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Lichtenegger AS, Posadas-Cantera S, Badr MT, Häcker G. Comparison of the diversity of anaerobic-cultured gut bacterial communities on different culture media using 16S rDNA sequencing. J Microbiol Methods 2024; 224:106988. [PMID: 38977080 DOI: 10.1016/j.mimet.2024.106988] [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: 02/16/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
The gut microbiome is a dense and diverse community of different microorganisms that deeply influence human physiology and that have important interactions with pathogens. For the correct antibiotic treatment of infections, with its twin goals of effective inhibition of the pathogen and limitation of collateral damage to the microbiome, the identification of infectious organisms is key. Microbiological culturing is still the mainstay of pathogen identification, and anaerobic species are among the most demanding bacterial communities to culture. This study aimed to evaluate the impact of growth media on the culture of an-aerobic bacteria from human stool samples. Stool samples from eight human subjects were cultured each on a yeast extract cysteine blood agar (HCB) and a modified peptone-yeast extract-glucose (MPYG) plate and subjected to Illumina NGS analysis after DNA extraction and amplification. The results showed tight clustering of sequencing samples belonging to the same human subject. Various differences in bacterial richness and evenness could be observed between the two media, with HCB plates supporting the growth of a more diverse microbial community, and MPYG plates improving the growth rates of certain taxa. No statistical significance was observed between the groups. This study highlights the importance of choosing the appropriate growth media for anaerobic bacterial culture and adjusting culture conditions to target specific pathological conditions. HCB plates are suitable for standard microbiological diagnostics, while MPYG plates may be more appropriate for targeting specific conditions. This work emphasizes the role of next-generation sequencing in supporting future research in clinical microbiology.
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Affiliation(s)
- Anne Sophie Lichtenegger
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany.
| | - Sara Posadas-Cantera
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Georg Häcker
- Institute of Medical Microbiology and Hygiene, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
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2
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Hulme JP. Emerging Diagnostics in Clostridioides difficile Infection. Int J Mol Sci 2024; 25:8672. [PMID: 39201359 PMCID: PMC11354687 DOI: 10.3390/ijms25168672] [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: 06/24/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Clostridioides difficile detection in community settings is time-intensive, resulting in delays in diagnosing and quarantining infected individuals. However, with the advent of semi-automated devices and improved algorithms in recent decades, the ability to discern CDI infection from asymptomatic carriage has significantly improved. This, in turn, has led to efficiently regulated monitoring systems, further reducing endemic risk, with recent concerns regarding a possible surge in hospital-acquired Clostridioides difficile infections post-COVID failing to materialize. This review highlights established and emerging technologies used to detect community-acquired Clostridioides difficile in research and clinical settings.
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Affiliation(s)
- John P Hulme
- Department of Bio-Nano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
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3
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Purwanti IF, Abdullah SRS, Hamzah A, Idris M, Basri H, Latif MT, Mukhlisin M, Kurniawan SB, Imron MF. Maximizing diesel removal from contaminated sand using Scirpus mucronatus and assessment of rhizobacteria addition effect. Heliyon 2023; 9:e21737. [PMID: 38027659 PMCID: PMC10665750 DOI: 10.1016/j.heliyon.2023.e21737] [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: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Phytoremediation is one of the green technologies that is friendly to nature, utilizes fewer chemicals, and exhibits good performance. In this study, phytoremediation was used to treat diesel-contaminated sand using a local aquatic plant species, Scirpus mucronatus, by analyzing the amount of total petroleum hydrocarbons (TPHs). Optimization of diesel removal was performed according to Response Surface Methodology (RSM) using Box-Behnken Design (BBD) under pilot-scale conditions. The quadratic model showed the best fit to describe the obtained data. Actual vs. predicted values from BBD showed a total of 9.1 % error for the concentration of TPH in sand and 0 % error for the concentration of TPH in plants. Maximum TPH removal of 42.3 ± 2.1 % was obtained under optimized conditions at a diesel initial concentration of 50 mg/kg, an aeration rate of 0.48 L/min, and a retention time of 72 days. The addition of two species of rhizobacteria (Bacillus subtilis and Bacillus licheniformis) at optimum conditions increased the TPH removal to 51.9 ± 2.6 %. The obtained model and optimum condition can be adopted to treat diesel-contaminated sand within the same TPH range (50-3000 mg/kg) in sand.
