grand Strand Medical Center, Myrtle Beach, USA
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Dichtl K, Klugherz I, Greimel H, Luxner J, Köberl J, Friedl S, Steinmetz I, Leitner E. A head-to-head comparison of three MALDI-TOF mass spectrometry systems with 16S rRNA gene sequencing. J Clin Microbiol 2023; 61:e0191322. [PMID: 37732759 PMCID: PMC10595064 DOI: 10.1128/jcm.01913-22] [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: 01/08/2023] [Accepted: 07/17/2023] [Indexed: 09/22/2023] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized diagnostics in culture-based microbiology. Commonly used MALDI-TOF MS systems in clinical microbiology laboratories are MALDI Biotyper (Bruker Daltonics) and Vitek MS (bioMérieux), but recently the new EXS2600 (Zybio) has been launched. This study aimed to evaluate the performance of the three devices by comparing the results to 16S rRNA gene sequencing. A set of 356 previously collected difficult-to-identify bacteria was tested in parallel with the three systems. Only the direct smear method and simple formic acid extraction were applied. Valid results were achieved for 98.6%, 94.4%, and 93.3% of all isolates by MALDI Biotyper, EXS2600, and Vitek MS, respectively. Of all valid results, agreement with sequencing data was achieved in 98.9%, 98.5%, and 99.7% by MALDI Biotyper, EXS2600, and Vitek MS, respectively. Considering only the isolates with valid measurements at the single-species level, misidentification rates were 0%, 2.6%, and 1.1% for MALDI Biotyper, EXS2600, and Vitek MS, respectively. Apart from minor performance differences, our data demonstrate that the three systems provide comparable results and are suitable for use in medical diagnostic laboratories.
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Affiliation(s)
- Karl Dichtl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
| | - Isabel Klugherz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
| | - Hanna Greimel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
| | - Josefa Luxner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
| | - Julian Köberl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
| | - Simone Friedl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
| | - Ivo Steinmetz
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz , Graz, Austria
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11
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Ishikawa K, Hasegawa R, Shibutani K, Mikami Y, Kawai F, Matsuo T, Uehara Y, Mori N. Probiotic-related Clostridium butyricum bacteremia: a case report and literature review. Anaerobe 2023; 83:102770. [PMID: 37544356 DOI: 10.1016/j.anaerobe.2023.102770] [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: 06/12/2022] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/08/2023]
Abstract
We report three cases of Clostridium butyricum bacteremia associated with taking C. butyricum-related probiotics. We performed a literature review and found 11 cases of C. butyricum bacteremia including our cases. Nine cases related to probiotics. We should consider that probiotics may infect clinically unstable patients.
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Affiliation(s)
- Kazuhiro Ishikawa
- Department of Infectious Diseases, St. Luke's International Hospital, Tokyo, Japan.
| | - Ryo Hasegawa
- Department of General Internal Medicine and Clinical Laboratory Medicine, Akita University Graduate School of Medicine, Akita, Japan
| | - Koko Shibutani
- Department of Infectious Diseases, St. Luke's International Hospital, Tokyo, Japan
| | - Yumiko Mikami
- Department of Clinical Laboratory, St. Luke's International Hospital, Tokyo, Japan
| | - Fujimi Kawai
- Library, Center for Academic Resources, St. Luke's International University, Japan
| | - Takahiro Matsuo
- Department of Infectious Diseases, St. Luke's International Hospital, Tokyo, Japan; Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuki Uehara
- Department of Infectious Diseases, St. Luke's International Hospital, Tokyo, Japan; Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | - Nobuyoshi Mori
- Department of Infectious Diseases, St. Luke's International Hospital, Tokyo, Japan
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12
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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Koizumi J, Nakase K, Hayashi N, Nasu Y, Hirai Y, Nakaminami H. Prevalence of antimicrobial-resistant Cutibacterium isolates and development of multiplex PCR method for Cutibacterium species identification. J Infect Chemother 2023; 29:198-204. [PMID: 36336238 DOI: 10.1016/j.jiac.2022.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/22/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022]
Abstract
INTRODUCTION Cutibacterium species such as C. acnes, C. avidum, and C. granulosum are known anaerobic skin inhabitants and often cause surgical site infections. These species are genetically similar and are difficult to identify rapidly. In addition, their pathogenicity and antimicrobial resistance remain unknown. In this study, antimicrobial resistance in Cutibacterium isolates was studied and a multiplex PCR method for their identification was developed. METHODS A total of 497 C. acnes, 71 C. avidum, and 25 C. granulosum strains which were isolated from the acne pustule and infectious regions, were used. RESULTS The antimicrobial resistance rates of C. acnes, C. avidum, and C. granulosum strains isolated from patients with acne vulgaris were higher than those of strains isolated from patients with infectious diseases. In particular, macrolide-clindamycin-resistant strains were isolated most frequently from all species. Among the resistant strains, strains with 23S rRNA mutations were the most common in C. acnes (24.3%, 71/292), whereas C. avidum and C. granulosum strains were most frequently found with erm(X). For the first time, a C. granulosum strain carrying pTZC1, which codes erm(50) and tet(W), was isolated from patients with acne vulgaris. Regarding the rapid identification of causative pathogens from infectious regions, three Cutibacterium species were identified with 100% sensitivity and specificity using multiplex PCR method. CONCLUSIONS Our data showed that antimicrobial resistance differed among Cutibacterium species. The multiplex PCR method may contribute to the rapid detection of Cutibacterium species and selection of appropriate antimicrobial agents.
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Affiliation(s)
- Juri Koizumi
- Department of Clinical Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
| | - Keisuke Nakase
- Department of Clinical Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan.
| | - Nobukazu Hayashi
- Department of Dermatology, Toranomon Hospital, 2-2-2 toranomon, minato-ku, Tokyo, 105-8470, Japan
| | - Yutaka Nasu
- Department of Infectious Diseases, Tokyo Medical University Hachioji Medical Center, 1163 Tatemachi, Hachioji, Tokyo, 193-0944, Japan
| | - Yuji Hirai
- Department of Infectious Diseases, Tokyo Medical University Hachioji Medical Center, 1163 Tatemachi, Hachioji, Tokyo, 193-0944, Japan
| | - Hidemasa Nakaminami
- Department of Clinical Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392, Japan
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14
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Asare PT, Lee CH, Hürlimann V, Teo Y, Cuénod A, Akduman N, Gekeler C, Afrizal A, Corthesy M, Kohout C, Thomas V, de Wouters T, Greub G, Clavel T, Pamer EG, Egli A, Maier L, Vonaesch P. A MALDI-TOF MS library for rapid identification of human commensal gut bacteria from the class Clostridia. Front Microbiol 2023; 14:1104707. [PMID: 36896425 PMCID: PMC9990839 DOI: 10.3389/fmicb.2023.1104707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction Microbial isolates from culture can be identified using 16S or whole-genome sequencing which generates substantial costs and requires time and expertise. Protein fingerprinting via Matrix-assisted Laser Desorption Ionization-time of flight mass spectrometry (MALDI-TOF MS) is widely used for rapid bacterial identification in routine diagnostics but shows a poor performance and resolution on commensal bacteria due to currently limited database entries. The aim of this study was to develop a MALDI-TOF MS plugin database (CLOSTRI-TOF) allowing for rapid identification of non-pathogenic human commensal gastrointestinal bacteria. Methods We constructed a database containing mass spectral profiles (MSP) from 142 bacterial strains representing 47 species and 21 genera within the class Clostridia. Each strain-specific MSP was constructed using >20 raw spectra measured on a microflex Biotyper system (Bruker-Daltonics) from two independent cultures. Results For validation, we used 58 sequence-confirmed strains and the CLOSTRI-TOF database successfully identified 98 and 93% of the strains, respectively, in two independent laboratories. Next, we applied the database to 326 isolates from stool of healthy Swiss volunteers and identified 264 (82%) of all isolates (compared to 170 (52.1%) with the Bruker-Daltonics library alone), thus classifying 60% of the formerly unknown isolates. Discussion We describe a new open-source MSP database for fast and accurate identification of the Clostridia class from the human gut microbiota. CLOSTRI-TOF expands the number of species which can be rapidly identified by MALDI-TOF MS.
