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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Burnham CAD, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. mBio 2024; 15:e0330023. [PMID: 38329369 PMCID: PMC10936198 DOI: 10.1128/mbio.03300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and the genomic determinants of disease outcomes. Across two wards over 6 months, we selectively cultured C. difficile from patients (n = 384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n = 79), 19 (24%) patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤2 core gene single nucleotide polymorphisms; two of these networks contain strains from different patients. Strain networks were temporally linked (P < 0.0001). To understand the genomic correlates of the disease, we conducted WGS on an additional cohort of C. difficile (n = 102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR, nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes (tcdABER and cdtR) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate that toxigenic and nontoxigenic C. difficile contamination persist in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease. IMPORTANCE Clostridioides difficile infection remains a leading cause of hospital-associated diarrhea, despite increased antibiotic stewardship and transmission prevention strategies. This suggests a changing genomic landscape of C. difficile. Our study provides insight into the nature of prevalent C. difficile strains in a hospital setting and transmission patterns among carriers. Longitudinal sampling of surfaces and patient stool revealed that both toxigenic and nontoxigenic strains of C. difficile clade 1 dominate these two wards. Moreover, quantification of transmission in carriers of these clade 1 isolates underscores the need to revisit infection prevention measures in this patient group. We identified unique genetic signatures associated with virulence in this clade. Our data highlight the complexities of preventing transmission of this pathogen in a hospital setting and the need to investigate the mechanisms of in vivo persistence and virulence of prevalent lineages in the host gut microbiome.
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Affiliation(s)
- Erin P. Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Skye R. S. Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kailun Zhang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zainab H. Iqbal
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Emily L. Struttmann
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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Dumm RE, Burnham CAD, Hink T, Reske KA, Struttmann E, Iqbal ZH, Cass C, Kwon JH, Olsen MA, Dubberke ER. Comparison of Clostridioides difficile nucleic acid amplification test (NAAT) results using fresh and frozen stool specimens and rectal swabs. J Clin Microbiol 2024; 62:e0103723. [PMID: 38078766 PMCID: PMC10793323 DOI: 10.1128/jcm.01037-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/27/2023] [Indexed: 01/18/2024] Open
Abstract
IMPORTANCE Nucleic acid amplification tests (NAATs) are frequently used in Clostridioides difficile research and diagnostic testing, but the effect of freezing specimens on C. difficile NAAT performance is not well characterized. This study evaluated the concordance of NAAT results between fresh and frozen specimens (fecal and rectal swabs) and found it to be very good to excellent. The results indicate that frozen fecal and rectal swab specimens may be used for C. difficile NAAT testing in research when fresh specimens are not available.
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Affiliation(s)
- Rebekah E. Dumm
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Emily Struttmann
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zainab Hassan Iqbal
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennie H. Kwon
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Margaret A. Olsen
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. medRxiv 2023:2023.09.26.23295023. [PMID: 38105952 PMCID: PMC10723495 DOI: 10.1101/2023.09.26.23295023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and genomic determinants of disease outcomes. Across two wards over six months, we selectively cultured C. difficile from patients (n=384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n=79), 19 (24%) of patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤ 2 core gene SNPs; 2 of these networks contain strains from different patients. Strain networks were temporally linked (p<0.0001). To understand genomic correlates of disease, we conducted WGS on an additional cohort of C. difficile (n=102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR , nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes ( tcdABER and cdtR ) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate toxigenic and nontoxigenic C. difficile contamination persists in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease.