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Affiliation(s)
- Ipung Fitri Purwanti
- Department of Environmental Engineering, Faculty of Civil, Planning, And Geo Engineering, Institut Teknologi Sepuluh Nopember, Kampus ITS Sukolilo, Surabaya 60111, Indonesia
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Siti Rozaimah Sheikh Abdullah
- Department of Chemical and Process Engineering, Faculty of Engineering and Built Environment, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Ainon Hamzah
- School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Mushrifah Idris
- Tasik Chini Research Center, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| | - Hassan Basri
- Department of Civil and Structural Engineering, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| | - Mohd Talib Latif
- School of Environmental Science and Natural Resources, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
| | - Muhammad Mukhlisin
- Department of Civil Engineering, Politeknik Negeri Semarang, 50275 Semarang, Indonesia
| | - Setyo Budi Kurniawan
- Laboratory of Algal Biotechnology, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Opatovický Mlýn, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - Muhammad Fauzul Imron
- Study Program of Environmental Engineering, Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Kampus C UNAIR, Jalan Mulyorejo, Surabaya 60115, Indonesia
- Department of Water Management, Faculty of Civil Engineering and Geosciences, Delft University of Technology, Stevinweg 1, CN Delft 2628, Netherlands
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Leite S, Cotias C, Rainha KC, Santos MG, Penna B, F Moraes RF, Harmanus C, Smits WK, Ferreira EDO. Prevalence of Clostridioides difficile in dogs (Canis familiaris) with gastrointestinal disorders in Rio de Janeiro. Anaerobe 2023; 83:102765. [PMID: 37573963 DOI: 10.1016/j.anaerobe.2023.102765] [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: 04/04/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023]
Abstract
Clostridioides difficile infections (CDI) have a high morbidity and mortality rate and have always been considered a nosocomial disease. Nonetheless, the number of cases of community-acquired CDI is increasing, and new evidence suggests additional C. difficile reservoirs exist. Pathogenic C. difficile strains have been found in livestock, domestic animals, and meat, so a zoonotic transmission has been proposed. OBJECTIVE The goal of this study was to isolate C. difficile strains in dogs at a veterinary clinic in Rio de Janeiro, Brazil, and characterize clinical and pathological findings associated with lower gastrointestinal tract disorders. METHODS Fifty stool samples and biopsy fragments from dogs were obtained and cultured in the CDBA selective medium. All suggestive C. difficile colonies were confirmed by MALDI-TOF MS and PCR (tpi gene). Vancomycin, metronidazole, moxifloxacin, erythromycin, and rifampicin were tested for antibiotic susceptibility. Biofilm, motility assays, and a PCR for the toxins (tcdA, tcdB, and cdtB), as well as ribotyping, were also performed. RESULTS Blood samples and colonic biopsy fragments were examined in C. difficile positive dogs. Ten animals (20%) tested positive for C. difficile by using stool samples, but not from biopsy fragments. Most C. difficile strains were toxigenic: six were A+B+ belonging to RT106; two were A+B+ belonging to RT014/020; and two were A-B- belonging to RT010. All strains were biofilm producers. In the motility test, 40% of strains were as motile as the positive control, CD630 (RT012). In the disc diffusion test, two strains (RT010) were resistant to erythromycin and metronidazole; and another to metronidazole (RT014/020). In terms of C. difficile clinicopathological correlations, no statistically significant morphological changes, such as pseudomembranous and "volcano" lesions, were observed. Regarding hematological data, dogs positive for C. difficile had leucopenia (p = 0.02) and lymphopenia (p = 0.03). There was a significant correlation between senility and the presence of C. difficile in the dogs studied (p = 0,02). CONCLUSIONS Although C. difficile has not been linked to canine diarrheal disorders, it appears to be more common in dogs with intestinal dysfunctions. The isolation of ribotypes frequently involved in human CDI outbreaks around the world supports the theory of C. difficile zoonotic transmission.
