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Karampatakis T, Kandilioti E, Katsifa H, Nikopoulou A, Harmanus C, Tsergouli K, Kuijper E, Kachrimanidou M. Clostridioides difficile infection epidemiology during the COVID-19 pandemic in Greece. Future Microbiol 2024:1-9. [PMID: 38913938 DOI: 10.1080/17460913.2024.2358653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/20/2024] [Indexed: 06/26/2024] Open
Abstract
Aim: The aim was to highlight the incidence and epidemiology of C. difficile infections (CDI) in a tertiary Greek hospital during the COVID-19 pandemic. Methods: A single-center prospective observational cohort study was conducted (October 2021 until April 2022). 125 C. difficile isolates were cultured from hospitalized patients stool samples and screened by PCR for toxin A (tcdA), toxin B (tcdB), binary toxin (cdtA and cdtB) genes and the regulating gene of tcdC. Results: The incidence of CDI increased to 13.1 infections per 10,000 bed days. The most common PCR ribotypes identified included hypervirulent RT027-related RT181 (73.6%), presumably hypervirulent RT126 (8.0%) and toxin A negative RT017 (7.2%). Conclusion: Although the incidence of CDI increased significantly, the CDI epidemiology remained stable.
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Affiliation(s)
| | - Eleni Kandilioti
- Microbiology Department, Papanikolaou General Hospital, 570 10, Thessaloniki, Greece
| | - Helen Katsifa
- Microbiology Department, Papanikolaou General Hospital, 570 10, Thessaloniki, Greece
| | - Anna Nikopoulou
- Infectious Disease Unit, Papanikolaou General Hospital, 570 10, Thessaloniki, Greece
| | - Celine Harmanus
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, European Study Group of C. difficile (ESGCD), 2333ZA, Leiden, The Netherlands
| | - Katerina Tsergouli
- Microbiology Department, Agios Pavlos General Hospital, 551 34, Thessaloniki, Greece
| | - Ed Kuijper
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, European Study Group of C. difficile (ESGCD), 2333ZA, Leiden, The Netherlands
| | - Melina Kachrimanidou
- Department of Microbiology, Aristotle University of Thessaloniki, Medical School, 541 24, Thessaloniki, Greece
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Li Z, Ouyang Z, Zhang H, Mi C, Dong N, Niu Y, Qiang C, Yang J, Wang W, Li Y, Zhao J. Novel target and PCR assay for identification of hypervirulent ST1 (BI/NAP1/027) Clostridioides difficile and detection of toxigenic C. Difficile. Clin Chim Acta 2024; 559:119728. [PMID: 38750779 DOI: 10.1016/j.cca.2024.119728] [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: 04/22/2024] [Accepted: 05/12/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND AND AIMS The incidence of Clostridioides difficile infection and the prevalence of hypervirulent ST1 (BI/NAP1/027)strain are increasing, especially in developing countries. We aimed to develop a new PCR assay for the identification of hypervirulent ST1 strains and toxigenic C. difficile in stool samples. MATERIALS AND METHODS We established a quadruplex TaqMan real-time PCR (pilW_4-plex PCR) assay targeting the pilW, a ST1-specific type Ⅳ minor pilin gene, and three C. difficile genes including cdtB, tcdB, and hsp. The sensitivity and specificity of the assay was tested using 403C. difficile isolates and 180 unformed stool sample. The results were compared with anaerobic culture-based conventional PCR method and MLST. RESULTS The pilW_4-plex PCR identified toxigenic C. difficile in 333 (82.6%, 333/403) isolates with 100% sensitivity and specificity, and in 78 (43.3%, 78/180) stool samples with the sensitivity and specificity of 94.7% and 93.3%, respectively. Hypervirulent ST1 were detected in 21 strains and nine stool samples by the pilW_4-plex PCR. The pilW_4-plex PCR assay has no cross-reaction with non-toxigenic C. difficile or other bacteria. CONCLUSION The pilW_4-plex PCR assay is an accurate and rapid method with high sensitivity and specificity for identification of ST1 and detection of toxigenic C. difficile in stool.
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Affiliation(s)
- Zhirong Li
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zirou Ouyang
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huimin Zhang
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chaoyi Mi
- Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang, China; Clinical Oncology Research Center, Shijiazhuang, China Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Shijiazhuang, ChinaClinical Oncology Research Center, Shijiazhuang, China
| | - Ning Dong
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yanan Niu
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Cuixin Qiang
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jing Yang
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Weigang Wang
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yanhong Li
- Comprehensive Surgical Department, Hebei Provincial Hospital of Traditional Chinese Medicine, Shijiazhuang, China
| | - Jianhong Zhao
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
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Heydari H, Iranikhah A, Ghasemi A, Mohammadbeigi A, Sadat-Mirei SA, Shams S, Kermani S. Evaluation of the prevalence of Aeromonas spp., Campylobacter spp., and Clostridioides difficile in immunocompromised children with diarrhea. BMC Infect Dis 2024; 24:512. [PMID: 38778271 PMCID: PMC11110422 DOI: 10.1186/s12879-024-09372-3] [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: 11/07/2023] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
AIM Diarrhea is a common disease in immunocompromised patients and can be associated with greater morbidity and even mortality. Therefore, the present study was designed to determine the prevalence of Aeromonas spp., Campylobacter spp., and C. difficile among immunocompromised children. METHODS This study was conducted on 130 stool samples from patients with diarrhea who had defects in the immune system and were referred to Hazrat Masoumeh Children's Hospital in Qom. Demographic information, clinical symptoms, immune status, and duration of chemotherapy were also recorded for each child. DNAs were extracted from the stool, and then direct PCR assays were done by specific primers for the detection of Aeromonas spp., Campylobacter spp., and toxigenic C. difficile, including tcdA/B and cdtA/B genes. Co-infection in patients was also evaluated. RESULTS 60.8% and 39.2% were male and female, respectively, with a m ± SD age of 56.72 ± 40.49 months. Most cases of immunocompromised states were related to Acute Lymphocytic Leukemia (77.7%) and Non-Hodgkin Lymphoma (14.6%). 93.1% of patients were undergoing chemotherapy during the study. Among patients, most clinical symptoms were related to bloody diarrhea (98.5%) and fever (92.3%). Based on PCR, 14.6, 9.2, and 1.5% were positive for Aeromonas spp., C. difficile, and C. jejuni, respectively. Among the C. difficile-positive cases, the tcdA gene was only detected in one patient. In total, three co-infections were identified, which included Aeromonas spp./C. difficile (tcdA+), C. jejuni/C. difficile, and C. jejuni/Aeromonas spp. CONCLUSIONS This is the first study in Iran to investigate the simultaneous prevalence of some pathogens in immunocompromised children with diarrhea. Because Aeromonas spp., Campylobacter spp., and C. difficile are not routinely detected in some laboratories, infections caused by them are underappreciated in the clinic. Our results showed that these pathogens are present in our region and can cause gastroenteritis in children, especially those with underlying diseases. Therefore, increasing the level of hygiene in some areas and controlling bacterial diarrheal diseases should be given more attention by health officials.
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Affiliation(s)
- Hosein Heydari
- Pediatric Medicine Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Abolfazl Iranikhah
- Gastroenterology and Hepatology Diseases Research Center, Qom University of Medical Sciences, Qom, Iran
| | - Ahmad Ghasemi
- Department of Microbiology, Research Center of Reference Health Laboratories, Ministry of Health and Medical Education, Tehran, Iran
| | - Abolfazl Mohammadbeigi
- Department of Epidemiology and Biostatistics, School of Health, Qom University of Medical Sciences, Qom, Iran
| | | | - Saeed Shams
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
| | - Somayeh Kermani
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran.
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Ziaei Chamgordani S, Yadegar A, Ghourchian H. C. difficile biomarkers, pathogenicity and detection. Clin Chim Acta 2024; 558:119674. [PMID: 38621586 DOI: 10.1016/j.cca.2024.119674] [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: 02/04/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is the main etiologic agent of antibiotic-associated diarrhea. CDI contributes to gut inflammation and can lead to disruption of the intestinal epithelial barrier. Recently, the rate of CDI cases has been increased. Thus, early diagnosis of C. difficile is critical for controlling the infection and guiding efficacious therapy. APPROACH A search strategy was set up using the terms C. difficile biomarkers and diagnosis. The found references were classified into two general categories; conventional and advanced methods. RESULTS The pathogenicity and biomarkers of C. difficile, and the collection manners for CDI-suspected specimens were briefly explained. Then, the conventional CDI diagnostic methods were subtly compared in terms of duration, level of difficulty, sensitivity, advantages, and disadvantages. Thereafter, an extensive review of the various newly proposed techniques available for CDI detection was conducted including nucleic acid isothermal amplification-based methods, biosensors, and gene/single-molecule microarrays. Also, the detection mechanisms, pros and cons of these methods were highlighted and compared with each other. In addition, approximately complete information on FDA-approved platforms for CDI diagnosis was collected. CONCLUSION To overcome the deficiencies of conventional methods, the potential of advanced methods for C. difficile diagnosis, their direction, perspective, and challenges ahead were discussed.
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Affiliation(s)
- Sepideh Ziaei Chamgordani
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hedayatollah Ghourchian
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
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Cerri FM, Basso RM, Pereira WAB, Silveira JMDS, Ferreira EDO, Haisi A, Araújo Júnior JP, Arroyo LG, de Castro YG, Silva ROS, Oliveira-Filho JPD, Borges AS. Fecal shedding of Clostridioides difficile in calves in Sao Paulo state, Brazil. Anaerobe 2024; 88:102861. [PMID: 38729514 DOI: 10.1016/j.anaerobe.2024.102861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
OBJECTIVE This study aimed to evaluate the fecal shedding of C. difficile in calves on farms in Sao Paulo State, Brazil. MATERIALS AND METHODS Fecal samples (n = 300) were collected from diarrheic (n = 78) and nondiarrheic (n = 222) calves less than 60 days of age from 20 farms. Fecal samples were inoculated into enrichment broth supplemented with taurocholate and cultured under anaerobic conditions. Colonies suspected to be C. difficile were harvested for DNA extraction and then multiplex PCR for the detection of genes encoding toxins A and B and binary toxins. All toxigenic isolates were ribotyped and tested for antimicrobial susceptibility, and five selected strains were subjected to whole-genome sequencing to determine their sequence type. RESULTS AND DISCUSSION C. difficile was isolated from 29.3 % (88/300) of the samples. All toxigenic isolates (17/88, 19.3 %) were classified as ribotypes RT046 (13/17-79.47 %, A+B+ CDT-) and RT126 (4/17 = 20.53 %, A+B+ CDT+). The sequenced strains from RT046 were classified as ST35 (Clade 1), while those from RT126 were classified as ST11 (Clade 5). No associations between the epidemiological factors in any of the groups and C. difficile isolation were observed. Most of the toxigenic isolates (16/17 = 94.41 %) were classified as multidrug-resistant. Calves can be an important source of toxigenic C. difficile strains, including multidrug-resistant isolates from ribotypes commonly observed in humans.
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Affiliation(s)
- Fabrício Moreira Cerri
- Sao Paulo State University (UNESP), School of Veterinary Medicine and Animal Science (FMVZ), Botucatu, Sao Paulo, Brazil
| | - Roberta Martins Basso
- Sao Paulo State University (UNESP), School of Veterinary Medicine and Animal Science (FMVZ), Botucatu, Sao Paulo, Brazil
| | | | - Júlia Meireles da Silva Silveira
- Federal University of Rio de Janeiro (UFRJ), Paulo de Góes Institute of Microbiology (IMPG), Department of Medical Microbiology, UFRJ, Rio de Janeiro, Rio Janeiro, Brazil
| | - Eliane de Oliveira Ferreira
- Federal University of Rio de Janeiro (UFRJ), Paulo de Góes Institute of Microbiology (IMPG), Department of Medical Microbiology, UFRJ, Rio de Janeiro, Rio Janeiro, Brazil
| | - Amanda Haisi
- Sao Paulo State University (UNESP), Institute of Biotechnology (IBTEC), Botucatu, Sao Paulo, Brazil
| | | | - Luis G Arroyo
- University of Guelph, Ontario Veterinary College, Department of Clinical Studies, Guelph, Ontario, Canada
| | - Yasmin Gonçalves de Castro
- Federal University of Minas Gerais (UFMG), School of Veterinary Medicine (EV), Belo Horizonte, Minas Gerais, Brazil
| | | | - José Paes de Oliveira-Filho
- Sao Paulo State University (UNESP), School of Veterinary Medicine and Animal Science (FMVZ), Botucatu, Sao Paulo, Brazil
| | - Alexandre Secorun Borges
- Sao Paulo State University (UNESP), School of Veterinary Medicine and Animal Science (FMVZ), Botucatu, Sao Paulo, Brazil.
