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Kamel S, Corbacho-Loarte MD, Escudero-Sánchez R, Halperin A, Llorente S, Quevedo SM, Suárez-Carantoña C, del Campo L, Hernández MS, Guillen SM, Cobo J. Impact of an Intervention Program on Clostridioides difficile Infections: Comparison of 2 Hospital Cohorts. Open Forum Infect Dis 2024; 11:ofae390. [PMID: 39050227 PMCID: PMC11267231 DOI: 10.1093/ofid/ofae390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Indexed: 07/27/2024] Open
Abstract
Background Clostridioides difficile infection (CDI) occurs in various contexts and care settings and is managed by multiple specialists who are not experts in its management. While there are many initiatives to improve the diagnosis and avoid overdiagnosis, there is less focus on the overall management of the infection. Methods We studied a cohort of patients with a positive test result for toxigenic C difficile in 2 hospitals. Hospital A has a program that provides advice from an infectious disease specialist (IDS) and promotes continuity of care by providing a phone number to contact the IDS. Hospital B does not have any specific CDI program. The evaluation assessed the proportion of patients not treated (carriers or self-limited disease), adherence to Infectious Diseases Society of America guidelines, access to novel therapies, recurrence and mortality rates, and readmission and emergency department visits due to CDI. We assessed the program's effectiveness through a logistic regression model adjusted for covariates chosen by clinical criteria. Results Hospital A avoided more unnecessary treatments (19.3% vs 11.5%), provided access to novel therapies more frequently (35.3% vs 13%), and adhered more closely to current guidelines (95.8% vs 71.3%). Although the mortality and recurrence rates did not differ, the absence of an intervention program was associated with greater odds of admission due to recurrence (odds ratio, 4.19; P = .037) and more visits to the emergency department due to CDI (odds ratio, 8.74; P = .001). Conclusions Implementation of a CDI intervention program based on recommendations from IDSs and improved access to specialized care during the follow-up is associated with enhanced quality of CDI management and potential reductions in hospital resource utilization.
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Affiliation(s)
- Sara Kamel
- Internal Medicine Department, Hospital Universitario Severo Ochoa, Madrid, Spain
| | - María Dolores Corbacho-Loarte
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Escudero-Sánchez
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Halperin
- Microbiology Department, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
| | - Sergio Llorente
- Internal Medicine Department, Hospital Universitario Severo Ochoa, Madrid, Spain
| | - Sara María Quevedo
- Microbiology Department, Hospital Universitario Severo Ochoa, IRYCIS, Madrid, Spain
| | - Cecilia Suárez-Carantoña
- IInternal Medicine Department, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
- Medicine Department, Alcalá University, Madrid, Spain
| | - Laura del Campo
- Biostatistics Department, CIBERESP, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
- CIBER de Epidemiologia y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Santiago Moreno Guillen
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, Alcalá University, Madrid, Spain
| | - Javier Cobo
- Infectious Diseases Department, Hospital Ramón y Cajal, IRYCIS, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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2
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Bloomfield M, Hutton S, Burton M, Tarring C, Velasco C, Clissold C, Balm M, Kelly M, Macartney-Coxson D, White R. Early identification of a ward-based outbreak of Clostridioides difficile using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance. Infect Control Hosp Epidemiol 2024:1-7. [PMID: 38706217 DOI: 10.1017/ice.2024.77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To describe an outbreak of sequence type (ST)2 Clostridioides difficile infection (CDI) detected by a recently implemented multilocus sequence type (MLST)-based prospective genomic surveillance system using Oxford Nanopore Technologies (ONT) sequencing. SETTING Hemato-oncology ward of a public tertiary referral centre. METHODS From February 2022, we began prospectively sequencing all C. difficile isolated from inpatients at our institution on the ONT MinION device, with the output being an MLST. Bed-movement data are used to construct real-time ST-specific incidence charts based on ward exposures over the preceding three months. RESULTS Between February and October 2022, 76 of 118 (64.4%) CDI cases were successfully sequenced. There was wide ST variation across cases and the hospital, with only four different STs being seen in >4 patients. A clear predominance of ST2 CDI cases emerged among patients with exposure to our hemato-oncology ward between May and October 2022, which totalled ten patients. There was no detectable rise in overall CDI incidence for the ward or hospital due to the outbreak. Following a change in cleaning product to an accelerated hydrogen peroxide wipe and several other interventions, no further outbreak-associated ST2 cases were detected. A retrospective phylogenetic analysis using original sequence data showed clustering of the suspected outbreak cases, with the exception of two cases that were retrospectively excluded from the outbreak. CONCLUSIONS Prospective genomic surveillance of C. difficile using ONT sequencing permitted the identification of an outbreak of ST2 CDI that would have otherwise gone undetected.