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Affiliation(s)
- Suzana Leite
- Departmento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes -IMPG, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Universidade Santa Úrsula, Rio de Janeiro, Brazil
| | - Carlos Cotias
- H&Diagnóstico, Veterinary Diagnosis Center, Rio de Janeiro, Brazil
| | | | | | - Bruno Penna
- Departmento de Microbiologia e Parasitologia, Instituto de Biomedicina, Universidade Federal Fluminense- UFF, Niterói, Brazil
| | | | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eliane de Oliveira Ferreira
- Departmento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes -IMPG, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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Baek C, Li YG, Yoo HJ, Cui WY, Kang JT, Son J, Min J. Simple and portable on-site system for nucleic acid-based detection of Clostridium difficile in stool samples using two columns containing microbeads and loop-mediated isothermal amplification. Anal Bioanal Chem 2021; 414:613-621. [PMID: 34341839 DOI: 10.1007/s00216-021-03557-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/10/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
It is challenging to employ nucleic acid-based diagnostics for the in situ detection of Clostridium difficile from complex fecal samples because essential sample preparation and amplification procedures require various experimental resources. In this study, a simple and effective on-site nucleic acid-based detection system was used to detect C. difficile in stool samples. Two columns containing different microbeads, namely, glass and functionalized graphene oxide-coated microbeads, were designed to remove relatively large impurities by filtration and concentrate bacteria, including C. difficile, from stool samples by adsorption. The bacterial nucleic acids were effectively extracted using a small bead beater. The effectiveness of enzyme inhibitors remaining in the sample was efficiently reduced by the direct buffer developed in this study. This sample preparation kit consisting of two simple columns showed better performance in real-time polymerase chain reaction (PCR) and equivalent performance in loop-mediated isothermal amplification (LAMP) than other sample preparation kits, despite 90% simplification of the process. The amplification-ready samples were introduced into two microtubes containing LAMP pre-mixtures (one each for E. coli as an external positive control and C. difficile) by a simple sample loader, which was operated using a syringe. LAMP, which indicates amplification based on color change, was performed at 65 °C in a small water bath. The limit of detection (L.O.D) and analytical sensitivity/specificity of our simple and effective kit were compared with those of a commercial kit. C. difficile in stool samples could be detected within 1 h with 103 cfu/10 mg using LAMP combined simple on-site detection kit.
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Affiliation(s)
- Changyoon Baek
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, South Korea
| | - Yun Guang Li
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, South Korea
| | - Hyun Jin Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, South Korea
| | - Wen Ying Cui
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, South Korea
| | - Jia Tong Kang
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, South Korea
| | - Juwon Son
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, South Korea
| | - Junhong Min
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, South Korea.
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Appert O, Garcia AR, Frei R, Roduit C, Constancias F, Neuzil-Bunesova V, Ferstl R, Zhang J, Akdis C, Lauener R, Lacroix C, Schwab C. Initial butyrate producers during infant gut microbiota development are endospore formers. Environ Microbiol 2020; 22:3909-3921. [PMID: 32686173 DOI: 10.1111/1462-2920.15167] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022]
Abstract
The acquisition of the infant gut microbiota is key to establishing a host-microbiota symbiosis. Microbially produced metabolites tightly interact with the immune system, and the fermentation-derived short-chain fatty acid butyrate is considered an important mediator linked to chronic diseases later in life. The intestinal butyrate-forming bacterial population is taxonomically and functionally diverse and includes endospore formers with high transmission potential. Succession, and contribution of butyrate-producing taxa during infant gut microbiota development have been little investigated. We determined the abundance of major butyrate-forming groups and fermentation metabolites in faeces, isolated, cultivated and characterized the heat-resistant cell population, which included endospores, and compared butyrate formation efficiency of representative taxa in batch cultures. The endospore community contributed about 0.001% to total cells, and was mainly composed of the pioneer butyrate-producing Clostridium sensu stricto. We observed an increase in abundance of Faecalibacterium prausnitzii, butyrate-producing Lachnospiraceae and faecal butyrate levels with age that is likely explained by higher butyrate production capacity of contributing taxa compared with Clostridium sensu stricto. Our data suggest that a successional arrangement and an overall increase in abundance of butyrate forming populations occur during the first year of life, which is associated with an increase of intestinal butyrate formation capacity.
