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Nakayama A, Morinaga Y, Izuno R, Morikane K, Yanagihara K. Evaluation of MALDI-TOF mass spectrometry coupled with ClinProTools as a rapid tool for toxin-producing Clostridioides difficile. J Infect Chemother 2024; 30:847-852. [PMID: 38423297 DOI: 10.1016/j.jiac.2024.02.024] [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: 01/07/2024] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
INTRODUCTION The performance of MALDI-TOF MS combined with analysis platform for identification of toxin-producing Clostridiodes difficile is yet to be known. METHODS Between August 2018 and September 2020, 61 isolates from stool specimens of patients with C. difficile-associated diarrhea were analyzed using the MALDI Biotyper system. A C. difficile toxin-producer detection model was developed using ClinProTools. The model was validated using 28 known strains that differed from the isolates used to develop the model. RESULTS The sensitivity and specificity of the Genetic Algorithm (GA) model using isolates grown on Brucella with hemin and vitamin K (BHK) agar plates were 91.7% and 44.4%, respectively. When isolates grown on cycloserine-cefoxitin mannitol agar were analyzed by the model, sensitivity and specificity were 6.3% and 100%, respectively. The GA model using BHK medium showed the highest discriminatory performance in detection of toxin-producing C. difficile. However, a discrepancy in detection of toxin-producing C. difficile was observed in the results generated when the model was being developed and when the model was validated which suggests that incubation conditions may have affected the results. CONCLUSION MALDI-TOF analysis using ClinProTools has a potential to be a cost-effective tool for rapid diagnosis and contribute to antimicrobial stewardship by differentiating toxin-producing C. difficile from non-producers.
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Affiliation(s)
- Asami Nakayama
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Laboratory Medicine, Tohoku University Hospital, Miyagi, Japan
| | - Yoshitomo Morinaga
- Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama, Japan; Center for Advanced Antibody Drug Development, University of Toyama, Toyama, Japan; Clinical and Research Center for Infectious Diseases, Toyama University Hospital, Toyama, Japan.
| | - Ryota Izuno
- Department of Laboratory Medicine, Yamagata University Hospital, Yamagata, Japan
| | - Keita Morikane
- Department of Laboratory Medicine, Yamagata University Hospital, Yamagata, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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2
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Benhasna S, Boudemagh A. Alternative protocol leading to rapid identification of Actinomycetes isolated from Algerian desertic soil by MALDI-TOF mass spectrometry. J Microbiol Methods 2024; 223:106984. [PMID: 38955305 DOI: 10.1016/j.mimet.2024.106984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/19/2024] [Accepted: 06/29/2024] [Indexed: 07/04/2024]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is the first-line method for the rapid identification of most cultured microorganisms. As for Streptomyces strains, MALDI-TOF MS identification is complicated by the characteristic incrustation of colonies in agar and the strong cell wall of Actinomycetes cells requiring the use of alternative protein extraction protocols. In this study, we developed a specific protocol to overcome these difficulties for the MALDI-TOF MS identification of Actinomycetes made on solid medium. This protocol includes incubation of colony removed from agar plate with the beta-agarase enzyme, followed by a mechanical lysis and two washes by phosphate buffer and ethanol. Twenty-four Streptomyces and two Lentzea strains isolated from Algerian desertic soils were first identified by 16S rRNA sequencing as gold standard method, rpoB gene was used as a secondary gene target when 16S rRNA did not allow species identification. In parallel the isolates were identified by using the MALDI-TOF MS protocol as reported. After the expansion of the database with the inclusion of this MSPS, the strains were analyzed again in MALDI Biotyper, and all were identified. This work demonstrates that the rapid identification of Actinomycetes can be obtained without protein extraction step frequently used in MALDI-TOF mass spectrometry with this type of microorganisms.
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Affiliation(s)
- Sarra Benhasna
- Laboratory of Molecular and Cellular Biology, Constantine1-Frères Mentouri University, Chaâbat Erssas Campus, Ain El Bey Road, 25000 Constantine, Algeria; Department of Microbiology, Constantine1-Frères Mentouri University, Ain El Bey Road, 25000 Constantine, Algeria.
| | - Allaoueddine Boudemagh
- Laboratory of Molecular and Cellular Biology, Constantine1-Frères Mentouri University, Chaâbat Erssas Campus, Ain El Bey Road, 25000 Constantine, Algeria
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Sasiene ZJ, LeBrun ES, Velappan N, Anderson AR, Patterson NH, Dufresne M, Farrow MA, Norris JL, Caprioli RM, Mach PM, McBride EM, Glaros TG. Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers. Analyst 2024; 149:3564-3574. [PMID: 38717518 DOI: 10.1039/d4an00325j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.
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Affiliation(s)
- Zachary J Sasiene
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Erick S LeBrun
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nileena Velappan
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Austin R Anderson
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Nathan H Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Martin Dufresne
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Melissa A Farrow
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37240, USA
| | - Phillip M Mach
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Ethan M McBride
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Trevor G Glaros
- Biochemistry and Biotechnology Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Gonfa TG, Negessa AK, Bulto AO. Isolation, screening, and identification of chitinase-producing bacterial strains from riverbank soils at Ambo, Western Ethiopia. Heliyon 2023; 9:e21643. [PMID: 38027800 PMCID: PMC10665737 DOI: 10.1016/j.heliyon.2023.e21643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Chitinases are hydrolytic enzymes that dissolve the glycosidic linkages in chitin. Chitin is a cell wall component of fungi and fund in exoskeleten of worms and arthropods. Chitinase has been applied in agriculture, as a biopesticide for the control of plant fungal infections, in medicine, and in waste management. This research aimed to isolate, screen, and identification of chitinase-producing bacteria from riverbank soils. Twenty nine chitinolytic bacteria were isolated from the river bank soil samples, from which 9 of them had strong chitinolytic properties. Chitinase production was determined by zones of hydrolysis produced after 96 h of incubation at 37 °C. The different bacterial isolates were characterized morphologically, microscopically, and biochemically and finally eight strain were identified at species level by Matrix Assisted Laser Desorption Ionization - Time of Flight Mass Spectrometry (MALDI-TOF MS). From the eight, bacterial isolates investigated in this study Stenotrophomonas maltophilia showed the highest chitinase enzyme activity (625 μg/mL) followed by Pseudomonas putida with the enzyme activity of (553 μg/mL) and the least enzyme activity was recorded for Lilliottia amnigena (80 μg/mL). An incubation temperature of 45 °C, neutral pH and an incubation period of 96 h are found to be the optimum condition for the chitinase enzyme production from Stenotrophomonas maltophilia. The results of this study indicated the possibility of the production of chitinase from the chitinolytic bacterial isolates, which was highly useful for a variety of applications, including biocontrol of harmful insects and pathogenic fungi as well as in the biochemical, pharmaceutical, and medical sectors.
