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Kunishima H, Ichiki K, Ohge H, Sakamoto F, Sato Y, Suzuki H, Nakamura A, Fujimura S, Matsumoto K, Mikamo H, Mizutani T, Morinaga Y, Mori M, Yamagishi Y, Yoshizawa S. Japanese Society for infection prevention and control guide to Clostridioides difficile infection prevention and control. J Infect Chemother 2024; 30:673-715. [PMID: 38714273 DOI: 10.1016/j.jiac.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 05/09/2024]
Affiliation(s)
- Hiroyuki Kunishima
- Department of Infectious Diseases. St. Marianna University School of Medicine, Japan.
| | - Kaoru Ichiki
- Department of Infection Control and Prevention, Hyogo Medical University Hospital, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
| | - Fumie Sakamoto
- Quality Improvement and Safety Center, Itabashi Chuo Medical Center, Japan
| | - Yuka Sato
- Department of Infection Control and Nursing, Graduate School of Nursing, Aichi Medical University, Japan
| | - Hiromichi Suzuki
- Department of Infectious Diseases, University of Tsukuba School of Medicine and Health Sciences, Japan
| | - Atsushi Nakamura
- Department of Infection Prevention and Control, Graduate School of Medical Sciences, Nagoya City University, Japan
| | - Shigeru Fujimura
- Division of Clinical Infectious Diseases and Chemotherapy, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Japan
| | - Kazuaki Matsumoto
- Division of Pharmacodynamics, Faculty of Pharmacy, Keio University, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, Japan
| | | | - Yoshitomo Morinaga
- Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
| | - Minako Mori
- Department of Infection Control, Hiroshima University Hospital, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Kochi Medical School, Kochi University, Japan
| | - Sadako Yoshizawa
- Department of Laboratory Medicine/Department of Microbiology and Infectious Diseases, Faculty of Medicine, Toho University, Japan
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Carling PC, Parry MF, Olmstead R. Environmental approaches to controlling Clostridioides difficile infection in healthcare settings. Antimicrob Resist Infect Control 2023; 12:94. [PMID: 37679758 PMCID: PMC10483842 DOI: 10.1186/s13756-023-01295-z] [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: 05/14/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
As today's most prevalent and costly healthcare-associated infection, hospital-onset Clostridioides difficile infection (HO-CDI) represents a major threat to patient safety world-wide. This review will discuss how new insights into the epidemiology of CDI have quantified the prevalence of C. difficile (CD) spore contamination of the patient-zone as well as the role of asymptomatically colonized patients who unavoidable contaminate their near and distant environments with resilient spores. Clarification of the epidemiology of CD in parallel with the development of a new generation of sporicidal agents which can be used on a daily basis without damaging surfaces, equipment, or the environment, led to the research discussed in this review. These advances underscore the potential for significantly mitigating HO-CDI when combined with ongoing programs for optimizing the thoroughness of cleaning as well as disinfection. The consequence of this paradigm-shift in environmental hygiene practice, particularly when combined with advances in hand hygiene practice, has the potential for significantly improving patient safety in hospitals globally by mitigating the acquisition of CD spores and, quite plausibly, other environmentally transmitted healthcare-associated pathogens.