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Farthing TS, Jolley A, Nickel KB, Hill C, Stwalley D, Reske KA, Kwon JH, Olsen MA, Burnham JP, Dubberke ER, Lanzas C. Early coronavirus disease 2019 (COVID-19) pandemic effects on individual-level risk for healthcare-associated infections in hospitalized patients. Infect Control Hosp Epidemiol 2023; 44:1966-1971. [PMID: 37381734 PMCID: PMC10755158 DOI: 10.1017/ice.2023.83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/08/2022] [Accepted: 04/10/2023] [Indexed: 06/30/2023]
Abstract
OBJECTIVE We compared the individual-level risk of hospital-onset infections with multidrug-resistant organisms (MDROs) in hospitalized patients prior to and during the coronavirus disease 2019 (COVID-19) pandemic. We also quantified the effects of COVID-19 diagnoses and intrahospital COVID-19 burden on subsequent MDRO infection risk. DESIGN Multicenter, retrospective, cohort study. SETTING Patient admission and clinical data were collected from 4 hospitals in the St. Louis area. PATIENTS Data were collected for patients admitted between January 2017 and August 2020, discharged no later than September 2020, and hospitalized ≥48 hours. METHODS Mixed-effects logistic regression models were fit to the data to estimate patients' individual-level risk of infection with MDRO pathogens of interest during hospitalization. Adjusted odds ratios were derived from regression models to quantify the effects of the COVID-19 period, COVID-19 diagnosis, and hospital-level COVID-19 burden on individual-level hospital-onset MDRO infection probabilities. RESULTS We calculated adjusted odds ratios for COVID-19-era hospital-onset Acinetobacter spp., P. aeruginosa and Enterobacteriaceae spp infections. Probabilities increased 2.64 (95% confidence interval [CI], 1.22-5.73) times, 1.44 (95% CI, 1.03-2.02) times, and 1.25 (95% CI, 1.00-1.58) times relative to the prepandemic period, respectively. COVID-19 patients were 4.18 (95% CI, 1.98-8.81) times more likely to acquire hospital-onset MDRO S. aureus infections. CONCLUSIONS Our results support the growing body of evidence indicating that the COVID-19 pandemic has increased hospital-onset MDRO infections.
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Affiliation(s)
| | - Ashlan Jolley
- North Carolina State University, Raleigh, North Carolina
| | - Katelin B. Nickel
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
| | - Cherie Hill
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
| | - Dustin Stwalley
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
| | - Jennie H. Kwon
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
| | - Margaret A. Olsen
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
| | - Jason P. Burnham
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University, St. Louis, Missouri
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Vogt LC, Reske KA, Park D, Habrock Bach T, Stewart HB, Arter OG, Stoeckel D, Steinkamp HM, Liang SY, Durkin MJ, Kwon JH. Personal protective equipment use among dental healthcare personnel during the coronavirus disease 2019 (COVID-19) pandemic and the impact of an educational video in clinical practice. Infect Control Hosp Epidemiol 2023; 44:1472-1480. [PMID: 36924218 PMCID: PMC10507497 DOI: 10.1017/ice.2023.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 03/18/2023]
Abstract
OBJECTIVE Dental healthcare personnel (DHCP) are at high risk of exposure to coronavirus disease 2019 (COVID-19). We sought to identify how DHCP changed their use of personal protective equipment (PPE) as a result of the COVID-19 pandemic, and to pilot an educational video designed to improve knowledge of proper PPE use. DESIGN The study comprised 2 sets of semistructured qualitative interviews. SETTING The study was conducted in 8 dental clinics in a Midwestern metropolitan area. PARTICIPANTS In total, 70 DHCP participated in the first set of interviews; 63 DHCP participated in the second set of interviews. METHODS In September-November 2020 and March-October 2021, we conducted 2 sets of semistructured interviews: (1) PPE use in the dental community during COVID-19, and (2) feedback on the utility of an educational donning and doffing video. RESULTS Overall, 86% of DHCP reported having prior training. DHCP increased the use of PPE during COVID-19, specifically N95 respirators and face shields. DHCP reported real-world challenges to applying infection control methods, often resulting in PPE modification and reuse. DHCP reported double masking and sterilization methods to extend N95 respirator use. Additional challenges to PPE included shortages, comfort or discomfort, and compatibility with specialty dental equipment. DHCP found the educational video helpful and relevant to clinical practice. Fewer than half of DHCP reported exposure to a similar video. CONCLUSIONS DHCP experienced significant challenges related to PPE access and routine use in dental clinics during the COVID-19 pandemic. An educational video improved awareness and uptake of appropriate PPE use among DHCP.