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Affiliation(s)
- Teshome Gudeta Gonfa
- Kotebe University of Education, College of Natural and Computational Sciences, Department of Biology, Addis Ababa, Ethiopia
| | - Asefa Keneni Negessa
- Kotebe University of Education, College of Natural and Computational Sciences, Department of Biology, Addis Ababa, Ethiopia
- Ambo Ubiversity, College of Natural and Computational Sceicnes, Department of Biology, Ambo, Ethiopia
- Animal Health Institute, Sebeta, Ethiopia
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Challenging the problematic detection of clostridial isolates causing late-blowing defect with MALDI-TOF MS. CZECH JOURNAL OF FOOD SCIENCES 2023. [DOI: 10.17221/199/2022-cjfs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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6
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Kalender H, Öngör H, Timurkaan N, Karagülle B, Karabulut B, İncili CA, Başar HE, Ekinci E, Çevik A, Atıl E, Çetinkaya B. Detection and molecular characterization of Clostridium perfringens, Paeniclostridium sordellii and Clostridium septicum from lambs and goat kids with hemorrhagic abomasitis in Turkey. BMC Vet Res 2023; 19:8. [PMID: 36639759 PMCID: PMC9837962 DOI: 10.1186/s12917-023-03569-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The pathogenic Clostridia cause neurotoxic, histotoxic and enterotoxic infections in humans and animals. Several Clostridium species have been associated with abomasitis in ruminants. The present study aimed to investigate the frequency, and the presence of virulence genes, of Clostridium perfringens, Paeniclostridium sordellii and Clostridium septicum in lambs and goat kids with hemorrhagic abomasitis. RESULTS A total of 38 abomasum samples, collected from lambs and goat kids of 1 week to 1 month of age in different farms located in eastern Turkey between 2021 and 2022, were evaluated by histopathology, culture and PCR. At necropsy, the abomasum of the animals was excessively filled with caseinized content and gas, and the abomasum mucosa was hemorrhagic in varying degrees. In histopathological evaluation, acute necrotizing hemorrhagic inflammation was noted in abomasum samples. The examination of swab samples by culture and PCR revealed that C. perfringens type A was the most frequently detected species (86.84%) either alone or in combination with other Clostridium species. P. sordellii, C. perfringens type F and C. septicum were also harboured in the samples, albeit at low rates. Beta2 toxin gene (cpb2) was found in three of C. perfringens type A positive samples. CONCLUSION It was suggested that vaccination of pregnant animals with toxoid vaccines would be beneficial in terms of protecting newborn animals against Clostridial infections. This study investigated the presence of clostridial toxin genes in abomasal samples for the first time in Turkey.
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Affiliation(s)
- Hakan Kalender
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Microbiology, Firat University, Elazig, Turkey
| | - Hasan Öngör
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Microbiology, Firat University, Elazig, Turkey
| | - Necati Timurkaan
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Pathology, Firat University, Elazig, Turkey
| | - Burcu Karagülle
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Microbiology, Firat University, Elazig, Turkey
| | - Burak Karabulut
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Pathology, Firat University, Elazig, Turkey
| | - Canan Akdeniz İncili
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Pathology, Firat University, Elazig, Turkey
| | - Hatip Enfal Başar
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Microbiology, Firat University, Elazig, Turkey
| | - Elif Ekinci
- grid.411690.b0000 0001 1456 5625Faculty of Veterinary Medicine, Department of Pathology, Dicle University, Diyarbakir, Turkey
| | - Aydın Çevik
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Pathology, Firat University, Elazig, Turkey
| | - Eray Atıl
- Pendik Veterinary Control Institute, Istanbul, Turkey
| | - Burhan Çetinkaya
- grid.411320.50000 0004 0574 1529Faculty of Veterinary Medicine, Department of Microbiology, Firat University, Elazig, Turkey
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de Oliveira Sant’Anna L, Cappelli EA, Batista Araújo MR, Ramos JN, Simpson-Lourêdo L, Cucinelli ADES, Pereira Baio PV, Vieira VV, Sanches dos Santos L, Mattos-Guaraldi AL. Virulence potential of the first Corynebacterium mycetoides strain isolated from human urine: a rare species of Corynebacterium. Microbes Infect 2022; 24:105001. [DOI: 10.1016/j.micinf.2022.105001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 10/31/2022]
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8
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Huang X, Yang Q, Yan Z, Wang P, Shi H, Li J, Shang X, Gun S. Combined Analysis of RRBS DNA Methylome and Transcriptome Reveal Novel Candidate Genes Related to Porcine Clostridium perfringens Type C-Induced Diarrhea. Front Genet 2022; 13:803477. [PMID: 35401691 PMCID: PMC8990837 DOI: 10.3389/fgene.2022.803477] [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: 10/28/2021] [Accepted: 02/24/2022] [Indexed: 11/29/2022] Open
Abstract
Clostridium perfringens type C (Cp) is one of the principal microorganisms responsible for bacterial diarrhea in neonatal and pre-weaning piglets. To better understand the molecular effects of Cp infection, we performed a genome-wide comparison of the changes in DNA methylation and gene expression in Cp infected resistant and susceptible piglets. We characterized the pattern of changes in methylation and found 6485, 5968, and 6472 differentially methylated regions (DMRs) of piglets infected with Cp in IR vs. IC, IS vs. IC, and IS vs. IR groups, respectively. These methylation changes for genes mainly involved in immune and inflammatory responses, cell adhesion, and activation of transcription factors. Gene ontology and KEGG pathway analyses showed that the differentially methylated genes (DMGs) were associated with negative regulation of transcription, apoptotic processes, protein binding, and kinase activity. In addition, they were enriched in immunity-related pathways, such as MAPK signaling pathway, Toll-like receptor signaling pathway, and NF-kappa B signaling pathway. Integrative analysis identified 168, 198, and 7 mRNAs showing inverse correlations between methylation and expression with Cp infection. Altered DNA methylation and expression of various genes suggested their roles and potential functional interactions upon Cp infection, 14 immune-associated mRNAs with differential methylation and transcriptional repression were identified in IS vs. IR, commonly revealing that the differentially expressed genes (DEGs) LBP, TBX21, and LCN2 were likely involved in the piglets against Cp infection. The present results provide further insight into the DNA methylation epigenetic alterations of C. perfringens type C infected piglet ileum tissues, and may advance the identification of biomarkers and drug targets for predicting susceptibility to and controlling C. perfringens type C-induced piglet diarrhea.