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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:S1341-321X(24)00065-5. [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] [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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van Prehn J, Crobach MJT, Baktash A, Duszenko N, Kuijper EJ. Diagnostic Guidance for C. difficile Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:33-56. [PMID: 38175470 DOI: 10.1007/978-3-031-42108-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Diagnosis of Clostridioides difficile infection (CDI) can be challenging. First of all, there has been debate on which of the two reference assays, cell cytotoxicity neutralization assay (CCNA) or toxigenic culture (TC), should be considered the gold standard for CDI detection. Although the CCNA suffers most from suboptimal storage conditions and subsequent toxin degradation, TC is reported to falsely increase CDI detection rates as it cannot differentiate CDI patients from patients asymptomatically colonised by toxigenic C. difficile. Several rapid assays are available for CDI detection and fall into three broad categories: (1) enzyme immunoassays for glutamate dehydrogenase, (2) enzyme immunoassays or single-molecule array assays for toxins A/B and (3) nucleic acid amplification tests detecting toxin genes. All three categories have their own limitations, being suboptimal specificity and/or sensitivity or the inability to discern colonised patients from CDI patients. In light of these limitations, multi-step algorithmic testing has been advocated by international guidelines (IDSA/SHEA and ESCMID) in order to optimize diagnostic accuracy. As a result, a survey performed in 2018-2019 in Europe revealed that most of all hospital sites reported using more than one test to diagnose CDI. CDI incidence rates are also influenced by sample selection criteria, as several studies have shown that if not all unformed stool samples are tested for CDI, many cases may be missed due to an absence of clinical suspicion. Since methods for diagnosing CDI remain imperfect, there has been a growing interest in alternative testing strategies like faecal microbiota biomarkers, immune modulating interleukins, cytokines and imaging methods. At the moment, these alternative methods might play an adjunctive role, but they are not suitable to replace conventional CDI testing strategies.
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Affiliation(s)
- Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Centre for Infectious Diseases (LU-CID), Leiden University Medical Centre, Leiden, The Netherlands.
- ESCMID Study Group for C. difficile (ESGCD) and Study Group for Host and Microbiota Interaction (ESGHAMI), Basel, Switzerland.
| | - Monique J T Crobach
- Department of Medical Microbiology, Leiden University Centre for Infectious Diseases (LU-CID), Leiden University Medical Centre, Leiden, The Netherlands
| | - Amoe Baktash
- Department of Medical Microbiology, Leiden University Centre for Infectious Diseases (LU-CID), Leiden University Medical Centre, Leiden, The Netherlands
| | - Nikolas Duszenko
- Department of Medical Microbiology, Leiden University Centre for Infectious Diseases (LU-CID), Leiden University Medical Centre, Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Centre for Infectious Diseases (LU-CID), Leiden University Medical Centre, Leiden, The Netherlands
- ESCMID Study Group for C. difficile (ESGCD) and Study Group for Host and Microbiota Interaction (ESGHAMI), Basel, Switzerland
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Ötleş E, Balczewski EA, Keidan M, Oh J, Patel A, Young VB, Rao K, Wiens J. Clostridioides difficile infection surveillance in intensive care units and oncology wards using machine learning. Infect Control Hosp Epidemiol 2023; 44:1776-1781. [PMID: 37088695 PMCID: PMC10665879 DOI: 10.1017/ice.2023.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 04/25/2023]
Abstract
OBJECTIVE Screening individuals admitted to the hospital for Clostridioides difficile presents opportunities to limit transmission and hospital-onset C. difficile infection (HO-CDI). However, detection from rectal swabs is resource intensive. In contrast, machine learning (ML) models may accurately assess patient risk without significant resource usage. In this study, we compared the effectiveness of swab surveillance to daily risk estimates produced by an ML model to identify patients who will likely develop HO-CDI in the intensive care unit (ICU) setting. DESIGN A prospective cohort study was conducted with patient carriage of toxigenic C. difficile identified by rectal swabs analyzed by anaerobic culture and polymerase chain reaction (PCR). A previously validated ML model using electronic health record data generated daily risk of HO-CDI for every patient. Swab results and risk predictions were compared to the eventual HO-CDI status. PATIENTS Adult inpatient admissions taking place in University of Michigan Hospitals' medical and surgical intensive care units and oncology wards between June 6th and October 8th, 2020. RESULTS In total, 2,979 admissions, representing 2,044 patients, were observed over the course of the study period, with 39 admissions developing HO-CDIs. Swab surveillance identified 9 true-positive and 87 false-positive HO-CDIs. The ML model identified 9 true-positive and 226 false-positive HO-CDIs; 8 of the true-positives identified by the model differed from those identified by the swab surveillance. CONCLUSION With limited resources, an ML model identified the same number of HO-CDI admissions as swab-based surveillance, though it generated more false-positives. The patients identified by the ML model were not yet colonized with C. difficile. Additionally, the ML model identifies at-risk admissions before disease onset, providing opportunities for prevention.
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Affiliation(s)
- Erkin Ötleş
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Industrial & Operations Engineering, College of Engineering, University of Michigan, Ann Arbor, Michigan
| | - Emily A. Balczewski
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Micah Keidan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jeeheh Oh
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, Michigan
| | - Alieysa Patel
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jenna Wiens
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, Michigan
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9
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Blau K, Berger FK, Mellmann A, Gallert C. Clostridioides difficile from Fecally Contaminated Environmental Sources: Resistance and Genetic Relatedness from a Molecular Epidemiological Perspective. Microorganisms 2023; 11:2497. [PMID: 37894155 PMCID: PMC10608975 DOI: 10.3390/microorganisms11102497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Clostridioides difficile is the most important pathogen causing antimicrobial-associated diarrhea and has recently been recognized as a cause of community-associated C. difficile infection (CA-CDI). This study aimed to characterize virulence factors, antimicrobial resistance (AMR), ribotype (RT) distribution and genetic relationship of C. difficile isolates from diverse fecally contaminated environmental sources. C. difficile isolates were recovered from different environmental samples in Northern Germany. Antimicrobial susceptibility testing was determined by E-test or disk diffusion method. Toxin genes (tcdA and tcdB), genes coding for binary toxins (cdtAB) and ribotyping were determined by PCR. Furthermore, 166 isolates were subjected to whole genome sequencing (WGS) for core genome multi-locus sequence typing (cgMLST) and extraction of AMR and virulence-encoding genes. Eighty-nine percent (148/166) of isolates were toxigenic, and 51% (76/148) were positive for cdtAB. Eighteen isolates (11%) were non-toxigenic. Thirty distinct RTs were identified. The most common RTs were RT127, RT126, RT001, RT078, and RT014. MLST identified 32 different sequence types (ST). The dominant STs were ST11, followed by ST2, ST3, and ST109. All isolates were susceptible to vancomycin and metronidazole and displayed a variable rate of resistance to moxifloxacin (14%), clarithromycin (26%) and rifampicin (2%). AMR genes, such as gyrA/B, blaCDD-1/2, aph(3')-llla-sat-4-ant(6)-la cassette, ermB, tet(M), tet(40), and tetA/B(P), conferring resistance toward fluoroquinolone, beta-lactam, aminoglycoside, macrolide and tetracycline antimicrobials, were found in 166, 137, 29, 32, 21, 72, 17, and 9 isolates, respectively. Eleven "hypervirulent" RT078 strains were detected, and several isolates belonged to RTs (i.e., RT127, RT126, RT023, RT017, RT001, RT014, RT020, and RT106) associated with CA-CDI, indicating possible transmission between humans and environmental sources pointing out to a zoonotic potential.
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Affiliation(s)
- Khald Blau
- Department of Microbiology–Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany;
| | - Fabian K. Berger
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, 66421 Homburg, Germany;
- German National Reference Center for Clostridioides Difficile, 66421 Homburg, Germany;
| | - Alexander Mellmann
- German National Reference Center for Clostridioides Difficile, 66421 Homburg, Germany;
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
| | - Claudia Gallert
- Department of Microbiology–Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany;
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Ito Y, Kaneko N, Yoshida M, Nakayama H. Evaluation of a novel Clostridioides difficile-selective growth broth under aerobic conditions. Diagn Microbiol Infect Dis 2023; 107:116020. [PMID: 37536259 DOI: 10.1016/j.diagmicrobio.2023.116020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 06/22/2023] [Accepted: 07/08/2023] [Indexed: 08/05/2023]
Abstract
A newly developed Clostridioides difficile-selective growth broth, which can be cultured under aerobic conditions, was found to have a sensitivity/specificity (98%/89%) comparable to conventional anaerobic culture methods. This might be a powerful tool for diagnosing Clostridioides difficile infection in resource-limited regions and health care settings in the future.
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Affiliation(s)
- Yukitaka Ito
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Meguro, Tokyo, Japan; Department of Infection and prevention, Toho University Ohashi Medical Center, Meguro, Tokyo, Japan.
| | - Naomi Kaneko
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Meguro, Tokyo, Japan
| | - Mieko Yoshida
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Meguro, Tokyo, Japan
| | - Haruo Nakayama
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Meguro, Tokyo, Japan; Department of Infection and prevention, Toho University Ohashi Medical Center, Meguro, Tokyo, Japan
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Ito Y, Tanimoto K, Chiba N, Otsuka M, Ota M, Yoshida M, Hashimoto Y, Nomura T, Tomita H. Molecular epidemiological analyses of Clostridioides difficile isolates in a university hospital in Japan. Heliyon 2023; 9:e20167. [PMID: 37800060 PMCID: PMC10550568 DOI: 10.1016/j.heliyon.2023.e20167] [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: 12/05/2022] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Background We performed molecular epidemiological analyses of Clostridioides difficile isolates in a university hospital in Japan to reveal the risk of C. difficile infection. Methods Cultured isolates from 919 stool samples from 869 patients obtained from July 2015 to August 2016 were subjected to toxin gene detection, ribotyping, multilocus sequence typing, antimicrobial susceptibility testing, and quantitative real-time polymerase chain reaction testing for C. difficile toxin gene expression. Results Of the 919 stool samples from 869 patients, C. difficile was isolated from 153 samples (16.6%), of which 49 (32%) and 104 (68%) were from patients with and without C. difficile infection, respectively. Analyses showed genetic diversity, with ST8 and ST17 strains of healthcare-associated infections, some of which caused C. difficile infections. There was no significant difference in the transcription levels of C. difficile toxin genes between isolates from patients with and without C. difficile infection. Conclusions Major Japanese clonal strains, ST8 and ST17, have been in the hospital environment for a long time and cause healthcare-associated C. difficile infections. The C. difficile toxin genes were transcribed in the isolates from both patients with and without C. difficile infection but were no significant relationship with the development of C. difficile infection.
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Affiliation(s)
- Yukitaka Ito
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Koichi Tanimoto
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Naoko Chiba
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Masanobu Otsuka
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masato Ota
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Mieko Yoshida
- Division of Clinical Microbiology Laboratory, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Takahiro Nomura
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Gunma, Japan
- Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Gunma, Japan
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Liu Y, Ma L, Sun W, Cheng J, Wang Y, Su J. Molecular epidemiology, antimicrobial susceptibility, and toxin production of clinical Clostridioides difficile isolates from a teaching hospital in Northern China. Diagn Microbiol Infect Dis 2023; 106:115972. [PMID: 37236133 DOI: 10.1016/j.diagmicrobio.2023.115972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/15/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
To grasp the epidemiological trend and drug resistance mechanisms of Clostridioides difficile (C. diff) in Beijing, 302 C. diff isolates were obtained from patients with diarrhea. The sequence types (STs) from mainstream strains were all susceptible to metronidazole, vancomycin, piperacillin/tazobactam, meropenem, and tigecycline but almost resistant to ciprofloxacin and clindamycin. The missense mutation of GyrA/GyrB and RpoB resulted in fluoroquinolone and rifamycin resistance, respectively. Toxigenic strains from clade IV were likely to be missed due to the deficiency of tcdA gene. Four tcdC genotypes were first detected in strains from clade III and IV. The truncating mutation of TcdC disabled its function working as a toxin suppressor. In conclusion, the molecular epidemiology of C. diff in Beijing is different from other regions of China. The antimicrobial resistance patterns and toxin-producing abilities of strains with different STs varied greatly, which suggests that continuous surveillance and control are meaningful and urgent.