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Affiliation(s)
- Olivia Appert
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Alejandro Ramirez Garcia
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Remo Frei
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Division of Respiratory Medicine, Department of Paediatrics, Inselspital, University of Bern, Bern, Switzerland
| | - Caroline Roduit
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,University Children's Hospital Zürich, Zürich, Switzerland.,Children's Hospital St. Gallen, St. Gallen, Switzerland
| | - Florentin Constancias
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Vera Neuzil-Bunesova
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague, Czech Republic
| | - Ruth Ferstl
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Jianbo Zhang
- Laboratory of Toxicology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Cezmi Akdis
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Roger Lauener
- Christine Kühne-Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.,Children's Hospital St. Gallen, St. Gallen, Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Clarissa Schwab
- Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland.,Division of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
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7
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Alimolaei M, Rahimi HR, Ezatkhah M, Shamsaddini Bafti M, Afzali S. Prevalence, characteristics and antimicrobial susceptibility patterns of Clostridioides difficile isolated from hospitals in Iran. J Glob Antimicrob Resist 2019; 19:22-27. [PMID: 30825696 DOI: 10.1016/j.jgar.2019.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Revised: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Clostridioides (previously Clostridium) difficile is a major growing cause of nosocomial diarrhoea known as C. difficile infection (CDI). This study investigated the prevalence and antimicrobial resistance patterns of C. difficile isolated from patients suffering from diarrhoea in Iran between 2016-2018. METHODS A total of 151 stool specimens were collected and were screened for the presence of C. difficile. Specimens were examined for toxins by culture, enzyme immunoassay (EIA) and PCR. Antimicrobial susceptibility testing was performed for 12 antibiotics (metronidazole, vancomycin, clindamycin, tetracycline, erythromycin, ciprofloxacin, levofloxacin, moxifloxacin, fusidic acid, piperacillin, piperacillin/tazobactam and rifampicin) by the disk diffusion method according to the guidelines of the CLSI, EUCAST and CA-SFM. RESULTS Of 151 stool specimens, 66 (43.7%) were positive for C. difficile by PCR, whereas 2 (1.3%) were only positive for C. difficile toxins based on EIA. A total of 292 clostridial isolates were obtained from specimens by culture, of which 133 (45.5%) were finally confirmed as C. difficile by PCR. Of 121 isolates resistant to at least one antibiotic, 107 (88.4%) were resistant to three or more antimicrobials and thus were defined as multidrug-resistant (MDR). Different and diverse resistance patterns to the antimicrobial drugs were seen among the isolates. CONCLUSION This is the first report of the isolation of C. difficile from different governmental hospitals of Iran and indicates that CDI might be an important nosocomial infection in different hospital wards. Moreover, this study provides a comprehensive picture of the MDR phenotype characteristics of C. difficile isolates in Iran.
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Affiliation(s)
- Mojtaba Alimolaei
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran; Department of Research and Technology, Kerman Branch, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kerman, Iran.