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Affiliation(s)
- Lucy C. Vogt
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Kimberly A. Reske
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel Park
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Tracey Habrock Bach
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Henry B. Stewart
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Olivia G. Arter
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel Stoeckel
- St. Louis University Center for Advanced Dental Education, St. Louis, Missouri
- St. Louis Children’s Hospital, St. Louis, Missouri
| | - Heidi M. Steinkamp
- St. Louis University Center for Advanced Dental Education, St. Louis, Missouri
| | - Stephen Y. Liang
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Emergency Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Michael J. Durkin
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jennie H. Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
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Kwon JH, Nickel KB, Reske KA, Stwalley D, Lyons PG, Michelson A, McMullen K, Sahrmann JM, Gandra S, Olsen MA, Dubberke ER, Burnham JP. Risk factors for hospital-onset Clostridioides difficile infections before and during the severe acute respiratory syndrome coronavirus 2 pandemic. Am J Infect Control 2023; 51:S0196-6553(23)00382-6. [PMID: 37263419 PMCID: PMC10228158 DOI: 10.1016/j.ajic.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
In this retrospective cohort from 3 Missouri hospitals from January 2017 to August 2020, hospital-onset Clostridioides difficile infections were more common during the severe acute respiratory syndrome coronavirus 2 pandemic at the tertiary care hospital. Risk factors associated with hospital-onset C difficile infection included the year of hospitalization, age, high-risk antibiotic use, acid-reducing medications, chronic comorbidities, and severe acute respiratory syndrome coronavirus 2 infection.
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Affiliation(s)
- Jennie H Kwon
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Katelin B Nickel
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Kimberly A Reske
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Dustin Stwalley
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Patrick G Lyons
- Division of Pulmonary and Critical Care Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Andrew Michelson
- Division of Pulmonary and Critical Care Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | | | - John M Sahrmann
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Sumanth Gandra
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Margaret A Olsen
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Jason P Burnham
- Division of Infectious Diseases, Washington University in St. Louis School of Medicine, St. Louis, MO.
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Gandra S, Alvarez-Uria G, Stwalley D, Nickel KB, Reske KA, Kwon JH, Dubberke ER, Olsen MA, Burnham JP. Microbiology Clinical Culture Diagnostic Yields and Antimicrobial Resistance Proportions before and during the COVID-19 Pandemic in an Indian Community Hospital and Two US Community Hospitals. Antibiotics (Basel) 2023; 12:antibiotics12030537. [PMID: 36978404 PMCID: PMC10044523 DOI: 10.3390/antibiotics12030537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
Studies comparing the impact of the COVID-19 pandemic on diagnostic microbiology culture yields and antimicrobial resistance proportions in low-to-middle-income and high-income countries are lacking. A retrospective study using blood, respiratory, and urine microbiology data from a community hospital in India and two community hospitals (Hospitals A and B) in St. Louis, MO, USA was performed. We compared the proportion of cultures positive for selected multi-drug-resistant organisms (MDROs) listed on the WHO’s priority pathogen list both before the COVID-19 pandemic (January 2017–December 2019) and early in the COVID-19 pandemic (April 2020–October 2020). The proportion of blood cultures contaminated with coagulase-negative Staphylococcus (CONS) was significantly higher during the pandemic in all three hospitals. In the Indian hospital, the proportion of carbapenem-resistant (CR) Klebsiella pneumoniae in respiratory cultures was significantly higher during the pandemic period, as was the proportion of CR Escherichia coli in urine cultures. In the US hospitals, the proportion of methicillin-resistant Staphylococcus aureus in blood cultures was significantly higher during the pandemic period in Hospital A, while no significant increase in the proportion of Gram-negative MDROs was observed. Continuity of antimicrobial stewardship activities and better infection prevention measures are critical to optimize outcomes and minimize the burden of antimicrobial resistance among COVID-19 patients.