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Affiliation(s)
- Yifeng Liu
- Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Liyan Ma
- Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Wei Sun
- Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jingwei Cheng
- Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Yaxuan Wang
- Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Jianrong Su
- Clinical Laboratory Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China.
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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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Crobach MJT, Hornung BVH, Verduin C, Vos MC, Hopman J, Kumar N, Harmanus C, Sanders I, Terveer EM, Stares MD, Lawley TD, Kuijper EJ. Screening for Clostridioides difficile colonization at admission to the hospital: a multi-centre study. Clin Microbiol Infect 2023:S1198-743X(23)00092-7. [PMID: 36871826 DOI: 10.1016/j.cmi.2023.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/13/2023] [Accepted: 02/25/2023] [Indexed: 03/07/2023]
Abstract
OBJECTIVE This study aimed to assess the value of C. difficile colonization (CDC) screening at hospital admission in an endemic setting. METHODS A multi-centre study was performed in 4 hospitals located across the Netherlands. Newly admitted patients were screened for CDC. The risk to develop C. difficile infection (CDI) during admission and one-year follow-up was assessed for colonized and non-colonized patients. C. difficile isolates from colonized patients were compared with isolates from incident CDI cases using core genome multi locus sequence typing (cgMLST) to determine if onwards transmission had occurred. RESULTS CDC was present in 108/2211 admissions (4.9%), while colonization with a toxigenic strain (tCDC) was present in 68/2211 (3.1%) of admissions. Among these 108 colonized patients, diverse PCR ribotypes were found and no 'hypervirulent' RT027 was detected ((95% CI, 0- 0.028). None of the colonized patients developed CDI during admission (0/49, 95% CI 0-0.073) or one-year follow-up (0/38, 95% CI 0-0.93). Core genome MLST identified 6 clusters with genetically related isolates from tCDC and CDI patients, but in these clusters only one possible transmission event from a tCDC to a CDI patient was identified by epidemiological data. CONCLUSION In this endemic setting with a low prevalence of 'hypervirulent' strains screening on CDC at admission did not detect any CDC patient who progressed to symptomatic CDI and only one possible transmission event from a colonized patient to a CDI patient. Thus, screening on CDC at admission is not useful in this setting.
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Affiliation(s)
- Monique J T Crobach
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.
| | - Bastian V H Hornung
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Cees Verduin
- former: Department of Medical Microbiology, Amphia Hospital Breda, The Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Joost Hopman
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Celine Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Ingrid Sanders
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Mark D Stares
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands; Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
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Stojanovic P, Harmanus C, Kuijper EJ. Community-onset Clostridioides difficile infection in south Serbia. Anaerobe 2023; 79:102669. [PMID: 36455757 DOI: 10.1016/j.anaerobe.2022.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Data from the past decade indicates that Clostridioides difficile infection (CDI) is not only a nosocomial infection but is also increasingly recognized as a disease in the community. OBJECTIVE We aimed to study community-onset (CO) CDI in the various age groups in south Serbia with its clinical characteristics, risk factors and microbiological characterization. METHODS The study group included 93 patients with CO-CDI (median age 62). The control group consisted of 186 patients with community-onset diarrhea and stool samples negative tested for CDI. RESULTS Of all CDI cases diagnosed with a community onset, 74.19% had a previous contact with a healthcare facility in the previous 12 weeks, but 34.40% have no record on hospitalization in the previous 12 months. Using a multivariate statistical regression model, the following risk factors for CO-CDI development were found; antacid usage (OR = 0.267, 95%C.I.:0.10-0.291, p < 0.01), chronic kidney disease (OR = 0.234, 95%C.I.:0.10-0.51, p < 0.01) and antibiotic use during the prior 2 months (OR = 0.061, 95%C.I.:0.02-0.17, p < 0.01), especially tetracycline's (OR = 0.146, 95% C.I.:0.07-0.22, p < 0.01) and cephalosporin's (OR = 0.110, 95%C.I.:0.14-0.42, p < 0.01). The most common ribotypes (RTs) detected in patients with CO-CDI were RT001 (32.3%) and RT027 (24.7%). All tested toxin producing C. difficile isolates were sensitive to metronidazole, vancomycin and tigecycline. A high rate of resistance to moxifloxacin (73.11%) and rifampicin (23.65%) was found. CONCLUSION Patients with CO-CDI had frequently contact with healthcare facility in the previous 12 weeks. Restriction of antacid usage and of high-risk antibiotics in the community may help reduce the incidence of CO-CDI.
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Affiliation(s)
- Predrag Stojanovic
- Faculty of Medicine, University of Niš, Zorana Đinđića 50, 18000, Niš, Serbia; Institute for Public Health Nis, Center of Microbiology, 18000, Niš, Serbia(1).
| | - Celine Harmanus
- Department of Medical Microbiology, Center for Infectious Diseases, National Expertise Center for Clostridioides difficile infections, National Institute of Public Health and the Environment, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, the Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Center for Infectious Diseases, National Expertise Center for Clostridioides difficile infections, National Institute of Public Health and the Environment, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, the Netherlands
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Blau K, Gallert C. Prevalence, Antimicrobial Resistance and Toxin-Encoding Genes of Clostridioides difficile from Environmental Sources Contaminated by Feces. Antibiotics (Basel) 2023; 12:antibiotics12010162. [PMID: 36671363 PMCID: PMC9855088 DOI: 10.3390/antibiotics12010162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Clostridioides difficile (C. difficile) is the most common pathogen causing antibiotic-associated intestinal diseases in humans and some animal species, but it can also be present in various environments outside hospitals. Thus, the objective of this study was to investigate the presence and the characteristics of toxin-encoding genes and antimicrobial resistance of C. difficile isolates from different environmental sources. C. difficile was found in 32 out of 81 samples (39.50%) after selective enrichment of spore-forming bacteria and in 45 samples (55.56%) using a TaqMan-based qPCR assay. A total of 169 C. difficile isolates were recovered from those 32 C. difficile-positive environmental samples. The majority of environmental C. difficile isolates were toxigenic, with many (88.75%) positive for tcdA and tcdB. Seventy-four isolates (43.78%) were positive for binary toxins, cdtA and cdtB, and 19 isolates were non-toxigenic. All the environmental C. difficile isolates were susceptible to vancomycin and metronidazole, and most isolates were resistant to ciprofloxacin (66.86%) and clindamycin (46.15%), followed by moxifloxacin (13.02%) and tetracycline (4.73%). Seventy-five isolates (44.38%) showed resistance to at least two of the tested antimicrobials. C. difficile strains are commonly present in various environmental sources contaminated by feces and could be a potential source of community-associated C. difficile infections.
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Kim J, Kim B, Pai H. Diversity of binary toxin positive Clostridioides difficile in Korea. Sci Rep 2023; 13:576. [PMID: 36631661 PMCID: PMC9834304 DOI: 10.1038/s41598-023-27768-0] [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: 08/18/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
The objective of this study is to determine the trend and diversity of binary toxin-positive Clostridioides difficile over 10 years in Korea. Binary toxin-positive strains were selected from a tertiary hospital in Korea in 2009-2018. The multi-locus sequence typing and antibiotic susceptibility test were performed. Among the 3278 isolates in 2009-2018, 58 possessed binary toxin genes (1.7%). The proportion of CDT- positive isolates was 0.51-4.82% in 2009-2018, which increased over the 10-year period (P = 0.023). Thirteen sequence types (STs) were identified; ST5 (14 [24%]), ST11 (11 [19%]), ST221 (10 [17%]), ST201 (7 [12%]) and ST1 (5 [9%]) were popular. All 58 isolates were susceptible to vancomycin and piperacillin/tazobactam, and clindamycin and moxifloxacin were active in 69.0% and 62% of isolates, respectively. ST1 strains were resistant to several antibiotics, including moxifloxacin (80%), clindamycin (60%) and rifaximin (60%). Moreover, four of five ST1 presented a metronidazole minimum inhibitory concentration of 4 µg/mL. Moxifloxacin resistance was highest (72.3%) for ST11. In conclusion, binary toxin-positive strains are non-prevalent in Korea and involve diverse STs. ST1 strains were resistant to several antibiotics.
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Affiliation(s)
- Jieun Kim
- grid.49606.3d0000 0001 1364 9317Division of Infectious Diseases, Department of Internal Medicine, Hanyang University College of Medicine, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763 Korea
| | - Bongyoung Kim
- grid.49606.3d0000 0001 1364 9317Division of Infectious Diseases, Department of Internal Medicine, Hanyang University College of Medicine, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763 Korea
| | - Hyunjoo Pai
- Division of Infectious Diseases, Department of Internal Medicine, Hanyang University College of Medicine, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Korea.
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Alves F, Castro R, Pinto M, Nunes A, Pomba C, Oliveira M, Silveira L, Gomes JP, Oleastro M. Molecular epidemiology of Clostridioides difficile in companion animals: Genetic overlap with human strains and public health concerns. Front Public Health 2023; 10:1070258. [PMID: 36684930 PMCID: PMC9853383 DOI: 10.3389/fpubh.2022.1070258] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction The changing epidemiology of Clostridioides difficile reflects a well-established and intricate community transmission network. With rising numbers of reported community-acquired infections, recent studies tried to identify the role played by non-human reservoirs in the pathogen's transmission chain. This study aimed at describing the C. difficile strains circulating in canine and feline populations, and to evaluate their genetic overlap with human strains to assess the possibility of interspecies transmission. Methods Fecal samples from dogs (n = 335) and cats (n = 140) were collected from two populations (group A and group B) in Portugal. C. difficile isolates were characterized for toxigenic profile and PCR-ribotyping. The presence of genetic determinants of antimicrobial resistance was assessed in all phenotypically resistant isolates. To evaluate the genetic overlap between companion animals and human isolates from Portugal, RT106 (n = 42) and RT014/020 (n = 41) strains from both sources were subjected to whole genome sequencing and integrated with previously sequenced RT106 (n = 43) and RT014/020 (n = 142) genomes from different countries. The genetic overlap was assessed based on core-single nucleotide polymorphism (SNP) using a threshold of 2 SNP. Results The overall positivity rate for C. difficile was 26% (76/292) in group A and 18.6% (34/183) in group B. Toxigenic strains accounted for 50% (38/76) and 52.9% (18/34) of animal carriage rates, respectively. The most prevalent ribotypes (RT) were the toxigenic RT106 and RT014/020, and the non-toxigenic RT010 and RT009. Antimicrobial resistance was found for clindamycin (27.9%), metronidazole (17.1%) and moxifloxacin (12.4%), associated with the presence of the ermB gene, the pCD-METRO plasmid and point mutations in the gyrA gene, respectively. Both RT106 and RT014/020 genetic analysis revealed several clusters integrating isolates from animal and human sources, supporting the possibility of clonal interspecies transmission or a shared environmental contamination source. Discussion This study shows that companion animals may constitute a source of infection of toxigenic and antimicrobial resistant human associated C. difficile isolates. Additionally, it contributes with important data on the genetic proximity between C. difficile isolates from both sources, adding new information to guide future work on the role of animal reservoirs in the establishment of community associated transmission networks and alerting for potential public health risk.
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Affiliation(s)
- Frederico Alves
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Castro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Alexandra Nunes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Constança Pomba
- Genevet–Veterinary Molecular Diagnostic Laboratory, Carnaxide, Portugal
- CIISA–Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Manuela Oliveira
- CIISA–Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Leonor Silveira
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Mónica Oleastro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
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Kracík M, Dolinová I, Žemličková H. Ribotyping of Clostridioides difficile in the Liberec Regional Hospital: a tertiary health care facility. Folia Microbiol (Praha) 2022; 68:315-320. [PMID: 36454512 PMCID: PMC9713161 DOI: 10.1007/s12223-022-01021-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022]
Abstract
The ribotyping of Clostridioides difficile is one of the basic methods of molecular epidemiology for monitoring the spread of C. difficile infections. In the Czech Republic, this procedure is mainly available in university hospitals. The introduction of ribotyping in a tertiary health care facility such as Liberec Regional Hospital not only increases safety in the facility but also supports regional professional development. In our study, 556 stool samples collected between June 2017 and June 2018 were used for C. difficile infection screening, followed by cultivation, toxinotyping, and ribotyping of positive samples. The toxinotyping of 96 samples revealed that 44.8% of typed strains could produce toxins A and B encoded by tcdA and tcdB, respectively. The ribotyping of the same samples revealed two epidemic peaks, caused by the regionally most prevalent ribotype 176 (n = 30, 31.3). C. difficile infection incidence ranged between 5.5 and 4.2 cases per 10,000 patient-bed days. Molecular diagnostics and molecular epidemiology are the two most developing parts of clinical laboratories. The correct applications of molecular methods help ensure greater safety in hospitals.