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Affiliation(s)
- Paul Tetteh Asare
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Chi-Hsien Lee
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Vera Hürlimann
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Youzheng Teo
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Nermin Akduman
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Cordula Gekeler
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Afrizal Afrizal
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Myriam Corthesy
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Claire Kohout
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | | | | | - Gilbert Greub
- Institute of Microbiology of the University of Lausanne, University Hospital Centre (CHUV), Lausanne, Switzerland
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Eric G Pamer
- Duchossois Family Institute, Division of Infectious Diseases and Global Health, University of Chicago, Chicago, IL, United States
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,Clinical Bacteriology and Mycology, University Hospital of Basel, Basel, Switzerland
| | - Lisa Maier
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University of Tübingen, Tübingen, Germany.,Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.,Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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Vecilla DF, Matheus MPR, Hidalgo GI, de Tuesta Del Arco JLD. Osteomyelitis caused by Pasteurella multocida and Bacteroides pyogenes after cat bite. Eur J Clin Microbiol Infect Dis 2023; 42:125-128. [PMID: 36348263 DOI: 10.1007/s10096-022-04520-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Domingo Fernández Vecilla
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao (Biscay), Spain.
- Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Barakaldo (Biscay), Spain.
| | - Mary Paz Roche Matheus
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao (Biscay), Spain
- Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Barakaldo (Biscay), Spain
| | - Gotzon Iglesias Hidalgo
- Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Barakaldo (Biscay), Spain
- Radiodiagnosis Service of Cruces University Hospital, Barakaldo, Spain
| | - José Luis Díaz de Tuesta Del Arco
- Clinical Microbiology Service, Basurto University Hospital, 18 Avenida Montevideo, 48013, Bilbao (Biscay), Spain
- Biocruces Bizkaia Health Research Institute, Cruces Plaza, 48903, Barakaldo (Biscay), Spain
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Vecilla DF, López IA, Yanes MLG, Toboso MCN, del Arco JLDDT. Is Propionimicrobium lymphophilum a new urinary tract infection cause? REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2023; 36:107-109. [PMID: 36458724 PMCID: PMC9910668 DOI: 10.37201/req/086.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Domingo Fernández Vecilla
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Correspondence: Domingo Fernández Vecilla, Clinical Microbiology and Parasitology. Hospital Universitario de Basurto. Avenida Montevideo nº18, Gurtubay pavilion, 3rd floor. Postal code: 48013, Bilbao (Basque country). Spain. E-mail:
| | - Itziar Angulo López
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
| | - María Luisa Gurruchaga Yanes
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
| | - María Carmen Nieto Toboso
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
| | - José Luis Díaz de Tuesta del Arco
- Clinical Microbiology and Parasitology Service. Basurto University Hospital. Bilbao (Vizcaya). Spain,Pathological Anatomy Service. Basurto University Hospital. Bilbao (Vizcaya). Spain
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Hleba L, Hlebova M, Kovacik A, Petrova J, Maskova Z, Cubon J, Massanyi P. Use of MALDI-TOF MS to Discriminate between Aflatoxin B1-Producing and Non-Producing Strains of Aspergillus flavus. Molecules 2022; 27:molecules27227861. [PMID: 36431961 PMCID: PMC9692738 DOI: 10.3390/molecules27227861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins. One of the producers of AFB1 is Aspergillus flavus. Therefore, its rapid identification plays a key role in various sectors of the food and feed industry. MALDI-TOF mass spectrometry is one of the fastest and most accurate methods today. Therefore, the aim of this research was to develop the rapid identification of producing and non-producing strains of A. flavus based on the entire mass spectrum. To accomplish the main goal a different confirmatory MALDI-TOF MS and TLC procedures such as direct AFB1 identification by scraping from TLC plates, A. flavus mycelium, nutrient media around A. flavus growth, and finally direct AFB1 identification from infected wheat and barley grains had to be conducted. In this experiment, MALDI-TOF mass spectrometry with various modifications was the main supporting technology. All confirmatory methods confirmed the presence of AFB1 in the samples of aflatoxin-producing strains of A. flavus and vice versa; AFB1 was not detected in the case of non-producing strains. Entire mass spectra (from 2 to 20 kDa) of aflatoxin-producing and non-producing A. flavus strains were collected, statistically analyzed and clustered. An in-depth analysis of the obtained entire mass spectra showed differences between AFB1-producing and non-producing strains of A. flavus. Statistical and cluster analysis divided AFB1-producing and non-producing strains of A. flavus into two monasteries. The results indicate that it is possible to distinguish between AFB1 producers and non-producers by comparing the entire mass spectra using MALDI-TOF MS. Finally, we demonstrated that if there are established local AFB1-producing and non-producing strains of A. flavus, the entire mass spectrum database identification of aflatoxigenic A. flavus strains can be even faster and cheaper, without the need to identify the toxin itself.
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Affiliation(s)
- Lukas Hleba
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
- Correspondence:
| | - Miroslava Hlebova
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 917 01 Trnava, Slovakia
| | - Anton Kovacik
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Jana Petrova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Zuzana Maskova
- Faculty of Biotechnology and Food Sciences, Institute of Biotechnology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Juraj Cubon
- Faculty of Biotechnology and Food Sciences, Institute of Food Sciences, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
| | - Peter Massanyi
- Faculty of Biotechnology and Food Sciences, Institute of Applied Biology, Slovak University of Agriculture in Nitra, Tr. Andreja Hlinku 2, 949 76 Nitra, Slovakia
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Larragoity González EA, Pérez Cavazos S, Tobías Ávila GDC, Rodríguez Saldívar MM, Vaquera Aparicio DN, Castillo Bejarano JI, Mascareñas de los Santos A. Capnocytophaga sputigena Bacteremia in an Immunocompromised Child, When to Suspect? A Case Report and Review of the Literature. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2022. [DOI: 10.1097/ipc.0000000000001163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Shinzato T, Yonaha T, Oshiro Y, Ishiki H. Clostridium ramosum bacteremia: A case series at a general acute care hospital. J Infect Chemother 2022; 29:78-81. [PMID: 36154869 DOI: 10.1016/j.jiac.2022.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022]
Abstract
Clostridium ramosum infections have been rarely reported, probably due to underestimating in clinical practice. Seven patients with bacteremia from gastrointestinal sources and skin and soft tissue were recognized between 2009 and 2020. Most of them were older and in compromised status, and they had risk factors including cancer, diabetes, liver cirrhosis, gangrene, and pressure ulcers. The source of infections was considered bacterial translocation from the gastrointestine and the skin and soft tissue infections. All patients were treated with antimicrobials, and two received surgical interventions. Four patients died secondary to sepsis due to C. ramosum. The bacteremia of C. ramosum should be appropriately evaluated and treated, especially in compromised hosts.