| | - Hamid-Reza Rahimi
- Department of Toxicology and Pharmacology, School of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran
| | - Majid Ezatkhah
- Department of Anaerobic Bacterial Vaccine Research and Production, Kerman Branch, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kerman, Iran
| | - Mehrdad Shamsaddini Bafti
- Department of Anaerobic Bacterial Vaccine Research and Production, Kerman Branch, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kerman, Iran
| | - Sadegh Afzali
- Department of Research and Technology, Kerman Branch, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Kerman, Iran
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8
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Development of an optimized broth enrichment culture medium for the isolation of Clostridium difficile. Anaerobe 2018; 54:92-99. [DOI: 10.1016/j.anaerobe.2018.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/26/2018] [Accepted: 08/13/2018] [Indexed: 02/04/2023]
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de Oliveira CA, de Paula Gabardo M, Guedes RMC, Poncet F, Blanc DS, Lobato FCF, Silva ROS. Rodents are carriers of Clostridioides difficile strains similar to those isolated from piglets. Anaerobe 2018; 51:61-63. [DOI: 10.1016/j.anaerobe.2018.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/08/2018] [Indexed: 02/04/2023]
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Biasizzo M, Vadnjal S, Henigman U, Krizman M, Kirbis A, Jamnikar-Ciglenecki U. Development and Validation of a New Protocol for Detecting and Recovering Clostridium difficile from Meat Samples. J Food Prot 2018; 81:561-568. [PMID: 29517350 DOI: 10.4315/0362-028x.jfp-17-354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is no recommended protocol for detecting and isolating Clostridium difficile present in food samples. Here, we have evaluated the recovery of C. difficile in meat samples after incubating them in various enrichment broths. The media were as follows: cycloserine-cefoxitin fructose broth supplemented with taurocholic acid, d-cycloserine, cefoxitin, and lysozyme; cycloserine-cefoxitin mannitol broth with taurocholate and lysozyme; and cycloserine-cefoxitin fructose broth supplemented with taurocholic acid, C. difficile moxalactam norfloxacin selective supplement, and lysozyme. Samples were inoculated with various strains and quantities of C. difficile and then enriched in the different broths for 1, 4, and 7 days. C. difficile was isolated on agar plates and detected with quantitative real-time PCR (qPCR). The procedure using enrichment in cycloserine-cefoxitin fructose broth supplemented with taurocholic acid, d-cycloserine, cefoxitin, and lysozyme and incubation for 4 days for qPCR detection and 7 days for isolation (plating on C. difficile agar base with added C. difficile selective supplement and 7% [v/v] defibrinated horse blood after alcoholic shock and centrifugation) was validated. Samples of different kinds of meat and meat preparation were contaminated and used for validation of the chosen protocol. The sensitivity of detection with qPCR was 100%, and the sensitivity of the isolation method was 96%.
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Affiliation(s)
- Majda Biasizzo
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Stanka Vadnjal
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Urska Henigman
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Manja Krizman
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Andrej Kirbis
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Urska Jamnikar-Ciglenecki
- Institute of Food Safety, Feed and Environment, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
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11
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Pickering DS, Vernon JJ, Freeman J, Wilcox MH, Chilton CH. Investigating the effect of supplementation on Clostridioides (Clostridium) difficile spore recovery in two solid agars. Anaerobe 2018; 50:38-43. [PMID: 29408598 DOI: 10.1016/j.anaerobe.2018.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 01/22/2018] [Accepted: 01/28/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND A variety of supplemented solid media are used within Clostridium difficile research to optimally recover spores. Our study sought to investigate different media and additives, providing a method of optimised C. difficile spore recovery. Additionally, due to the results observed in the initial experiments, the inhibitory effects of three amino acids (glycine, l-histidine &l-phenylalanine) on C. difficile spore outgrowth were investigated. METHODS Spores of five C. difficile strains (PCR ribotypes 001,015,020,027,078) were recovered on two commonly used solid media (BHI & CCEY, or cycloserine-cefoxitin egg yolk) supplemented with various concentrations of germinants (taurocholate, glycine & lysozyme). Agar-incorporation minimum inhibitory concentration (MIC) testing was carried out for glycine and taurocholate on vegetative cells and spores of all five strains. Additionally a BHI broth microassay method was utilised to test the growth of C. difficile in the presence of increasing concentrations (0,1,2,3,4%) of three amino acids (glycine,l-histidine,l-phenyalanine). RESULTS CCEY agar alone and BHI supplemented with taurocholate (0.1/1%) provided optimal recovery for C. difficile spores. Glycine was inhibitory to spore recovery at higher concentrations, although these varied between the two media used. In agar-incorporated MIC testing, glycine concentrations higher than 2% (20 g/L) were inhibitory to both C. difficile spore and vegetative cell growth versus the control (mean absorbance = 0.33 ± 0.02 vs 0.12 ± 0.01) (P < 0.001). This indicates a potential mechanism whereby glycine interferes with vegetative cell growth. Further microbroth testing provided evidence of inhibition by two amino acids other than glycine, l-histidine and l-phenylalanine. CONCLUSIONS We provide two media for optimal recovery of C. difficile spores (CCEY alone and BHI supplemented with 0.1/1% taurocholate). CCEY is preferred for isolation from faecal samples. For pure cultures, either CCEY or supplemented BHI agar are appropriate. The inhibitory nature of three amino acids (glycine,l-histidine,l-phenylalanine) to C. difficile vegetative cell proliferation is also highlighted.