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Affiliation(s)
- Martin Kracík
- Department of Genetics and Molecular Diagnostics, Liberec Regional Hospital, 46001 Liberec, Czech Republic ,Department of Microbiology and Immunology, Liberec Regional Hospital, 46001 Liberec, Czech Republic ,Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, 50005 Hradec Kralove, Czech Republic
| | - Iva Dolinová
- Department of Genetics and Molecular Diagnostics, Liberec Regional Hospital, 46001 Liberec, Czech Republic
| | - Helena Žemličková
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, 50005 Hradec Kralove, Czech Republic ,National Reference Laboratory for Antibiotics, Centre for Epidemiology and Microbiology, National Institute of Public Health, 10000 Prague, Czech Republic ,Department of Microbiology, 3rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, 10000 Prague, Czech Republic
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Clostridioides difficile in Foods with Animal Origins; Prevalence, Toxigenic Genes, Ribotyping Profile, and Antimicrobial Resistance. J FOOD QUALITY 2022. [DOI: 10.1155/2022/4868409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Clostridioides difficile is an important nosocomial pathogen and is considered as a reason of diarrhea and gastrointestinal infections. As a majority of community-originated C. difficile cases are not related to antibiotic prescription and hospitalization, the food portion as a vector of infection transmission has been raised. An existing survey was aimed evaluating the prevalence, antimicrobial resistance, profile of toxigenic genes, and ribotypes of C. difficile isolated from raw meat and carcass surface swab samples. In total, 485 raw meat and carcass surface swab samples were collected. C. difficile was isolated via culture and a diverse biochemical examination. The assessment of minimum inhibitory concentration (MIC) was addressed to evaluate the antibiotic resistance of isolates. Toxin genes detection and ribotyping were used for isolates characterization. The prevalence of C. difficile contamination in all examined samples was 3.71%. The bacterium was detected in 2.91% of raw meat and 4.48% of carcass surface swab samples. Raw sheep meat (5%) and sheep carcass swab (7.50%) samples harbored the highest C. difficile prevalence. The highest rate of antibiotic resistance was observed toward clindamycin (38.88%), ciprofloxacin (38.88%), metronidazole (44.44%), erythromycin (72.22%), and tetracycline (77.77%). C. difficile bacteria showed the minimum rate of resistance meropenem (16.66%) and chloramphenicol (16.66%). TcdA, tcdB, cdtA, and cdtB toxigenic genes were detected in 22.22%, 44.44%, and 16.66% of isolates, respectively. TcdB + tcdA (27.77%) were the most prevalent combined toxigenic gene profile. Both 027 and 078 ribotypes were identified in C. difficile isolates. The role of raw meat and carcass surface swab samples as toxigenic and antibiotic-resistant C. difficile strains vectors was signified. This study authorizes that food animals, particularly sheep and cattle, are C. difficile carriers at slaughter stages and ribotypes are equal in human cases. Subsequently, contamination of carcasses occurs inside the slaughterhouse.
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Wen GL, Li SH, Qin Z, Yang YJ, Bai LX, Ge WB, Liu XW, Li JY. Isolation, molecular typing and antimicrobial resistance of Clostridium difficile in dogs and cats in Lanzhou city of Northwest China. Front Vet Sci 2022; 9:1032945. [DOI: 10.3389/fvets.2022.1032945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/20/2022] Open
Abstract
Clostridium difficile infection (CDI) in human and animals belonged usually to antibiotic-associated diarrhea, ranging in severity from mild to life-threatening intestinal tract illnesses. This study aimed to isolation and characterization, toxin genes test, molecular typing, and drug sensitivity of Clostridium difficile (C. difficile) which were isolated from clinical diseased dogs and cats. A total of 247 clinical samples were collected from five animal hospitals in Lanzhou City of Northwest China, of which dogs and cats accounted for 74.9% (185/247) and 25.1% (62/247), respectively. We successfully identified 24 C. difficile strains by 16S rRNA and Matrix-Assisted Laser Desorption/Ionization Time of Fight Mass Spectroscopy (MALDI-TOF-MS). 10.3% (19/185) of dogs and 8.1% (5/62) of cats were positive for C. difficile. Among them, 16 strains were toxic and 8 were non-toxic, with a toxic rate of 57.9% (11/19) in dogs and 100% (5/5) in cats. A total of 10 STs and 10 RTs were identified in this study. The percentages of ST42 (RT106) and ST2 (RT014/LW01) among 16 toxic strains were 41.7 and 12.5%, respectively. However, ST3 (RT001), ST1 (RT027), ST133 (LW04), and ST-UN (LW04) had only one strain. ST42 (RT106) was the most common genotype and RT027 strain was first isolated in China from pets. Antimicrobial susceptibility test showed that isolates were extremely sensitive to vancomycin and metronidazole but were resistant to erythromycin and ciprofloxacin. The drug resistant rates to clindamycin, levofloxacin, moxifloxacin and meropenem were 62.5, 20.8, 16.7, and 8.3%, respectively. In conclusion, C. difficile was quietly prevalent in dogs and cats in Lanzhou city with RT106 and RT014 as the main ribotypes. The CDI in pets should be paying more attention and further studies are needed.
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Li Y, Liao J, Jian Z, Li H, Chen X, Liu Q, Liu P, Wang Z, Liu X, Yan Q, Liu W. Molecular epidemiology and clinical characteristics of
Clostridioides difficile
infection in patients with inflammatory bowel disease from a teaching hospital. J Clin Lab Anal 2022; 36:e24773. [DOI: 10.1002/jcla.24773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yan‐ming Li
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Jing‐zhong Liao
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Zi‐juan Jian
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Hong‐ling Li
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Xia Chen
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Qing‐xia Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Pei‐lin Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Zhi‐qian Wang
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Xuan Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
- National Clinical Research Center for Geriatric Disorders Xiangya Hospital Changsha China
| | - Wen‐en Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
- National Clinical Research Center for Geriatric Disorders Xiangya Hospital Changsha China
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Gomez-Simmonds A, Annavajhala MK, Nunez MP, Macesic N, Park H, Uhlemann AC. Intestinal Dysbiosis and Risk of Posttransplant Clostridioides difficile Infection in a Longitudinal Cohort of Liver Transplant Recipients. mSphere 2022; 7:e0036122. [PMID: 36135360 PMCID: PMC9599498 DOI: 10.1128/msphere.00361-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/07/2022] [Indexed: 01/21/2023] Open
Abstract
Clostridioides difficile infection (CDI) has a higher incidence in solid organ transplant recipients than other hospitalized patients and can lead to poor outcomes. Perturbations to the intestinal microbiome are common in patients undergoing liver transplant (LT); however, the impacts of microbial diversity and composition on risk of CDI in this patient population is incompletely understood. Here, we assessed patients in an established, longitudinal LT cohort for development of CDI within 1 year of transplant. Clinical data were compared for patients with and without CDI using univariable models. 16S rRNA sequencing of fecal samples was performed at multiple pre- and posttransplant time points to compare microbiome α- and β-diversity and enrichment of specific taxa in patients with and without CDI. Of 197 patients who underwent LT, 18 (9.1%) developed CDI within 1 year. Pre-LT Child-Pugh class C liver disease, postoperative biliary leak, and use of broad-spectrum antibiotics were significantly associated with CDI. Patients who developed CDI had significantly lower α-diversity than patients without CDI overall and in samples collected at months 1, 3, and 6. Microbial composition (β-diversity) differed between patients with and without CDI and across sampling time points, particularly later in their posttransplant course. We also identified 15 (8%) patients with toxigenic C. difficile colonization who did not develop CDI and may have had additional protective factors. In summary, clinical and microbiome factors are likely to converge to impart CDI risk. Along with enhanced preventive measures, there may be a role for microbiome modulation to restore microbial diversity in high-risk LT patients. IMPORTANCE Liver transplant (LT) recipients have high rates of Clostridioides difficile infection (CDI), which has been associated with poor outcomes, including graft-related complications and mortality, in prior studies. Susceptibility to CDI is known to increase following perturbations in intestinal commensal bacteria that enable germination of C. difficile spores and bacterial overgrowth. In LT patients, changes in the intestinal microbiome resulting from advanced liver disease, surgery, and other clinical factors is common and most pronounced during the early posttransplant period. However, the relationship between microbiome changes and CDI risk after LT remains unclear. In this study, we investigated clinical and microbiome factors associated with development of CDI within the first year after LT. The importance of this work is to identify patients with high-risk features that should receive enhanced preventive measures and may benefit from the study of novel strategies to reconstitute the intestinal microbiome after LT.
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Affiliation(s)
- Angela Gomez-Simmonds
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Medini K. Annavajhala
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Maria Patricia Nunez
- Department of Microbiology & Immunology, Columbia University, New York, New York, USA
| | - Nenad Macesic
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia
| | - Heekuk Park
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
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Matsumoto A, Yamagishi Y, Miyamoto K, Higashi S, Oka K, Takahashi M, Mikamo H. Comparison of clinical severity, genotype and toxin gene expression of binary toxin-producing Clostridioides difficile clinical isolates in Japan. Access Microbiol 2022; 4:acmi000362. [PMID: 36415735 PMCID: PMC9675170 DOI: 10.1099/acmi.0.000362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/14/2022] [Indexed: 11/07/2023] Open
Abstract
The emerging Clostridioides difficile strain BI/NAP1/027 has been reported to be associated with more severe clinical symptoms and higher mortality rates, thought in part due to production of a novel binary toxin alongside conventional A and B toxins. However, recent studies suggest that this may not always be the case. Therefore, the purpose of this report was to investigate the correlation between clinical severity and microbiological characteristics of CDT-producing C. difficile isolates in Japan. Eight Japanese isolates of CDT producing C. difficile were investigated using genotyping, cytotoxic activity assays and toxin gene expression. Correlation with clinical severity was performed retrospectively using the patient record. Three of eight patients were assessed as having severe C. difficile infection (CDI). PCR ribotyping resolved six ribotypes including ribotype 027. No specific genes were identified determining severe compared with non-severe cases. Positive correlation of expression levels of tcdA, tcdB and cdtB were observed although these expression levels were not correlated with cytotoxicity. CDI severity index neither correlated with toxin gene expression level nor cytotoxicity. These data indicate that the possession of the CDT gene and toxin gene expression levels may not relate to C. difficile cytotoxicity or clinical severity.
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Affiliation(s)
- Asami Matsumoto
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- Department of Clinical Infectious Diseases, Kochi Medical School, 185-1, Kohasu, Oko-cho, Nankoku City, Kochi 783-8505, Japan
| | - Kentaro Miyamoto
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Seiya Higashi
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Kentaro Oka
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Motomichi Takahashi
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- R&D Division, Miyarisan Pharmaceutical Co., Ltd., 2-22-9, Toro-cho, Kita-ku, Saitama 331-0804, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, 1-1, Yazakokarimata, Nagakute City, Aichi 480-1195, Japan
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1, Yazakokarimata, Nagakute City, Aichi, 480-1195, Japan
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Son YJ, Kim YR, Oh SH, Jung S, Ciufolini MA, Hwang HJ, Kwak JH, Pai H. Micrococcin P2 Targets Clostridioides difficile. JOURNAL OF NATURAL PRODUCTS 2022; 85:1928-1935. [PMID: 35816693 DOI: 10.1021/acs.jnatprod.2c00120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clostridioides difficile infection is a global public health threat. Extensive in vitro assays using clinical isolates have identified micrococcin P2 (MP2, 1) as a particularly effective anti-C. difficile agent. MP2 possesses a mode of action that differs from other antibiotics and pharmacokinetic properties that render it especially promising. Its time-kill studies have been investigated using hypervirulent C. difficile ribotype 027. DSS (dextran sulfate sodium)-induced in vivo mouse studies with that strain indicate that 1 is better than vancomycin and fidaxomicin. Thus, micrococcin P2 is a valuable platform to be exploited for the development of new anti-C. difficile antibiotics.
