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Bogiel T, Dura A, Woźniak M, Mikucka A, Kanarek P. Usefulness of Capillary Gel Electrophoresis-Based PCR for Detection of Clostridioides difficile Strains with Hypervirulent Ribotypes. Gels 2024; 10:343. [PMID: 38786259 PMCID: PMC11121280 DOI: 10.3390/gels10050343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Clostridioides difficile is a complex of anaerobic bacteria responsible for the epidemics of post-antibiotic diarrhea as one of the examples of CDI (Clostridioides difficile infection). As many as 70% of cases concern hospitalized patients, particularly those in intensive care units. Ribotyping is one of the most common methods for differentiating bacterial strains. The purpose of this work was to show the effectiveness of the gel electrophoresis-based PCR ribotyping method and the Webribo database for typing C. difficile isolates, including the hypervirulent 027 ribotype. DNA samples extracted from 69 C. difficile strains with previously marked genotypes were included in this study. PCR was performed using 16S-23S primers, and capillary gel electrophoresis was performed on the Applied Biosystem 3130xl Genetic Analyzer. The Webribo database was applied for ribotype assignment. Out of 69 samples, 48 belonged to already known ribotypes, 13 represented new ribotypes and 8 was indicated as similar to the existing ones, having some differences. Capillary gel electrophoresis-based PCR is an effective method for the differentiation of C. difficile ribotypes and can be recognized as a very useful tool in epidemiological studies, while the Webribo database is a useful and an accessible database for a quick analysis of C. difficile ribotypes.
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Affiliation(s)
- Tomasz Bogiel
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland;
- Department of Clinical Microbiology, Antoni Jurasz University Hospital No. 1, 85-094 Bydgoszcz, Poland
| | - Alicja Dura
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland; (A.D.)
| | - Marcin Woźniak
- Department of Forensic Medicine, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, 87-100 Toruń, Poland; (A.D.)
| | - Agnieszka Mikucka
- Department of Microbiology, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, 85-094 Bydgoszcz, Poland;
- Department of Clinical Microbiology, Antoni Jurasz University Hospital No. 1, 85-094 Bydgoszcz, Poland
| | - Piotr Kanarek
- Department of Microbiology and Food Technology, Faculty of Agriculture and Biotechnology, Bydgoszcz University of Science and Technology, 85-029 Bydgoszcz, Poland
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High Prevalence of Clostridioides difficile Ribotype 176 in the University Hospital in Kosice. Pathogens 2023; 12:pathogens12030430. [PMID: 36986352 PMCID: PMC10055383 DOI: 10.3390/pathogens12030430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Dysbiosis of the gut microbiota, caused by antibiotics, plays a key role in the establishment of Clostridioides difficile CD). Toxin-producing strains are involved in the pathogenesis of Clostridioides difficile infection (CDI), one of the most common hospital-acquired infections. We cultured a total of 84 C. difficile isolates from stool samples of patients hospitalized at Louis Pasteur University Hospital in Kosice, Slovakia, that were suspected of CDI and further characterized by molecular methods. The presence of genes encoding toxin A, toxin B, and binary toxin was assessed by toxin-specific PCR. CD ribotypes were detected using capillary-based electrophoresis ribotyping. A total of 96.4% of CD isolates carried genes encoding toxins A and B, and 54.8% of them were positive for the binary toxin. PCR ribotyping showed the presence of three major ribotypes: RT 176 (n = 40, 47.6%); RT 001 (n = 23, 27.4%); and RT 014 (n = 7, 8.3%). Ribotype 176 predominated among clinical CD isolates in our hospital. The proportion of RT 176 and RT 001 in four hospital departments with the highest incidence of CDI cases was very specific, pointing to local CDI outbreaks. Based on our data, previous use of antibiotics represents a significant risk factor for the development of CDI in patients over 65 years of age.