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Affiliation(s)
- Takashi Shinzato
- Department of General Internal Medicine, Nakagami Hospital. 610 Noborikawa, Okinawa-shi, Okinawa, 904-2195, Japan; Department of Infectious Diseases, Nakagami Hospital. 610 Noborikawa, Okinawa-shi, Okinawa, 904-2195, Japan.
| | - Tadahiro Yonaha
- Department of General Internal Medicine, Nakagami Hospital. 610 Noborikawa, Okinawa-shi, Okinawa, 904-2195, Japan
| | - Yusuke Oshiro
- Department of Infectious Diseases, Nakagami Hospital. 610 Noborikawa, Okinawa-shi, Okinawa, 904-2195, Japan
| | - Haruka Ishiki
- Department of Infectious Diseases, Nakagami Hospital. 610 Noborikawa, Okinawa-shi, Okinawa, 904-2195, Japan
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20
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Evaluation of salivary parameters and Streptococcus' Mutans count in children with cerebral palsy in Egypt: a case control study. BMC Oral Health 2022; 22:411. [PMID: 36123671 PMCID: PMC9487054 DOI: 10.1186/s12903-022-02447-0] [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: 03/14/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Children with cerebral palsy (CP) are at high risk for dental caries. Alteration of some salivary properties encountered among them compared to healthy children, could play a role in this elevated risk. OBJECTIVES The aim of the present study was to assess salivary physicochemical properties; including total antioxidant (TAC), flow rate, viscosity, pH and buffering capacity, as well as Streptococcus mutans level among children with CP, also to correlate these variables to their caries experience. MATERIALS AND METHODS This case control study included 80 children with CP, study group (SG) and matched number of healthy children for control group (CG). Interview-based questionnaire, clinical examination, salivary biochemical and microbiological investigations using MALDI-TOF were done. RESULTS In SG, the caries experience in primary teeth dmft and S. mutans log value were significantly higher than CG (P = 0.039, P = 0.002) while unstimulated salivary flow rate, buffering capacity and salivary TAC were significantly lower (P < 0.0001). Multivariate linear regression showed that the presence of CP was significantly associated with the greatest variation in caries experience in the primary teeth and permanent teeth. Higher unstimulated salivary flow rate, or an increase in buffering capacity by 1 ml of acid/ml of saliva were associated with lower number of the affected primary and permanent teeth. On the other hand, One-unit increase in S. mutans log count and higher salivary TAC were associated with higher caries experience. CONCLUSION Children with CP have higher caries experience (dmf) due to lower salivary protective factors and higher S. mutans counts.
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Church DL, Griener T, Gregson D. Multi-year comparison of VITEK® MS and 16S rRNA gene sequencing performance for the identification of rarely encountered anaerobes causing invasive human infections in a large Canadian region: can our laboratory abandon 16S rRNA gene sequencing? Anaerobe 2022; 78:102640. [PMID: 36126828 DOI: 10.1016/j.anaerobe.2022.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/13/2022] [Accepted: 09/07/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10-13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum). METHODS VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates. RESULTS 489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups. CONCLUSIONS MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.
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Affiliation(s)
- D L Church
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada.
| | - T Griener
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
| | - D Gregson
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
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22
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Prevotella oris: A lesser KNOWN etiological agent of pleural effusion. Anaerobe 2022; 78:102644. [PMID: 36116686 DOI: 10.1016/j.anaerobe.2022.102644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/07/2022] [Accepted: 09/11/2022] [Indexed: 11/20/2022]
Abstract
Prevotella are gram negative, obligate anaerobes and includes pigmented and non-pigmented species. They are typically regarded as commensals, especially of the gastrointestinal tract and oral cavity, although opportunistic endogenous infections are known to be caused by a small number of strains. We report a case of a 51-year-old man with right-sided chest pain. Chest X-ray showed mild haziness in the right lung and he was diagnosed with right sided pleural effusion. Prevotella oris was isolated after pleural pus culture.
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Legaria M, Barberis C, Famiglietti A, De Gregorio S, Stecher D, Rodriguez C, Vay C. Urinary tract infection caused by anaerobic bacteria. Utility of anaerobic urine culture. Anaerobe 2022; 78:102636. [DOI: 10.1016/j.anaerobe.2022.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/01/2022]
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Hilt EE, Ferrieri P. Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases. Genes (Basel) 2022; 13:genes13091566. [PMID: 36140733 PMCID: PMC9498426 DOI: 10.3390/genes13091566] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.
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25
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Wang H, Yang JL, Chen C, Zheng Y, Chen M, Qi J, Tang S, Zhan XY. Identification of Peptoniphilus vaginalis-Like Bacteria, Peptoniphilus septimus sp. nov., From Blood Cultures in a Cervical Cancer Patient Receiving Chemotherapy: Case and Implications. Front Cell Infect Microbiol 2022; 12:954355. [PMID: 35880078 PMCID: PMC9307962 DOI: 10.3389/fcimb.2022.954355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
A 39-year-old woman with a 3-year human papillomavirus (HPV) 18 infection history was admitted to the hospital for a 16-day history of vaginal bleeding after sex. She was diagnosed with cervical cancer based on the results of the electronic colposcopy, cervical cytology, microscopy, and magnetic resonance imaging (MRI). Then, she received chemotherapy, with paclitaxel 200 mg (day 1), cisplatin 75 mg (day 2), and bevacizumab 700 mg (day 3) twice with an interval of 27 days. During the examination for the diagnosis and treatment, many invasive operations, including removal of intrauterine device, colposcopy, and ureteral dilatation, were done. After that, the patient was discharged and entered the emergency department about 2.5 months later with a loss of consciousness probably caused by septic shock. The patient finally died of multiple organ failure and bacterial infection, although she has received antimicrobial therapy. The blood cultures showed a monobacterial infection with an anaerobic Gram-positive bacterial strain, designated as SAHP1. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI–TOF MS) indicated that the patient was infected with Peptoniphilus asaccharolyticus, while molecular analysis and genome-based taxonomy confirmed the infection with a novel Peptoniphilus species that has a close genetic relationship with Peptoniphilus vaginalis and proposed provisionally as Peptoniphilus septimus sp. nov., which may also act as a commensal of the human vagina. Genomic features of SAHP1 have been fully described, and comparative genomic analysis reveals the known prokaryote relative of Peptoniphilus septimus sp. nov. in the genus Peptoniphilus. The invasive operations on the genital tract during the diagnosis and treatment of the patient and the tumor tissue damage and bleeding may have a certain role in the bloodstream infection. This study casts a new light on the Peptoniphilus bacteria and prompts clinicians to include anaerobic blood cultures as part of their blood culture procedures, especially on patients with genital tract tumors. Furthermore, due to the incomplete database and unsatisfying resolution of the MALDI–TOF MS for Peptoniphilus species identification, molecular identification, especially whole-genome sequencing, is required for those initially identified as bacteria belonging to Peptoniphilus in the clinical laboratory.