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Crivaro AN, Carasi P, Salto I, Hugo A, Soldavini Pelichotti PC, Bengoa A, Fragomeno M, Serradell MA, Minnaard J, Rolny I, Alul E, Arregui L, Fabra Martinez ME, Moreno Valero OJ, Facente A, Magariños F, Jewtuchowicz V, Pérez PF, Trejo FM. Clostridioides difficile: Characterization of the circulating toxinotypes in an Argentinean public hospital. Rev Argent Microbiol 2023; 55:73-82. [PMID: 35840437 DOI: 10.1016/j.ram.2022.05.010] [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: 08/09/2021] [Revised: 02/22/2022] [Accepted: 05/02/2022] [Indexed: 02/07/2023] Open
Abstract
Clostridioides difficile is a spore-forming anaerobe microorganism associated to nosocomial diarrhea. Its virulence is mainly associated with TcdA and TcdB toxins, encoded by their respective tcdA and tcdB genes. These genes are part of the pathogenicity locus (PaLoc). Our aim was to characterize relevant C. difficile toxinotypes circulating in the hospital setting. The tcdA and tcdB genes were amplified and digested with different restriction enzymes: EcoRI for tcdA; HincII and AccI for tcdB. In addition, the presence of the cdtB (binary toxin) gene, TcdA and TcdB toxins by dot blot and the cytotoxic effect of culture supernatants on Vero cells, were evaluated. Altogether, these studies revealed three different circulating toxinotypes according to Rupnik's classification: 0, I and VIII, being the latter the most prevalent one. Even though more studies are certainly necessary (e.g. sequencing analysis), it is worth noting that the occurrence of toxinotype I could be related to the introduction of bacteria from different geographical origins. The multivariate analysis conducted on the laboratory values of individuals infected with the most prevalent toxinotype (VIII) showed that the isolates associated with fatal outcomes (GCD13, GCD14 and GCD22) are located in regions of the biplots related to altered laboratory values at admission. In other patients, although laboratory values at admission were not correlated, levels of urea, creatinine and white blood cells were positively correlated after the infection was diagnosed. Our study reveals the circulation of different toxinotypes of C. difficile strains in this public hospital. The variety of toxinotypes can arise from pre-existing microorganisms as well as through the introduction of bacteria from other geographical regions. The existence of microorganisms with different pathogenic potential is relevant for the control, follow-up, and treatment of the infections.
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Affiliation(s)
- Andrea N Crivaro
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, B1900AJI La Plata, Argentina; IIFP, Universidad Nacional de La Plata, CONICET, Facultad de Ciencias Exactas, Departamento de Ciencias Biológicas, La Plata, Argentina
| | - Paula Carasi
- IIFP, Universidad Nacional de La Plata, CONICET, Facultad de Ciencias Exactas, Departamento de Ciencias Biológicas, La Plata, Argentina
| | - Ileana Salto
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, B1900AJI La Plata, Argentina; IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calles 47 y 115 (1900), La Plata, Argentina
| | - Ayelen Hugo
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP-CIC PBA, 47 y 116 (s/n), La Plata 1900, Argentina
| | - P Cecilia Soldavini Pelichotti
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, B1900AJI La Plata, Argentina; Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP-CIC PBA, 47 y 116 (s/n), La Plata 1900, Argentina
| | - Agustina Bengoa
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP-CIC PBA, 47 y 116 (s/n), La Plata 1900, Argentina
| | - Melisa Fragomeno
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP-CIC PBA, 47 y 116 (s/n), La Plata 1900, Argentina
| | - María A Serradell
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, B1900AJI La Plata, Argentina
| | - Jessica Minnaard
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, B1900AJI La Plata, Argentina; Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP-CIC PBA, 47 y 116 (s/n), La Plata 1900, Argentina
| | - Ivanna Rolny
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, B1900AJI La Plata, Argentina; IIFP, Universidad Nacional de La Plata, CONICET, Facultad de Ciencias Exactas, Departamento de Ciencias Biológicas, La Plata, Argentina
| | - Eduardo Alul
- Luisa G de Gandulfo Hospital, Lomas de Zamora, Buenos Aires, Argentina
| | - Leandro Arregui
- Luisa G de Gandulfo Hospital, Lomas de Zamora, Buenos Aires, Argentina
| | | | | | - Andrea Facente
- Luisa G de Gandulfo Hospital, Lomas de Zamora, Buenos Aires, Argentina
| | | | | | - Pablo F Pérez
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, B1900AJI La Plata, Argentina; Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP-CIC PBA, 47 y 116 (s/n), La Plata 1900, Argentina.