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Affiliation(s)
- Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Hairen Shi
- Tibet Academy of Agricultural and Animal Husbandry Science, Lasa, China
| | - Jie Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xuefeng Shang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
- Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China
- *Correspondence: Shuangbao Gun,
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Sulaiman IM, Miranda N, Simpson S. MALDI-TOF Mass Spectrometry and 16S rRNA Gene Sequence Analysis for the Identification of Foodborne Clostridium Spp. J AOAC Int 2021; 104:1381-1388. [PMID: 33982069 DOI: 10.1093/jaoacint/qsab070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND Clostridium is a genus of Gram-positive, spore-forming, anaerobic bacteria comprising approximately 100 species. Some Clostridium spp. (C. botulinum, C. perfringens, C. tetani and C. difficile) were recognized to cause acute food poisoning, botulism, tetanus, and diarrheal illness in humans. Thus, rapid identification of Clostridium spp. is critical for source tracking of contaminated food and to understand the transmission dynamics of these foodborne pathogens. OBJECTIVE This study was carried out to rapidly identify Clostridium-like isolates by MALDI-TOF MS and rRNA sequencing methods. METHODS Thirty-three Clostridium-like isolates were recovered from various baby food and surveillance samples. Species identification of these isolates was accomplished using VITEK MS system. Sequence characterization of the 16S rRNA region was done on an ABI 3500XL Genetic Analyzer. RESULTS The VITEK MS system identified 28 of the 33 Clostridium-like isolates with a high confidence value (99.9%); no ID was observed for the rest of the five isolates. Nucleotide sequencing of 16S rRNA region identified all 33 Clostridium-like isolates. Furthermore, while characterizing the 16S rRNA gene, eleven distinct Clostridium spp. (Clostridium aciditolerans, Clostridium aerotolerans, Clostridium argentinense, Clostridium beijerinckii, Clostridium bifermentans, Clostridium butyricum, Clostridium cochlearium, Clostridium difficile, Clostridium perfringens, Clostridium sporogenes, and Clostridium subterminale) were recognized among the 33 Clostridium-like isolates. One of the Clostridium-like isolate was identified as the Citrobacter amalonaticus by both diagnostic methods. The generated 16S rRNA sequences matched completely (100%) with sequences available in GenBank for Clostridium and Citrobacter species. Species identification attained by the VITEK MS for the Clostridium-like isolates was comparable to the 16S rRNA sequencing based data. HIGHLIGHTS MALDI-TOF mass spectrometry and 16S rRNA sequencing can be used in the species identification of Clostridium species.
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Affiliation(s)
- Irshad M Sulaiman
- U.S. Food and Drug Administration, Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, 60 8th Street NE, Atlanta, GA, 30309, USA
| | - Nancy Miranda
- U.S. Food and Drug Administration, Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, 60 8th Street NE, Atlanta, GA, 30309, USA
| | - Steven Simpson
- U.S. Food and Drug Administration, Microbiological Sciences Branch, Southeast Food and Feed Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, 60 8th Street NE, Atlanta, GA, 30309, USA
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Tsuyuki Y, Nakazawa S, Kubo S, Goto M, Takahashi T. Antimicrobial susceptibility patterns of anaerobic bacteria identified from clinical specimens of diseased dogs and cats. J Vet Med Sci 2020; 82:1316-1320. [PMID: 32713891 PMCID: PMC7538322 DOI: 10.1292/jvms.20-0294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We aimed to clarify antimicrobial susceptibility patterns of anaerobes from diseased companion animals. Bacterial identification was based on the Japanese 2012
guidelines for the testing of anaerobic bacteria. AST was performed using the broth microdilution method. The anaerobe-containing samples collected from 2014 to
2018 included blood (anaerobe recovery rate, 5.0%), bile (9.4%), joint fluids (0.6%), pleural effusions (42.6%), ascites (64.1%), cerebrospinal fluids (3.0%),
and punctures (75.0%). The anaerobes identified included Bacteroides spp. (33.2%), Peptostreptococcus spp. (19.6%),
Prevotella spp. (13.6%), Propionibacterium spp. (10.3%), Clostridium spp. (9.3%), and
Fusobacterium spp. (7.5%). Bacteroides fragilis group isolates were resistant to penicillin G (100%), ampicillin (100%),
cefmetazole (63.6%), ceftizoxime (90.0%), and clindamycin (40.0%). Our observations demonstrated antimicrobial susceptibility in anaerobes isolated from
Japanese companion animals.