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Affiliation(s)
- Huacheng Wang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jin-Lei Yang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Chunmei Chen
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Ying Zheng
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- School of Clinical Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Mingming Chen
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Junhua Qi
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shihuan Tang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiao-Yong Zhan
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Xiao-Yong Zhan,
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Time for Some Group Therapy: Update on Identification, Antimicrobial Resistance, Taxonomy, and Clinical Significance of the Bacteroides fragilis Group. J Clin Microbiol 2022; 60:e0236120. [PMID: 35700139 DOI: 10.1128/jcm.02361-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteroides fragilis group (BFG) species are common members of the human microbiota that provide several benefits to healthy hosts, yet BFG are also the most common anaerobes isolated from human infections, including intra-abdominal infections, abscesses, and bloodstream infection. Compared to many other anaerobes associated with disease, members of the BFG are more likely to be resistant to commonly used antimicrobials, including penicillin (>90% resistant), carbapenems (2 to 20% resistant), and metronidazole (0.2 to 4% resistant). As a result, infection with BFG bacteria can be associated with poor clinical outcomes. Here, we discuss the role of BFG in human health and disease, proposed taxonomic reclassifications within the BFG, and updates in methods for species-level identification. The increasing availability of whole-genome sequencing (WGS) supports recent proposals that the BFG now span two families (Bacteroidaceae and "Tannerellaceae") and multiple genera (Bacteroides, Parabacteroides, and Phocaeicola) within the phylum Bacteroidota. While members of the BFG are often reported to "group" rather than "species" level in many clinical settings, new reports of species-specific trends in antimicrobial resistance profiles and improved resolution of identification tools support routine species-level reporting in clinical practice. Empirical therapy may not be adequate for treatment of serious infections with BFG, warranting susceptibility testing for serious infections. We summarize methods for antimicrobial susceptibility testing and resistance prediction for BFG, including broth microdilution, agar dilution, WGS, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). We examine global trends in BFG antimicrobial resistance and review genomics of BFG, revealing insights into rapid activation and dissemination of numerous antimicrobial resistance mechanisms.
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Li Y, Li W, Luo R, Sakandar HA, Zhang H, Liu W. Lentilactobacillus rapi subsp. dabitei subsp. nov., a lactic acid bacterium isolated from naturally fermented dairy product. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005359] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two lactic acid bacterial strains (IMAU80584T and IMAU92037) were isolated from naturally fermented dairy products (kurut and yoghurt) in China and Russia. Based on sequence analysis of the 16S rRNA gene it was revealed that these strains belonged to
Lentilactobacillus rapi
. However, phylogenetic tree analyses of two housekeeping genes, rpoA (encoding RNA polymerase alpha subunit) and pheS (encoding phenylalanyl-tRNA synthase alpha subunit), and 88 core genes, indicated the two strains were separated into an independent monophyletic branch from
L. rapi
DSM 19907T, forming an infra-specific subgroup. The average nucleotide identity and digital DNA–DNA hybridization values between IMAU80584T and
L. rapi
DSM 19907T were 93.1 and 52.8 %, respectively. Strains IMAU80584T and IMAU92037 are distinguished from
L. rapi
DSM 19907T because they have different polar lipids and fatty acids. The novel subgroup strains could not ferment gluconate potassium. The DNA G+C content of strain IMAU80584T was 42.3 mol%. The major cellular fatty acids were C16 : 0, C18 : 1
ω9t and summed feature 5 (C18 : 0 ante and/or C18 : 2
ω6c and/or C18 : 2
ω9c). Therefore, based on the results of polyphasic taxonomic analysis, IMAU80584T and IMAU92037 could be considered as a novel subspecies in the species
L. rapi
with the proposed name
Lentilactobacillus rapi
subsp. dabitei subsp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).
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Affiliation(s)
- Yu Li
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Weicheng Li
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Rui Luo
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Hafiz Arbab Sakandar
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Heping Zhang
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
| | - Wenjun Liu
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Key Laboratory of Dairy Biotechnology and Engineering (IMAU), Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Collaborative Innovative Center of Ministry of Education for Lactic Acid Bacteria and Fermented Dairy Products, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, PR China
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Pascale MR, Bisognin F, Mazzotta M, Girolamini L, Marino F, Dal Monte P, Cordovana M, Scaturro M, Ricci ML, Cristino S. Use of Fourier-Transform Infrared Spectroscopy With IR Biotyper® System for Legionella pneumophila Serogroups Identification. Front Microbiol 2022; 13:866426. [PMID: 35558114 PMCID: PMC9090449 DOI: 10.3389/fmicb.2022.866426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/11/2022] [Indexed: 01/09/2023] Open
Abstract
Legionella spp. are Gram-negative bacteria that inhabit freshwater environments representing a serious risk for human health. Legionella pneumophila (Lp) is the species most frequently responsible for a severe pneumonia known as Legionnaires' disease. Lp consists of 15 serogroups (Sgs), usually identified by monoclonal or polyclonal antibodies. With regard to Lp serogrouping, it is well known that phenotyping methods do not have a sufficiently high discriminating power, while genotypic methods although very effective, are expensive and laborious. Recently, mass spectrometry and infrared spectroscopy have proved to be rapid and successful approaches for the microbial identification and typing. Different biomolecules (e.g., lipopolysaccharides) adsorb infrared radiation originating from a specific microbial fingerprint. The development of a classification system based on the intra-species identification features allows a rapid and reliable typing of strains for diagnostic and epidemiological purposes. The aim of the study was the evaluation of Fourier Transform Infrared Spectroscopy using the IR Biotyper® system (Bruker Daltonik, Germany) for the identification of Lp at the serogroup (Sg) level for diagnostic purposes as well as in outbreak events. A large dataset of Lp isolates (n = 133) and ATCC reference strains representing the 15 Lp serogroups were included. The discriminatory power of the instrument's classifier, was tested by Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). All isolates were classified as follows: 12/133 (9.0%) as Lp Sg1 and 115/133 (86.5%) as Lp Sg 2-15 (including both ATCC and environmental Lp serogroup). Moreover, a mis-classification for 2/133 (1.5%) isolates of Lp Sg 2-15 that returned as Lp Sg1 was observed, and 4/133 (3.0%) isolates were not classified. An accuracy of 95.49% and an error rate of 4.51% were calculated. IR Biotyper® is able provide a quick and cost-effective reliable Lp classification with advantages compared with agglutination tests that show ambiguous and unspecific results. Further studies including a larger number of isolates could be useful to implement the classifier obtaining a robust and reliable tool for the routine Lp serogrouping. IR Biotyper® could be a powerful and easy-to-use tool to identify Lp Sgs, especially during cluster/outbreak investigations, to trace the source of the infection and promptly adopt preventive and control strategies.
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Affiliation(s)
- Maria Rosaria Pascale
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Francesco Bisognin
- Microbiology Unit, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, IRCCS S. Orsola-Malpighi University Hospital, Bologna, Italy
| | - Marta Mazzotta
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Luna Girolamini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Federica Marino
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Paola Dal Monte
- Microbiology Unit, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, IRCCS S. Orsola-Malpighi University Hospital, Bologna, Italy
| | | | - Maria Scaturro
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Luisa Ricci
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Sandra Cristino
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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Gregory CW, Zersen KM, Schlemmer SN, Daniels JB. Retroperitoneal abscess and splenitis with
Clostridium
spp. in a dog. Vet Clin Pathol 2022; 51:560-564. [DOI: 10.1111/vcp.13112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Carly W. Gregory
- Department of Clinical Sciences Colorado State University Fort Collins Colorado USA
| | - Kristin M. Zersen
- Department of Clinical Sciences Colorado State University Fort Collins Colorado USA
| | - Samantha N. Schlemmer
- Department of Clinical Sciences Colorado State University Fort Collins Colorado USA
- University of Georgia, Department of Pathology Athens Georgia USA
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30
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Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022; 27:molecules27082411. [PMID: 35458608 PMCID: PMC9031286 DOI: 10.3390/molecules27082411] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
Mass Spectrometry (MS) allows the analysis of proteins and peptides through a variety of methods, such as Electrospray Ionization-Mass Spectrometry (ESI-MS) or Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry (MALDI-MS). These methods allow identification of the mass of a protein or a peptide as intact molecules or the identification of a protein through peptide-mass fingerprinting generated upon enzymatic digestion. Tandem mass spectrometry (MS/MS) allows the fragmentation of proteins and peptides to determine the amino acid sequence of proteins (top-down and middle-down proteomics) and peptides (bottom-up proteomics). Furthermore, tandem mass spectrometry also allows the identification of post-translational modifications (PTMs) of proteins and peptides. Here, we discuss the application of MS/MS in biomedical research, indicating specific examples for the identification of proteins or peptides and their PTMs as relevant biomarkers for diagnostic and therapy.