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Affiliation(s)
- Young-Jin Son
- A&J Science Co., Ltd., 80 Chumbok Road, Dong Gu, Daegu, 41061, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak Road, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Young-Rok Kim
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Sang-Hun Oh
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Sungji Jung
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Marco A Ciufolini
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6K 1Z1, Canada
| | - Hee-Jong Hwang
- A&J Science Co., Ltd., 80 Chumbok Road, Dong Gu, Daegu, 41061, Republic of Korea
| | - Jin-Hwan Kwak
- School of Life Science, Handong Global University, 558 Handong Road, Heunghae-eup, Buk-gu, Pohang, 37554, Republic of Korea
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, 222 Wangsimni Road, Seongdong-gu, Seoul, 04763, Republic of Korea
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Antibiotic Resistance Profile of RT 027/176 Versus Other Clostridioides difficile Isolates in Silesia, Southern Poland. Pathogens 2022; 11:pathogens11080949. [PMID: 36015069 PMCID: PMC9416131 DOI: 10.3390/pathogens11080949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/12/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Clostridioides difficile is an important health care-associated pathogen. The aim of this study was to analyze the antibiotic susceptibility of C. difficile isolates from feces of patients from 13 hospitals in Silesia, Poland. The incidence of CDI per 100.000 people in Silesia in 2018−2019 was higher than the average in Poland (39.3−38.7 vs. 30.2−29.5, respectively). The incidence doubled from 26.4 in 2020 to 55.1 in 2021. Two hundred and thirty stool samples tested positive for GDH (glutamate dehydrogenase) and toxins were cultured anaerobically for C. difficile. The isolates were characterized, typed, and tested for susceptibility to 11 antibiotics by E-test (EUCAST, 2021). The genes of toxins A/B and binary were detected by mPCR. Of 215 isolates, 166 (77.2%) were classified as RT 027 and 6 (2.8%) as related RT 176. Resistance to ciprofloxacin (96.7%), moxifloxacin (79.1%), imipenem (78.1%), penicillin (67%), and rifampicin (40.5%) was found. The ermB gene was detected in 79 (36.7%) strains. Multidrug resistance (MDR) was confirmed in 50 (23.3%) strains of RT 027 (94%). We concluded that a high prevalence of MDR among hypervirulent RT 027/176 C. difficile was found in the Silesian region of Poland, emphasizing the need to enhance regional infection control on CDI and antibiotic stewardships.
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27
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Detection of Plasmid-Mediated Resistance to Metronidazole in Clostridioides difficile from River Water. Microbiol Spectr 2022; 10:e0080622. [PMID: 35950844 PMCID: PMC9431275 DOI: 10.1128/spectrum.00806-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile is one of the most important human pathogens. The identification of its possible sources is important for the understanding of C. difficile infection (CDI) epidemiology. A total of 16 water samples from wastewater and surface water in South Moravia in the Czech Republic and 82 samples of fish and gulls were collected between May and July 2019. C. difficile isolates were cultured by direct plating and after enrichment on chromogenic media. Susceptibility testing to eight antimicrobials was performed by Etest. C. difficile isolates were characterized by ribotyping, multilocus sequence typing, multilocus tandem repeats analysis, and toxin gene detection. Samples from fish and gulls were C. difficile negative; a total of 15 C. difficile isolates from 8 out of 16 water samples were cultured (6 out of 14 surface water samples yielded 6 isolates, and 2 out of 2 wastewater samples yielded 9 isolates). Direct plating was culture positive in 6 out of 16 samples (12 isolates), and enrichment culture was positive in an additional 2 out of 16 samples (3 isolates). Twelve different ribotyping profiles and 14 sequence types of clades 1, 4, and 5 were identified. Five isolates did not carry genes for toxins, and eight isolates carried genes for toxins A and B; the remaining two isolates (RT078) carried the genes for toxins A, B, and binary. All C. difficile isolates were susceptible to amoxicillin, moxifloxacin, tetracycline, and vancomycin and resistant to ciprofloxacin. A high level of erythromycin resistance (>256 mg/L) was detected in eight isolates. Clindamycin resistance was found in 14 isolates, 6 of which showed a high level of resistance (>256 mg/L) and carried ermB. Surprisingly, one isolate (RT010, ST15) showed resistance to metronidazole (12 mg/L) with the presence of the plasmid pCD-METRO. In conclusion, a diverse spectrum of C. difficile strains was found in wastewater and surface water. A recently discovered plasmid-bound resistance to metronidazole was detected in C. difficile from the surface water sample. IMPORTANCE The combination of direct plating and culture after enrichment was used in order to gain a spectrum of C. difficile ribotypes present in the water samples. Toxigenic C. difficile ribotypes detected in surface water and in wastewater treatment plants overlapped with those derived from patients with CDI and/or animals. Importantly, a recently discovered plasmid-mediated resistance to metronidazole, a drug used for the treatment of CDI, was detected in C. difficile from river water.
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Schroeder CP, Hengel RL, Nathan RV, Ritter TE, Obi EN, Lancaster C, Van Anglen LJ, Garey KW. Appropriate cleaning reduces potential risk of spore transmission from patients with Clostridioides difficile infection treated in outpatient infusion centers. Anaerobe 2022; 77:102617. [DOI: 10.1016/j.anaerobe.2022.102617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/28/2022] [Accepted: 07/21/2022] [Indexed: 11/01/2022]
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Aleksić A, Stojanović-Radić Z, Harmanus C, Kuijper E, Stojanović P. In vitro anti-clostridial action and potential of the spice herbs essential oils to prevent biofilm formation of hypervirulent Clostridioides difficile strains isolated from hospitalized patients with CDI. Anaerobe 2022; 76:102604. [PMID: 35709937 DOI: 10.1016/j.anaerobe.2022.102604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Clostridioides difficile is the most common causative agent of antibiotic-acquired diarrhea in hospitalized patients associated with substantial morbidity and mortality. The global epidemic of CDI (Clostridioides difficile infection) began in the early 20th century with the emergence of the hypervirulent and resistant ribotype 027 strains, and requires an urgent search for new therapeutic agents. OBJECTIVE The aim of this study is to investigate the antibacterial activity of the three essential oils isolated from spice herbs (wild oregano, garlic and black pepper) against C. difficile clinical isolates belonging to 6 different PCR ribotypes and their potential inhibitory effect on the biofilm production in in vitro conditions. RESULTS Wild oregano essential oil showed strong inhibitory activity in concentrations 0.02-1.25 mg/mL and bactericidal activity in concentrations from 0.08 to 10 mg/mL. Garlic essential oil was effective in the concentration range of 0.02-40 mg/mL, and 0.16 - > 40 mg/mL. MIC and MBC for black pepper oil ranged from 0.04 to 40 mg/mL, and 0.08 - > 40 mg/mL, respectively. All the tested oils reduced in vitro biofilm production, with the best activity of oregano oil. CONCLUSION Essential oils of wild oregano, black pepper and garlic are candidates for adjunctive therapeutics in the treatment of CDI. Oregano oil should certainly be preferred due to the lack of selectivity of action in relation to the ribotype, the strength of the produced biofilm and/or antibiotic-susceptibility patterns.
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Affiliation(s)
- Ana Aleksić
- Faculty of Sciences and Mathematics, Department of Biology and Ecology, University of Nis, Serbia
| | - Zorica Stojanović-Radić
- Faculty of Sciences and Mathematics, Department of Biology and Ecology, University of Nis, Serbia.
| | - Celine Harmanus
- National Reference Laboratory for Clostridioides Difficile, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - EdJ Kuijper
- National Reference Laboratory for Clostridioides Difficile, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Predrag Stojanović
- Faculty of Medicine, University of Nis, Serbia; Institute for Public Health Nis, Center of Microbiology, Serbia
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Kachrimanidou M, Metallidis S, Tsachouridou O, Harmanus C, Lola V, Protonotariou E, Skoura L, Kuijper E. Predominance of Clostridioides difficile PCR ribotype 181 in northern Greece, 2016-2019. Anaerobe 2022; 76:102601. [PMID: 35688364 DOI: 10.1016/j.anaerobe.2022.102601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 05/22/2022] [Accepted: 06/03/2022] [Indexed: 11/01/2022]
Abstract
OBJECTIVES The epidemiology of Clostridioides difficile infection (CDI) has undergone many changes since the beginning of this century and continues to evolve based on recent studies. Here, we performed a molecular analysis of C. difficile isolates in northern Greece across 10 health-care facilities, spanning from 2016 to 2019. METHODS 221 C. difficile isolates were cultured from stool samples of hospitalized patients with diarrhea and screened by PCR for the presence of the toxin A (tcdA), toxin B (tcdB), the binary toxin (cdtA and cdtB) genes and the regulating gene of tcdC. PCR ribotyping of the cultured isolates was performed by a standardized protocol for capillary gel-based PCR ribotyping and an international database with well-documented reference strains. RESULTS Thirty-five different PCR ribotypes were identified. The most common RTs identified were: 181 (36%, 80/221), 017 (10%, 21/221), 126 (9%, 19/221), 078 (4%, 9/221) and 012 (4%, 8/221). Notably, the predominant RT181, with toxin profile tcdA+tcdB+cdtA+cdtB+, was identified in seven out of ten participating hospitals. CONCLUSIONS Multiple C. difficile ribotypes have been circulating in the northern Greece region with RTs 181 (closely related to 027), 017, 126 and 078 being predominant.
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Affiliation(s)
- Melina Kachrimanidou
- First Department of Microbiology, Aristotle University of Thessaloniki, Medical School, Thessaloniki, Greece.
| | - Symeon Metallidis
- First Internal Medicine Department, Infectious Diseases Division, AHEPA Hospital, Medical School, Aristotle University of Thessaloniki, Greece
| | - Olga Tsachouridou
- First Internal Medicine Department, Infectious Diseases Division, AHEPA Hospital, Medical School, Aristotle University of Thessaloniki, Greece
| | - Celine Harmanus
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, And National Institute of Public Health, Bilthoven, the Netherlands
| | - Vassiliki Lola
- First Department of Microbiology, Aristotle University of Thessaloniki, Medical School, Thessaloniki, Greece
| | - Efthymia Protonotariou
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lemonia Skoura
- Department of Microbiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ed Kuijper
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, And National Institute of Public Health, Bilthoven, the Netherlands
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Moosavian M, Keshavarzi R, Abbasi Montazeri E, Hajiani E. Loop mediated isothermal amplification of Clostridioides difficile isolates in gastrointestinal patients. AMB Express 2022; 12:42. [PMID: 35412160 PMCID: PMC9005576 DOI: 10.1186/s13568-022-01382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/01/2022] [Indexed: 11/10/2022] Open
Abstract
This study investigated the prevalence of Clostridioides difficile by culture, multiplex polymerase chain reaction (M-PCR), and loop mediated isothermal amplification (LAMP) in patients with suspected C. difficile infections (CDIs). Also, the results of three methods were compared. All stool specimens collected from CDI suspected patients were cultured on selective C. difficile cycloserine-cefoxitin fructose agar and incubated in an anaerobic jar up to 7 days. The bacterial isolates were identified using standard tests. Multiplex-PCR (M-PCR) was performed for detection of tcdA, tcdB, and tpi genes. The LAMP assay was performed to detect the tcdB gene of C. difficile. C. difficile was isolated from 20.0% (n = 10/50) of samples by culture. M-PCR showed that 34.0% (n = 17/50) of the specimens were positive for C. difficile based on the presence of tpi gene. Out of the 17 C. difficile, 13 strains (76.0%) were positive for tcdB gene using M-PCR. However, the LAMP assay showed that 30.0% (15/50) of specimens were positive for the presence of tcdB gene. M-PCR and LAMP methods showed 100.0% sensitivity compared to the culture method. However, the specificity of the LAMP (87.5%) was relatively higher than the M-PCR (82.5%) compared to the culture. Based on the results of this study, the prevalence of toxigenic C. difficile strains was high in suspected CDI patients. So, the differentiation between toxigenic and non-toxigenic strains is necessary. Our data showed that the LAMP assay is a good method for direct detection of toxigenic C. difficile strains from stool specimens.