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Affiliation(s)
- D S Pickering
- Healthcare Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, West Yorkshire, UK.
| | - J J Vernon
- Healthcare Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, West Yorkshire, UK
| | - J Freeman
- Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
| | - M H Wilcox
- Healthcare Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, West Yorkshire, UK; Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
| | - C H Chilton
- Healthcare Associated Infections Research Group, Molecular Gastroenterology, Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, West Yorkshire, UK
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12
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PCR-ribotype distribution of Clostridium difficile in Irish pigs. Anaerobe 2017; 48:237-241. [DOI: 10.1016/j.anaerobe.2017.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/25/2017] [Accepted: 10/07/2017] [Indexed: 01/05/2023]
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Martínez-Meléndez A, Camacho-Ortiz A, Morfin-Otero R, Maldonado-Garza HJ, Villarreal-Treviño L, Garza-González E. Current knowledge on the laboratory diagnosis of Clostridium difficile infection. World J Gastroenterol 2017; 23:1552-1567. [PMID: 28321156 PMCID: PMC5340807 DOI: 10.3748/wjg.v23.i9.1552] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/21/2017] [Accepted: 02/17/2017] [Indexed: 02/06/2023] Open
Abstract
Clostridium difficile (C. difficile) is a spore-forming, toxin-producing, gram-positive anaerobic bacterium that is the principal etiologic agent of antibiotic-associated diarrhea. Infection with C. difficile (CDI) is characterized by diarrhea in clinical syndromes that vary from self-limited to mild or severe. Since its initial recognition as the causative agent of pseudomembranous colitis, C. difficile has spread around the world. CDI is one of the most common healthcare-associated infections and a significant cause of morbidity and mortality among older adult hospitalized patients. Due to extensive antibiotic usage, the number of CDIs has increased. Diagnosis of CDI is often difficult and has a substantial impact on the management of patients with the disease, mainly with regards to antibiotic management. The diagnosis of CDI is primarily based on the clinical signs and symptoms and is only confirmed by laboratory testing. Despite the high burden of CDI and the increasing interest in the disease, episodes of CDI are often misdiagnosed. The reasons for misdiagnosis are the lack of clinical suspicion or the use of inappropriate tests. The proper diagnosis of CDI reduces transmission, prevents inadequate or unnecessary treatments, and assures best antibiotic treatment. We review the options for the laboratory diagnosis of CDI within the settings of the most accepted guidelines for CDI diagnosis, treatment, and prevention of CDI.
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Coinfection and Emergence of Rifamycin Resistance during a Recurrent Clostridium difficile Infection. J Clin Microbiol 2016; 54:2689-2694. [PMID: 27558181 DOI: 10.1128/jcm.01025-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/15/2016] [Indexed: 01/04/2023] Open
Abstract
Clostridium difficile (Peptoclostridium difficile) is a common health care-associated infection with a disproportionately high incidence in elderly patients. Disease symptoms range from mild diarrhea to life-threatening pseudomembranous colitis. Around 20% of patients may suffer recurrent disease, which often requires rehospitalization of patients. C. difficile was isolated from stool samples from a patient with two recurrent C. difficile infections. PCR ribotyping, whole-genome sequencing, and phenotypic assays were used to characterize these isolates. Genotypic and phenotypic screening of C. difficile isolates revealed multiple PCR ribotypes present and the emergence of rifamycin resistance during the infection cycle. Understanding both the clinical and bacterial factors that contribute to the course of recurrent infection could inform strategies to reduce recurrence. (This study has been registered at ClinicalTrials.gov under registration no. NCT01670149.).
