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Dost I, Abdel-Glil M, Persson S, Conza KL, Oleastro M, Alves F, Maurischat S, Scholtzek A, Mazuet C, Diancourt L, Tenson T, Schmoock G, Neubauer H, Schwarz S, Seyboldt C. Genomic study of European Clostridioides difficile ribotype 002/sequence type 8. Microb Genom 2024; 10. [PMID: 39051872 DOI: 10.1099/mgen.0.001270] [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] [Indexed: 07/27/2024] Open
Abstract
Clostridioides difficile has significant clinical importance as a leading cause of healthcare-associated infections, with symptoms ranging from mild diarrhoea to severe colitis, and possible life-threatening complications. C. difficile ribotype (RT) 002, mainly associated with MLST sequence type (ST) 8, is one of the most common RTs found in humans. This study aimed at investigating the genetic characteristics of 537 C. difficile genomes of ST8/RT002. To this end, we sequenced 298 C. difficile strains representing a new European genome collection, with strains from Germany, Denmark, France and Portugal. These sequences were analysed against a global dataset consisting of 1,437 ST8 genomes available through Enterobase. Our results showed close genetic relatedness among the studied ST8 genomes, a diverse array of antimicrobial resistance (AMR) genes and the presence of multiple mobile elements. Notably, the pangenome analysis revealed an open genomic structure. ST8 shows relatively low overall variation. Thus, clonal isolates were found across different One Health sectors (humans, animals, environment and food), time periods, and geographical locations, suggesting the lineage's stability and a universal environmental source. Importantly, this stability did not hinder the acquisition of AMR genes, emphasizing the adaptability of this bacterium to different selective pressures. Although only 2.4 % (41/1,735) of the studied genomes originated from non-human sources, such as animals, food, or the environment, we identified 9 cross-sectoral core genome multilocus sequence typing (cgMLST) clusters. Our study highlights the importance of ST8 as a prominent lineage of C. difficile with critical implications in the context of One Health. In addition, these findings strongly support the need for continued surveillance and investigation of non-human samples to gain a more comprehensive understanding of the epidemiology of C. difficile.
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Affiliation(s)
- Ines Dost
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
- Present address: Landesuntersuchungsamt Rheinland-Pfalz, Koblenz, Germany
| | - Mostafa Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Søren Persson
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Karen Loaiza Conza
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Mónica Oleastro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Frederico Alves
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Chief Scientific Office, European Food Safety Authority (EFSA), Parma, Italy
| | - Sven Maurischat
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Anissa Scholtzek
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Christelle Mazuet
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Laure Diancourt
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Gernot Schmoock
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
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Li X, Wang Y, Cao R, Xiao F, Wang X, Ye L, Xiao Y, Li D, Zhang T. Antimicrobial Resistance of Clostridioides difficile in Children from a Tertiary Pediatric Hospital in Shanghai, China. Infect Drug Resist 2024; 17:329-339. [PMID: 38293314 PMCID: PMC10826549 DOI: 10.2147/idr.s441312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/13/2023] [Indexed: 02/01/2024] Open
Abstract
Background Our previous study reported a high rate of recurrence in children with Clostridioides difficile (C. difficile) infection (CDI) after conventional antibiotic therapy. Here, we aimed to explore whether metronidazole and vancomycin resistant C. difficile isolates are circulating in pediatric CDI. Methods Antimicrobial susceptibility testing (AST) using the agar dilution method according to the Clinical and Laboratory Standard Institute (CLSI) were performed on C. difficile isolates collected from children with CDI between 2019 and 2022 at the Shanghai Children's Hospital. Whole-genome sequencing (WGS) was performed on all C. difficile isolates, and the presence of antibiotic resistance genes (ARGs) were identified using Resfinder and the Comprehensive Antibiotic Resistance Database (CARD). The presence of plasmid pCD-METRO was detected using SRST2 (v0.2.0) against 8 pCD-METRO coding sequences. Results A total of 50 C. difficile isolates were collected from stools of CDI children. The overall resistance rate on all isolates was 30.00% for metronidazole, 6.00% for vancomycin, 0% for rifaximin, 2.00% for rifampin, 24.00% for meropenem, 100.00% for ceftriaxone and clindamycin, 86.00% for erythromycin, 30.0% for levofloxacin, and 50.0% for tetracycline. Multidrug-resistant (MDR) was presented in 44 isolates (88.00%). Sixteen reported potential ARGs relating with resistance to antibiotic classes of aminoglycoside (AAC(6')-Ie-APH(2")-Ia, aad(6), ANT(6)-Ib, APH(2")-If, APH(3')-IIIa), lincosamide-clindamycin-erythromycin (ErmB, ErmQ), fluoroquinolones (CdeA), glycopeptides (vanRG), nucleoside (SAT-4), tetracycline (tetM, tetA(P), tetB(P), tetO), and trimethoprim (dfrF) were identified. However, the pCD-METRO plasmid and vanA/B were not detected in any isolates. Conclusion C. difficile isolates from children with reduced susceptibility to metronidazole and vancomycin are emerging in pediatric CDI in China. The lack of pCD-METRO plasmid and vanA/B associated with reduced antibiotic susceptibility suggests there are additional mechanisms of resistance.
