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Knight DR, Riley TV. Genomic Delineation of Zoonotic Origins of Clostridium difficile. Front Public Health 2019; 7:164. [PMID: 31281807 PMCID: PMC6595230 DOI: 10.3389/fpubh.2019.00164] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/03/2019] [Indexed: 01/27/2023] Open
Abstract
Clostridium difficile is toxin-producing antimicrobial resistant (AMR) enteropathogen historically associated with diarrhea and pseudomembranous colitis in hospitalized patients. In recent years, there have been dramatic increases in the incidence and severity of C. difficile infection (CDI), and associated morbidity and mortality, in both healthcare and community settings. C. difficile is an ancient and diverse species that displays a sympatric lifestyle, establishing itself in a range of ecological niches external to the healthcare system. These sources/reservoirs include food, water, soil, and over a dozen animal species, in particular, livestock such as pigs and cattle. In a manner analogous to human infection, excessive antimicrobial exposure, particularly to cephalosporins, is driving the expansion of C. difficile in livestock populations worldwide. Subsequent spore contamination of meat, vegetables grown in soil containing animal feces, agricultural by-products such as compost and manure, and the environment in general (households, lawns, and public spaces) is contributing to a persistent community source/reservoir of C. difficile and the insidious rise of CDI in the community. The whole-genome sequencing era continues to redefine our view of this complex pathogen. The application of high-resolution microbial genomics in a One Health framework (encompassing clinical, veterinary, and environment derived datasets) is the optimal paradigm for advancing our understanding of CDI in humans and animals. This approach has begun to yield critical insights into the genetic diversity, evolution, AMR, and zoonotic potential of C. difficile. In Europe, North America, and Australia, microevolutionary analysis of the C. difficile core genome shows strains common to humans and animals (livestock or companion animals) do not form distinct populations but share a recent evolutionary history. Moreover, for C. difficile sequence type 11 and PCR ribotypes 078 and 014, major lineages of One Health importance, this approach has substantiated inter-species clonal transmission between animals and humans. These findings indicate either a zoonosis or anthroponosis. Moreover, they challenge the existing paradigm and the long-held misconception that CDI is primarily a healthcare-associated infection. In this article, evolutionary, and zoonotic aspects of CDI are discussed, including the anthropomorphic factors that contribute to the spread of C. difficile from the farm to the community.
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Affiliation(s)
- Daniel R Knight
- Medical, Molecular, and Forensic Sciences, Murdoch University, Perth, WA, Australia
| | - Thomas V Riley
- Medical, Molecular, and Forensic Sciences, Murdoch University, Perth, WA, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.,School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia.,PathWest Laboratory Medicine, Department of Microbiology, Nedlands, WA, Australia
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Balsells E, Shi T, Leese C, Lyell I, Burrows J, Wiuff C, Campbell H, Kyaw MH, Nair H. Global burden of Clostridium difficile infections: a systematic review and meta-analysis. J Glob Health 2019; 9:010407. [PMID: 30603078 PMCID: PMC6304170 DOI: 10.7189/jogh.09.010407] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Clostridium difficile is a leading cause of morbidity and mortality in several countries. However, there are limited evidence characterizing its role as a global public health problem. We conducted a systematic review to provide a comprehensive overview of C. difficile infections (CDI) rates. Methods Seven databases were searched (January 2016) to identify studies and surveillance reports published between 2005 and 2015 reporting CDI incidence rates. CDI incidence rates for health care facility-associated (HCF), hospital onset-health care facility-associated, medical or general intensive care unit (ICU), internal medicine (IM), long-term care facility (LTCF), and community-associated (CA) were extracted and standardized. Meta-analysis was conducted using a random effects model. Results 229 publications, with data from 41 countries, were included. The overall rate of HCF-CDI was 2.24 (95% confidence interval CI = 1.66-3.03) per 1000 admissions/y and 3.54 (95%CI = 3.19-3.92) per 10 000 patient-days/y. Estimated rates for CDI with onset in ICU or IM wards were 11.08 (95%CI = 7.19-17.08) and 10.80 (95%CI = 3.15-37.06) per 1000 admission/y, respectively. Rates for CA-CDI were lower: 0.55 (95%CI = 0.13-2.37) per 1000 admissions/y. CDI rates were generally higher in North America and among the elderly but similar rates were identified in other regions and age groups. Conclusions Our review highlights the widespread burden of disease of C. difficile, evidence gaps, and the need for sustainable surveillance of CDI in the health care setting and the community.