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31
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Kim E, Yang SM, Kim HJ, Kim HY. Differentiating between Enterococcusfaecium and Enterococcuslactis by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry. Foods 2022; 11:foods11071046. [PMID: 35407133 PMCID: PMC8997568 DOI: 10.3390/foods11071046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 03/30/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
Unlike Enterococcus faecium strains, some Enterococcus lactis strains are considered potential probiotic strains as they lack particular virulence and antibiotic resistance genes. However, these closely related species are difficult to distinguish via conventional taxonomic methods. Here, for the first time, we used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with BioTyper and in-house databases to distinguish between E. faecium and E. lactis. A total of 58 reference and isolated strains (89.2%) were correctly identified at the species level using MALDI-TOF MS with in-house databases. However, seven strains (10.8%) were not accurately differentiated as a single colony was identified as a different species with a similar score value. Specific mass peaks were identified by analyzing reference strains, and mass peaks at 10,122 ± 2 m/z, 3650 ± 1 m/z, and 7306 ± 1 m/z were unique to E. faecium and E. lactis reference strains, respectively. Mass peaks verified reproducibility in 60 isolates and showed 100% specificity, whereas 16S rRNA sequencing identified two different candidates for some isolates (E. faecium and E. lactis). Our specific mass peak method helped to differentiate two species, with high accuracy and high throughput, and provided a viable alternative to 16S rRNA sequencing.
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Affiliation(s)
| | | | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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32
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Bächli P, Baars S, Simmler A, Zbinden R, Schulthess B. Impact of MALDI-TOF MS identification on anaerobic species and genus diversity in routine diagnostics. Anaerobe 2022; 75:102554. [DOI: 10.1016/j.anaerobe.2022.102554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/08/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022]
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33
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MALDI-Based Mass Spectrometry in Clinical Testing: Focus on Bacterial Identification. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062814] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The term “proteome” refers to the total of all proteins expressed in an organism. The term “proteomics” refers to the field of research that includes not only information on the expression levels of individual proteins, but also their higher-order structures, intermolecular interactions, and post-translational modifications. The core technology, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), is available for protein analysis thanks to the work of Koichi Tanaka and John Fenn, who were awarded the Nobel Prize in Chemistry in 2002. The most successful proteome analysis in clinical practice is rapid microbial identification. This method determines the bacterial species by comparing the proteome profile of the bacteria obtained by matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF MS) with a database. MS is superior in simplicity, speed, and accuracy to classic speciation by staining and phenotyping. In clinical microbiology, MS has had a large impact on the diagnosis and treatment of infectious disease. Early diagnosis and treatment of infectious disease are important, and rapid identification by MALDI-TOF MS has made a major contribution to this field.
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34
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Lu Y, Zeng L, Li M, Yan B, Gao D, Zhou B, Lu W, He Q. Use of GC-IMS for detection of volatile organic compounds to identify mixed bacterial culture medium. AMB Express 2022; 12:31. [PMID: 35244795 PMCID: PMC8897540 DOI: 10.1186/s13568-022-01367-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
In order to explore the possibility to identify common wound infection bacteria in mixed culture with gas chromatograph-ion migration spectroscopy (GC-IMS), the headspace gas of single and mixed cultures of Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa were detected and analyzed by GC-IMS system. The bacteria were cultured in thioglycolate medium tubes then transferred to the sampling bottles (indirect method), or directly cultured in the sampling bottles (direct method) to allow accumulation of volatile compounds and facilitate automation. The specific microorganism volatile organic compounds (mVOCs) of the three bacteria were obtained. Some of them have been known to certain substance, for example, ethanol, isoamyl acetate, Phenylacetaldehyde, 2-heptanone etc., while others have not. Principal component analysis (PCA) showed that a higher separability can be achieved with direct method than indirect method. This work indicated that it is possible to identify compound bacteria by detecting specific mVOCs with GC-IMS, and the specific mVOCs should be medium-dependent.
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35
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Cobo F, Pérez-Carrasco V, Rodríguez-Guerrero E, Sampedro A, Rodríguez-Granger J, García-Salcedo JA, Navarro-Marí JM. Misidentification of Phocaeicola (Bacteroides) dorei in two patients with bacteremia. Anaerobe 2022; 75:102544. [PMID: 35247588 DOI: 10.1016/j.anaerobe.2022.102544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/09/2022] [Accepted: 02/28/2022] [Indexed: 11/17/2022]
Abstract
Phocaeicola (Bacteroides) dorei is a Gram-negative anaerobic bacillus that is rarely isolated from human specimens. Its accurate identification can be hampered by its close taxonomic relationship with Bacteroides vulgatus. We report on two patients with bacteremia due to P. (B.) dorei, which was initially identified as B. vulgatus by MALDI-TOF MS.
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Affiliation(s)
- Fernando Cobo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves. Granada, Spain.
| | - Virginia Pérez-Carrasco
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves. Granada, Spain; GENYO, Pfizer-University of Granada- Junta de Andalucía for Genomics and Oncological Research, Spain
| | - Enrique Rodríguez-Guerrero
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves. Granada, Spain
| | - Antonio Sampedro
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves. Granada, Spain
| | - Javier Rodríguez-Granger
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves. Granada, Spain
| | - José A García-Salcedo
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves. Granada, Spain; GENYO, Pfizer-University of Granada- Junta de Andalucía for Genomics and Oncological Research, Spain
| | - José María Navarro-Marí
- Department of Microbiology and Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospital Virgen de las Nieves. Granada, Spain
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Chen YC, Kuo YC, Chen MC, Zhang YD, Chen CL, Le PH, Chiu CH. Case–Control Study of Clostridium innocuum Infection, Taiwan. Emerg Infect Dis 2022. [DOI: 10.3201/2803.204421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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37
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Chen YC, Kuo YC, Chen MC, Zhang YD, Chen CL, Le PH, Chiu CH. Case-Control Study of Clostridium innocuum Infection, Taiwan. Emerg Infect Dis 2022; 28:599-607. [PMID: 35195517 PMCID: PMC8888209 DOI: 10.3201/eid2803.204421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Vancomycin-resistant Clostridium innocuum was recently identified as an etiologic agent for antibiotic-associated diarrhea in humans. We conducted a case–control study involving 152 C. innocuum-infected patients during 2014–2019 in Taiwan, using 304 cases of Clostridioides difficile infection (CDI) matched by diagnosis year, age (+2 years), and sex as controls. The baseline characteristics were similar between the 2 groups. C. innocuum–infected patients experienced more extraintestinal clostridial infection and gastrointestinal tract–related complications than did patients with CDI. The 30-day mortality rate among C. innocuum–infected patients was 14.5%, and the overall rate was 23.0%. Chronic kidney disease, solid tumor, intensive care unit admission, and shock status were 4 independent risk factors for death. C. innocuum identified from clinical specimens should be recognized as a pathogen requiring treatment, and because of its intrinsic vancomycin resistance, precise identification is necessary to guide appropriate and timely antimicrobial therapy.