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Real-time quantitative PCR method for detection and quantification of Clostridioides difficile cells and spores. METHODS IN MICROBIOLOGY 2022; 196:106458. [DOI: 10.1016/j.mimet.2022.106458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022]
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Faecal carriage of Clostridioides difficile is low among veterinary healthcare workers in the Netherlands. Epidemiol Infect 2022; 150:e63. [PMID: 35296372 PMCID: PMC8931804 DOI: 10.1017/s0950268822000383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Williamson CHD, Stone NE, Nunnally AE, Roe CC, Vazquez AJ, Lucero SA, Hornstra H, Wagner DM, Keim P, Rupnik M, Janezic S, Sahl JW. Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations. Microb Genom 2022; 8. [PMID: 35166655 PMCID: PMC8942030 DOI: 10.1099/mgen.0.000742] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a pathogen often associated with hospital-acquired infection or antimicrobial-induced disease; however, increasing evidence indicates infections can result from community or environmental sources. Most genomic sequencing of C. difficile has focused on clinical strains, although evidence is growing that C. difficile spores are widespread in soil and water in the environment. In this study, we sequenced 38 genomes collected from soil and water isolates in Flagstaff (AZ, USA) and Slovenia in an effort targeted towards environmental surveillance of C. difficile. At the average nucleotide identity (ANI) level, the genomes were divergent to C. difficile at a threshold consistent with different species. A phylogenetic analysis of these divergent genomes together with Clostridioides genomes available in public repositories confirmed the presence of three previously described, cryptic Clostridioides species and added two additional clades. One of the cryptic species (C-III) was almost entirely composed of Arizona and Slovenia genomes, and contained distinct sub-groups from each region (evidenced by SNP and gene-content differences). A comparative genomics analysis identified multiple unique coding sequences per clade, which can serve as markers for subsequent environmental surveys of these cryptic species. Homologues to the C. difficile toxin genes, tcdA and tcdB, were found in cryptic species genomes, although they were not part of the typical pathogenicity locus observed in C. difficile, and in silico PCR suggested that some would not amplify with widely used PCR diagnostic tests. We also identified gene homologues in the binary toxin cluster, including some present on phage and, for what is believed to be the first time, on a plasmid. All isolates were obtained from environmental samples, so the function and disease potential of these toxin homologues is currently unknown. Enzymatic profiles of a subset of cryptic isolates (n=5) demonstrated differences, suggesting that these isolates contain substantial metabolic diversity. Antimicrobial resistance (AMR) was observed across a subset of isolates (n=4), suggesting that AMR mechanisms are intrinsic to the genus, perhaps originating from a shared environmental origin. This study greatly expands our understanding of the genomic diversity of Clostridioides. These results have implications for C. difficile One Health research, for more sensitive C. difficile diagnostics, as well as for understanding the evolutionary history of C. difficile and the development of pathogenesis.
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Affiliation(s)
| | - Nathan E Stone
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Amalee E Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Chandler C Roe
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Adam J Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Samantha A Lucero
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Heidie Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Prvomajska Ulica 1, 2000 Maribor, Slovenia
| | - Sandra Janezic
- Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia
| | - Jason William Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
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Gu W, Wang W, Li W, Li N, Wang Y, Zhang W, Lu C, Tong P, Han Y, Sun X, Lu J, Wu Y, Dai J. New ribotype Clostridioides difficile from ST11 group revealed higher pathogenic ability than RT078. Emerg Microbes Infect 2021; 10:687-699. [PMID: 33682630 PMCID: PMC8023612 DOI: 10.1080/22221751.2021.1900748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/07/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022]
Abstract
Clostridioides difficile is the predominant antibiotic-associated enteropathogen associated with diarrhoea or pseudomembranous colitis in patients worldwide. Previously, we identified C. difficile RT078 isolates (CD21062) from elderly patients in China, including two new ribotype strains (CD10010 and CD12038) belonging to the ST11 group, and their genomic features were also investigated. This study compared sporulation, spore germination, toxin expression, flagellar characteristics, and adhesion among these strains in vitro and analysed their pathogenic ability in vivo using animal models. The results showed sporulation and spore germination did not significantly differ among the three C. difficile strains. CD10010 and CD12038 showed higher transcriptional levels of toxins until 48 h; thereafter, the transcriptional levels of toxins remained constant among RT078, CD10010, and CD12038. RT078 showed a loss of flagellum and its related genes, whereas CD12038 showed the highest motility in vitro. Both CD10010 and CD12038 initially showed flg phase OFF, and the flagellar switch reversed to phase ON after 48 h in swim agar. Flagellar proteins and toxins were both upregulated when flg phase OFF changed to flg phase ON status, enhancing their pathogenic ability. CD12038 showed the highest adhesion to Hep-2 cells. Histopathology and inflammation scores demonstrated that CD12038 caused the most severe tissue damage and infection in vivo. The new ribotype strains, particularly CD12038, exhibit higher pathogenic ability than the typical RT078 strain, both in vitro and in vivo. Therefore, more attention should be paid to this new C. difficile strain in epidemiological research; further studies are warranted.
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Affiliation(s)
- Wenpeng Gu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wenguang Wang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Li
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yuanyuan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenzhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Caixia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Pinfen Tong
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yuanyuan Han
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Xiaomei Sun
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
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Tsai MS, Newman C, Macdonald DW, Buesching CD. Stress-Related Herpesvirus Reactivation in Badgers Can Result in Clostridium Proliferation. ECOHEALTH 2021; 18:440-450. [PMID: 34870778 PMCID: PMC8742816 DOI: 10.1007/s10393-021-01568-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 09/21/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Clostridium perfringens is an important food-borne zoonotic pathogen and a member of the commensal gut microbiome of many mammals. Predisposing factors such as coinfection with other pathogens or diet change can, however, cause overgrowth and subsequent disease development. Here we investigated the occurrence of C. perfringens in a free-ranging badger population with up to 100% prevalence of herpesvirus infection. Herpesvirus reactivation is known to be associated with increased susceptibility bacterial infections. PCR screening of rectal swabs from 69 free-ranging badgers revealed 15.9% (11/69, 95% CI = 9.1-26.3%) prevalence of detectable C. perfringens (Type A) DNA in the digestive tracts of assymptomatic animals. The results of Fisher's exact test revealed C. perfringens detection was not biased by age, sex and seasons. However, badgers with genital tract gammaherpesvirus (MusGHV-1) reactivation (p = 0.007) and infection with a specific MusGHV-1 genotype (p = 0.019) were more prone to of C. perfringens proliferation, indicating coinfection biased dynamics of intestinal C. perfringens. An inclusion pattern analysis further indicated that, causally, MusGHV-1 reactivation potentiated C. perfringens detection. Whether or not specific MusGHV-1 genotype infection or reactivation plays a role in C. perfringens overgrowth or disease development in badgers will require further investigation. Nevertheless, a postmortem examination of a single badger that died of fatal disease, likely associated with C. perfringens, revealed MusGHV-1 detection in the small intestine.
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Affiliation(s)
- Ming-Shan Tsai
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Abingdon Road, Tubney House, Tubney, Oxfordshire, OX13 5QL, UK.
| | - Chris Newman
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Abingdon Road, Tubney House, Tubney, Oxfordshire, OX13 5QL, UK
- Cook's Lake Farming Forestry and Wildlife Inc (Ecological Consultancy), Queens County, NS, Canada
| | - David W Macdonald
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Abingdon Road, Tubney House, Tubney, Oxfordshire, OX13 5QL, UK
| | - Christina D Buesching
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Abingdon Road, Tubney House, Tubney, Oxfordshire, OX13 5QL, UK
- Cook's Lake Farming Forestry and Wildlife Inc (Ecological Consultancy), Queens County, NS, Canada
- Department of Biology, Irving K. Barber Faculty of Science, The University of British Columbia, Okanagan, Kelowna, BC, Canada
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Abdehagh M, Azimirad M, Houri H, Nadalian B, Azimirad F, Olfatifar M, Nasir Shoeibi OK, Yadegar A, Shahrokh S, Mahdavi Roshan M, Asadzadeh Aghdaei H, Zali MR. Serum procalcitonin levels associate with Clostridioides difficile infection in patients with inflammatory bowel disease. BMC Infect Dis 2021; 21:1103. [PMID: 34702217 PMCID: PMC8549175 DOI: 10.1186/s12879-021-06804-2] [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: 07/10/2021] [Accepted: 10/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is a major cause of morbidity among patients with inflammatory bowel disease (IBD). Diagnostic biomarkers for early detection of CDI are needed in clinical practice. The relationship between serum procalcitonin and CDI in IBD patients has not been investigated so far. Therefore, we aimed to evaluate the usefulness of measuring serum procalcitonin level to detect CDI in patients with the flare of IBD. METHODS One hundred twenty patients with IBD were enrolled in this study. Bacterial identification was performed using standard microbiological and molecular methods. The serum procalcitonin levels were measured in all patients. Receiver operating characteristic (ROC) curve analysis was applied to assess the value of procalcitonin for the prediction of CDI among IBD patients. RESULTS The median serum procalcitonin level was significantly increased in IBD patients with CDI compared to non-CDI IBD patients (0.69 ng/mL vs 0.32 ng/mL). In univariate analysis, log10 procalcitonin was associated with CDI (OR 2.81, 95% CI 1.54-4.09, P-value < 0.001). Procalcitonin 1.1 ng/mL was 85% sensitive and 88% specific for the prediction of CDI. In the multivariable model including the covariates log10 procalcitonin, age, hospitalization, type of IBD, duration of the disease, and antibiotic usage, procalcitonin showed a robust association with CDI (OR 4.59, 95% CI 2.49-6.70, P-value < 0.001). An elevated procalcitonin level was associated with the presence of CDI among IBD patients. CONCLUSIONS Our results indicate that procalcitonin level can be a good candidate biomarker for assessing the CDI in IBD patients. Further studies are required to decipher whether procalcitonin can predict CDI therapy or its recurrence.
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Affiliation(s)
- Mohammad Abdehagh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamidreza Houri
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Banafsheh Nadalian
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fahimeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Meysam Olfatifar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ome Kolsoum Nasir Shoeibi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shabnam Shahrokh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehran Mahdavi Roshan
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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38
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Kwon JH, O'Neil CA, Hink T, Reske KA, Bosserman RE, Dubberke ER, Burnham CAD. Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile. J Appl Lab Med 2021; 7:437-443. [PMID: 34609483 DOI: 10.1093/jalm/jfab110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C. difficile toxin enzyme immunoassay (tEIA) testing after an initial tEIA test was negative. METHODS For patients age ≥18 years who had a second C. difficile tEIA test ordered within 96 h after a negative tEIA test, remnant fecal specimens from the first (negative) tEIA test were evaluated using the BioFire FilmArray Gastrointestinal Panel PCR, C. difficile toxigenic culture, and culture on a blood agar plate (BAP) to identify other potential causes of infectious diarrhea. Growth of organisms on the BAP was also used to assess potential disruptions in the gastrointestinal microbiota. RESULTS Among 84 remnant specimens, toxigenic C. difficile was identified in 9 (11%) by culture or PCR, while potential alternative causes of infectious diarrhea, including norovirus, rotavirus, enteropathogenic Escherichia coli, and Salmonella, were identified in 11 specimens (13%) by PCR. For the majority of patients, no infectious cause of diarrhea was identified, but 84% exhibited disrupted gastrointestinal microbiota, which may contribute to diarrhea. CONCLUSIONS When a hospitalized patient has a negative C. difficile tEIA test but continues to have diarrhea, alternative infectious and noninfectious causes of diarrhea should be considered. If the patient has clinical signs and symptoms suggestive of infection or risk factors for gastrointestinal infection, laboratory testing for other etiologic agents may be appropriate.