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Affiliation(s)
- Max Bloomfield
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | - Samantha Hutton
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Megan Burton
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Claire Tarring
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Charles Velasco
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
| | - Carolyn Clissold
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | - Michelle Balm
- Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | - Matthew Kelly
- Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand
| | | | - Rhys White
- Institute of Environmental Science and Research, Health Group, Porirua, New Zealand
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3
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O’Grady K, Hong S, Putsathit P, George N, Hemphill C, Huntington PG, Korman TM, Kotsanas D, Lahra M, McDougall R, McGlinchey A, Levy A, Moore CV, Nimmo G, Prendergast L, Robson J, Speers DJ, Waring L, Wehrhahn MC, Weldhagen GF, Wilson RM, Riley TV, Knight DR. Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia. Microb Genom 2024; 10:001232. [PMID: 38717815 PMCID: PMC11165652 DOI: 10.1099/mgen.0.001232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/27/2024] [Indexed: 06/13/2024] Open
Abstract
Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLSB agents in vitro, but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, n=36) to 115.6 (RT002, ST8, n=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, n=169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, n=14; RT002, n=3; RT056, n=2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse C. difficile strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.
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Affiliation(s)
- Keeley O’Grady
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Stacey Hong
- Communicable Disease Control Directorate, WA Department of Health, East Perth, Western Australia, Australia
| | - Papanin Putsathit
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Narelle George
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Peter G. Huntington
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Tony M. Korman
- Monash University, Monash Health, Clayton, Victoria, Australia
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Monash Medical Centre, Clayton, Victoria, Australia
| | - Monica Lahra
- Department of Microbiology, The Prince of Wales Hospital, Randwick, New South Wales, Australia
| | | | | | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Casey V. Moore
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Graeme Nimmo
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Jennifer Robson
- Sullivan Nicolaides Pathology, Taringa, Queensland, Australia
| | - David J. Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | | | | | - Gerhard F. Weldhagen
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Richard M. Wilson
- Australian Clinical Labs, Microbiology Department, Wayville, South Australia, Australia
| | - Thomas V. Riley
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Daniel R. Knight
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [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: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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5
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Sundermann AJ, Griffith MP, Srinivasa VR, Waggle K, Snyder GM, Van Tyne D, Pless L, Harrison LH. Prolonged bacterial carriage and hospital transmission detected by whole genome sequencing surveillance. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2024; 4:e11. [PMID: 38415095 PMCID: PMC10897709 DOI: 10.1017/ash.2024.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 02/29/2024]
Affiliation(s)
- Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marissa P. Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Vatsala Rangachar Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kady Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, PA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lora Pless
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Epidemiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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6
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Janezic S, Garneau JR, Monot M. Comparative Genomics of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:199-218. [PMID: 38175477 DOI: 10.1007/978-3-031-42108-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile, a Gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of large numbers of genome sequences, mainly due to the use of next-generation sequencing methods, has undoubtedly shown their immense advantages in the determination of C. difficile population structure. The implementation of fine-scale comparative genomic approaches has paved the way for global transmission and recurrence studies, as well as more targeted studies, such as the PaLoc or CRISPR/Cas systems. In this chapter, we provide an overview of recent and significant findings on C. difficile using comparative genomic studies with implications for epidemiology, infection control and understanding of the evolution of C. difficile.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia.
- Faculty of Medicine, University of Maribor, Maribor, Slovenia.
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France
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7
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Doyle H, Valek AL, Murillo T, Ayres AM, Slaughter J, Berg ML, Snyder GM. A novel approach to correcting attribution of Clostridioides difficile in a healthcare setting. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e246. [PMID: 38156213 PMCID: PMC10753511 DOI: 10.1017/ash.2023.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 12/30/2023]
Abstract
Objective To describe a novel attribution metric estimating the causal source location of healthcare-associated Clostridioides difficile and compare it with the current US National Healthcare Safety Network (NHSN) surveillance reporting standard. Design Quality improvement study. Setting Two acute care facilities. Methods A novel attribution metric assigned days of attribution to locations where patients were located for 14 days before and the day of their C. difficile diagnosis. We correlated the NHSN-assigned unit attribution with the novel attribution measure and compared the proportion of attribution assigned to inpatient units. Results During a 30-month period, there were 727 NHSN C. difficile healthcare-associated infections (HAIs) and 409 non-HAIs; the novel metric attributed 17,034 days. The correlation coefficients for NHSN and novel attributions among non-ICU units were 0.79 (95% CI, 0.76-0.82) and 0.74 (95% CI, 0.70-0.78) and among ICU units were 0.70 (95% CI, 0.63-0.76) and 0.69 (95% CI, 0.60-0.77) at facilities A and B, respectively. The distribution of difference in percent attribution showed higher inpatient unit attribution using NHSN measure than the novel attribution metric: 38% of ICU units and 15% of non-ICU units in facility A, and 20% of ICU units and 25% of non-ICU units in facility B had a median difference >0; no inpatient units showed a greater attribution using the novel attribution metric. Conclusion The novel attribution metric shifts attribution from inpatient units to other settings and correlates modestly with NHSN methodology of attribution. If validated, the attribution metric may more accurately target C. difficile reduction efforts.