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38
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Ko YJ, Lee OJ, Lee SB, Kim CM, Lee J, Kook JK, Park SN, Shin JH, Kim SH, Won EJ, Park G, Kang SH, Jang SJ. Accuracy of ASTA MicroIDSys, a New Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System, for the Identification of Korean Reference and Clinical Bacterial and Yeast Strains. Diagn Microbiol Infect Dis 2022; 103:115658. [DOI: 10.1016/j.diagmicrobio.2022.115658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 11/03/2022]
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Wan X, Wang S, Wang M, Liu J, Zhang Y. Identification of Peptoniphilus harei From Blood Cultures in an Infected Aortic Aneurysm Patient: Case Report and Review Published Literature. Front Cell Infect Microbiol 2022; 11:755225. [PMID: 35004343 PMCID: PMC8730293 DOI: 10.3389/fcimb.2021.755225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Gram-positive anaerobic cocci (GPAC) are a commensal part of human flora but are also opportunistic pathogens. This is possibly the first study to report a case of Peptoniphilus harei bacteremia in an abdominal aortic aneurysm (AAA) patient. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) failed to identify the isolate and molecular analysis confirmed it as P. harei. A comprehensive literature review revealed that P. harei is an emergent pathogen. This study serves as a reminder for practicing clinicians to include anaerobic blood cultures as part of their blood culture procedures; this is particularly important situations with a high level of suspicion of infection factors in some noninfectious diseases, as mentioned in this publication. Clinical microbiologists should be aware that the pathogenic potential of GPAC can be greatly underestimated leading to incorrect diagnosis on using only one method for pathogen identification. Upgradation and correction of the MALDI-TOF MS databases is recommended to provide reliable and rapid identification of GPAC at species level in medical diagnostic microbiology laboratories.
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Affiliation(s)
- Xue Wan
- Laboratory Department of Clinical Laboratory, The Second Hospital of Jilin University, Changchun, China
| | - Shuang Wang
- Department of Dermatology, The Second Hospital of Jilin University, Changchun, China
| | - Min Wang
- Department of General Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Jinhua Liu
- Changchun Customs Technology Center, Changchun, China
| | - Yu Zhang
- Laboratory Department of Clinical Laboratory, The Second Hospital of Jilin University, Changchun, China
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Chauhan N, Porte S, Joshi V, Shah K. Plants' steroidal saponins - A review on its pharmacology properties and analytical techniques. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2022. [DOI: 10.4103/2311-8571.353503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Carbapenemase Producing Klebsiella pneumoniae (KPC): What Is the Best MALDI-TOF MS Detection Method. Antibiotics (Basel) 2021; 10:antibiotics10121549. [PMID: 34943761 PMCID: PMC8698427 DOI: 10.3390/antibiotics10121549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/21/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria is a group of highly dangerous antibiotic resistant Gram-negative Enterobacteriaceae. They cause infections associated with significant morbidity and mortality. Therefore, the rapid detection of KPC-producing bacteria plays a key role in clinical microbiology. Matrix assisted laser desorption/ionization time-of- flight (MALDI-TOF) is a rapidly evolving technology that finds application in various clinical, scientific, and industrial disciplines. In the present study, we demonstrated three different procedures of carbapenemase-producing K. pneumoniae (KPC) detection. The most basic model of MALDI-TOF instrument MS Microflex LT was used, operating in the linear ion-positive mode, commonly used in modern clinical laboratories. The first procedure was based on indirect monitoring of carbapenemase production with direct detection of hydrolyzed carbapenem antibiotic degradation products in the mass spectrum. The second procedure was based on direct detection of blaKPC accompanying peak with an 11,109 Da in the mass spectrum of carbapenemase-producing K. pneumoniae (KPC), which represents the cleaved protein (pKpQIL_p019) expressed by pKpQIL plasmid. In addition, several unique peaks were detected in the carbapenemase-producing K. pneumoniae (KPC) mass spectrum. The third procedure was the identification of carbapenemase-producing K. pneumoniae (KPC) based on the protein fingerprint using local database created from the whole mass spectra. By comparing detection procedures, we determined that the third procedure was very fast and relatively easy. However, it requires previous verification of carbapenemase-producing K. pneumoniae (KPC) using other methods as genetic blaKPC identification, detection of carbapenem degradation products, and accompanying peak with 11,109 Da, which represents cleaved pKpQIL_p019 protein expressed by pKpQIL plasmid. Detection of carbapenemase-producing K. pneumoniae using MALDI-TOF provides fast and accurate results that may help to reduce morbidity and mortality in hospital setting when applied in diagnostic situations.
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Souna D, Drissi M, Almahmoud I, Maurin M. Enterobacter cloacae Complex and CTX-M Extended-Spectrum β-Lactamases in Algeria. Microb Drug Resist 2021; 28:346-354. [PMID: 34890283 DOI: 10.1089/mdr.2020.0535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We evaluated the β-lactam resistance phenotypes of clinical and environmental strains of the Enterobacter cloacae complex (ECC) isolated from three Algerian hospitals. The first combination of API 20E, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and hsp60 genetic clustering methodologies were carried out for the identification of ECC strains. Our research showed that API 20E and MALDI TOF MS are satisfactory in genus identification of ECC strains, but sequence-based methods are then necessary to discriminate the species and subspecies levels. Among 36 ECC strains, 94.44% belonged to Enterobacter hormaechei species. Twenty-five isolates clustered with the reference strain of E. hormaechei subsp. xiangfangensis, making it the most frequently isolated subspecies. Enterobacter kobei was found only once (2.77%). All ECC isolates were phenotypically extended-spectrum β-lactamase (ESBL) producers and were resistant to ticarcillin, piperacillin, cefoxitin, cefotaxime, ceftazidime, ceftriaxone, and aztreonam, but susceptible to ertapenem and imipenem. The genetic analyses only allowed the detection of resistance genes of the CTX-M-1 group (32 strains, 88.9%), including CTX-M-15 (30 strains), CTX-M-3 (1 strain), and CTX-M-22 (1 strain). We report for the first time the detection of CTX-M-22 among ECC strains in an Algerian hospital (Tlemcen hospital). None of the isolated strains harbored CTX-M-2, CTX-M-9, or CTX-M-8/25 group genes. In this review, we address recent comparison in the identification methods of multidrug-resistant E. cloacae complex in Algeria, focusing also on the CTX-M ESBLs. This represents a serious public health challenge, which requires the clarification of the current situation and warrants the reinforcement of hygiene measures in the Algerian hospitals.