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Affiliation(s)
- Yuzo Tsuyuki
- Division of Clinical Laboratory, Sanritsu Zelkova Veterinary Laboratory, 3-5-5 Ogibashi, Koto-ku, Tokyo 135-0011, Japan.,Division of Clinical Laboratory, Sanritsu Laboratory, 1353-25 Kamitakano, Yachio, Chiba 276-0022, Japan.,Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Sayaka Nakazawa
- Division of Clinical Laboratory, Sanritsu Zelkova Veterinary Laboratory, 3-5-5 Ogibashi, Koto-ku, Tokyo 135-0011, Japan
| | - Setsuko Kubo
- Division of Clinical Laboratory, Sanritsu Laboratory, 1353-25 Kamitakano, Yachio, Chiba 276-0022, Japan
| | - Mieko Goto
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Takashi Takahashi
- Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences & Ōmura Satoshi Memorial Institute, Kitasato University, Shirokane, Minato-ku, Tokyo 108-8641, Japan
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Poirier I, Benhaïm D, Poizot E, Gallon RK, Cauvin E, Lemarchand A, Bertrand M, Lelièvre C, Murat A, Benoit F, Méar Y. Marine aggregates in North Atlantic coast: Microbial characteristics and potential interactions with farmed Atlantic salmon (Salmo salar). MARINE ENVIRONMENTAL RESEARCH 2020; 157:104864. [PMID: 32275501 DOI: 10.1016/j.marenvres.2019.104864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 06/11/2023]
Abstract
Microbial contamination of aggregates collected near an Atlantic salmon farm, in the Cherbourg roadstead, was followed monthly over one year to study the dynamics of Vibrio spp. and explore their impact on farmed fish. Salmon state of health was followed through blood and histopathological analyses. Vibrio were systematically found in aggregates with particularly high concentration in August. The Splendidus clade was strongly dominant in aggregates as well as in gills, and an increase in Vibrio diversity was observed in summer and autumn. Results did not demonstrate that aggregates directly impact the bacterial community of gills, but they suggested an aggregates-gills interaction. Gill contamination was correlated with water temperature and probably impacted by amoebae. Vibrio renipiscarius and Vibrio toranzoniae were isolated in North Atlantic for the first time. A better understanding of the interaction between marine aggregates, Vibrio spp. and fish is essential to improve salmon cage farming.
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Affiliation(s)
- Isabelle Poirier
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110, Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
| | - David Benhaïm
- Hólar University, Department of Aquaculture and Fish Biology, Háeyri 1, 550 Saudárkrókur, Iceland; Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110, Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
| | - Emmanuel Poizot
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110, Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
| | - Régis Kévin Gallon
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110, Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
| | - Elodie Cauvin
- LABÉO MANCHE, 1352 avenue de Paris, CS 33608, 50008, Saint-Lô, France.
| | - Alexis Lemarchand
- GMG, ZA Produimer, Rue Port des Flamands, 50110, Cherbourg en Cotentin, France.
| | - Martine Bertrand
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110, Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
| | - Céline Lelièvre
- Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
| | - Anne Murat
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110, Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
| | - Fabienne Benoit
- LABÉO MANCHE, 1352 avenue de Paris, CS 33608, 50008, Saint-Lô, France.
| | - Yann Méar
- Conservatoire National des Arts et Métiers, Institut National des Sciences et Techniques de la Mer, EPN8, Boulevard Collignon, Tourlaville, 50110, Cherbourg en Cotentin, France; Laboratoire Universitaire des Sciences Appliquées de Cherbourg, EA4253, Normandie Université, UNICAEN, 50130, Cherbourg en Cotentin, France.
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12
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Junior CAO, Silva ROS, Lobato FCF, Navarro MA, Uzal FA. Gas gangrene in mammals: a review. J Vet Diagn Invest 2020; 32:175-183. [PMID: 32081096 DOI: 10.1177/1040638720905830] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Gas gangrene is a necrotizing infection of subcutaneous tissue and muscle that affects mainly ruminants and horses, but also other domestic and wild mammals. Clostridium chauvoei, C. septicum, C. novyi type A, C. perfringens type A, and C. sordellii are the etiologic agents of this disease, acting singly or in combination. Although a presumptive diagnosis of gas gangrene can be established based on clinical history, clinical signs, and gross and microscopic changes, identification of the clostridia involved is required for confirmatory diagnosis. Gross and microscopic lesions are, however, highly suggestive of the disease. Although the disease has a worldwide distribution and can cause significant economic losses, the literature is limited mostly to case reports. Thus, we have reviewed the current knowledge of gas gangrene in mammals.
