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Hulme JP. Emerging Diagnostics in Clostridioides difficile Infection. Int J Mol Sci 2024; 25:8672. [PMID: 39201359 PMCID: PMC11354687 DOI: 10.3390/ijms25168672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Clostridioides difficile detection in community settings is time-intensive, resulting in delays in diagnosing and quarantining infected individuals. However, with the advent of semi-automated devices and improved algorithms in recent decades, the ability to discern CDI infection from asymptomatic carriage has significantly improved. This, in turn, has led to efficiently regulated monitoring systems, further reducing endemic risk, with recent concerns regarding a possible surge in hospital-acquired Clostridioides difficile infections post-COVID failing to materialize. This review highlights established and emerging technologies used to detect community-acquired Clostridioides difficile in research and clinical settings.
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Affiliation(s)
- John P Hulme
- Department of Bio-Nano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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Williamson CHD, Roe CC, Terriquez J, Hornstra H, Lucero S, Nunnally AE, Vazquez AJ, Vinocur J, Plude C, Nienstadt L, Stone NE, Celona KR, Wagner DM, Keim P, Sahl JW. A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment. Microb Genom 2023; 9. [PMID: 37347682 DOI: 10.1099/mgen.0.001046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C. difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.
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Affiliation(s)
| | - Chandler C Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Heidie Hornstra
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samantha Lucero
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Amalee E Nunnally
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam J Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | | | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kimberly R Celona
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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Kuttappan DA, Mooyottu S, Sponseller BA. An Overview of Equine Enteric Clostridial Diseases. Vet Clin North Am Equine Pract 2023; 39:15-23. [PMID: 36737289 DOI: 10.1016/j.cveq.2022.11.012] [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: 02/04/2023] Open
Abstract
The understanding of the pathogenesis of equine enteric clostridial organisms is an active, evolving field. Advances will improve our knowledge both from the animal welfare and human health perspectives. The zoonotic nature of this group of diseases makes them relevant in the age of One health, as a significant amount of close human-equine interactions occurs for business and pleasure. Economic and welfare reasons prompt a better understanding of enteric clostridial pathogenesis, treatment, and control of the infection in horses and ongoing efforts are needed to advance clinical outcomes.
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Affiliation(s)
| | - Shankumar Mooyottu
- Department of Pathobiology, Auburn University, College of Veterinary Medicine, 1130 Wire Road, Auburn, AL 36849, USA
| | - Brett A Sponseller
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, 2134 College of Veterinary Medicine, Ames, IA 50011-1134, USA; Department of Veterinary Clinical Sciences, Iowa State University, Ames, IA 50014, USA.
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Lee YR, Lee K, Byun JW, Kim H, So B, Ku BK, Kim HY, Moon BY. Prevalence, genetic characteristics, and antimicrobial resistance of Clostridioides difficile isolates from horses in Korea. Anaerobe 2023; 80:102700. [PMID: 36716814 DOI: 10.1016/j.anaerobe.2023.102700] [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: 07/18/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
OBJECTIVES Clostridioides difficile is an etiological agent of enteric diseases in humans and animals. Animals are considered a potential reservoir due to the genetic and antimicrobial resistance similarities between human and animal C. difficile isolates. In this study, we evaluated the genetic characteristics and antimicrobial resistance profiles of C. difficile isolated from 942 fecal samples collected from horses in South Korea during 2019-2020. METHODS The C. difficile isolates were tested for toxin genes including tcdA (A), tcdB (B), and cdtAB (CDT) and deletions of the tcdC gene by PCR. In addition, ribotyping, multilocus sequence typing, and antimicrobial susceptibility tests were performed. RESULTS Twenty-three (2.4%) C. difficile isolates were associated with diarrhea in foals under 1 year old during the spring-summer period. Of these, 82.6% were toxigenic strains, determined to be A+B+CDT+ (52.1%) or A+B+CDT‒ (30.4%). All isolates were susceptible to metronidazole and vancomycin, and resistant to cefotaxime and gentamicin, and 76.2% were multidrug resistant (MDR). RT078/ST11/Clade 5 was the most common genotype (47.8%), which was also found in animals and humans worldwide. All RT078/ST11/Clade 5 strains were toxigenic and had deletions of the tcdC gene. About half of these strains were resistant to moxifloxacin, and 63.6% were MDR. CONCLUSIONS C. difficile isolates in this study consisted mostly of toxigenic and MDR strains, and their genetic properties were highly similar to human C. difficile isolates. These results suggest high possibilities of zoonotic transmission and can provide knowledge for establishing strategies for the treatment and prevention of C. difficile infection.
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Affiliation(s)
- Yu-Ran Lee
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Kichan Lee
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Jae-Won Byun
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Heejung Kim
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - ByungJae So
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Bok-Kyung Ku
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Ha-Young Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
| | - Bo-Youn Moon
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea.
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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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Wright S. Highlights of recent clinically relevant papers. EQUINE VET EDUC 2022. [DOI: 10.1111/eve.13631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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