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Affiliation(s)
- Sumanth Gandra
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
- Correspondence: ; Tel.: +1-314-454-8354; Fax: +1-314-454-8687
| | - Gerardo Alvarez-Uria
- Department of Infectious Diseases, Rural Development Trust Hospital, Bathalapalli, Anantapur 515661, India
| | - Dustin Stwalley
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
| | - Katelin B. Nickel
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
| | - Kimberly A. Reske
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
| | - Jennie H. Kwon
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
| | - Erik R. Dubberke
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
| | - Margaret A. Olsen
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
| | - Jason P. Burnham
- Department of Internal Medicine, Division of Infectious Diseases, Washington University in St. Louis School of Medicine, 4523 Clayton Avenue, Campus Box 8051, St. Louis, MO 63110, USA
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Kwon JH, Nickel KB, Reske KA, Stwalley D, Dubberke ER, Lyons PG, Michelson A, McMullen K, Sahrmann JM, Gandra S, Olsen MA, Burnham JP. Risk factors for hospital-acquired infection during the SARS-CoV-2 pandemic. J Hosp Infect 2023; 133:8-14. [PMID: 36493966 PMCID: PMC9724556 DOI: 10.1016/j.jhin.2022.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To evaluate risk factors for hospital-acquired infection (HAI) in patients during the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic, including historical and concurrent cohorts. DESIGN Retrospective cohort. SETTING Three Missouri hospitals, data from 1st January 2017 to 30th September 2020. PARTICIPANTS Patients aged ≥18 years and admitted for ≥48 h. METHODS Univariate and multi-variate Cox proportional hazards models incorporating the competing risk of death were used to determine risk factors for HAI. A-priori sensitivity analyses were performed to assess the robustness of the urine-, blood- and respiratory-culture-based HAI definition. RESULTS The cohort included 254,792 admissions, with 7147 (2.8%) HAIs (1661 blood, 3407 urine, 2626 respiratory). Patients with SARS-CoV-2 had increased risk of HAI (adjusted hazards ratio 1.65, 95% confidence interval 1.38-1.96), and SARS-CoV-2 infection was one of the strongest risk factors for development of HAI. Other risk factors for HAI included certain admitting services, chronic comorbidities, intensive care unit stay during index admission, extremes of body mass index, hospital, and selected medications. Factors associated with lower risk of HAI included year of admission (declined over the course of the study), admitting service and medications. Risk factors for HAI were similar in sensitivity analyses restricted to patients with diagnostic codes for pneumonia/upper respiratory infection and urinary tract infection. CONCLUSIONS SARS-CoV-2 was associated with significantly increased risk of HAI.
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Affiliation(s)
- J H Kwon
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - K B Nickel
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - K A Reske
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - D Stwalley
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - E R Dubberke
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - P G Lyons
- Division of Pulmonary and Critical Care Medicine, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - A Michelson
- Division of Pulmonary and Critical Care Medicine, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - K McMullen
- Mercy, Infection Prevention, St Louis, MO, USA
| | - J M Sahrmann
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - S Gandra
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - M A Olsen
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - J P Burnham
- Division of Infectious Diseases, Washington University in St Louis School of Medicine, St Louis, MO, USA.
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Reske KA, Park D, Bach TH, Stewart HB, Vogt LC, Arter OG, Stoeckel D, Steinkamp HM, Liang SY, Durkin MJ, Kwon JH. Assessment of dental health care personnel protocol deviations and self-contamination during personal protective equipment donning and doffing. J Am Dent Assoc 2022; 153:1070-1077.e1. [PMID: 36175202 PMCID: PMC9511115 DOI: 10.1016/j.adaj.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/24/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Background Dental health care personnel (DHCP) may be at increased risk of exposure to severe acute respiratory syndrome coronavirus 2, the virus that causes COVID-19, as well as other clinically important pathogens. Proper use of personal protective equipment (PPE) reduces occupational exposure to pathogens. The authors performed an assessment of PPE donning and doffing practices among DHCP, using a fluorescent marker as a surrogate for pathogen transmission. Methods Participants donned PPE (that is, disposable gown, gloves, face mask, and eye protection) and the fluorescent marker was applied to their palms and abdomen. DHCP then doffed PPE according to their usual practices. The donning and doffing processes were video recorded, areas of fluorescence were noted, and protocol deviations were assessed. Statistical analyses included frequency, type, and descriptions of protocol deviations and factors associated with fluorescence. Results Seventy DHCP were enrolled. The donning and doffing steps with the highest frequency of protocol deviations were hand hygiene (66% of donning and 78% of doffing observations involved a deviation) and disposable gown use (63% of donning and 60% of doffing observations involved a deviation). Fluorescence was detected on 69% of DHCP after doffing, most frequently on hands. An increasing number of protocol deviations was significantly associated with increased risk of fluorescence. DHCP with a gown doffing deviation, excluding doffing out of order, were more likely to have fluorescence detected. Conclusions DHCP self-contamination was common with both donning and doffing PPE. Practical Implications Proper use of PPE is an important component of occupational health.