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Affiliation(s)
- Carlos A Oliveira Junior
- Veterinary School, Federal University of Minas Gerais, Brazil (Oliveira Junior, Silva, Lobato).,California Animal Health and Food Safety Laboratory, University of California, Davis, CA (Navarro, Uzal)
| | - Rodrigo O S Silva
- Veterinary School, Federal University of Minas Gerais, Brazil (Oliveira Junior, Silva, Lobato).,California Animal Health and Food Safety Laboratory, University of California, Davis, CA (Navarro, Uzal)
| | - Francisco C F Lobato
- Veterinary School, Federal University of Minas Gerais, Brazil (Oliveira Junior, Silva, Lobato).,California Animal Health and Food Safety Laboratory, University of California, Davis, CA (Navarro, Uzal)
| | - Mauricio A Navarro
- Veterinary School, Federal University of Minas Gerais, Brazil (Oliveira Junior, Silva, Lobato).,California Animal Health and Food Safety Laboratory, University of California, Davis, CA (Navarro, Uzal)
| | - Francisco A Uzal
- Veterinary School, Federal University of Minas Gerais, Brazil (Oliveira Junior, Silva, Lobato).,California Animal Health and Food Safety Laboratory, University of California, Davis, CA (Navarro, Uzal)
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13
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Posthaus H, Kittl S, Tarek B, Bruggisser J. Clostridium perfringens type C necrotic enteritis in pigs: diagnosis, pathogenesis, and prevention. J Vet Diagn Invest 2020; 32:203-212. [PMID: 31955664 DOI: 10.1177/1040638719900180] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Clostridium perfringens type C causes severe and lethal necrotic enteritis (NE) in newborn piglets. NE is diagnosed through a combination of pathology and bacteriologic investigations. The hallmark lesion of NE is deep, segmental mucosal necrosis with marked hemorrhage of the small intestine. C. perfringens can be isolated from intestinal samples in acute cases but it is more challenging to identify pathogenic strains in subacute-to-chronic cases. Toxinotyping or genotyping is required to differentiate C. perfringens type C from commensal type A strains. Recent research has extended our knowledge about the pathogenesis of the disease, although important aspects remain to be determined. The pathogenesis involves rapid overgrowth of C. perfringens type C in the small intestine, inhibition of beta-toxin (CPB) degradation by trypsin inhibitors in the colostrum of sows, and most likely initial damage to the small intestinal epithelial barrier. CPB itself acts primarily on vascular endothelial cells in the mucosa and can also inhibit platelet function. Prevention of the disease is achieved by immunization of pregnant sows with C. perfringens type C toxoid vaccines, combined with proper sanitation on farms. For the implementation of prevention strategies, it is important to differentiate between disease-free and pathogen-free status of a herd. The latter is more challenging to maintain, given that C. perfringens type C can persist for a long time in the environment and in the intestinal tract of adult animals and thus can be distributed via clinically and bacteriologically inapparent carrier animals.
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Affiliation(s)
- Horst Posthaus
- Institute of Animal Pathology (Posthaus, Tarek, Bruggisser), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology (Kittl), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sonja Kittl
- Institute of Animal Pathology (Posthaus, Tarek, Bruggisser), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology (Kittl), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Basma Tarek
- Institute of Animal Pathology (Posthaus, Tarek, Bruggisser), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology (Kittl), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Julia Bruggisser
- Institute of Animal Pathology (Posthaus, Tarek, Bruggisser), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology (Kittl), Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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14
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Li Y, Shan M, Zhu Z, Mao X, Yan M, Chen Y, Zhu Q, Li H, Gu B. Application of MALDI-TOF MS to rapid identification of anaerobic bacteria. BMC Infect Dis 2019; 19:941. [PMID: 31699042 PMCID: PMC6836477 DOI: 10.1186/s12879-019-4584-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been rapidly developed and widely used as an analytical technique in clinical laboratories with high accuracy in microorganism identification. OBJECTIVE To validate the efficacy of MALDI-TOF MS in identification of clinical pathogenic anaerobes. METHODS Twenty-eight studies covering 6685 strains of anaerobic bacteria were included in this meta-analysis. Fixed-effects models based on the P-value and the I-squared were used for meta-analysis to consider the possibility of heterogeneity between studies. Statistical analyses were performed by using STATA 12.0. RESULTS The identification accuracy of MALDI-TOF MS was 84% for species (I2 = 98.0%, P < 0.1), and 92% for genus (I2 = 96.6%, P < 0.1). Thereinto, the identification accuracy of Bacteroides was the highest at 96% with a 95% CI of 95-97%, followed by Lactobacillus spp., Parabacteroides spp., Clostridium spp., Propionibacterium spp., Prevotella spp., Veillonella spp. and Peptostreptococcus spp., and their correct identification rates were all above 90%, while the accuracy of rare anaerobic bacteria was relatively low. Meanwhile, the overall capabilities of two MALDI-TOF MS systems were different. The identification accuracy rate was 90% for VITEK MS vs. 86% for MALDI biotyper system. CONCLUSIONS Our research showed that MALDI-TOF-MS was satisfactory in genus identification of clinical pathogenic anaerobic bacteria. However, this method still suffers from different drawbacks in precise identification of rare anaerobe and species levels of common anaerobic bacteria.
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Affiliation(s)
- Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Mingzhu Shan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, 214200, China
| | - Mingju Yan
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Qiuju Zhu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hongchun Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Bing Gu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
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15
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Evaluation of the Vitek MS and the MALDI Biotyper systems for the identification of less commonly isolated but clinically relevant anaerobes and facultative anaerobes. Anaerobe 2018; 54:210-216. [DOI: 10.1016/j.anaerobe.2018.05.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/25/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022]
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16
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Schaumann R, Dallacker-Losensky K, Rosenkranz C, Genzel GH, Stîngu CS, Schellenberger W, Schulz-Stübner S, Rodloff AC, Eschrich K. Discrimination of Human Pathogen Clostridium Species Especially of the Heterogeneous C. sporogenes and C. botulinum by MALDI-TOF Mass Spectrometry. Curr Microbiol 2018; 75:1506-1515. [PMID: 30120528 DOI: 10.1007/s00284-018-1552-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022]
Abstract
Clostridium species cause several local and systemic diseases. Conventional identification of these microorganisms is in part laborious, not always reliable, time consuming or does not always distinguish different species, i.e., C. botulinum and C. sporogenes. All in, there is a high interest to find out a reliable, powerful and rapid method to identify Clostridium spp. not only on genus but also on species level. The aim of the present study was to identify Clostridium spp. strains and also to find differences and metabolic groups of C. botulinum by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS). A total of 123 strains of Clostridium spp. (C. botulinum, n = 40, C. difficile, n = 11, C. tetani, n = 11, C. sordellii, n = 20, C. sporogenes, n = 18, C. innocuum, n = 10, C. perfringens, n = 13) were analyzed by MALDI-TOF MS in combination with methods of multivariate statistical analysis. MALDI-TOF MS analysis in combination with methods of multivariate statistical analysis was able to discriminate between the different tested Clostridium spp., even between species which are closely related and difficult to differentiate by traditional methods, i.e., C. sporogenes and C. botulinum. Furthermore, the method was able to separate the different metabolic groups of C. botulinum. Especially, E gene-positive C. botulinum strains are clearly distinguishable from the other species but also from those producing other toxin types. Thus, MALDI-TOF MS represents a reliable and above all quick method for identification of cultivated Clostridium species.