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Rodriguez C, Warszawski N, Korsak N, Taminiau B, Van Broeck J, Delmée M, Daube G. Laboratory identification of anaerobic bacteria isolated on Clostridium difficile selective medium. Acta Microbiol Immunol Hung 2016; 63:171-84. [PMID: 27352971 DOI: 10.1556/030.63.2016.2.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite increasing interest in the bacterium, the methodology for Clostridium difficile recovery has not yet been standardized. Cycloserine-cefoxitin fructose taurocholate (CCFT) has historically been the most used medium for C. difficile isolation from human, animal, environmental, and food samples, and presumptive identification is usually based on colony morphologies. However, CCFT is not totally selective. This study describes the recovery of 24 bacteria species belonging to 10 different genera other than C. difficile, present in the environment and foods of a retirement establishment that were not inhibited in the C. difficile selective medium. These findings provide insight for further environmental and food studies as well as for the isolation of C. difficile on supplemented CCFT.
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Affiliation(s)
- Cristina Rodriguez
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège , Liège, Belgium
| | - Nathalie Warszawski
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège , Liège, Belgium
| | - Nicolas Korsak
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège , Liège, Belgium
| | - Bernard Taminiau
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège , Liège, Belgium
| | - Johan Van Broeck
- Belgian Reference Centre for Clostridium difficile (NRC), Pôle de microbiologiemédicale, UniversitéCatholique de Louvain , Brussels, Belgium
| | - Michel Delmée
- Belgian Reference Centre for Clostridium difficile (NRC), Pôle de microbiologiemédicale, UniversitéCatholique de Louvain , Brussels, Belgium
| | - Georges Daube
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège , Liège, Belgium
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Rodriguez C, Van Broeck J, Taminiau B, Delmée M, Daube G. Clostridium difficile infection: Early history, diagnosis and molecular strain typing methods. Microb Pathog 2016; 97:59-78. [PMID: 27238460 DOI: 10.1016/j.micpath.2016.05.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 01/05/2023]
Abstract
Recognised as the leading cause of nosocomial antibiotic-associated diarrhoea, the incidence of Clostridium difficile infection (CDI) remains high despite efforts to improve prevention and reduce the spread of the bacterium in healthcare settings. In the last decade, many studies have focused on the epidemiology and rapid diagnosis of CDI. In addition, different typing methods have been developed for epidemiological studies. This review explores the history of C. difficile and the current scope of the infection. The variety of available laboratory tests for CDI diagnosis and strain typing methods are also examined.
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Affiliation(s)
- C Rodriguez
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - J Van Broeck
- Belgian Reference Centre for Clostridium Difficile (NRC), Pôle de microbiologie médicale, Université Catholique de Louvain, Brussels, Belgium
| | - B Taminiau
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - M Delmée
- Belgian Reference Centre for Clostridium Difficile (NRC), Pôle de microbiologie médicale, Université Catholique de Louvain, Brussels, Belgium
| | - G Daube
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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Abstract
The best laboratory diagnostic approach to detect Clostridium difficile infection (CDI) is the subject of ongoing debate. In the United States, nucleic acid amplification tests (NAAT) have become the most widely used tests for making this diagnosis. Detection of toxin in stool may be a better predictor of CDI disease and severity. Laboratories that have switched from toxin-based to NAAT-based methods have significantly higher CDI detection rates. The important issue is whether all NAAT-positive patients have CDI or at least some of those patients are excretors of the organism and do not have clinical disease.
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Affiliation(s)
- Peter H Gilligan
- Clinical Microbiology-Immunology Laboratories, Microbiology-Immunology, UNC Health Care, UNC School of Medicine, CB 7600, Chapel Hill, NC 27516, USA; Pathology-Laboratory Medicine, UNC School of Medicine, CB 7600, Chapel Hill, NC 27516, USA.
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