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Affiliation(s)
- Djahida Souna
- Department of Biology, Faculty of Science of Nature and Life, University of Hassiba Ben Bouali Chlef, Chlef, Algeria.,Laboratory of Molecular Biology, Genomic and Bioinformatic, Team 1: Microbial Genomics and Molecular Epidemiology of Infectious Diseases, University of Hassiba Ben Bouali Chlef, Chlef, Algeria
| | - Mourad Drissi
- Department of Biology, Faculty of Science of Nature and Life and Science of Earth and Universe, University Bekr Belkaid-Tlemcen, Tlemcen, Algeria
| | - Iyad Almahmoud
- Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Max Maurin
- Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France.,Grenoble Alpes University, CNRS, TIMC-IMAG, Grenoble, France
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Gonzalez LE, Szalwinski LJ, Marsh BM, Wells JM, Cooks RG. Immediate and sensitive detection of sporulated Bacillus subtilis by microwave release and tandem mass spectrometry of dipicolinic acid. Analyst 2021; 146:7104-7108. [PMID: 34757350 DOI: 10.1039/d1an01796a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spore lysis of Bacillus species is achieved by brief (1 min) microwave irradiation while tandem mass spectrometry (MS/MS) allows identification of the characteristic spore marker, dipicolinic acid. This rapid measurement, made on 105-108 spores, has significant implications for biothreat recognition.
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Affiliation(s)
- L Edwin Gonzalez
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Lucas J Szalwinski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | - Brett M Marsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
| | | | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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Fleming E, Pabst V, Scholar Z, Xiong R, Voigt AY, Zhou W, Hoyt A, Hardy R, Peterson A, Beach R, Ondouah-Nzutchi Y, Dong J, Bateman L, Vernon SD, Oh J. Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota. BMC Microbiol 2021; 21:278. [PMID: 34649516 PMCID: PMC8515726 DOI: 10.1186/s12866-021-02314-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, level. High-resolution genomics to investigate species- and strain-level diversity and mechanistic studies, however, rely on the availability of individual microbes from a complex microbial consortia. High-throughput approaches are needed to acquire and identify the significant species- and strain-level diversity present in the oral, skin, and gut microbiome. Here, we describe and validate a streamlined workflow for cultivating dominant bacterial species and strains from the skin, oral, and gut microbiota, informed by metagenomic sequencing, mass spectrometry, and strain profiling. RESULTS Of total genera discovered by either metagenomic sequencing or culturomics, our cultivation pipeline recovered between 18.1-44.4% of total genera identified. These represented a high proportion of the community composition reconstructed with metagenomic sequencing, ranging from 66.2-95.8% of the relative abundance of the overall community. Fourier-Transform Infrared spectroscopy (FT-IR) was effective in differentiating genetically distinct strains compared with whole-genome sequencing, but was less effective as a proxy for genetic distance. CONCLUSIONS Use of a streamlined set of conditions selected for cultivation of skin, oral, and gut microbiota facilitates recovery of dominant microbes and their strain variants from a relatively large sample set. FT-IR spectroscopy allows rapid differentiation of strain variants, but these differences are limited in recapitulating genetic distance. Our data highlights the strength of our cultivation and characterization pipeline, which is in throughput, comparisons with high-resolution genomic data, and rapid identification of strain variation.
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Affiliation(s)
- Elizabeth Fleming
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Victor Pabst
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Zoe Scholar
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Ruoyun Xiong
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Anita Y Voigt
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Wei Zhou
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Amelia Hoyt
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Rachel Hardy
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | - Anna Peterson
- The University of Connecticut Health Center, Farmington, CT, USA
| | - Ryan Beach
- The University of Connecticut Health Center, Farmington, CT, USA
| | | | - Jinhong Dong
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA
| | | | | | - Julia Oh
- The Jackson Laboratory, 10 Discovery Drive, Farmington, CT, 860-837-2014, USA.
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Microbial Reduction of Fumonisin B1 by the New Isolate Serratia marcescens 329-2. Toxins (Basel) 2021; 13:toxins13090638. [PMID: 34564642 PMCID: PMC8473028 DOI: 10.3390/toxins13090638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
The mycotoxin fumonisin (FB) has become a major problem in maize products in southeastern Asia. Fumonisin can affect the health of humans and many animals. Fumonisin contamination can be reduced by detoxifying microbial enzyme. Screening of 95 potent natural sources resulted in 5.3% of samples yielding a total of five bacterial isolates that were a promising solution, reducing approximately 10.0-30.0% of fumonisin B1 (FB1). Serratia marcescens, one of the dominant degrading bacteria, was identified with Gram staining, 16S rRNA gene, and MALDI-TOF/TOF MS. Cell-free extract showed the highest fumonisin reduction rates, 30.3% in solution and 37.0% in maize. Crude proteins from bacterial cells were analyzed with a label-free quantification technique. The results showed that hydrolase enzymes and transferase enzymes that can cooperate in the fumonisin degradation process were highly expressed in comparison to their levels in a control. These studies have shown that S. marcescens 329-2 is a new potential bacterium for FB1 reduction, and the production of FB1-reducing enzymes should be further explored.
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Alves MLF, Ferreira MRA, Donassolo RA, Rodrigues RR, Conceição FR. Clostridium septicum: A review in the light of alpha-toxin and development of vaccines. Vaccine 2021; 39:4949-4956. [PMID: 34312008 DOI: 10.1016/j.vaccine.2021.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/31/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Clostridium septicum (CS) is a pathogen that can cause the death of animals in livestock worldwide through its main virulence factor, alpha-toxin (ATX). The aspects involved in diseases caused by ATX, such as economic impact, prevalence, and rapid clinical course, require that animals should be systematically immunized. This review provides an overview of CS in livestock farming and discusses current immunization methods. Currently, commercial vaccines available against CS involve the cultivation and inactivation of microorganisms and toxins using a time-consuming, expensive, and high biological risk-carrying production platform, and some have been reported to be ineffective. An alternative to this process is the recombinant DNA technology, although recombinant ATX obtained thus far is no longer efficient in stimulating protective antibody titers despite improvements in the production methods. On the other hand, immunized animals have highly favorable levels of survival when subjected to challenge tests, suggesting that high titers of circulating serum antibodies may not be representative of protection after immunization and that the non-immune cellular defenses associated with the particularities of the mechanism of action of ATX may be involved in the immune response of the host. To contribute to the future of global livestock farming through the development of more efficient recombinant vaccines, we suggest novel perspectives and strategies, such as the location of immunodominant epitopes, expression of relevant functional domains, and construction of chimeras, in the rational design of recombinant ATX.
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Affiliation(s)
- Mariliana Luiza Ferreira Alves
- Instituto Federal Sul-rio-grandense - IFSUL, Praça Vinte de Setembro, 455, Centro, CEP 96.015-360, Pelotas, RS, Brazil; Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, CP 354, CEP 96160-000, Pelotas, RS, Brazil.
| | - Marcos Roberto Alves Ferreira
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, CP 354, CEP 96160-000, Pelotas, RS, Brazil
| | - Rafael Amaral Donassolo
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, CP 354, CEP 96160-000, Pelotas, RS, Brazil
| | - Rafael Rodrigues Rodrigues
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, CP 354, CEP 96160-000, Pelotas, RS, Brazil
| | - Fabricio Rochedo Conceição
- Centro de Desenvolvimento Tecnológico, Núcleo de Biotecnologia, Universidade Federal de Pelotas, CP 354, CEP 96160-000, Pelotas, RS, Brazil
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Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, Huang JJ, Zhang JJ, Xu YC, Hsueh PR. Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review. Microorganisms 2021; 9:microorganisms9071536. [PMID: 34361971 PMCID: PMC8304613 DOI: 10.3390/microorganisms9071536] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xin Hou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Wei Cheng
- Center of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100053, China;
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
- Correspondence: (Y.-C.X.); (P.-R.H.)
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 40447, Taiwan;
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence: (Y.-C.X.); (P.-R.H.)