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Affiliation(s)
- Hunter Doyle
- Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, PA, USA
| | - Abby L. Valek
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Theresa Murillo
- Department of Infection Prevention and Control, UPMC Senior Communities, Pittsburgh, PA, USA
| | - Ashley M. Ayres
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Julie Slaughter
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Madeline L. Berg
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
| | - Graham M. Snyder
- Department of Infection Prevention and Control, UPMC Presbyterian/Shadyside, Pittsburgh, PA, USA
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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8
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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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9
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Kiu R, Shaw AG, Sim K, Acuna-Gonzalez A, Price CA, Bedwell H, Dreger SA, Fowler WJ, Cornwell E, Pickard D, Belteki G, Malsom J, Phillips S, Young GR, Schofield Z, Alcon-Giner C, Berrington JE, Stewart CJ, Dougan G, Clarke P, Douce G, Robinson SD, Kroll JS, Hall LJ. Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains. Nat Microbiol 2023; 8:1160-1175. [PMID: 37231089 PMCID: PMC10234813 DOI: 10.1038/s41564-023-01385-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/17/2023] [Indexed: 05/27/2023]
Abstract
Clostridium perfringens is an anaerobic toxin-producing bacterium associated with intestinal diseases, particularly in neonatal humans and animals. Infant gut microbiome studies have recently indicated a link between C. perfringens and the preterm infant disease necrotizing enterocolitis (NEC), with specific NEC cases associated with overabundant C. perfringens termed C. perfringens-associated NEC (CPA-NEC). In the present study, we carried out whole-genome sequencing of 272 C. perfringens isolates from 70 infants across 5 hospitals in the United Kingdom. In this retrospective analysis, we performed in-depth genomic analyses (virulence profiling, strain tracking and plasmid analysis) and experimentally characterized pathogenic traits of 31 strains, including 4 from CPA-NEC patients. We found that the gene encoding toxin perfringolysin O, pfoA, was largely deficient in a human-derived hypovirulent lineage, as well as certain colonization factors, in contrast to typical pfoA-encoding virulent lineages. We determined that infant-associated pfoA+ strains caused significantly more cellular damage than pfoA- strains in vitro, and further confirmed this virulence trait in vivo using an oral-challenge C57BL/6 murine model. These findings suggest both the importance of pfoA+ C. perfringens as a gut pathogen in preterm infants and areas for further investigation, including potential intervention and therapeutic strategies.
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Affiliation(s)
- Raymond Kiu
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Kathleen Sim
- Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Harley Bedwell
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sally A Dreger
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Wesley J Fowler
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Emma Cornwell
- Faculty of Medicine, Imperial College London, London, UK
| | - Derek Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gusztav Belteki
- Neonatal Intensive Care Unit, The Rosie Hospital, Cambridge, UK
| | - Jennifer Malsom
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | - Gregory R Young
- Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, UK
| | - Zoe Schofield
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
| | | | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Neonatal Services, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Paul Clarke
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Gillian Douce
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Stephen D Robinson
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - J Simon Kroll
- Faculty of Medicine, Imperial College London, London, UK
| | - Lindsay J Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Intestinal Microbiome, School of Life Sciences, ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany.
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10
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Whole Genome Sequencing Evidences High Rates of Relapse in Clostridioides difficile Infection Caused by the Epidemic Ribotype 106. Appl Microbiol 2023. [DOI: 10.3390/applmicrobiol3010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
An increasing prevalence and spread of Clostridioides difficile infection (CDI) caused by DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or by the higher resistance rates observed for some strains. Based on the results of our previous study where RT106 showed higher recurrence rates than other relevant ribotypes, a genetic analysis by whole-genome sequencing (WGS) of primary and recurrent RT106 isolates from ten patients was performed to determine whether the higher rate of recurrence associated with RT106 is due to relapses, caused by the same strain, or reinfections, caused by different strains. MLST profiles, resistance mutations, and phylogenetic relatedness were determined by comparative single nucleotide variant (SNV) analysis. All isolates were classified as ST42, and those belonging to the same patient were isogenic, with one exception; strains belonging to different patients were not with two exceptions, pointing to putative transmission events. Phylogenetic analysis also suggested the presence of similar local epidemic lineages associated with moxifloxacin resistance, except for one patient whose isolates clustered with different nonresistant US strains. Our results show that recurrent CDIs caused by RT06/ST42 are mainly due to relapses caused by the primary strains, showing the higher capacity of RT106/ST42 to persist and cause recurrences as compared to other ribotypes.