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Gandra S, Li T, Reske KA, Peacock K, Hock KG, Bommarito S, Miller C, Stewart H, Dang NL, Farnsworth CW, Olsen MA, Kwon JH, Warren DK, Fraser VJ. Longitudinal analysis of risk factors associated with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among hemodialysis patients and healthcare personnel in outpatient hemodialysis centers. Antimicrob Steward Healthc Epidemiol 2022; 2:e125. [PMID: 36483341 PMCID: PMC9726589 DOI: 10.1017/ash.2022.269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 06/17/2023]
Abstract
In this prospective, longitudinal study, we examined the risk factors for severe acute respiratory coronavirus virus 2 (SARS-CoV-2) infection among a cohort of chronic hemodialysis (HD) patients and healthcare personnel (HCPs) over a 6-month period. The risk of SARS-CoV-2 infection among HD patients and HCPs was consistently associated with a household member having SARS-CoV-2 infection.
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Affiliation(s)
- Sumanth Gandra
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Tingting Li
- Division of Nephrology, Washington University School of Medicine, St Louis, Missouri
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Kate Peacock
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Karl G. Hock
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Silvana Bommarito
- Division of Nephrology, Washington University School of Medicine, St Louis, Missouri
| | - Candace Miller
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Henry Stewart
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Na Le Dang
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri
| | - Margaret A. Olsen
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Jennie H. Kwon
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - David K. Warren
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
| | - Victoria J. Fraser
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, Missouri
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11
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Anthony WE, Wang B, Sukhum KV, D'Souza AW, Hink T, Cass C, Seiler S, Reske KA, Coon C, Dubberke ER, Burnham CAD, Dantas G, Kwon JH. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults. Cell Rep 2022; 39:110649. [PMID: 35417701 PMCID: PMC9066705 DOI: 10.1016/j.celrep.2022.110649] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/07/2022] [Accepted: 03/17/2022] [Indexed: 02/09/2023] Open
Abstract
Antibiotics are deployed against bacterial pathogens, but their targeting of conserved microbial processes means they also collaterally perturb the commensal microbiome. To understand acute and persistent effects of antibiotics on the gut microbiota of healthy adult volunteers, we quantify microbiome dynamics before, during, and 6 months after exposure to 4 commonly used antibiotic regimens. We observe an acute decrease in species richness and culturable bacteria after antibiotics, with most healthy adult microbiomes returning to pre-treatment species richness after 2 months, but with an altered taxonomy, resistome, and metabolic output, as well as an increased antibiotic resistance burden. Azithromycin delays the recovery of species richness, resulting in greater compositional distance. A subset of volunteers experience a persistent reduction in microbiome diversity after antibiotics and share compositional similarities with patients hospitalized in intensive care units. These results improve our quantitative understanding of the impact of antibiotics on commensal microbiome dynamics, resilience, and recovery. How are robust microbiomes affected by antibiotics? Anthony et al. characterize “antibiotic scarring” in healthy volunteers, identifying universal compositional changes and treatment-specific effects on resistance burden and time to recovery of diversity. Three low-sdiversity microbiomes end compositionally similar to ICU patient microbiomes, highlighting the need for antibiotic stewardship in medicine.