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Affiliation(s)
- Evelyn Balsells
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Joint first authorship
| | - Ting Shi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Joint first authorship
| | - Callum Leese
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Iona Lyell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - John Burrows
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | | | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Moe H Kyaw
- Sanofi Pasteur, Swiftwater, Pennsylvania, USA.,Joint last authorship
| | - Harish Nair
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Joint last authorship
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Eyre DW, Tracey L, Elliott B, Slimings C, Huntington PG, Stuart RL, Korman TM, Kotsiou G, McCann R, Griffiths D, Fawley WN, Armstrong P, Dingle KE, Walker AS, Peto TE, Crook DW, Wilcox MH, Riley TV. Emergence and spread of predominantly community-onset Clostridium difficile PCR ribotype 244 infection in Australia, 2010 to 2012. ACTA ACUST UNITED AC 2015; 20:21059. [PMID: 25788254 DOI: 10.2807/1560-7917.es2015.20.10.21059] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe an Australia-wide Clostridium difficile outbreak in 2011 and 2012 involving the previously uncommon ribotype 244. In Western Australia, 14 of 25 cases were community-associated, 11 were detected in patients younger than 65 years, 14 presented to emergency/outpatient departments, and 14 to non-tertiary/community hospitals. Using whole genome sequencing, we confirm ribotype 244 is from the same C. difficile clade as the epidemic ribotype 027. Like ribotype 027, it produces toxins A, B, and binary toxin, however it is fluoroquinolone-susceptible and thousands of single nucleotide variants distinct from ribotype 027. Fifteen outbreak isolates from across Australia were sequenced. Despite their geographic separation, all were genetically highly related without evidence of geographic clustering, consistent with a point source, for example affecting the national food chain. Comparison with reference laboratory strains revealed the outbreak clone shared a common ancestor with isolates from the United States and United Kingdom (UK). A strain obtained in the UK was phylogenetically related to our outbreak. Follow-up of that case revealed the patient had recently returned from Australia. Our data demonstrate new C. difficile strains are an on-going threat, with potential for rapid spread. Active surveillance is needed to identify and control emerging lineages.
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Affiliation(s)
- D W Eyre
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
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Foster NF, Collins DA, Ditchburn SL, Duncan CN, van Schalkwyk JW, Golledge CL, Keed ABR, Riley TV. Epidemiology of Clostridium difficile infection in two tertiary-care hospitals in Perth, Western Australia: a cross-sectional study. New Microbes New Infect 2014; 2:64-71. [PMID: 25356346 PMCID: PMC4184660 DOI: 10.1002/nmi2.43] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/20/2014] [Accepted: 03/05/2014] [Indexed: 12/03/2022] Open
Abstract
The epidemiology of Clostridium difficile infection (CDI) has changed over time and between countries. It is therefore essential to monitor the characteristics of patients at risk of infection and the circulating strains to recognize local and global trends, and improve patient management. From December 2011 to May 2012 we conducted a prospective, observational epidemiological study of patients with laboratory-confirmed CDI at two tertiary teaching hospitals in Perth, Western Australia to determine CDI incidence and risk factors in an Australian setting. The incidence of CDI varied from 5.2 to 8.1 cases/10 000 occupied bed days (OBDs) at one hospital and from 3.9 to 16.3/10 000 OBDs at the second hospital. In total, 80 patients with laboratory-confirmed CDI met eligibility criteria and consented to be in the study. More than half (53.8%) had hospital-onset disease, 28.8% had community-onset and healthcare facility-associated disease and 7.5% were community-associated infections according to the definitions used. Severe CDI was observed in 40.0% of these cases but the 30-day mortality rate for all cases was only 2.5%. Besides a shorter length of stay among cases of community-onset CDI, no characteristics were identified that were significantly associated with community-onset or severe CDI. From 70 isolates, 34 different ribotypes were identified. The predominant ribotypes were 014 (24.3%), 020 (5.7%), 056 (5.7%) and 070 (5.7%). Whereas this study suggests that the characteristics of CDI cases in Australia are not markedly different from those in other developed countries, the increase in CDI rate observed emphasizes the importance of surveillance.