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11
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Alves F, Castro R, Pinto M, Nunes A, Pomba C, Oliveira M, Silveira L, Gomes JP, Oleastro M. Molecular epidemiology of Clostridioides difficile in companion animals: Genetic overlap with human strains and public health concerns. Front Public Health 2023; 10:1070258. [PMID: 36684930 PMCID: PMC9853383 DOI: 10.3389/fpubh.2022.1070258] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/12/2022] [Indexed: 01/09/2023] Open
Abstract
Introduction The changing epidemiology of Clostridioides difficile reflects a well-established and intricate community transmission network. With rising numbers of reported community-acquired infections, recent studies tried to identify the role played by non-human reservoirs in the pathogen's transmission chain. This study aimed at describing the C. difficile strains circulating in canine and feline populations, and to evaluate their genetic overlap with human strains to assess the possibility of interspecies transmission. Methods Fecal samples from dogs (n = 335) and cats (n = 140) were collected from two populations (group A and group B) in Portugal. C. difficile isolates were characterized for toxigenic profile and PCR-ribotyping. The presence of genetic determinants of antimicrobial resistance was assessed in all phenotypically resistant isolates. To evaluate the genetic overlap between companion animals and human isolates from Portugal, RT106 (n = 42) and RT014/020 (n = 41) strains from both sources were subjected to whole genome sequencing and integrated with previously sequenced RT106 (n = 43) and RT014/020 (n = 142) genomes from different countries. The genetic overlap was assessed based on core-single nucleotide polymorphism (SNP) using a threshold of 2 SNP. Results The overall positivity rate for C. difficile was 26% (76/292) in group A and 18.6% (34/183) in group B. Toxigenic strains accounted for 50% (38/76) and 52.9% (18/34) of animal carriage rates, respectively. The most prevalent ribotypes (RT) were the toxigenic RT106 and RT014/020, and the non-toxigenic RT010 and RT009. Antimicrobial resistance was found for clindamycin (27.9%), metronidazole (17.1%) and moxifloxacin (12.4%), associated with the presence of the ermB gene, the pCD-METRO plasmid and point mutations in the gyrA gene, respectively. Both RT106 and RT014/020 genetic analysis revealed several clusters integrating isolates from animal and human sources, supporting the possibility of clonal interspecies transmission or a shared environmental contamination source. Discussion This study shows that companion animals may constitute a source of infection of toxigenic and antimicrobial resistant human associated C. difficile isolates. Additionally, it contributes with important data on the genetic proximity between C. difficile isolates from both sources, adding new information to guide future work on the role of animal reservoirs in the establishment of community associated transmission networks and alerting for potential public health risk.
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Affiliation(s)
- Frederico Alves
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Rita Castro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Alexandra Nunes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Constança Pomba
- Genevet–Veterinary Molecular Diagnostic Laboratory, Carnaxide, Portugal
- CIISA–Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Manuela Oliveira
- CIISA–Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Leonor Silveira
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Mónica Oleastro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
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12
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Sundermann AJ, Chen J, Miller JK, Martin EM, Snyder GM, Van Tyne D, Marsh JW, Dubrawski A, Harrison LH. Whole-genome sequencing surveillance and machine learning for healthcare outbreak detection and investigation: A systematic review and summary. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e91. [PMID: 36483409 PMCID: PMC9726481 DOI: 10.1017/ash.2021.241] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 06/17/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) has traditionally been used in infection prevention to confirm or refute the presence of an outbreak after it has occurred. Due to decreasing costs of WGS, an increasing number of institutions have been utilizing WGS-based surveillance. Additionally, machine learning or statistical modeling to supplement infection prevention practice have also been used. We systematically reviewed the use of WGS surveillance and machine learning to detect and investigate outbreaks in healthcare settings. METHODS We performed a PubMed search using separate terms for WGS surveillance and/or machine-learning technologies for infection prevention through March 15, 2021. RESULTS Of 767 studies returned using the WGS search terms, 42 articles were included for review. Only 2 studies (4.8%) were performed in real time, and 39 (92.9%) studied only 1 pathogen. Nearly all studies (n = 41, 97.6%) found genetic relatedness between some isolates collected. Across all studies, 525 outbreaks were detected among 2,837 related isolates (average, 5.4 isolates per outbreak). Also, 35 studies (83.3%) only utilized geotemporal clustering to identify outbreak transmission routes. Of 21 studies identified using the machine-learning search terms, 4 were included for review. In each study, machine learning aided outbreak investigations by complementing methods to gather epidemiologic data and automating identification of transmission pathways. CONCLUSIONS WGS surveillance is an emerging method that can enhance outbreak detection. Machine learning has the potential to identify novel routes of pathogen transmission. Broader incorporation of WGS surveillance into infection prevention practice has the potential to transform the detection and control of healthcare outbreaks.
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Affiliation(s)
- Alexander J. Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jieshi Chen
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - James K. Miller
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Elise M. Martin
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Infection Prevention and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Graham M. Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Infection Prevention and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jane W. Marsh
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Artur Dubrawski
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Lee H. Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
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13
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Miller AC, Arakkal AT, Sewell DK, Segre AM, Pemmaraju SV, Polgreen PM. Risk for Asymptomatic Household Transmission of Clostridioides difficile Infection Associated with Recently Hospitalized Family Members. Emerg Infect Dis 2022; 28:932-939. [PMID: 35447064 PMCID: PMC9045444 DOI: 10.3201/eid2805.212023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We evaluated whether hospitalized patients without diagnosed Clostridioides difficile infection (CDI) increased the risk for CDI among their family members after discharge. We used 2001–2017 US insurance claims data to compare monthly CDI incidence between persons in households with and without a family member hospitalized in the previous 60 days. CDI incidence among insurance enrollees exposed to a recently hospitalized family member was 73% greater than enrollees not exposed, and incidence increased with length of hospitalization among family members. We identified a dose-response relationship between total days of within-household hospitalization and CDI incidence rate ratio. Compared with persons whose family members were hospitalized <1 day, the incidence rate ratio increased from 1.30 (95% CI 1.19–1.41) for 1–3 days of hospitalization to 2.45 (95% CI 1.66–3.60) for >30 days of hospitalization. Asymptomatic C. difficile carriers discharged from hospitals could be a major source of community-associated CDI cases.