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Affiliation(s)
- Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Rong Cao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Fangfei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Xufei Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lin Ye
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Dan Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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Yin C, Song Z, Wang X, Li H, Liu Y, Wang Q, Feng X, Song X. Development and clinical application of a rapid, visually interpretable polymerase spiral reaction for tcdB gene of Clostridioides difficile in fecal cultures. FEMS Microbiol Lett 2023; 370:fnad080. [PMID: 37537148 DOI: 10.1093/femsle/fnad080] [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: 02/01/2023] [Revised: 06/14/2023] [Accepted: 08/02/2023] [Indexed: 08/05/2023] Open
Abstract
In the surveillance of outbreaks of Clostridioides difficile infection, the rapid detection and diagnosis of C. difficile remain a major challenge. Polymerase spiral reaction (PSR) is a nucleic acid amplification technique that uses mixed primers and the strand displacement activity of Bst DNA polymerase to achieve a pair of primers and a single enzyme in an isothermal environment. The primer design is simple, the reaction is efficient, and a color indicator can be used to visualize the result. In this study, we developed a rapid and visually interpretable PSR to detect C. difficile by analyzing artificially contaminated feces samples and clinical isolates from patient feces samples. We designed two pairs of primers for a PSR that specifically targeted the conserved tcdB gene of C. difficile. The amplification results were visualized with the chromogenic dye hydroxynaphthol blue. The entire process was accomplished in 50 min at 64°C, with high specificity. The limit of detection of C. difficile with PSR was 150 fg/μl genomic DNA or 2 × 10 CFU/ml in artificially contaminated feces samples. With this method, we analyzed four clinical isolates and also compared the PSR with an isolation-and-culture detection method, polymerase chain reaction, and the Sanger sequencing. The four clinical isolates were found positive for tcdB, which confirmed the high specificity of the primers. The positive rates of tcdB in toxigenic C. difficile detected with PSR, PCR, and Sanger sequencing were 100%. The proportions of toxin types in these clinical C. difficile strains were 50% tcdA+tcdB+CDT- and 50% tcdA+tcdB+CDT+. The assay described should extend our understanding of the incidence of C. difficile. This may allow the rapid diagnosis and screening of C. difficile-related disease outbreaks in the field.
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Affiliation(s)
- Caihong Yin
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
| | - Zhanyun Song
- Changchun Customs Technology Center, 4448 Freedom Road, Changchun, China
| | - Xianghui Wang
- Changchun Customs Technology Center, 4448 Freedom Road, Changchun, China
| | - Hui Li
- Changchun Customs Technology Center, 4448 Freedom Road, Changchun, China
| | - Yue Liu
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
| | - Qiulin Wang
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
| | - Xin Feng
- School of Public Health, College of Veterinary Medicine, Jilin University, 5333 Xi 'an Road, Changchun, China
| | - Xiuling Song
- Department of Hygienic Inspection, School of Public Health, Jilin University, 1163 Xinmin Street, Changchun 130021, China
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Molecular characterization and antibiotic resistance of Clostridioides difficile in patients with inflammatory bowel disease from two hospitals in China. J Glob Antimicrob Resist 2022; 30:252-258. [PMID: 35764214 DOI: 10.1016/j.jgar.2022.06.017] [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: 09/27/2021] [Revised: 05/27/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Patients with inflammatory bowel disease (IBD) are susceptible to Clostridioides difficile infection (CDI), resulting in poor outcomes and recurrence; therefore, the molecular characterization of C. difficle in IBD patients in China needs further investigation. METHODS C. difficile strains were isolated and identified from fecal samples of adult and pediatric IBD patients. Toxigenic strains were typed using multilocus sequence typing (MLST) and whole genomic sequencing (WGS) to construct the phylogenetic tree. Susceptibility to 10 antimicrobials was evaluated using the E-test. RESULTS Among the 838 IBD patients, 82 toxigenic C. difficile were identified, which comprised 46 from adults and 36 children. 90.2% (74/82) of the isolates were positive for both toxin A and toxin B genes (A+B+), while the remaining 9.8% were negative for toxin A gene, but positive for toxin B gene (A-B+). These toxigenic strains were susceptible to metronidazole and vancomycin, but highly resistant to clindamycin, erythromycin, and fluoroquinolones. All moxifloxacin-resistant isolates had mutations resulting in an amino acid substitution in gryA (T82I). The dominant types were ST-35 (20.7%), ST-2 (17.1%), ST-54 (13.4%), and ST-3 (13.4%) in all patients. CONCLUSION The incidence and molecular epidemiology of C. difficile infection in adult IBD patients resembled CDI in the general inpatient population. A higher antibiotic resistance rate was identified among the C. difficile isolates obtained from pediatric IBD patients than adult patients, and few STs accounted for most multidrug-resistant strains. However, the molecular genetic features of the same ST-type between these two groups remains highly correlated.