| | - Fernando M Trejo
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP-CIC PBA, 47 y 116 (s/n), La Plata 1900, Argentina
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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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Jo J, Gonzales-Luna AJ, Lancaster CK, McPherson JK, Begum K, Jahangir Alam M, Garey KW. Multi-country surveillance of Clostridioides difficile demonstrates high prevalence of spores in non-healthcare environmental settings. Anaerobe 2022; 75:102543. [DOI: 10.1016/j.anaerobe.2022.102543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/27/2022] [Accepted: 02/23/2022] [Indexed: 01/05/2023]
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Health Care Environmental Hygiene: New Insights and Centers for Disease Control and Prevention Guidance. Infect Dis Clin North Am 2021; 35:609-629. [PMID: 34362536 DOI: 10.1016/j.idc.2021.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Recent research has significantly clarified the impact of optimizing patient-zone environmental hygiene. New insights into the environmental microbial epidemiology of many hospital-associated pathogens, especially Clostridioides difficile, have clarified and quantified the role of ongoing occult pathogen transmission from the near-patient environment. The recent development of safe, broadly effective surface chemical disinfectants has led to new opportunities to broadly enhance environmental hygiene in all health care settings. The Centers for Disease Control and Prevention has recently developed a detailed guidance to assist all health care settings in implementing optimized programs to mitigate health care-associated pathogen transmission from the near-patient surfaces.
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7
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Kuenzli AB, Burri S, Casanova C, Sommerstein R, Buetti N, Seth-Smith HMB, Bodmer T, Egli A, Marschall J. Successful management of a Clostridioides difficile ribotype 027 outbreak with a lean intervention bundle. J Hosp Infect 2020; 106:240-245. [PMID: 32745592 DOI: 10.1016/j.jhin.2020.07.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/27/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND In a 2015 point-prevalence study, Clostridioides difficile 027, a hypervirulent ribotype, was absent from healthcare institutions in Switzerland. In late 2016, we detected an outbreak of C. difficile infection (CDI) with ribotype 027 occurring across several hospitals in the same hospital network. METHODS The first cases of CDI due to ribotype 027 triggered an outbreak investigation, including whole genome sequencing (WGS) to identify outbreak strains. FINDINGS Twenty-eight patients with CDI caused by ribotype 027 between December 2016 and December 2017 were identified, out of which 20 were caused by a single clone. Commonalities among these patients were hospitalization in the same room or on the same ward, receiving care from the same healthcare workers, and shared toilet areas. In addition to the epidemiological links suggesting possible transmission pathways between cases, WGS confirmed the clonality of this C. difficile 027 outbreak. The outbreak was contained by isolation precautions, raising awareness among healthcare workers, harmonizing diagnostic algorithms, and switching to a sporicidal agent for environmental disinfection. Of note, neither default gowning and gloving nor hand washing with water and soap were implemented. CONCLUSION This C. difficile 027 outbreak was recognized belatedly due to lack of screening for this ribotype in some hospitals, and was contained by a swift response with simple infection prevention measures and adapting the laboratory approach. In order to have a better understanding of C. difficile epidemiology, diagnostic approaches should be standardized, CDI declared notifiable, and longitudinal data on prevalent ribotypes collected in countries where this is not established.
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Affiliation(s)
- A B Kuenzli
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - S Burri
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - C Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - R Sommerstein
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - N Buetti
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; University of Paris, INSERM IAME, U1137, Team DesCID, Paris, France
| | - H M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - T Bodmer
- labormedizinisches zentrum Dr. Risch, Liebefeld, Switzerland
| | - A Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland; Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - J Marschall
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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Shen A. Clostridioides difficile Spores: Bile Acid Sensors and Trojan Horses of Transmission. Clin Colon Rectal Surg 2020; 33:58-66. [PMID: 32104157 DOI: 10.1055/s-0040-1701230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Gram-positive, spore-forming bacterium, Clostridioides difficile is the leading cause of healthcare-associated infections in the United States, although it also causes a significant number of community-acquired infections. C. difficile infections, which range in severity from mild diarrhea to toxic megacolon, cost more to treat than matched infections, with an annual treatment cost of approximately $6 billion for almost half-a-million infections. These high-treatment costs are due to the high rates of C. difficile disease recurrence (>20%) and necessity for special disinfection measures. These complications arise in part because C. difficile makes metabolically dormant spores, which are the major infectious particle of this obligate anaerobe. These seemingly inanimate life forms are inert to antibiotics, resistant to commonly used disinfectants, readily disseminated, and capable of surviving in the environment for a long period of time. However, upon sensing specific bile salts in the vertebrate gut, C. difficile spores transform back into the vegetative cells that are responsible for causing disease. This review discusses how spores are ideal vectors for disease transmission and how antibiotics modulate this process. We also describe the resistance properties of spores and how they create challenges eradicating spores, as well as promote their spread. Lastly, environmental reservoirs of C. difficile spores and strategies for destroying them particularly in health care environments will be discussed.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