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14
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Lanzas C, Jara M, Tucker R, Curtis S. A review of epidemiological models of Clostridioides difficile transmission and control (2009-2021). Anaerobe 2022; 74:102541. [PMID: 35217149 DOI: 10.1016/j.anaerobe.2022.102541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/09/2022] [Accepted: 02/20/2022] [Indexed: 02/08/2023]
Abstract
Clostridioides difficile is the leading cause of infectious diarrhea and one of the most common healthcare-acquired infections worldwide. We performed a systematic search and a bibliometric analysis of mathematical and computational models for Clostridioides difficile transmission. We identified 33 publications from 2009 to 2021. Models have underscored the importance of asymptomatic colonized patients in maintaining transmission in health-care settings. Infection control, antimicrobial stewardship, active testing, and vaccination have often been evaluated in models. Despite active testing and vaccination being not currently implemented, they are the most commonly evaluated interventions. Some aspects of C. difficile transmission, such community transmission and interventions in health-care settings other than in acute-care hospitals, remained less evaluated through modeling.
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Affiliation(s)
- Cristina Lanzas
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA.
| | - Manuel Jara
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Rachel Tucker
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Savannah Curtis
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
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- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
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15
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Jenior ML, Papin JA. Computational approaches to understanding Clostridioides difficile metabolism and virulence. Curr Opin Microbiol 2022; 65:108-115. [PMID: 34839237 PMCID: PMC8792252 DOI: 10.1016/j.mib.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 02/03/2023]
Abstract
The progress of infection by Clostridioides difficile is strongly influenced by metabolic cues it encounters as it colonizes the gastrointestinal tract. Both colonization and regulation of virulence have a multi-factorial interaction between host, microbiome, and gene expression cascades. While these connections with metabolism have been understood for some time, many mechanisms of control have remained difficult to directly assay due to high metabolic variability among C. difficile isolates and difficult genetic systems. Computational systems offer a means to interrogate structure of complex or noisy datasets and generate useful, tractable hypotheses to be tested in the laboratory. Recently, in silico techniques have provided powerful insights into metabolic elements of C. difficile infection ranging from virulence regulation to interactions with the gut microbiota. In this review, we introduce and provide context to the methods of computational modeling that have been applied to C. difficile metabolism and virulence thus far. The techniques discussed here have laid the foundation for future multi-scale efforts aimed at understanding the complex interplay of metabolic activity between pathogen, host, and surrounding microbial community in the regulation of C. difficile pathogenesis.
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Affiliation(s)
- Matthew L Jenior
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA,denotes co-corresponding author
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA, Department of Medicine, Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, VA, USA, Department of Biochemistry & Molecular Genetics, University of Virginia, Charlottesville, VA, USA,denotes co-corresponding author
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16
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Chandra H, Sharma KK, Tuovinen OH, Sun X, Shukla P. Pathobionts: mechanisms of survival, expansion, and interaction with host with a focus on Clostridioides difficile. Gut Microbes 2022; 13:1979882. [PMID: 34724858 PMCID: PMC8565823 DOI: 10.1080/19490976.2021.1979882] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Pathobionts are opportunistic microbes that emerge as a result of perturbations in the healthy microbiome due to complex interactions of various genetic, exposomal, microbial, and host factors that lead to their selection and expansion. Their proliferations can aggravate inflammatory manifestations, trigger autoimmune diseases, and lead to severe life-threatening conditions. Current surge in microbiome research is unwinding these complex interplays between disease development and protection against pathobionts. This review summarizes the current knowledge of pathobiont emergence with a focus on Clostridioides difficile and the recent findings on the roles of immune cells such as iTreg cells, Th17 cells, innate lymphoid cells, and cytokines in protection against pathobionts. The review calls for adoption of innovative tools and cutting-edge technologies in clinical diagnostics and therapeutics to provide insights in identification and quantification of pathobionts.