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Su T, Chen W, Wang D, Cui Y, Ni Q, Jiang C, Dong D, Peng Y. Complete Genome Sequencing and Comparative Phenotypic Analysis Reveal the Discrepancy Between Clostridioides difficile ST81 and ST37 Isolates. Front Microbiol 2021; 12:776892. [PMID: 34992586 PMCID: PMC8725731 DOI: 10.3389/fmicb.2021.776892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/22/2021] [Indexed: 11/26/2022] Open
Abstract
Toxin A-negative, toxin B-positive Clostridioides difficile strains, which primarily include the ST81 and ST37 genotypes, are predominant in C. difficile infections leading to antibiotic-associated diarrhea in China. Recently, ST81 has been reported as the most prevalent genotype rather than ST37, although the genetic and functional characteristics of the two genotypes remain ambiguous. In this study, we conducted comprehensive comparative analysis of these two genotypes through complete genome sequencing and phenotypic profiling. The whole genome sequencing revealed that the ST81 and ST37 isolates were closely related genetically with similar gene compositions, and high rate of the core genome shared. The integrative and conjugative elements identified in ST81 were similar to those in ST37, albeit with more diverse and insertion regions. By characterizing the phenotypes related to colonization or survival in the host, we found that the ST81 isolates exhibited robust colonization ability and survival both in vitro and in vivo, enhanced spore production, and slightly increased motility, which may be attributable to the discrepancy in non-synonymous single-nucleotide polymorphisms in the relevant functional genes. Furthermore, the ST81 isolates displayed a significantly higher rate of resistance to fluoroquinolones compared with the ST37 isolates (94.12% vs. 62.5%) and mostly carried the amino acid substitution Asp426Val in GyrB. In summary, the results of our study indicate that ST81 isolates exhibit enhanced ability to transmit between hosts and survive in harsh environments, providing key genetic insights for further epidemiological investigations and surveillance of C. difficile infection.
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Affiliation(s)
- Tongxuan Su
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Chen
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Daosheng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingchao Cui
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Ni
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Danfeng Dong,
| | - Yibing Peng
- Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Yibing Peng,
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Ahn SW, Lee SH, Kim UJ, Jang HC, Choi HJ, Choy HE, Kang SJ, Roh SW. Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection. Gut Pathog 2021; 13:55. [PMID: 34530913 PMCID: PMC8447795 DOI: 10.1186/s13099-021-00451-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/08/2021] [Indexed: 12/14/2022] Open
Abstract
Background Clostridioides difficile infection (CDI) is an infectious nosocomial disease caused by Clostridioides difficile, an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens. Results Nine C. difficile strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60 C. difficile strains belong to the genus Clostridioides, while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine C. difficile strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes. Conclusion In this study, we identified the specific genomic characteristics of Korean C. difficile strains, which could serve as basic information for CDI prevention and treatment in Korea. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00451-3.
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Affiliation(s)
- Seung Woo Ahn
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Uh Jin Kim
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hee-Chang Jang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, 61469, Gwangju, Republic of Korea
| | - Seung Ji Kang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea.
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea.
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