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Affiliation(s)
- Reiner Schaumann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | - Kevin Dallacker-Losensky
- Department of Trauma Surgery and Orthopedics, Reconstructive and Septic Surgery, and Sports Traumatology, German Armed Forces Hospital Ulm, Ulm, Germany.
| | - Christiane Rosenkranz
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | | | - Catalina S Stîngu
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | | | | | - Arne C Rodloff
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital of Leipzig, Leipzig, Germany
| | - Klaus Eschrich
- Institute of Biochemistry, University Hospital of Leipzig, Leipzig, Germany
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17
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Fong P, Francis MJ, Hamblin JF, Korman TM, Graham M. Identification and diversity of Actinomyces species in a clinical microbiology laboratory in the MALDI-TOF MS era. Anaerobe 2018; 54:151-158. [PMID: 30261272 DOI: 10.1016/j.anaerobe.2018.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/13/2018] [Accepted: 09/22/2018] [Indexed: 11/28/2022]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable tool for bacterial identification. This study compared the Bruker MALDI-TOF BioTyper MS (MBT) and 16S rRNA gene sequencing for the identification of Actinomyces and Actinotignum spp. The MBT identified 68/77 (88.3%) of Actinomyces isolates to the genus-level and 44/77 (57.1%) of Actinomyces isolates to the species-level using the manufacturer's identification criteria. The MBT did not yield reliable identification for only 1/77 (1.3%) and generated no identification for 8/77 (10.4%) of the isolates. No misidentifications were found. Discordance at the species level was observed for eight isolates. Overall, the MBT demonstrated good concordance with the 16S rRNA gene sequencing with the exception of the closely related species A. naeslundii, A. viscosus and A. oris. A variety of Actinomyces spp. were isolated from orocervicofacial/dental specimens, but only a limited number of species were isolated from urine or intra-abdominal specimens. This study confirms the utility of MBT in the identification of Actinomyces spp. and describes the diversity and anatomic niche of species in human clinical specimens from various body sites.
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Affiliation(s)
- Peivern Fong
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia.
| | | | - John F Hamblin
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia
| | - Tony M Korman
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia; Monash Infectious Diseases, Monash University, Monash Health, Clayton, Victoria, Australia
| | - Maryza Graham
- Department of Microbiology, Monash Health, Clayton, Victoria, Australia; Monash Infectious Diseases, Monash University, Monash Health, Clayton, Victoria, Australia
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18
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Bakhtiary F, Sayevand HR, Remely M, Hippe B, Indra A, Hosseini H, Haslberger AG. Identification of Clostridium spp. derived from a sheep and cattle slaughterhouse by matrix-assisted laser desorption and ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequencing. Journal of Food Science and Technology 2018; 55:3232-3240. [PMID: 30065434 DOI: 10.1007/s13197-018-3255-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 05/22/2018] [Accepted: 05/28/2018] [Indexed: 11/30/2022]
Abstract
Clostridia are widespread and some of them are serious human pathogens. Identification of Clostridium spp. is important for managing microbiological risks in the food industry. Samples derived from sheep and cattle carcasses from a slaughterhouse in Iran were analyzed by MALDI-TOF MS using direct transfer and extended direct transfer sample preparation methods and 16S rDNA sequencing. MALDI-TOF MS could identify ten species in 224 out of 240 Clostridium isolates. In comparison to the 16S rDNA sequencing, correct identification rate of the Clostridium spp. at the species level by MALDI-TOF MS technique was 93.3%. 16 isolates were not identified by MALDI-TOF MS but 16s rDNA sequencing identified them as C. estertheticum, C. frigidicarnis, and C. gasigenes species. The most frequently identified Clostridium species were: C. sporogenes (13%), C. cadaveris (12.5%), C. cochlearium (12%) and C. perfringens (10%). Extended direct transfer method [2.26 ± 0.18 log (score)] in comparison to direct transfer method [2.15 ± 0.23 log (score)] improved Clostridium spp. IDENTIFICATION Using a cut-off score of 1.7 was sufficient for accurate identification of Clostridium species. MALDI-TOF MS identification scores for Clostridium spp. decreased with longer incubation time. Clostridium species predominantly were isolated from carcasses after skinning and evisceration steps in the slaughterhouse. MALDI-TOF MS could be an accurate way to identify Clostridium species. Moreover, continuous improvement of the database and MALDI-TOF MS instrument enhance its performance in food control laboratories.
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Affiliation(s)
- Farzaneh Bakhtiary
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | - Hamid Reza Sayevand
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | - Marlene Remely
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | - Berit Hippe
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
| | | | - Hedayat Hosseini
- 3Faculty of Nutrition Sciences and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alexander G Haslberger
- 1Department of Nutritional Sciences, University of Vienna, Althanstrasse 14, UZAII;2D541, 1090 Vienna, Austria
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19
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Zasada AA, Mosiej E. Contemporary microbiology and identification of Corynebacteria spp. causing infections in human. Lett Appl Microbiol 2018; 66:472-483. [PMID: 29573441 DOI: 10.1111/lam.12883] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 11/29/2022]
Abstract
The Corynebacterium is a genus of bacteria of growing clinical importance. Progress in medicine results in growing population of immunocompromised patients and growing number of infections caused by opportunistic pathogens. A new infections caused by new Corynebacterium species and species previously regarded as commensal micro-organisms have been described. Parallel with changes in Corynebacteria infections, the microbiological laboratory diagnostic possibilities are changing. But identification of this group of bacteria to the species level remains difficult. In the paper, we present various manual, semi-automated and automated assays used in clinical laboratories for Corynebacterium identification, such as API Coryne, RapID CB Plus, BBL Crystal Gram Positive ID System, MICRONAUT-RPO, VITEK 2, BD Phoenix System, Sherlock Microbial ID System, MicroSeq Microbial Identification System, Biolog Microbial Identification Systems, MALDI-TOF MS systems, polymerase chain reaction (PCR)-based and sequencing-based assays. The presented assays are based on various properties, like biochemical tests, specific DNA sequences, composition of cellular fatty acids, protein profiles and have specific limitations. SIGNIFICANCE AND IMPACT OF THE STUDY The number of opportunistic infections caused by Corynebacteria is increasing due to increase in number of immunocompromised patients. New Corynebacterium species and new human infections, caused by this group of bacteria, has been described recently. However, identification of Corynebacteria is still a challenge despite application of sophisticated laboratory methods. In the study we present possibilities and limitations of various commercial systems for identification of Corynebacteria.