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Gonzales-Luna AJ, Carlson TJ, Dotson KM, Poblete K, Costa G, Miranda J, Lancaster C, Walk ST, Tupy S, Begum K, Alam MJ, Garey KW. PCR ribotypes of Clostridioides difficile across Texas from 2011 to 2018 including emergence of ribotype 255. Emerg Microbes Infect 2020; 9:341-347. [PMID: 32037964 PMCID: PMC7033716 DOI: 10.1080/22221751.2020.1721335] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 12/22/2022]
Abstract
Clostridioides difficile infection (CDI) is the most prevalent healthcare-associated infection in the United States and carries a significant healthcare system burden. As part of an ongoing, active surveillance system of C. difficile throughout Texas, the objective of this study was to assess changes in C. difficile ribotypes of clinical isolates obtained from hospitalized patients in Texas over the past seven years. Fifty hospitals located in Texas, USA sent C. difficile positive stool specimens to a centralized laboratory for PCR ribotyping and toxin characterization between 2011 and 2018. Data collected included specimen collection date, patient age, and sex. Strain genotypes were compiled, and changes in ribotype distribution over time were assessed. Overall, 7796 samples were ribotyped from predominately female patients (58.4%) aged 62 ± 19 years. Samples were obtained from all geographic regions of Texas including Houston/Southwest region (n = 5129; 85%), Dallas/North Texas (n = 579, 9.6%), Central Texas (n = 164; 2.7%), and South Texas (n = 162; 2.6%). The 10 most common ribotypes comprised 73% of all isolates tested during the study period. The most common ribotypes were 027 (17.5%), followed by 014-020 (16.1%), 106 (11.6%), and 002 (9.1%). The prevalence of ribotypes 027, 001, and 078-126 declined significantly over time, while ribotypes 106 and 054 increased in prevalence (P < 0.001). Furthermore, the emergence of a novel ribotype 255 strain was observed. Differences in ribotype distribution were also noted based on age and geographic distribution (P < 0.001, each). This seven-year study demonstrated changing molecular epidemiology of C. difficile in Texas, including the emergence of a novel ribotype 255.
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Affiliation(s)
- Anne J. Gonzales-Luna
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
| | - Travis J. Carlson
- Department of Clinical Sciences, Fred Wilson
School of Pharmacy, High Point University, High Point, NC,
USA
| | - Kierra M. Dotson
- Division of Clinical and Administrative Science,
Xavier University of Louisiana College of Pharmacy, New Orleans, LA,
USA
| | - Kelley Poblete
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
| | - Gabriela Costa
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
| | - Julie Miranda
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
| | - Chris Lancaster
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
| | - Seth T. Walk
- Department of Microbiology & Immunology,
Montana State University, Bozeman, MO, USA
| | - Shawn Tupy
- Texas Department of State Health
Services, Austin, TX, USA
| | - Khurshida Begum
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
| | - M. Jahangir Alam
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
| | - Kevin W. Garey
- Department of Pharmacy Practice and Translational
Research, University of Houston College of Pharmacy, Houston, TX,
USA
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Carlson TJ, Endres BT, Le Pham J, Gonzales-Luna AJ, Alnezary FS, Nebo K, Miranda J, Lancaster C, Bassères E, Begum K, Alam MJ, Reveles KR, Garey KW. Eosinopenia and Binary Toxin Increase Mortality in Hospitalized Patients With Clostridioides difficile Infection. Open Forum Infect Dis 2020; 7:ofz552. [PMID: 31993458 PMCID: PMC6979314 DOI: 10.1093/ofid/ofz552] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/01/2020] [Indexed: 12/18/2022] Open
Abstract
Background Patients with Clostridioides difficile infection (CDI) with either eosinopenia or infected with a binary toxin strain have increased likelihood of mortality. However, the relationship between binary toxin and eosinopenia to synergistically increase mortality has not been studied in humans. We hypothesized that patients with CDI due to binary toxin strains and concomitant peripheral eosinopenia would have a higher likelihood of inpatient mortality. Methods This multicenter, retrospective cohort study included adult patients with CDI of known ribotypes stratified by eosinopenia, defined as an absence of eosinophils in the peripheral blood (Houston cohort). The primary outcome was inpatient mortality. Results were supported by a separate national cohort of veterans with CDI (Veterans’ cohort). Results In the Houston cohort, a total of 688 patients from 13 institutions in 6 cities were included. Of these, 132 (19%) had an eosinophil count of 0.0 cells/µL (0.0 cells*109/L) and 109 (16%) were infected with a binary toxin strain. After adjusting for covariates, the combination of eosinopenia and infection with a binary toxin strain was an independent predictor of inpatient mortality (odds ratio [OR], 7.8; 95% confidence interval [CI], 1.9–33.2; P = .005). In the separate Veterans’ cohort (n = 790), this combination was also a significant predictor of inpatient mortality (OR, 6.1; 95% CI, 1.5–23.9; P = .009). Conclusions In conclusion, the combination of eosinopenia and CDI due to a binary toxin strain was correlated with increased mortality in hospitalized patients from 2 independent cohorts. Prospective studies should further study this important subset of patients at the time of CDI diagnosis.