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Affiliation(s)
- Jennie H Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline A O'Neil
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiffany Hink
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Kimberly A Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Bosserman
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Erik R Dubberke
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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Kabała M, Gofron Z, Aptekorz M, Sacha K, Harmanus C, Kuijper E, Martirosian G. Clostridioides difficile Ribotype 027 (RT027) Outbreak Investigation Due to the Emergence of Rifampicin Resistance Using Multilocus Variable-Number Tandem Repeat Analysis (MLVA). Infect Drug Resist 2021; 14:3247-3254. [PMID: 34429622 PMCID: PMC8380304 DOI: 10.2147/idr.s324745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/24/2021] [Indexed: 12/29/2022] Open
Abstract
Objective The aim of this study was Clostridioides difficile outbreak investigation due to the emergence of rifampicin resistant ribotype 027 (RT 027) fecal isolates from patients of Polish tertiary care hospital between X. 2017 and II. 2018 using multilocus variable tandem repeat analysis (MLVA). Materials and Methods Twenty-nine C. difficile fecal isolates from patients of tertiary care hospital in Southern Poland were ribotyped and analyzed by MLVA. Multiplex PCR (mPCR) for genes encoding GDH (gluD), toxins A (tcdA)/ B (tcdB), 16S rDNA and binary toxin genes (ctdA and ctdB) was performed. The antibiotic susceptibility profile was determined by E-test. Results The A, B and binary toxins encoding genes were detected in all 29 C. difficile strains which were sensitive to metronidazole, vancomycin and were resistant to erythromycin, clindamycin, and moxifloxacin; resistance to imipenem demonstrated 97%, to rifampicin – 45% isolates. C. difficile strains could be grouped by MLVA into 5 distinct clusters, and the largest cluster II contains 16 strains. The comparison of rifampicin GM MIC of cluster II (n=16 strains) with all others (n=13) showed that strains from clusters I, III, IV and V possessed significantly (p <0.005) higher GM MIC and were more resistant to rifampicin. Conclusion MLVA analysis proved transmission and recognized outbreak due to multidrug-resistant RT 027 C. difficile among patients of tertiary care hospital in Southern Poland. The reason for this is probably the widespread occurrence of spores in the hospital environment, which includes, among others, neglect of hygienic procedures and epidemic supervision. High resistance to imipenem (97%) and to rifampicin (45%) among C. difficile RT 027 Silesian isolates is threatening and requires further studies to elucidate this phenomenon.
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Affiliation(s)
- Monika Kabała
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Zygmunt Gofron
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Małgorzata Aptekorz
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Krzysztof Sacha
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
| | - Celine Harmanus
- Department of Medical Microbiology Leiden University Medical Center, Leiden, the Netherlands
| | - Ed Kuijper
- Department of Medical Microbiology Leiden University Medical Center, Leiden, the Netherlands
| | - Gayane Martirosian
- Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland
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Noori M, Ghalavand Z, Azimirad M, Yadegar A, Eslami G, Krutova M, Brajerova M, Goudarzi M, Zali MR. Genetic diversity and phylogenetic analysis of the surface layer protein A gene (slpA) among Clostridioides difficile clinical isolates from Tehran, Iran. Anaerobe 2021; 70:102403. [PMID: 34111549 DOI: 10.1016/j.anaerobe.2021.102403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022]
Abstract
Clostridioides difficile is the most common causative agent of healthcare-associated diarrhea. C. difficile strains produce a crystalline surface layer protein (SlpA), encoded by the slpA gene. Previous studies have shown that SlpA varies among C. difficile strains. In this study, we used the SlpA sequence-based typing system (SlpAST) for the molecular genotyping of C. difficile clinical isolates identified in Iran; the PCR ribotypes (RTs) and toxin profiles of the isolates were also characterized. Forty-eight C. difficile isolates were obtained from diarrheal patients, and characterized by capillary electrophoresis (CE) PCR ribotyping and the detection of toxin genes. In addition, the genetic diversity of the slpA gene was investigated by Sanger sequencing. The most common RTs were RT126 (20.8%), followed by RT001 (12.5%) and RT084 (10.4%). The intact PaLoc arrangement representing cdu2+/tcdR+/tcdB+/tcdE+/tcdA+/tcdC+/cdd3+ profile was the predominant pattern and cdtA and cdtB genes were found in one-third of the isolates. Using the SlpA genotyping, 12 main genotypes and 16 subtypes were identified. The SlpA type 078-1 was the most prevalent genotype (20.8%), and identified within the isolates of RT126. The yok-1, gr-1, cr-1 and kr-3 genotypes were detected in 14.5%, 12.5%, 12.5% and 8.3% of isolates, respectively. Almost all the isolates with the same RT were clustered in similar SlpA sequence types. In comparison to PCR ribotyping, SlpAST, as a simple and highly reproducible sequenced-based technique, can discriminate well between C. difficile isolates. This typing method appears to be a valuable tool for the epidemiological study of C. difficile isolates worldwide.
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Affiliation(s)
- Maryam Noori
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Ghalavand
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Gita Eslami
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Marie Brajerova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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AlJindan R, AlEraky DM, Borgio JF, AbdulAzeez S, Abdalhamid B, Mahmoud N, Farhat M. Diagnostic deficiencies of C. difficile infection among patients in a tertiary hospital in Saudi Arabia: A laboratory-based case series. Saudi J Biol Sci 2021; 28:4472-4477. [PMID: 34354432 PMCID: PMC8324924 DOI: 10.1016/j.sjbs.2021.04.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/19/2022] Open
Abstract
Clostridioides difficile infection (CDI) has become a threatening public health problem in the developed world. In the kingdom of Saudi Arabia, prevalence of CDI is still unknown due to limited surveillance protocols and diagnostic resources. We used a two-step procedure to study and confirm C. difficile cases. We also studied toxin profiles of these isolates. Stool samples were collected from symptomatic patients and clinically suspected of CDI for almost 12 months. Isolates were confirmed by culture method followed by 16S rRNA sequencing. Multiplex PCR was performed for the identification of toxin A, toxin B and binary toxin genes and compared to Gene Expert results. Out of the 47 collected samples, 27 were successfully grown on culture media. 18 samples were confirmed as C. difficile by both culture and 16S rRNA sequencing. Interestingly, the rest of the isolates (9 species) belonged to different genera. Our results showed 95% of samples were positive for both toxin A and B (tcdA, tcdB) and all samples exhibited the toxin gene regulator tcdC. All samples were confirmed negative for the binary toxin gene ctdB and 11% of the isolates were positive for ctdA gene. Interestingly, one isolate harbored the binary toxin gene (cdtA +) and tested negative for both toxins A and B. We believe that combining the standard culture method with molecular techniques can make the detection of C. difficile more accurate.
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Affiliation(s)
- Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Doaa M AlEraky
- Department of Biomedical Dental Science, Microbiology and Immunology Division, Collage of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Baha Abdalhamid
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nehal Mahmoud
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Maha Farhat
- Department of Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Corresponding author.
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Hassanain WA, Spoors J, Johnson CL, Faulds K, Keegan N, Graham D. Rapid ultra-sensitive diagnosis of clostridium difficile infection using a SERS-based lateral flow assay. Analyst 2021; 146:4495-4505. [PMID: 34184680 DOI: 10.1039/d1an00726b] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Clostridium difficile (C. diff) infection is one of the most contagious diseases associated with high morbidity and mortality rates in hospitalised patients. Accurate diagnosis can slow its spread by determining the most effective treatment. Herein, we report a novel testing platform as a proof-of-concept for the selective, sensitive, rapid and cost-effective diagnosis of C. diff infection (CDI) based on a duplex measurement. This was achieved by detecting two specific biomarkers, surface layer protein A (SlpA) and toxin B (ToxB), using a surface enhanced Raman scattering-based lateral flow assay (SERS-based LFA). The simultaneous duplex detection of SlpA with ToxB has not been described for the clinical diagnosis of CDI previously. The SlpA biomarker "AKDGSTKEDQLVDALA" was first reported by our group in 2018 as a species-specific identification tool. The second biomarker, ToxB, is the essential virulence biomarker of C. diff pathogenic strains and is required to confirm true infection pathogenicity. The proposed SERS-based LFA platform enabled rapid duplex detection of SlpA and ToxB on separate test lines using a duplex LF test strip within 20 minutes. The use of a handheld Raman spectrometer to scan test lines allowed for the highly sensitive quantitative detection of both biomarkers with a lowest observable concentration of 0.01 pg μL-1. The use of a handheld device in this SERS-based LFA instead of benchtop machine paves the way for rapid, selective, sensitive and cheap clinical evaluation of CDI at the point of care (POC) with minimal sample backlog.
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Affiliation(s)
- Waleed A Hassanain
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, G1 1RD, UK.
| | - Julia Spoors
- Diagnostic and Therapeutic Technologies, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, NE2 4HH, UK.
| | - Christopher L Johnson
- Diagnostic and Therapeutic Technologies, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, NE2 4HH, UK.
| | - Karen Faulds
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, G1 1RD, UK.
| | - Neil Keegan
- Diagnostic and Therapeutic Technologies, Translational and Clinical Research Institute, Newcastle University, Newcastle-Upon-Tyne, NE2 4HH, UK.
| | - Duncan Graham
- Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, Glasgow, G1 1RD, UK.
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von Schwartzenberg RJ, Bisanz JE, Lyalina S, Spanogiannopoulos P, Ang QY, Cai J, Dickmann S, Friedrich M, Liu SY, Collins SL, Ingebrigtsen D, Miller S, Turnbaugh JA, Patterson AD, Pollard KS, Mai K, Spranger J, Turnbaugh PJ. Caloric restriction disrupts the microbiota and colonization resistance. Nature 2021; 595:272-277. [PMID: 34163067 PMCID: PMC8959578 DOI: 10.1038/s41586-021-03663-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/21/2021] [Indexed: 12/14/2022]
Abstract
Diet is a major factor that shapes the gut microbiome1, but the consequences of diet-induced changes in the microbiome for host pathophysiology remain poorly understood. We conducted a randomized human intervention study using a very-low-calorie diet (NCT01105143). Although metabolic health was improved, severe calorie restriction led to a decrease in bacterial abundance and restructuring of the gut microbiome. Transplantation of post-diet microbiota to mice decreased their body weight and adiposity relative to mice that received pre-diet microbiota. Weight loss was associated with impaired nutrient absorption and enrichment in Clostridioides difficile, which was consistent with a decrease in bile acids and was sufficient to replicate metabolic phenotypes in mice in a toxin-dependent manner. These results emphasize the importance of diet-microbiome interactions in modulating host energy balance and the need to understand the role of diet in the interplay between pathogenic and beneficial symbionts.
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Affiliation(s)
- Reiner Jumpertz von Schwartzenberg
- Charité Universitätsmedizin Berlin, Department of Endocrinology and Metabolic Diseases, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Center for Cardiovascular Research (CCR), Berlin, Germany
| | - Jordan E Bisanz
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
| | | | - Peter Spanogiannopoulos
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Qi Yan Ang
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Jingwei Cai
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Sophia Dickmann
- Charité Universitätsmedizin Berlin, Department of Endocrinology and Metabolic Diseases, Berlin, Germany
| | - Marie Friedrich
- Charité Universitätsmedizin Berlin, Department of Endocrinology and Metabolic Diseases, Berlin, Germany
| | - Su-Yang Liu
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie L Collins
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Danielle Ingebrigtsen
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jessie A Turnbaugh
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Knut Mai
- Charité Universitätsmedizin Berlin, Department of Endocrinology and Metabolic Diseases, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Joachim Spranger
- Charité Universitätsmedizin Berlin, Department of Endocrinology and Metabolic Diseases, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Center for Cardiovascular Research (CCR), Berlin, Germany.
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA.
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Wongkuna S, Janvilisri T, Phanchana M, Harnvoravongchai P, Aroonnual A, Aimjongjun S, Malaisri N, Chankhamhaengdecha S. Temporal Variations in Patterns of Clostridioides difficile Strain Diversity and Antibiotic Resistance in Thailand. Antibiotics (Basel) 2021; 10:antibiotics10060714. [PMID: 34199301 PMCID: PMC8231780 DOI: 10.3390/antibiotics10060714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 01/04/2023] Open
Abstract
Clostridioides difficile has been recognized as a life-threatening pathogen that causes enteric diseases, including antibiotic-associated diarrhea and pseudomembranous colitis. The severity of C. difficile infection (CDI) correlates with toxin production and antibiotic resistance of C. difficile. In Thailand, the data addressing ribotypes, toxigenic, and antimicrobial susceptibility profiles of this pathogen are scarce and some of these data sets are limited. In this study, two groups of C. difficile isolates in Thailand, including 50 isolates collected from 2006 to 2009 (THA group) and 26 isolates collected from 2010 to 2012 (THB group), were compared for toxin genes and ribotyping profiles. The production of toxins A and B were determined on the basis of toxin gene profiles. In addition, minimum inhibitory concentration of eight antibiotics were examined for all 76 C. difficile isolates. The isolates of the THA group were categorized into 27 A−B+CDT− (54%) and 23 A-B-CDT- (46%), while the THB isolates were classified into five toxigenic profiles, including six A+B+CDT+ (23%), two A+B+CDT− (8%), five A−B+CDT+ (19%), seven A−B+CDT− (27%), and six A−B−CDT− (23%). By visually comparing them to the references, only five ribotypes were identified among THA isolates, while 15 ribotypes were identified within THB isolates. Ribotype 017 was the most common in both groups. Interestingly, 18 unknown ribotyping patterns were identified. Among eight tcdA-positive isolates, three isolates showed significantly greater levels of toxin A than the reference strain. The levels of toxin B in 3 of 47 tcdB-positive isolates were significantly higher than that of the reference strain. Based on the antimicrobial susceptibility test, metronidazole showed potent efficiency against most isolates in both groups. However, high MIC values of cefoxitin (MICs 256 μg/mL) and chloramphenicol (MICs ≥ 64 μg/mL) were observed with most of the isolates. The other five antibiotics exhibited diverse MIC values among two groups of isolates. This work provides evidence of temporal changes in both C. difficile strains and patterns of antimicrobial resistance in Thailand.