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Affiliation(s)
- A A Zasada
- Department of Sera and Vaccines Evaluation, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
| | - E Mosiej
- Department of Sera and Vaccines Evaluation, National Institute of Public Health - National Institute of Hygiene, Warsaw, Poland
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20
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Hepworth-Warren KL, Hay Kraus BL, Wong DM, Krull AC, Metcalf GL. Septic peritonitis in a Percheron mare associated with Clostridium haemolyticum. EQUINE VET EDUC 2017. [DOI: 10.1111/eve.12531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- K. L. Hepworth-Warren
- Lloyd Veterinary Medical Center; College of Veterinary Medicine; Iowa State University; Ames Iowa USA
| | - B. L. Hay Kraus
- Lloyd Veterinary Medical Center; College of Veterinary Medicine; Iowa State University; Ames Iowa USA
| | - D. M. Wong
- Lloyd Veterinary Medical Center; College of Veterinary Medicine; Iowa State University; Ames Iowa USA
| | - A. C. Krull
- Lloyd Veterinary Medical Center; College of Veterinary Medicine; Iowa State University; Ames Iowa USA
| | - G. L. Metcalf
- Lloyd Veterinary Medical Center; College of Veterinary Medicine; Iowa State University; Ames Iowa USA
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21
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Comparison of biomarker based Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) and conventional methods in the identification of clinically relevant bacteria and yeast. BMC Microbiol 2017; 17:128. [PMID: 28545528 PMCID: PMC5445374 DOI: 10.1186/s12866-017-1037-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Background MALDI-TOF MS is an analytical method that has recently become integral in the identification of microorganisms in clinical laboratories. It relies on databases that majorly employ pattern recognition or fingerprinting. Biomarker based databases have also been developed and there is optimism that these may be superior to pattern recognition based databases. This study compared the performance of ribosomal biomarker based MALDI-TOF MS and conventional methods in the identification of selected bacteria and yeast. Methods The study was a cross sectional study identifying clinically relevant bacteria and yeast isolated from varied clinical specimens submitted to a clinical laboratory. The identification of bacteria using conventional Vitek 2™ automated system, serotyping and MALDI-TOF MS was performed as per standard operating procedures. Comparison of sensitivities were then carried out using Pearson Chi-Square test and p-value of <0.05 was considered statistically significant. Secondary outcomes analyzed included the major and minor error rates. Results Of the 383 isolates MALDI-TOF MS and conventional methods identified 97.6 and 95.7% (p = 0.231) to the genus level and 97.4 and 88.0% (p = 0.000) to the species level respectively. Biomarker based MALDI-TOF MS was significantly superior to Vitek 2™ in the identification of Gram negative bacteria and Gram positive bacteria to the species level. For the Gram positive bacteria, significant difference was observed in the identification of Coagulase negative Staphylococci (p = 0.000) and Enterococcus (p = 0.008). Significant difference was also observed between serotyping and MALDI-TOF MS (p = 0.005) and this was attributed to the lack of identification of Shigella species by MALDI-TOF MS. There was no significant difference observed in the identification of yeast however some species of Candida were unidentified by MALDI-TOF MS. Conclusion Biomarker based MALDI-TOF MS had good performance in a clinical laboratory setting with high sensitivities in the identification of clinically relevant microorganisms.
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Abstract
Alteration in the host microbiome at skin and mucosal surfaces plays a role in the function of the immune system, and may predispose immunocompromised patients to infection. Because obligate anaerobes are the predominant type of bacteria present in humans at skin and mucosal surfaces, immunocompromised patients are at increased risk for serious invasive infection due to anaerobes. Laboratory approaches to the diagnosis of anaerobe infections that occur due to pyogenic, polymicrobial, or toxin-producing organisms are described. The clinical interpretation and limitations of anaerobe recovery from specimens, anaerobe-identification procedures, and antibiotic-susceptibility testing are outlined. Bacteriotherapy following analysis of disruption of the host microbiome has been effective for treatment of refractory or recurrent Clostridium difficile infection, and may become feasible for other conditions in the future.
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Affiliation(s)
- Deirdre L Church
- Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, and Division of Microbiology, Calgary Laboratory Services, Calgary, Alberta, Canada T2N 1N4
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MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species. Anaerobe 2016; 40:73-5. [PMID: 27296834 DOI: 10.1016/j.anaerobe.2016.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/02/2016] [Accepted: 06/09/2016] [Indexed: 11/20/2022]
Abstract
All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF.
For 18 non-difficile Clostridium strains, the identification results were correct in 2, 0, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively [corrected].