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Matsuoka T, Shimizu T, Minagawa T, Hiranuma W, Takeda M, Kakuta R, Kawamoto S. First case of an invasive Bacteroides dorei infection detected in a patient with a mycotic aortic aneurysm-raising a rebellion of major indigenous bacteria in humans: a case report and review. BMC Infect Dis 2021; 21:625. [PMID: 34193073 PMCID: PMC8247135 DOI: 10.1186/s12879-021-06345-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/21/2021] [Indexed: 02/05/2023] Open
Abstract
Background Bacteroides dorei is an anaerobic gram-negative bacterium first described in 2006. Because of the high similarity in mass spectra between B. dorei and Bacteroides vulgatus, discriminating between these species is arduous in clinical practice. In recent decades, 16S rRNA gene sequencing has been a complementary method for distinguishing taxonomically close bacteria, including B. dorei and B. vulgatus, at the genus and species levels. Consequently, B. dorei has been shown to contribute to some diseases, including type 1 autoimmune diabetes mellitus and atherosclerotic diseases. However, there are no reports on invasive infectious diseases caused by B. dorei. This report describes the first case of direct invasion and colonisation of human tissue by B. dorei, thus providing a warning regarding the previously proposed application of B. dorei as a live biotherapeutic for atherosclerotic diseases. Case presentation A 78-year-old Japanese man complained of intermittent chest/back pain and was diagnosed with a mycotic thoracic aortic aneurysm by enhanced computed tomography on admission. Despite strict blood pressure control and empirical antibiotic therapy, the patient’s condition worsened. To prevent aneurysmal rupture and eliminate infectious foci, the patient underwent surgical treatment. The resected specimen was subjected to tissue culture and 16S rRNA gene sequencing analysis to identify pathogenic bacteria. A few days after the surgery, culture and sequencing results revealed that the pathogen was B. dorei/B. vulgatus and B. dorei, respectively. The patient was successfully treated with appropriate antibacterial therapy and after improvement, was transferred to another hospital for rehabilitation on postoperative day 34. There was no recurrence of infection or aneurysm after the patient transfer. Conclusions This report describes the first case of invasive infectious disease caused by B. dorei, casting a shadow over its utilisation as a probiotic for atherosclerotic diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-06345-8.
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Affiliation(s)
- Takayuki Matsuoka
- Department of Cardiovascular Surgery, Tohoku Medical and Pharmaceutical University, 1-12-1 Fukumuro, Miyagino Ward, Sendai, Miyagi, 983-8512, Japan.
| | - Takuya Shimizu
- Department of Cardiovascular Surgery, Tohoku Medical and Pharmaceutical University, 1-12-1 Fukumuro, Miyagino Ward, Sendai, Miyagi, 983-8512, Japan
| | - Tadanori Minagawa
- Department of Cardiovascular Surgery, Tohoku Medical and Pharmaceutical University, 1-12-1 Fukumuro, Miyagino Ward, Sendai, Miyagi, 983-8512, Japan
| | - Wakiko Hiranuma
- Department of Cardiovascular Surgery, Tohoku Medical and Pharmaceutical University, 1-12-1 Fukumuro, Miyagino Ward, Sendai, Miyagi, 983-8512, Japan
| | - Miki Takeda
- Department of Cardiovascular Surgery, Tohoku Medical and Pharmaceutical University, 1-12-1 Fukumuro, Miyagino Ward, Sendai, Miyagi, 983-8512, Japan
| | - Risako Kakuta
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shunsuke Kawamoto
- Department of Cardiovascular Surgery, Tohoku Medical and Pharmaceutical University, 1-12-1 Fukumuro, Miyagino Ward, Sendai, Miyagi, 983-8512, Japan
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Lamoureux C, Guilloux CA, Beauruelle C, Gouriou S, Ramel S, Dirou A, Le Bihan J, Revert K, Ropars T, Lagrafeuille R, Vallet S, Le Berre R, Nowak E, Héry-Arnaud G. An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches. Sci Rep 2021; 11:6845. [PMID: 33767218 PMCID: PMC7994387 DOI: 10.1038/s41598-021-85592-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Strict anaerobes are undeniably important residents of the cystic fibrosis (CF) lung but are still unknowns. The main objectives of this study were to describe anaerobic bacteria diversity in CF airway microbiota and to evaluate the association with lung function. An observational study was conducted during eight months. A hundred and one patients were enrolled in the study, and 150 sputum samples were collected using a sterile sample kit designed to preserve anaerobic conditions. An extended-culture approach on 112 sputa and a molecular approach (quantitative PCR targeting three of the main anaerobic genera in CF lung: Prevotella, Veillonella, and Fusobacterium) on 141 sputa were developed. On culture, 91.1% of sputa were positive for at least one anaerobic bacterial species, with an average of six anaerobic species detected per sputum. Thirty-one anaerobic genera and 69 species were found, which is the largest anaerobe diversity ever reported in CF lungs. Better lung function (defined as Forced Expiratory Volume in one second > 70%) was significantly associated with higher quantification of Veillonella. These results raise the question of the potential impact of anaerobes on lung function.
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Affiliation(s)
- Claudie Lamoureux
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Clémence Beauruelle
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Sophie Ramel
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Anne Dirou
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Jean Le Bihan
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Krista Revert
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Thomas Ropars
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | | | - Sophie Vallet
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | - Rozenn Le Berre
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Pulmonary and Internal Medicine, Brest University Hospital, Brest, France
| | - Emmanuel Nowak
- INSERM CIC 1412, Brest University Hospital, Brest, France
| | - Geneviève Héry-Arnaud
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France. .,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France.
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Dai Y, Xu X, Yan X, Li D, Cao W, Tang L, Hu M, Jiang C. Evaluation of a Rapid and Simplified Protocol for Direct Identification of Microorganisms From Positive Blood Cultures by Using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Front Cell Infect Microbiol 2021; 11:632679. [PMID: 33777845 PMCID: PMC7990877 DOI: 10.3389/fcimb.2021.632679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Early and rapid identification of microorganisms is critical for reducing the mortality rate caused by bloodstream infections (BSIs). The accuracy and feasibility of directly identifying pathogens in positive blood cultures by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been intensely confirmed. In this study, we combined density centrifugation and extra chemical lysis-extraction to develop an optimized method in the blood culture process, which significantly improved the effectiveness of direct identification by MALDI-TOF MS. The accuracy was evaluated by 2,032 positive blood culture samples (115 species of microorganism). The overall MALDI-TOF MS based identification rate with scores ≥ 1.700 was 87.60%. 94.06% of gram-negative bacteria were identified consistently to the genus level, followed by anaerobes (93.33%), gram-positive bacteria (84.46%), and fungi (60.87%). This protocol could obtain results within 10–20 min at a cost of less than $0.1 per sample, which saved up to 24 h in identifying 87.60% of the microorganism from positive blood cultures. This rapid and simplified protocol facilitates the direct identification of microorganism in positive blood cultures, and exhibits the advantages of cost-effective, time-saving, and easy-to-use. It could provide the causative organism of the patient to clinicians in time for targeted treatment and reduce mortality.
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Affiliation(s)
- Yufeng Dai
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xinyi Xu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xue Yan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Daming Li
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Cao
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lingli Tang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Molecular Diagnostic Center of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Min Hu
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Molecular Diagnostic Center of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Chuanhao Jiang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.,Clinical Molecular Diagnostic Center of Hunan Province, The Second Xiangya Hospital, Central South University, Changsha, China
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