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Affiliation(s)
- Harish Chandra
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India,Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Krishna Kant Sharma
- Laboratory of Enzymology and Recombinant DNA Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Olli H. Tuovinen
- Department of Microbiology, Ohio State University, Columbus, OH, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA,Xingmin Sun Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India,Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India,CONTACT Pratyoosh Shukla School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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17
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Sundermann AJ, Chen J, Kumar P, Ayres AM, Cho ST, Ezeonwuka C, Griffith MP, Miller JK, Mustapha MM, Pasculle AW, Saul MI, Shutt KA, Srinivasa V, Waggle K, Snyder DJ, Cooper VS, Van Tyne D, Snyder GM, Marsh JW, Dubrawski A, Roberts MS, Harrison LH. Whole Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection. Clin Infect Dis 2021; 75:476-482. [PMID: 34791136 PMCID: PMC9427134 DOI: 10.1093/cid/ciab946] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Most hospitals use traditional infection prevention (IP) methods for outbreak detection. We developed the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines whole genome sequencing (WGS) surveillance and machine learning (ML) of the electronic health record (EHR) to identify undetected outbreaks and the responsible transmission routes, respectively. METHODS We performed WGS surveillance of healthcare-associated bacterial pathogens from November 2016 to November 2018. EHR ML was used to identify the transmission routes for WGS-detected outbreaks, which were investigated by an IP expert. Potential infections prevented were estimated and compared to traditional IP practice during the same period. RESULTS Of 3,165 isolates, there were 2,752 unique patient isolates in 99 clusters involving 297 (10.8%) patient isolates were identified by WGS; clusters ranged from 2-14 patients. At least one transmission route was detected for 65.7% of clusters. During the same time, traditional IP investigation prompted WGS for 15 suspected outbreaks involving 133 patients, for which transmission events were identified for 5 (3.8%). If EDS-HAT had been running in real-time, 25-63 transmissions could have been prevented. EDS-HAT was found to be cost-saving and more effective than traditional IP practice, with overall savings of $192,408 - $692,532. CONCLUSION EDS-HAT detected multiple outbreaks not identified using traditional IP methods, correctly identified the transmission routes for most outbreaks, and would save the hospital substantial costs. Traditional IP practice misidentified outbreaks for which transmission did not occur. WGS surveillance combined with EHR ML has the potential to save costs and enhance patient safety.
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Affiliation(s)
- Alexander J Sundermann
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jieshi Chen
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Praveen Kumar
- Department of Health Policy and Management, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ashley M Ayres
- Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania, USA
| | - Shu-Ting Cho
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Chinelo Ezeonwuka
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Marissa P Griffith
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James K Miller
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Mustapha M Mustapha
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - A William Pasculle
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Melissa I Saul
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kathleen A Shutt
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vatsala Srinivasa
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kady Waggle
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel J Snyder
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pennsylvania, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pennsylvania, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Graham M Snyder
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Infection Control and Hospital Epidemiology, UPMC Presbyterian, Pittsburgh, Pennsylvania, USA
| | - Jane W Marsh
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Artur Dubrawski
- Auton Lab, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
| | - Mark S Roberts
- Department of Health Policy and Management, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lee H Harrison
- Microbial Genomic Epidemiology Laboratory, Center for Genomic Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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18
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Meijer SE, Harel N, Ben-Ami R, Nahari M, Yakubovsky M, Oster HS, Kolomansky A, Halutz O, Laskar O, Henig O, Stern A, Paran Y. Unraveling a Nosocomial Outbreak of COVID-19: The Role of Whole-Genome Sequence Analysis. Open Forum Infect Dis 2021; 8:ofab120. [PMID: 34631912 PMCID: PMC7989189 DOI: 10.1093/ofid/ofab120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic poses many epidemiological challenges. The investigation of nosocomial transmission is usually performed via thorough investigation of an index case and subsequent contact tracing. Notably, this approach has a subjective component, and there is accumulating evidence that whole-genome sequencing of the virus may provide more objective insight. METHODS We report a large nosocomial outbreak in 1 of the medicine departments in our institution. Following intensive epidemiological investigation, we discovered that 1 of the patients involved was suffering from persistent COVID-19 while initially thought to be a recovering patient. She was therefore deemed to be the most likely source of the outbreak. We then performed whole-genome sequencing of the virus of 14 infected individuals involved in the outbreak. RESULTS Surprisingly, the results of whole-genome sequencing refuted our initial hypothesis. A phylogenetic tree of the samples showed multiple introductions of the virus into the ward, 1 of which led to a cluster of 10 of the infected individuals. Importantly, the results pointed in the direction of a specific index patient that was different from the 1 that arose from our initial investigation. CONCLUSIONS These results underscore the important added value of using whole-genome sequencing in epidemiological investigations as it may reveal unexpected connections between cases and aid in understanding transmission dynamics, especially in the setting of a pandemic where multiple possible index cases exist simultaneously.