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Affiliation(s)
- Supapit Wongkuna
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (S.W.); (T.J.)
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Phurt Harnvoravongchai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Amornrat Aroonnual
- Department of Tropical Nutrition and Food Science, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand;
| | - Sathid Aimjongjun
- Graduate Program in Molecular Medicine, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Natamon Malaisri
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (P.H.); (N.M.)
- Correspondence:
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Martínez-Meléndez A, Tijerina-Rodríguez L, Collins N, Baines SD, Morfin-Otero R, Camacho-Ortíz A, Villarreal-Treviño L, Garza-González E. Diversity of Circulating Clostridioides difficile Ribotypes in Mexico and Susceptibility to Fidaxomicin, Vancomycin, and Metronidazole. Microb Drug Resist 2021; 27:1672-1676. [PMID: 34037477 DOI: 10.1089/mdr.2020.0583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we report the results of the epidemiological analysis of Clostridioides difficile ribotypes (RTs) and antimicrobial susceptibility testing. Most isolates were RT027, representing 73% (84/115) of isolates. No isolates with reduced susceptibility to fidaxomicin were found; however, 38 (33.04%) isolates had reduced susceptibility to metronidazole, and 7 isolates (6.1%) had reduced susceptibility to vancomycin. These findings highlight the need for continuous surveillance of C. difficile RTs and antimicrobial susceptibility testing.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Laura Tijerina-Rodríguez
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Nathania Collins
- Department of Clinical, Pharmaceutical, and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Simon D Baines
- Department of Clinical, Pharmaceutical, and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Rayo Morfin-Otero
- Centro Universitario de Ciencias de la Salud, Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Universidad de Guadalajara, Guadalajara, Mexico
| | - Adrián Camacho-Ortíz
- Hospital Universitario "Dr. José Eleuterio González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Licet Villarreal-Treviño
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Elvira Garza-González
- Hospital Universitario "Dr. José Eleuterio González," Universidad Autónoma de Nuevo León, Monterrey, Mexico
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Frentrup M, Thiel N, Junker V, Behrens W, Münch S, Siller P, Kabelitz T, Faust M, Indra A, Baumgartner S, Schepanski K, Amon T, Roesler U, Funk R, Nübel U. Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile. Environ Microbiol 2021; 23:7591-7602. [PMID: 33998128 DOI: 10.1111/1462-2920.15601] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 11/30/2022]
Abstract
During a field experiment applying broiler manure for fertilization of agricultural land, we detected viable Clostridioides (also known as Clostridium) difficile in broiler faeces, manure, dust and fertilized soil. A large diversity of toxigenic C. difficile isolates was recovered, including PCR ribotypes common from human disease. Genomic relatedness of C. difficile isolates from dust and from soil, recovered more than 2 years after fertilization, traced their origins to the specific chicken farm that had delivered the manure. We present evidence of long-term contamination of agricultural soil with manure-derived C. difficile and demonstrate the potential for airborne dispersal of C. difficile through dust emissions during manure application. Clostridioides genome sequences virtually identical to those from manure had been recovered from chicken meat and from human infections in previous studies, suggesting broiler-associated C. difficile are capable of zoonotic transmission.
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Affiliation(s)
- Martinique Frentrup
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nadine Thiel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vera Junker
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wiebke Behrens
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Steffen Münch
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Paul Siller
- Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany
| | - Tina Kabelitz
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Matthias Faust
- Leibniz-Institute for Tropospheric Research (TROPOS), Leipzig, Germany
| | - Alexander Indra
- AGES-Austrian Agency for Health and Food Safety, Vienna, Austria.,Paracelsus Medical University of Salzburg, Salzburg, Austria
| | | | | | - Thomas Amon
- Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany.,Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany
| | - Roger Funk
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Ulrich Nübel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.,Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
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47
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Global Landscape of Clostridioides Difficile Phylogeography, Antibiotic Susceptibility, and Toxin Polymorphisms by Post-Hoc Whole-Genome Sequencing from the MODIFY I/II Studies. Infect Dis Ther 2021; 10:853-870. [PMID: 33751421 PMCID: PMC8116447 DOI: 10.1007/s40121-021-00426-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/26/2021] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Clostridioides (Clostridium) difficile infection, the leading cause of healthcare-associated diarrhea, represents a significant burden on global healthcare systems. Despite being a global issue, information on C. difficile from a global perspective is lacking. The aim of this study is to model the global phylogeography of clinical C. difficile. METHODS Using samples collected from the MODIFY I and II studies (NCT01241552, NCT01513239), we performed whole-genome sequencing of 1501 clinical isolates including 37 novel sequence types (STs), representing the largest worldwide collection to date. RESULTS Our data showed ribotypes, multi-locus sequence typing clades, and whole-genome phylogeny were in good accordance. The clinical C. difficile genome was found to be more conserved than previously reported (61% core genes), and modest recombination rates of 1.4-5.0 were observed across clades. We observed a significant continent distribution preference among five C. difficile clades (Benjamini-Hochberg corrected Fisher's exact test P < 0.01); moreover, weak association between geographic and genetic distance among ribotypes suggested sources beyond healthcare-related transmission. Markedly different trends of antibiotic susceptibility among lineages and regions were identified, and three novel mutations (in pyridoxamine 5'-phosphate oxidase family protein: Tyr130Ser, Tyr130Cys, and a promoter SNP) associated with metronidazole-reduced susceptibility were discovered on a nim-related gene and its promotor by genome-wide association study. Toxin gene polymorphisms were shown to vary within and between prevalent ribotypes, and novel severe mutations were found on the tcdC toxin regulator protein. CONCLUSION Our systematic characterization of a global set of clinical trial C. difficile isolates from infected individuals demonstrated the complexity of the genetic makeup of this pathogenic organism. The geographic variability of clades, variability in toxin genes, and mutations associated with antibiotic susceptibility indicate a highly complex interaction of C. difficile between host and environment. This dataset will provide a useful resource for validation of findings and future research of C. difficile.
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48
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Weese JS, Slovis N, Rousseau J. Clostridioides (Clostridium) difficile in neonatal foals and mares at a referral hospital. J Vet Intern Med 2021; 35:1140-1146. [PMID: 33656757 PMCID: PMC7995440 DOI: 10.1111/jvim.16094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Understanding the epidemiology of Clostridium difficile is important for the development and assessment of infection prevention and control practices, as well as surveillance methods and interpretation of diagnostic testing results. OBJECTIVE Our objective was to longitudinally evaluate C. difficile shedding in neonatal foals and mares admitted to a referral hospital neonatal intensive care unit. ANIMALS Foals admitted to a neonatal intensive care unit, along with their dams. METHODS Rectal swabs were collected from mares and foals at admission, and then approximately every 3 days, when possible. Selective culture for C. difficile was performed and isolates were characterized by toxin gene PCR and ribotyping. RESULTS Clostridium difficile was isolated from 103/409 (25%) samples; 65/208 (31%) from foals and 38/201 (19%) from mares. Cumulatively, C. difficile was isolated from at least 1 sample from 50/113 (44%) foals and 30/97 (31%) mares. No association was found between hospitalization day and isolation of C. difficile (P = .13). Twenty-three different ribotypes were identified, with ribotype 078 predominating. Fifteen foals had 2 positive samples during hospitalization. In only 6/15 (40%) foals was the same strain identified both times (5 ribotype 078 and 1 ribotype 012). CONCLUSIONS AND CLINICAL IMPORTANCE Clostridium difficile is an important pathogen in adult horses and foals, and our findings highlight the complexity surrounding the epidemiology of this opportunistic pathogen. It can be found commonly, transiently, and cluster within a facility in the absence of identifiable disease occurrences or clusters.
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Affiliation(s)
- Jeffrey Scott Weese
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Nathan Slovis
- McGee Medical Center, Hagyard Equine Medical Institute, Lexington, Kentucky, USA
| | - Joyce Rousseau
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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49
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Comparison of Clostridioides difficile strains from animals and humans: First results after introduction of C. difficile molecular typing and characterization at the Istituto Zooprofilattico Sperimentale of Piemonte, Liguria e Valle d'Aosta, Italy. Comp Immunol Microbiol Infect Dis 2021; 75:101623. [PMID: 33607397 DOI: 10.1016/j.cimid.2021.101623] [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: 09/28/2020] [Revised: 01/27/2021] [Accepted: 02/05/2021] [Indexed: 11/24/2022]
Abstract
PCR ribotypes (RTs027 and 078) are known causes of Clostridioides difficile infection (CDI) in humans. Molecular typing and characterization of 39 C. difficile strains isolated from samples from humas and animals in 2016-2018 indicated an overlap of RTs between community-acquired patients (CA-CDI) and domestic animals from the same geographical area; 14 RTs were identified: 12 RTs were positive for toxins A/B; RT078, RT080 and RT126 were also positive for binary toxin (CDT). Most of the RTs from the animals (RTs020, 078, 106, 126) were also detected in the samples from humans. Strains grouped into three clusters: cluster I included prevalently human strains, mainly RT 018; clusters II and III included strains from humans and animals, mainly RT078 and RT020. The CA-CDI strains suggested animals as a reservoir of C. difficile isolated together with other microorganisms from animals, highlighting the association of enteric pathogens as a cause of infection and death.
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50
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van Rossen TM, van Prehn J, Koek A, Jonges M, van Houdt R, van Mansfeld R, Kuijper EJ, Vandenbroucke-Grauls CMJE, Budding AE. Simultaneous detection and ribotyping of Clostridioides difficile, and toxin gene detection directly on fecal samples. Antimicrob Resist Infect Control 2021; 10:23. [PMID: 33514422 PMCID: PMC7845108 DOI: 10.1186/s13756-020-00881-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/26/2020] [Indexed: 12/17/2022] Open
Abstract
Background Clostridioides difficile is the most common cause of nosocomial diarrhea. Ribotyping of cultured strains by a PCR-based test is used to study potential transmission between patients. We aimed to develop a rapid test that can be applied directly on fecal samples for simultaneous detection and ribotyping of C. difficile, as well as detection of toxin genes. Methods We developed a highly specific and sensitive primer set for simultaneous detection and ribotyping of C. difficile directly on total fecal DNA. Toxin genes were detected with primers adapted from Persson et al. (Clin Microbiol Infect 14(11):1057–1064). Our study set comprised 130 fecal samples: 65 samples with positive qPCR for C. difficile toxin A/B genes and 65 C. difficile qPCR negative samples. PCR products were analyzed by capillary gel electrophoresis. Results Ribosomal DNA fragment peak profiles and toxin genes were detected in all 65 C. difficile positive fecal samples and in none of the 65 C. difficile negative samples. The 65 samples were assigned to 27 ribotypes by the Dutch reference laboratory. Our peak profiles corresponded to these ribotypes, except for two samples. During a C. difficile outbreak, patients were correctly allocated to the outbreak-cluster based on the results of direct fecal ribotyping, before C. difficile isolates were cultured and conventionally typed. Conclusion C. difficile ribotyping directly on fecal DNA is feasible, with sensitivity and specificity comparable to that of diagnostic toxin gene qPCR and with ribotype assignment similar to that obtained by conventional typing on DNA from cultured isolates. This supports simultaneous diagnosis and typing to recognize an outbreak.
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Affiliation(s)
- Tessel M van Rossen
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands.
| | - Joffrey van Prehn
- Center for Infectious Diseases, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Alex Koek
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Robin van Houdt
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Rosa van Mansfeld
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
| | - Ed J Kuijper
- Center for Infectious Diseases, Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, Leiden, The Netherlands
| | - Christina M J E Vandenbroucke-Grauls
- Department of Medical Microbiology and Infection Control, Amsterdam Infection and Immunity Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, PK 2X132, De Boelelaan 1117, Amsterdam, The Netherlands
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