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Affiliation(s)
- Travis J Carlson
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Julie Le Pham
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Faris S Alnezary
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA.,Department of Clinical and Hospital Pharmacy, College of Pharmacy, Taibah University, Medinah, Saudi Arabia
| | - Kimberly Nebo
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Julie Miranda
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Chris Lancaster
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Eugénie Bassères
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Khurshida Begum
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - M Jahangir Alam
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Kelly R Reveles
- College of Pharmacy, University of Texas at Austin, Austin, Texas, USA.,Pharmacotherapy Education and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
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Janezic S, Rupnik M. Development and Implementation of Whole Genome Sequencing-Based Typing Schemes for Clostridioides difficile. Front Public Health 2019; 7:309. [PMID: 31709221 PMCID: PMC6821651 DOI: 10.3389/fpubh.2019.00309] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022] Open
Abstract
Clostridioides difficile is an important nosocomial pathogen increasingly observed in the community and in different non-human reservoirs. The epidemiology and transmissibility of C. difficile has been studied using a variety of typing methods, including more recently developed whole-genome sequence (WGS) analysis that is becoming used routinely for bacterial typing worldwide. Here we review the schemes for WGS-based typing methods available for C. difficile and their applications in the field of human C. difficile infection (CDI). The two main approaches to discover genomic variations are single nucleotide variant (SNV) analysis and methods based on gene-by-gene comparisons (frequently called core genome or whole genome MLST, cgMLST, or wgMLST). SNV analysis currently provides the ultimate resolution, however, typing nomenclature and standardized methodology are missing. On the other hand, gene-by-gene approaches allow portability and standardized nomenclature, and are therefore becoming increasingly popular in bacterial epidemiology and outbreak investigation. Two commercial software packages (BioNumerics and Ridom SeqSphere+) and an open source database (EnteroBase) for allele and sequence type determination for C. difficile are currently available. Proof-of-concept WGS studies have already enabled advances in the investigation of the population structure of C. difficile species, microevolution within the epidemic strains, intercontinental transmission over time and in tracking of transmission events. WGS of clinical C. difficile isolates demonstrated a considerable genetic diversity suggesting diverse reservoirs for CDI. WGS was also shown to aid in resolving relapses and reinfections in recurrent CDI and has potential for use as a tool for assessing hospital infection prevention and control performance.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Medical Faculty, University of Maribor, Maribor, Slovenia
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Seth-Smith HMB, Egli A. Whole Genome Sequencing for Surveillance of Diphtheria in Low Incidence Settings. Front Public Health 2019; 7:235. [PMID: 31497588 PMCID: PMC6713046 DOI: 10.3389/fpubh.2019.00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/06/2019] [Indexed: 12/29/2022] Open
Abstract
Corynebacterium diphtheriae (C. diphtheriae) is a relatively rare pathogen in most Western countries. While toxin producing strains can cause pharyngeal diphtheria with potentially fatal outcomes, the more common presentation is wound infections. The diphtheria toxin is encoded on a prophage and can also be carried by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis. Currently, across Europe, infections are mainly diagnosed in travelers and refugees from regions where diphtheria is more endemic, patients from urban areas with poor hygiene, and intravenous drug users. About half of the cases are non-toxin producing isolates. Rapid identification of the bacterial pathogen and toxin production is a critical element of patient and outbreak management. Beside the immediate clinical management of the patient, public health agencies should be informed of toxigenic C. diphtheriae diagnoses as soon as possible. The collection of case-related epidemiological data from the patient is often challenging due to language barriers and social circumstances. However, information on patient contacts, vaccine status and travel/refugee route, where appropriate, is critical, and should be documented. In addition, isolates should