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Affiliation(s)
- Suzy E Meijer
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noam Harel
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel
| | - Ronen Ben-Ami
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Meital Nahari
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Yakubovsky
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Howard S Oster
- Department of Internal Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Albert Kolomansky
- Department of Internal Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ora Halutz
- Laboratory of Microbiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Orly Laskar
- The Department of Infectious Diseases, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Oryan Henig
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
- Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Tel Aviv, Israel
| | - Yael Paran
- Department of Infectious Diseases and Epidemiology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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19
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Evaluation of a Combined Multilocus Sequence Typing and Whole-Genome Sequencing Two-Step Algorithm for Routine Typing of Clostridioides difficile. J Clin Microbiol 2021; 59:JCM.01955-20. [PMID: 33177119 DOI: 10.1128/jcm.01955-20] [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] [Received: 07/26/2020] [Accepted: 10/21/2020] [Indexed: 01/05/2023] Open
Abstract
Multilocus sequence typing (MLST) is a low-resolution but rapid genotyping method for Clostridioides difficile Whole-genome sequencing (WGS) has emerged as the new gold standard for C. difficile typing, but cost and lack of standardization still limit broad utilization. In this study, we evaluated the potential to combine the portability of MLST with the increased resolution of WGS for a cost-saving approach to routine C. difficile typing. C. difficile strains from two New York City hospitals (hospital A and hospital B) were selected. WGS single-nucleotide polymorphism (wgSNP) was performed using established methods. Sequence types (ST) were determined using PubMLST, while wgSNP analysis was performed using the Bionumerics software. An additional analysis of a subset of data (hospital A) was made comparing the Bionumerics software to the CosmosID pipeline. Cost and turnaround time to results were compared for the algorithmic approach of MLST followed by wgSNP versus direct wgSNP. Among the 202 C. difficile isolates typed, 91% (n = 185/203) clustered within the representative ST, showing a high agreement between MLST and wgSNP. While clustering was similar between the Bionumerics and CosmosID pipelines, large differences in the overall number of SNPs were noted. A two-step algorithm for routine typing results in significantly lower cost than routine use of WGS. Our results suggest that using MLST as a first step in routine typing of C. difficile followed by WGS for MLST concordant strains is a less technically demanding, cost-saving approach for performing C. difficile typing than WGS alone without loss of discriminatory power.
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McLean K, Balada-Llasat JM, Waalkes A, Pancholi P, Salipante SJ. Whole-genome sequencing of clinical Clostridioides difficile isolates reveals molecular epidemiology and discrepancies with conventional laboratory diagnostic testing. J Hosp Infect 2020; 108:64-71. [PMID: 33227298 DOI: 10.1016/j.jhin.2020.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/06/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND The high clinical burden of Clostridioides difficile infections merits rapid and sensitive identification of affected individuals. However, effective diagnosis remains challenging. Current best practice guidelines recommend molecular and/or direct toxin detection-based screening for symptomatic individuals, but previous work has called into question the concordance and performance of extant clinical assays. AIM To better correlate the genomic and phenotypic properties of clinical C. difficile isolates with laboratory testing outcomes in both C. difficile-infected patients and asymptomatic carriers. METHODS Whole-genome sequencing of clinical C. difficile isolates collected from an inpatient population at a single healthcare institution was performed, enabling examination of their molecular epidemiology and toxigenic gene content. Genomic findings were compared with clinical testing outcomes, identifying multiple diagnostic discrepancies. FINDINGS Toxigenic culture, considered a 'reference standard', provided perfect sensitivity and specificity in predicting toxigenic gene content, whereas reduced performance was observed for Simplexa C. difficile Direct Assay (100% specificity, 88% sensitivity), Gene Xpert CD/Epi Assay (86% specificity, 83% sensitivity), and Quick Check Complete Tox A/B (100% specificity, 30% sensitivity). Genomic analysis additionally revealed variability in toxin gene sequences among C. difficile strains, phylogenomic equivalency between isolates from affected patients and carriers, and patient carriage with uncommon environmentally derived C. difficile lineages, as well as presenting opportunities for tracing pathogen transmission events. CONCLUSION These results highlight the variable performance of clinical stool-based testing approaches as well as the potential diagnostic utility of whole-genome sequencing as an alternative to conventional testing algorithms.
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Affiliation(s)
- K McLean
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - J-M Balada-Llasat
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA
| | - A Waalkes
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - P Pancholi
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA.
| | - S J Salipante
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA.
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21
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Impact of the coronavirus disease 2019 (COVID-19) pandemic on nosocomial Clostridioides difficile infection. Infect Control Hosp Epidemiol 2020; 42:406-410. [PMID: 32895065 PMCID: PMC7520631 DOI: 10.1017/ice.2020.454] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVES The coronavirus disease 2019 (COVID-19) pandemic has induced a reinforcement of infection control measures in the hospital setting. Here, we assess the impact of the COVID-19 pandemic on the incidence of nosocomial Clostridioides difficile infection (CDI). METHODS We retrospectively compared the incidence density (cases per 10,000 patient days) of healthcare-facility-associated (HCFA) CDI in a tertiary-care hospital in Madrid, Spain, during the maximum incidence of COVID-19 (March 11 to May 11, 2020) with the same period of the previous year (control period). We also assessed the aggregate in-hospital antibiotic use (ie, defined daily doses [DDD] per 100 occupied bed days [BD]) and incidence density (ie, movements per 1,000 patient days) of patient mobility during both periods. RESULTS In total, 2,337 patients with reverse transcription-polymerase chain reaction-confirmed COVID-19 were admitted to the hospital during the COVID-19 period. Also, 12 HCFA CDI cases were reported at this time (incidence density, 2.68 per 10,000 patient days), whereas 34 HCFA CDI cases were identified during the control period (incidence density, 8.54 per 10,000 patient days) (P = .000257). Antibiotic consumption was slightly higher during the COVID-19 period (89.73 DDD per 100 BD) than during the control period (79.16 DDD per 100 BD). The incidence density of patient movements was 587.61 per 1,000 patient days during the control period and was significantly lower during the COVID-19 period (300.86 per 1,000 patient days) (P < .0001). CONCLUSIONS The observed reduction of ~70% in the incidence density of HCFA CDI in a context of no reduction in antibiotic use supports the importance of reducing nosocomial transmission by healthcare workers and asymptomatic colonized patients, reinforcing cleaning procedures and reducing patient mobility in the epidemiological control of CDI.