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Affiliation(s)
- N F Foster
- School of Pathology and Laboratory Medicine, The University of Western Australia Perth, Western Australia, Australia
| | - D A Collins
- School of Pathology and Laboratory Medicine, The University of Western Australia Perth, Western Australia, Australia
| | - S L Ditchburn
- Sir Charles Gairdner Hospital Perth, Western Australia, Australia
| | - C N Duncan
- Sir Charles Gairdner Hospital Perth, Western Australia, Australia
| | | | - C L Golledge
- Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre Perth, Western Australia, Australia
| | - A B R Keed
- Department of Infectious Diseases and Microbiology, Royal Perth Hospital Perth, Western Australia, Australia
| | - T V Riley
- School of Pathology and Laboratory Medicine, The University of Western Australia Perth, Western Australia, Australia ; Division of Microbiology and Infectious Diseases, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre Perth, Western Australia, Australia
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Slimings C, Armstrong P, Beckingham WD, Bull AL, Hall L, Kennedy KJ, Marquess J, McCann R, Menzies A, Mitchell BG, Richards MJ, Smollen PC, Tracey L, Wilkinson IJ, Wilson FL, Worth LJ, Riley TV. Increasing incidence of Clostridium difficile infection, Australia, 2011–2012. Med J Aust 2014; 200:272-6. [DOI: 10.5694/mja13.11153] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/27/2014] [Indexed: 11/17/2022]
Affiliation(s)
- Claudia Slimings
- Pathology and Laboratory Medicine, University of Western Australia, Perth, WA
| | | | - Wendy D Beckingham
- Infectious Diseases and Infection Prevention and Control Unit, ACT Health, Canberra, ACT
| | - Ann L Bull
- Victorian Healthcare Associated Infection Surveillance System (VICNISS) Coordinating Centre, Melbourne, VIC
| | - Lisa Hall
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD
- Centre for Healthcare Related Infection Surveillance and Prevention, Queensland Health, Brisbane, QLD
| | | | - John Marquess
- Centre for Healthcare Related Infection Surveillance and Prevention, Queensland Health, Brisbane, QLD
| | | | | | - Brett G Mitchell
- Faculty of Nursing and Health, Avondale College for Higher Education, Sydney, NSW
| | - Michael J Richards
- Victorian Healthcare Associated Infection Surveillance System (VICNISS) Coordinating Centre, Melbourne, VIC
| | | | | | - Irene J Wilkinson
- Communicable Disease Control Branch, Department of Health and Ageing, Adelaide, SA
| | - Fiona L Wilson
- Tasmanian Infection Prevention and Control Unit, Department of Health and Human Services, Hobart, TAS
| | - Leon J Worth
- Victorian Healthcare Associated Infection Surveillance System (VICNISS) Coordinating Centre, Melbourne, VIC
| | - Thomas V Riley
- Pathology and Laboratory Medicine, University of Western Australia, Perth, WA
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Foster NF, Riley TV. Clostridium difficile infection in Australia. MICROBIOLOGY AUSTRALIA 2014. [DOI: 10.1071/ma14008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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