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Affiliation(s)
- Winston E Anthony
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kimberley V Sukhum
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alaric W D'Souza
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tiffany Hink
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Candice Cass
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sondra Seiler
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kimberly A Reske
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christopher Coon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erik R Dubberke
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Jennie H Kwon
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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12
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Li T, Gandra S, Reske KA, Olsen MA, Bommarito S, Miller C, Hock KG, Ballman CA, Su C, Le Dang N, Kwon JH, Warren DK, Fraser VJ, Farnsworth CW. Predictors of humoral response to SARS-CoV-2 mRNA vaccine BNT162b2 in patients receiving maintenance dialysis. Antimicrob Steward Healthc Epidemiol 2022; 2:e48. [PMID: 36310813 PMCID: PMC9615013 DOI: 10.1017/ash.2022.31] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 06/16/2023]
Abstract
Objective Patients on dialysis are at high risk for severe COVID-19 and associated morbidity and mortality. We examined the humoral response to SARS-CoV-2 mRNA vaccine BNT162b2 in a maintenance dialysis population. Design Single-center cohort study. Setting and participants Adult maintenance dialysis patients at 3 outpatient dialysis units of a large academic center. Methods Participants were vaccinated with 2 doses of BNT162b2, 3 weeks apart. We assessed anti-SARS-CoV-2 spike antibodies (anti-S) ∼4-7 weeks after the second dose and evaluated risk factors associated with insufficient response. Definitions of antibody response are as follows: nonresponse (anti-S level, <50 AU/mL), low response (anti-S level, 50-839 AU/mL), and sufficient response (anti-S level, ≥840 AU/mL). Results Among the 173 participants who received 2 vaccine doses, the median age was 60 years (range, 28-88), 53.2% were men, 85% were of Black race, 86% were on in-center hemodialysis and 14% were on peritoneal dialysis. Also, 7 participants (4%) had no response, 27 (15.6%) had a low response, and 139 (80.3%) had a sufficient antibody response. In multivariable analysis, factors significantly associated with insufficient antibody response included end-stage renal disease comorbidity index score ≥5 and absence of prior hepatitis B vaccination response. Conclusions Although most of our study participants seroconverted after 2 doses of BNT162b2, 20% of our cohort did not achieve sufficient humoral response. Our findings demonstrate the urgent need for a more effective vaccine strategy in this high-risk patient population and highlight the importance of ongoing preventative measures until protective immunity is achieved.
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Affiliation(s)
- Tingting Li
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri
| | - Sumanth Gandra
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Kimberly A. Reske
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Margaret A. Olsen
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Silvana Bommarito
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri
| | - Candace Miller
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Karl G. Hock
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Claire A. Ballman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Christina Su
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri
| | - Na Le Dang
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Jennie H. Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - David K. Warren
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Victoria J. Fraser
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Christopher W. Farnsworth
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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13
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Sung A, Bailey AL, Stewart HB, McDonald D, Wallace MA, Peacock K, Miller C, Reske KA, O’Neil CA, Fraser VJ, Diamond MS, Burnham CAD, Babcock HM, Kwon JH. Isolation of SARS-CoV-2 in Viral Cell Culture in Immunocompromised Patients With Persistently Positive RT-PCR Results. Front Cell Infect Microbiol 2022; 12:804175. [PMID: 35186791 PMCID: PMC8847756 DOI: 10.3389/fcimb.2022.804175] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022] Open
Abstract
Immunocompromised adults can have prolonged acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive RT-PCR results, long after the initial diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to determine if SARS-CoV-2 virus can be recovered in viral cell culture from immunocompromised adults with persistently positive SARS-CoV-2 RT-PCR tests. We obtained 20 remnant SARS-CoV-2 PCR positive nasopharyngeal swabs from 20 immunocompromised adults with a positive RT-PCR test ≥14 days after the initial positive test. The patients' 2nd test samples underwent SARS-CoV-2 antigen testing, and culture with Vero-hACE2-TMPRSS2 cells. Viral RNA and cultivable virus were recovered from the cultured cells after qRT-PCR and plaque assays. Of 20 patients, 10 (50%) had a solid organ transplant and 5 (25%) had a hematologic malignancy. For most patients, RT-PCR Ct values increased over time. There were 2 patients with positive viral cell cultures; one patient had chronic lymphocytic leukemia treated with venetoclax and obinutuzumab who had a low viral titer of 27 PFU/mL. The second patient had marginal zone lymphoma treated with bendamustine and rituximab who had a high viral titer of 2 x 106 PFU/mL. Most samples collected ≥7 days after an initial positive SARS-CoV-2 RT-PCR had negative viral cell cultures. The 2 patients with positive viral cell cultures had hematologic malignancies treated with chemotherapy and B cell depleting therapy. One patient had a high concentration titer of cultivable virus. Further data are needed to determine risk factors for persistent viral shedding and methods to prevent SARS-CoV-2 transmission from immunocompromised hosts.