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Novakova E, Kotlebova N, Gryndlerova A, Novak M, Vladarova M, Wilcox M, Kuijper E, Krutova M. An Outbreak of Clostridium ( Clostridioides) difficile Infections within an Acute and Long-Term Care Wards Due to Moxifloxacin-Resistant PCR Ribotype 176 Genotyped as PCR Ribotype 027 by a Commercial Assay. J Clin Med 2020; 9:jcm9113738. [PMID: 33233843 PMCID: PMC7699857 DOI: 10.3390/jcm9113738] [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] [Received: 10/06/2020] [Revised: 11/09/2020] [Accepted: 11/18/2020] [Indexed: 01/05/2023] Open
Abstract
We aimed to characterize Clostridioides difficile isolates cultured during a six-month single-center study from stool samples of patients with C. difficile infection (CDI) genotyped by the Xpert®C. difficile/Epi assay by polymerase chain reaction (PCR) ribotyping, toxin genes’ detection and multi-locus variable number tandem repeats analysis (MLVA). The susceptibility to metronidazole, vancomycin and moxifloxacin was determined by agar dilution. In addition, the presence of Thr82Ile in the GyrA and a single nucleotide deletion at position (Δ117) in the tcdC gene were investigated. Between January 1 and June 30, 2016, of 114 CDIs, 75 cases were genotyped as presumptive PCR ribotype (RT) 027 infections using a commercial assay. C. difficile isolates cultured from presumptive RT027 stool samples belonged to RT176. These isolates carried genes for toxin A (tcdA), B (tcdB), binary (cdtA/B) and had Δ117 in the tcdC gene. Using MLVA, the 71/75 isolates clustered into two clonal complexes (CCs). Of these, 39 isolates (54.9%) were from patients hospitalized in acute care and 32 isolates (45.1%) were isolated from patients hospitalized in the long-term care department. All isolates were susceptible to metronidazole and vancomycin, and 105 isolates were resistant to moxifloxacin (92%) carrying Thr83Ile in the GyrA. An outbreak of RT176 CDIs, suspected as RT027, was recognized in a Slovakian hospital. In order to monitor the emergence and spread of RT027-variants, the identification of a presumptive RT027 CDI should be confirmed at a strain level by PCR ribotyping.
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Affiliation(s)
- Elena Novakova
- Department of Microbiology and Immunology, Comenius University Jessenius Faculty of Medicine, 036 01 Martin, Slovakia; (E.N.); (N.K.); (M.N.)
| | - Nina Kotlebova
- Department of Microbiology and Immunology, Comenius University Jessenius Faculty of Medicine, 036 01 Martin, Slovakia; (E.N.); (N.K.); (M.N.)
| | - Anezka Gryndlerova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, 150 06 Prague, Czech Republic;
| | - Martin Novak
- Department of Microbiology and Immunology, Comenius University Jessenius Faculty of Medicine, 036 01 Martin, Slovakia; (E.N.); (N.K.); (M.N.)
| | - Michala Vladarova
- Department of Clinical Microbiology, Clinical Biochemistry Inc., 012 07 Zilina, Slovakia;
| | - Mark Wilcox
- Healthcare Associated Infection Research Group, Leeds Teaching Hospitals NHS Trust & University of Leeds, Leeds LS2 9JT, UK;
| | - Ed Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, 2300 Leiden, The Netherlands;
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, 150 06 Prague, Czech Republic;
- Correspondence:
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Novakova E, Stefkovicova M, Kopilec MG, Novak M, Kotlebova N, Kuijper E, Krutova M. The emergence of Clostridium difficile ribotypes 027 and 176 with a predominance of the Clostridium difficile ribotype 001 recognized in Slovakia following the European standardized Clostridium difficile infection surveillance of 2016. Int J Infect Dis 2020; 90:111-115. [PMID: 31707136 PMCID: PMC6912155 DOI: 10.1016/j.ijid.2019.10.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/26/2022] Open
Abstract
AIM To obtain standardized epidemiological data for Clostridium difficile infection (CDI) in Slovakia. METHODS Between October and December 2016, 36 hospitals in Slovakia used the European Centre for Disease Prevention and Control (ECDC) Clostridium difficile infection (CDI) surveillance protocol. RESULTS The overall mean CDI incidence density was 2.8 (95% confidence interval 1.9-3.9) cases per 10 000 patient-days. Of 332 CDI cases, 273 (84.9%) were healthcare-associated, 45 (15.1%) were community-associated, and 14 (4.2%) were cases of recurrent CDI. A complicated course of CDI was reported in 14.8% of cases (n=51). CDI outcome data were available for 95.5% of cases (n=317). Of the 35 patients (11.1%) who died, 34 did so within 30 days after their CDI diagnosis. Of the 78 isolates obtained from 12 hospitals, 46 belonged to PCR ribotype 001 (59.0%; 11 hospitals) and 23 belonged to ribotype 176 (29.5%; six hospitals). A total of 73 isolates (93.6%) showed reduced susceptibility to moxifloxacin (ribotypes 001 and 176; p< 0.01). A reduced susceptibility to metronidazole was observed in 13 isolates that subsequently proved to be metronidazole-susceptible when, after thawing, they were retested using the agar dilution method. No reduced susceptibility to vancomycin was found. CONCLUSIONS These results show the emergence of C. difficile ribotypes 027 and 176 with a predominance of ribotype 001 in Slovakia in 2016. Given that an almost homogeneous reduced susceptibility to moxifloxacin was detected in C. difficile isolates, this stresses the importance of reducing fluoroquinolone prescriptions in Slovak healthcare settings.