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AlMogbel MS. Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry for identification of Clostridium species isolated from Saudi Arabia. Braz J Microbiol 2016; 47:410-3. [PMID: 26991272 PMCID: PMC4874676 DOI: 10.1016/j.bjm.2016.01.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 08/20/2015] [Indexed: 11/27/2022] Open
Abstract
The aim of this study was to identify different Clostridium spp. isolated from currency notes from the Ha'il region of Saudi Arabia in September 2014 using MALDI-TOF-MS. Clostridium spp. were identified by Bruker MALDI-TOF-MS and compared with VITEK 2. The confirmation of the presence of different Clostridium spp. was performed by determining the sequence of the 16S ribosomal RNA gene. In this study, 144 Clostridium spp. were isolated. Among these specimens, MALDI-TOF-MS could identify 88.8% (128/144) of the isolates to the species level and 92.3% (133/144) to the genus level, whereas, VITEK 2 identified 77.7% of the (112/144) isolates. The correct identification of the 144 isolates was performed by sequence analysis of the 500bp 16S rRNA gene. The most common Clostridium spp. identified were Clostridium perfringens (67.36%), Clostridium subterminale (14.58%), Clostridium sordellii (9%) and Clostridium sporogenes (9%). The results of this study demonstrate that MALDI-TOF-MS is a rapid, accurate and user friendly technique for the identification of Clostridium spp. Additionally, MALDI-TOF-MS has advantages over VITEK 2 in the identification of fastidious micro-organisms, such as Clostridium spp. Incorporating this technique into routine microbiology would lead to more successful and rapid identification of pathogenic and difficult to identify micro-organisms.
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Affiliation(s)
- Mohammed Suliman AlMogbel
- Molecular Diagnostic and Personalized Therapeutics Unit, College of Applied Medical Sciences, University of Ha'il, Hail, Saudi Arabia.
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25
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Rimoldi G, Uzal F, Chin RP, Palombo EA, Awad M, Lyras D, Shivaprasad HL. Necrotic Enteritis in Chickens Associated with Clostridium sordellii. Avian Dis 2015; 59:447-51. [PMID: 26478166 DOI: 10.1637/11077-033115-case.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Three outbreaks of necrotic enteritis-like disease associated with Clostridium sordelii were diagnosed in commercial broiler chicken flocks with 18,000 to 31,000 birds between 18 and 26 days old. Clinical signs in the affected flocks included high mortality up to 2% a day, depression, and diarrhea. The main gross changes included segmental dilation of the small intestine with watery contents, gas, mucoid exudate, and roughened and uneven mucosa, occasionally covered with a pseudomembrane. Microscopic lesions in the small intestine were characterized by extensive areas of coagulative necrosis of the villi, fibrinous exudate in the lumen, and high numbers of large, Gram-positive rods, occasionally containing subterminal spores, seen in the necrotic tissue and lumen. These rods were identified as C. sordellii by immunohistochemistry. Clostridium sordellii was isolated in an almost pure culture from the intestine of affected birds. A retrospective study of commercial broiler chicken and turkey submissions to the California Animal Health and Food Safety Laboratory System revealed that C. sordellii had been isolated from intestinal lesions in outbreaks of necrotic enteritis-like disease in 8 of 39 cases, 5 times together with Clostridium perfringens and 3 times alone. The latter three cases are reported here.
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Kiyosuke M, Kibe Y, Oho M, Kusaba K, Shimono N, Hotta T, Kang D, Shoubuike T, Miyamoto H. Comparison of two types of matrix-assisted laser desorption/ionization time-of-flight mass spectrometer for the identification and typing of Clostridium difficile. J Med Microbiol 2015; 64:1144-1150. [DOI: 10.1099/jmm.0.000136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Makiko Kiyosuke
- Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
- Center for the Study of Global Infection, Kyushu University Hospital, Fukuoka, Japan
| | - Yasushi Kibe
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Megumi Oho
- Department of Laboratory Medicine, Saga University Hospital, Saga, Japan
| | - Koji Kusaba
- Department of Laboratory Medicine, Saga University Hospital, Saga, Japan
| | - Nobuyuki Shimono
- Center for the Study of Global Infection, Kyushu University Hospital, Fukuoka, Japan
| | - Taeko Hotta
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Takeo Shoubuike
- Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
| | - Hiroshi Miyamoto
- Division of Microbiology, Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, Japan
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Randazzo A, Kornreich A, Lissoir B. A Clostridium hathewayi isolate in blood culture of a patient with an acute appendicitis. Anaerobe 2015; 35:44-7. [PMID: 26187681 DOI: 10.1016/j.anaerobe.2015.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/01/2015] [Accepted: 07/14/2015] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Clostridium species is a group of anaerobic bacteria constituting the colonic microflora of the intestinal tract. Since molecular methodologies based on 16 rRNA have been established for the classification and the recognition of bacterial species, more than 150 species of Clostridium have been described. Most are considered harmless saprophytes; however, these bacteria may be involved in a wide variety of infections and may be a common cause of enteritis and enterotoxemias in humans. CASE PRESENTATION We present the case of a 60-year-old Asian patient admitted in the emergency room with an acute appendicitis where a blood culture showed the presence of a Clostridium hathewayi. This microorganism is an anaerobic bacteria described in 2001 as a Gram negative end-pointed bacillus, usually endospore-forming. It was reclassified in 2014 as Hungatella hathewayi. A literature review has been performed to find articles relating to this bacteria in a clinical case. CONCLUSION C. hathewayi is microorganism recently reclassified as Hungatella hathewayi. Its growth in blood cultures has been reported in a few cases in the literature. Although only a few articles have reported its involvement in clinical infections, we assess that its part in the cause of the illness should be evaluated.
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Affiliation(s)
- Adrien Randazzo
- Medical Laboratory, Grand Hôpital de Charleroi, Rue Marguerite Depasse 6, 6060 Gilly, Belgium.
| | - Anne Kornreich
- Medical Laboratory, Grand Hôpital de Charleroi, Rue Marguerite Depasse 6, 6060 Gilly, Belgium.
| | - Bénédicte Lissoir
- Department of Microbiology, Medical Laboratory, Grand Hôpital de Charleroi, Rue Marguerite Depasse 6, 6060 Gilly, Belgium.
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Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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