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Affiliation(s)
- Abby Sung
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Adam L. Bailey
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Henry B. Stewart
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - David McDonald
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Kate Peacock
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Candace Miller
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Kimberly A. Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Caroline A. O’Neil
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Victoria J. Fraser
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Michael S. Diamond
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Departments of Medicine and Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Hilary M. Babcock
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Jennie H. Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
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14
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Fishbein SR, Robinson JI, Hink T, Reske KA, Newcomer EP, Burnham CAD, Henderson JP, Dubberke ER, Dantas G. Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis. eLife 2022; 11:72801. [PMID: 35083969 PMCID: PMC8794467 DOI: 10.7554/elife.72801] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile infection (CDI) imposes a substantial burden on the health care system in the United States. Understanding the biological basis for the spectrum of C. difficile-related disease manifestations is imperative to improving treatment and prevention of CDI. Here, we investigate the correlates of asymptomatic C. difficile colonization using a multi-omics approach. We compared the fecal microbiome and metabolome profiles of patients with CDI versus asymptomatically colonized patients, integrating clinical and pathogen factors into our analysis. We found that CDI patients were more likely to be colonized by strains with the binary toxin (CDT) locus or strains of ribotype 027, which are often hypervirulent. We find that microbiomes of asymptomatically colonized patients are significantly enriched for species in the class Clostridia relative to those of symptomatic patients. Relative to CDI microbiomes, asymptomatically colonized patient microbiomes were enriched with sucrose degradation pathways encoded by commensal Clostridia, in addition to glycoside hydrolases putatively involved in starch and sucrose degradation. Fecal metabolomics corroborates the carbohydrate degradation signature: we identify carbohydrate compounds enriched in asymptomatically colonized patients relative to CDI patients. Further, we reveal that across C. difficile isolates, the carbohydrates sucrose, rhamnose, and lactulose do not serve as robust growth substrates in vitro, consistent with their enriched detection in our metagenomic and metabolite profiling of asymptomatically colonized individuals. We conclude that pathogen genetic variation may be strongly related to disease outcome. More interestingly, we hypothesize that in asymptomatically colonized individuals, carbohydrate metabolism by other commensal Clostridia may prevent CDI by inhibiting C. difficile proliferation. These insights into C. difficile colonization and putative commensal competition suggest novel avenues to develop probiotic or prebiotic therapeutics against CDI.
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Affiliation(s)
- Skye Rs Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, United States
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Kimberly A Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Erin P Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, United States.,Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, United States
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, United States.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, United States
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15
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Kwon JH, O'Neil CA, Hink T, Reske KA, Bosserman RE, Dubberke ER, Burnham CAD. Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile. J Appl Lab Med 2021; 7:437-443. [PMID: 34609483 DOI: 10.1093/jalm/jfab110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C. difficile toxin enzyme immunoassay (tEIA) testing after an initial tEIA test was negative. METHODS For patients age ≥18 years who had a second C. difficile tEIA test ordered within 96 h after a negative tEIA test, remnant fecal specimens from the first (negative) tEIA test were evaluated using the BioFire FilmArray Gastrointestinal Panel PCR, C. difficile toxigenic culture, and culture on a blood agar plate (BAP) to identify other potential causes of infectious diarrhea. Growth of organisms on the BAP was also used to assess potential disruptions in the gastrointestinal microbiota. RESULTS Among 84 remnant specimens, toxigenic C. difficile was identified in 9 (11%) by culture or PCR, while potential alternative causes of infectious diarrhea, including norovirus, rotavirus, enteropathogenic Escherichia coli, and Salmonella, were identified in 11 specimens (13%) by PCR. For the majority of patients, no infectious cause of diarrhea was identified, but 84% exhibited disrupted gastrointestinal microbiota, which may contribute to diarrhea. CONCLUSIONS When a hospitalized patient has a negative C. difficile tEIA test but continues to have diarrhea, alternative infectious and noninfectious causes of diarrhea should be considered. If the patient has clinical signs and symptoms suggestive of infection or risk factors for gastrointestinal infection, laboratory testing for other etiologic agents may be appropriate.
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Affiliation(s)
- Jennie H Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline A O'Neil
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiffany Hink
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Kimberly A Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Bosserman
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Erik R Dubberke
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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16
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Gandra S, Li T, Reske KA, Dang NL, Farnsworth CW, Hock KG, Miller C, Olsen MA, Kwon JH, Warren DK, Fraser VJ. SARS-CoV-2 Infection Risk Factors among Maintenance Hemodialysis Patients and Health Care Personnel In Outpatient Hemodialysis Centers. Kidney360 2021; 2:996-1001. [PMID: 35373088 PMCID: PMC8791360 DOI: 10.34067/kid.0001282021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/16/2021] [Indexed: 01/06/2023]
Abstract
Increased risk of SARS-CoV-2 infection was associated with community prevalence.Increased risk of SARS-CoV-2 infection was associated with exposure to infected family members and personal infection prevention measures.