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22
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Frentrup M, Zhou Z, Steglich M, Meier-Kolthoff JP, Göker M, Riedel T, Bunk B, Spröer C, Overmann J, Blaschitz M, Indra A, von Müller L, Kohl TA, Niemann S, Seyboldt C, Klawonn F, Kumar N, Lawley TD, García-Fernández S, Cantón R, del Campo R, Zimmermann O, Groß U, Achtman M, Nübel U. A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics. Microb Genom 2020; 6:mgen000410. [PMID: 32726198 PMCID: PMC7641423 DOI: 10.1099/mgen.0.000410] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/30/2020] [Indexed: 01/02/2023] Open
Abstract
Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled C. difficile genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of C. difficile at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (P<10-4) or single wards (P=0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with k-mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled C. difficile genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile.
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Affiliation(s)
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, UK
| | - Matthias Steglich
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
| | | | | | - Thomas Riedel
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Jörg Overmann
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
- Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
| | - Marion Blaschitz
- AGES-Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Alexander Indra
- AGES-Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | - Thomas A. Kohl
- Research Center Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Germany
| | - Stefan Niemann
- Research Center Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Germany
| | | | - Frank Klawonn
- Biostatistics, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Information Engineering, Ostfalia University, Wolfenbüttel, Germany
| | | | | | - Sergio García-Fernández
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | | | - Uwe Groß
- University Medical Center Göttingen, Germany
| | - Mark Achtman
- Warwick Medical School, University of Warwick, UK
| | - Ulrich Nübel
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
- Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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24
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Miller AC, Segre AM, Pemmeraju SV, Sewell DK, Polgreen PM. Association of Household Exposure to Primary Clostridioides difficile Infection With Secondary Infection in Family Members. JAMA Netw Open 2020; 3:e208925. [PMID: 32589232 PMCID: PMC7320299 DOI: 10.1001/jamanetworkopen.2020.8925] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/14/2020] [Indexed: 12/14/2022] Open
Abstract
Importance Clostridioides difficile infection (CDI) is a common hospital-acquired infection. Whether family members are more likely to experience a CDI following CDI in another separate family member remains to be studied. Objective To determine the incidence of potential family transmission of CDI. Design, Setting, and Participants In this case-control study comparing the incidence of CDI among individuals with prior exposure to a family member with CDI to those without prior family exposure, individuals were binned into monthly enrollment strata based on exposure status (eg, family exposure) and confounding factors (eg, age, prior antibiotic use). Data were derived from population-based, longitudinal commercial insurance claims from the Truven Marketscan Commercial Claims and Encounters and Medicare Supplemental databases from 2001 to 2017. Households with at least 2 family members continuously enrolled for at least 1 month were eligible. CDI incidence was computed within each stratum. A regression model was used to compare incidence of CDI while controlling for possible confounding characteristics. Exposures Index CDI cases were identified using inpatient and outpatient diagnosis codes. Exposure risks 60 days prior to infection included CDI diagnosed in another family member, prior hospitalization, and antibiotic use. Main Outcomes and Measures The primary outcome was the incidence of CDI in a given monthly enrollment stratum. Separate analyses were considered for CDI diagnosed in outpatient or hospital settings. Results A total of 224 818 cases of CDI, representing 194 424 enrollees (55.9% female; mean [SD] age, 52.8 [22.2] years) occurred in families with at least 2 enrollees. Of these, 1074 CDI events (4.8%) occurred following CDI diagnosis in a separate family member. Prior family exposure was significantly associated with increased incidence of CDI, with an incidence rate ratio (IRR) of 12.47 (95% CI, 8.86-16.97); this prior family exposure represented the factor with the second highest IRR behind hospital exposure (IRR, 16.18 [95% CI, 15.31-17.10]). For community-onset CDI cases without prior hospitalization, the IRR for family exposure was 21.74 (95% CI, 15.12-30.01). Age (IRR, 9.90 [95% CI, 8.92-10.98] for ages ≥65 years compared with ages 0-17 years), antibiotic use (IRR, 3.73 [95% CI, 3.41-4.08] for low-risk and 14.26 [95% CI, 13.27-15.31] for high-risk antibiotics compared with no antibiotics), and female sex (IRR, 1.44 [95% CI, 1.36-1.53]) were also positively associated with incidence. Conclusions and Relevance This study found that individuals with family exposure may be at significantly greater risk for acquiring CDI, which highlights the importance of the shared environment in the transmission and acquisition of C difficile.
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Affiliation(s)
| | | | | | | | - Philip M. Polgreen
- Department of Epidemiology, University of Iowa, Iowa City
- Department of Internal Medicine, University of Iowa, Iowa City
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25
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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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