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Affiliation(s)
- Elena Novakova
- Department of Microbiology and Immunology, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Maria Stefkovicova
- Department of Epidemiology, Regional Public Health Authority, Trenčín, Slovakia; Department of Laboratory Medicine and Public Health, Faculty of Health Care, Alexander Dubcek University, Trenčín, Slovakia
| | | | - Martin Novak
- Department of Public Health, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Nina Kotlebova
- Department of Microbiology and Immunology, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Ed Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University in Prague, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
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Melegh S, Nyul A, Kovács K, Kovács T, Ghidán Á, Dombrádi Z, Szabó J, Berta B, Lesinszki V, Pászti J, Tóth Á, Mestyán G. Dissemination of VanA-TypeEnterococcus faeciumIsolates in Hungary. Microb Drug Resist 2018; 24:1376-1390. [DOI: 10.1089/mdr.2017.0296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Szilvia Melegh
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Adrienn Nyul
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | - Krisztina Kovács
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
| | | | - Ágoston Ghidán
- Department of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Dombrádi
- Department of Medical Microbiology, University of Debrecen, Debrecen, Hungary
| | - Judit Szabó
- Department of Medical Microbiology, University of Debrecen, Debrecen, Hungary
| | | | | | - Judit Pászti
- National Public Health Institute, Budapest, Hungary
| | - Ákos Tóth
- National Public Health Institute, Budapest, Hungary
| | - Gyula Mestyán
- Department of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
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Krehelova M, Nyč O, Sinajová E, Krutova M. The predominance and clustering of Clostridioides (Clostridium) difficile PCR ribotype 001 isolates in three hospitals in Eastern Slovakia, 2017. Folia Microbiol (Praha) 2018; 64:49-54. [PMID: 29971567 DOI: 10.1007/s12223-018-0629-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022]
Abstract
This study aimed to implement a toxigenic culture as an optional third diagnostic step for glutamate dehydrogenase (GDH)-positive and toxin A/B-negative diarrheal stool samples into a diagnostic algorithm for Clostridioides (Clostridium) difficile infection (CDI), and to characterise C. difficile isolates for epidemiological purposes. During the 5-month study, 481 diarrhoeal stool samples from three Slovak hospitals were investigated and 66 non-duplicated GDH-positive stool samples were found. Of them, 36 were also toxin A/B-positive. Twenty-three GDH-positive and toxin A/B-negative stool samples were shown subsequently to be positive following toxigenic culture (TC). Molecular characterisation of C. difficile isolates showed the predominance of PCR ribotype (RT) 001 (n = 37, 56.1%) and the occurrence of RT 176 (n = 3, 4.5%). C. difficile RT 001 isolates clustered to eight clonal complexes (CCs) using multiple-locus variable-number tandem repeats analysis (MLVA). Interestingly, one third of RT 001 isolates clustering in these CCs were cultured from toxin A/B-negative stool samples. Our observations highlight the need of use multiple step diagnostic algorithm in CDI diagnosis in order to detect all CDI cases and to avoid the spread of C. difficile in healthcare settings.
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Affiliation(s)
| | - Otakar Nyč
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Eva Sinajová
- Department of Microbiology, Medirex Group, Kosice, Slovakia
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic.
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Nagy E. What do we know about the diagnostics, treatment and epidemiology of Clostridioides (Clostridium) difficile infection in Europe? J Infect Chemother 2017; 24:164-170. [PMID: 29289484 DOI: 10.1016/j.jiac.2017.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/17/2022]
Abstract
Clostridium difficile, recently reclassified as Clostridioides difficile is responsible for a significant part of diarrheal diseases in the hospitals and in the community. Besides the main pathogenic factors, toxin A, toxin B and the binary toxin, several other putative virulence factors have been investigated. This manuscript summarize recent findings in Europe concerning source of infection, epidemiology of CDI, the changing pattern of PCR ribotypes of C. difficile strains in different European countries, recommendations for diagnosis and treatment of CDI.
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Affiliation(s)
- Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary.
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Phillips TM. Recent advances in CE and microchip-CE in clinical applications: 2014 to mid-2017. Electrophoresis 2017; 39:126-135. [PMID: 28853177 DOI: 10.1002/elps.201700283] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/11/2022]
Abstract
CE and microchip CE (ME) are powerful tools for the analysis of a number of different analytes and have been applied to a variety of clinical fields and human samples. This review will present an overview of the most recent applications of these techniques to different areas of clinical medicine during the period of 2014 to mid-2017. CE and ME have been applied to clinical chemistry, drug detection and monitoring, hematology, infectious diseases, oncology, endocrinology, neonatology, nephrology, and genetic screening. Samples examined range from serum, plasma, and urine to lest utilized materials such as tears, cerebral spinal fluid, sweat, saliva, condensed breath, single cells, and biopsy tissue. Examples of clinical applications will be given along with the various detection systems employed.
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Affiliation(s)
- Terry M Phillips
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
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Increasing incidence of Clostridium difficile ribotype 001 associated with severe course of the infection and previous fluoroquinolone use in the Czech Republic, 2015. Eur J Clin Microbiol Infect Dis 2017; 36:2251-2258. [DOI: 10.1007/s10096-017-3055-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/22/2017] [Indexed: 02/04/2023]
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