be characterized using high resolution typing, in order to identify transmissions and outbreaks. In recent years, whole genome sequencing (WGS) has become the gold standard of high-resolution typing methods, allowing detailed investigations of pathogen transmissions. De-centralized sequencing strategies with redundancy in sequencing capacities, followed by data exchange may be a valuable future option, especially since WGS becomes more available and portable. In this context, the sharing of sequence data, using public available platforms, is essential. A close interaction between microbiology laboratories, treating physicians, refugee centers, social workers, and public health officials is a key element in successful management of suspected outbreaks. Analyzing bacterial isolates at reference centers may further help to provide more specialized microbiological techniques and to standardize information, but this is also more time consuming during an outbreak. Centralized communication strategies between public health agencies and laboratories helps considerably in establishing and coordinating effective surveillance and infection control. We review the current literature on high-resolution typing of C. diphtheriae and share our own experience with the coordination of a Swiss-German outbreak.
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Affiliation(s)
- Helena M. B. Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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Endres BT, Begum K, Sun H, Walk ST, Memariani A, Lancaster C, Gonzales-Luna AJ, Dotson KM, Bassères E, Offiong C, Tupy S, Kuper K, Septimus E, Arafat R, Alam MJ, Zhao Z, Hurdle JG, Savidge TC, Garey KW. Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains. Open Forum Infect Dis 2019; 6:ofz013. [PMID: 30793006 PMCID: PMC6368847 DOI: 10.1093/ofid/ofz013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
Background The epidemic Clostridioides difficile ribotype 027 strain resulted from the dissemination of 2 separate fluoroquinolone-resistant lineages: FQR1 and FQR2. Both lineages were reported to originate in North America; however, confirmatory large-scale investigations of C difficile ribotype 027 epidemiology using whole genome sequencing has not been undertaken in the United States. Methods Whole genome sequencing and single-nucleotide polymorphism (SNP) analysis was performed on 76 clinical ribotype 027 isolates obtained from hospitalized patients in Texas with C difficile infection and compared with 32 previously sequenced worldwide strains. Maximum-likelihood phylogeny based on a set of core genome SNPs was used to construct phylogenetic trees investigating strain macro- and microevolution. Bayesian phylogenetic and phylogeographic analyses were used to incorporate temporal and geographic variables with the SNP strain analysis. Results Whole genome sequence analysis identified 2841 SNPs including 900 nonsynonymous mutations, 1404 synonymous substitutions, and 537 intergenic changes. Phylogenetic analysis separated the strains into 2 prominent groups, which grossly differed by 28 SNPs: the FQR1 and FQR2 lineages. Five isolates were identified as pre-epidemic strains. Phylogeny demonstrated unique clustering and resistance genes in Texas strains indicating that spatiotemporal bias has defined the microevolution of ribotype 027 genetics. Conclusions Clostridioides difficile ribotype 027 lineages emerged earlier than previously reported, coinciding with increased use of fluoroquinolones. Both FQR1 and FQR2 ribotype 027 epidemic lineages are present in Texas, but they have evolved geographically to represent region-specific public health threats.
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Affiliation(s)
- Bradley T Endres
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Khurshida Begum
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Hua Sun
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston
| | - Seth T Walk
- Department of Microbiology and Immunology, Montana State University, Bozeman
| | - Ali Memariani
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Chris Lancaster
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Kierra M Dotson
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Eugénie Bassères
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | | | - Shawn Tupy
- Texas Department of State Health Services, Austin
| | - Kristi Kuper
- Center for Pharmacy Practice Excellence, Vizient, Houston, Texas
| | - Edward Septimus
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | | | - M Jahangir Alam
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston
| | - Tor C Savidge
- Texas Children's Microbiome Center, Texas Children's Hospital, Houston.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Texas
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