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17
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Langdon A, Schwartz DJ, Bulow C, Sun X, Hink T, Reske KA, Jones C, Burnham CAD, Dubberke ER, Dantas G. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. Genome Med 2021; 13:28. [PMID: 33593430 PMCID: PMC7888090 DOI: 10.1186/s13073-021-00843-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI. METHODS An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms. RESULTS Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted. CONCLUSIONS Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others. TRIAL REGISTRATION ClinicalTrials.gov, NCT01925417 ; registered on August 19, 2013.
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Affiliation(s)
- Amy Langdon
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Clinical Research Training Center, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Drew J. Schwartz
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Christopher Bulow
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Tiffany Hink
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Kimberly A. Reske
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | | | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Erik R. Dubberke
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO USA
| | - for the CDC Prevention Epicenter Program
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Clinical Research Training Center, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Rebiotix, Inc., Minneapolis, MN USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO USA
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Kwak S, Choi J, Hink T, Reske KA, Blount K, Jones C, Bost MH, Sun X, Burnham CAD, Dubberke ER, Dantas G. Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial. Microbiome 2020; 8:125. [PMID: 32862830 PMCID: PMC7457799 DOI: 10.1186/s40168-020-00907-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome. RESULTS All patients exhibited significant recovery of gut microbiome diversity and a decrease of ARG relative abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts toward average configurations from unperturbed individuals were more significant and longer-lasting in RBX2660 recipients compared to placebo. We quantified microbiome and resistome modification by RBX2660 using a novel "transplantation index" metric. We identified taxonomic and metabolic features distinguishing the baseline microbiome of non-transplanted patients and taxa specifically enriched during the process of transplantation. We elucidated the correlation between resistome and taxonomic transplantations and post-treatment dynamics of patient-specific and RBX2660-specific ARGs. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs. CONCLUSIONS Through shotgun metagenomic sequencing, we elucidated the effects of RBX2660 in the microbiome and resistome. Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG relative abundance, but RBX2660 administration more rapidly and completely changed the composition of patients' microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product-a proxy for the donor-than an antibiotic perturbed state. TRIAL REGISTRATION ClinicalTrials.gov, NCT02299570 . Registered 19 November 2014 Video Abstract.
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Affiliation(s)
- Suryang Kwak
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - JooHee Choi
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Tiffany Hink
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Kimberly A. Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Kenneth Blount
- Rebiotix Inc. a Ferring Company, Minneapolis, MN 55113 USA
| | - Courtney Jones
- Rebiotix Inc. a Ferring Company, Minneapolis, MN 55113 USA
| | - Margaret H. Bost
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Erik R. Dubberke
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - for the CDC Prevention Epicenter Program
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Rebiotix Inc. a Ferring Company, Minneapolis, MN 55113 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
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Abstract
PURPOSE OF REVIEW Accurate and timely diagnosis of Clostridioides difficile infection (CDI) is imperative to prevent C. difficile transmission and reduce morbidity and mortality due to CDI, but CDI laboratory diagnostics are complex. The purpose of this article is to review the role of laboratory tests in the diagnosis of CDI, and the role of diagnostic stewardship in optimization of C. difficile testing. RECENT FINDINGS Results from C. difficile diagnostic tests should be interpreted with an understanding of the strengths and limitations inherent in each testing approach. Use of highly sensitive molecular diagnostic tests without accounting for clinical signs and symptoms may lead to over-diagnosis of CDI and increased facility CDI rates. Current guidelines recommend a two-step, algorithmic approach for testing. Diagnostic stewardship interventions, such as education, order sets, order search menus, reflex orders, hard and soft stop alerts, electronic references, feedback and benchmarking, decision algorithms, and predictive analytics may help improve use of C. difficile laboratory tests and CDI diagnosis. The diagnostic stewardship approaches with the highest reported success rates include computerized clinical decision support (CCDS) interventions, face-to-face feedback, and real-time evaluations. SUMMARY CDI is a clinical diagnosis supported by laboratory findings. Together, clinical evaluation combined with diagnostic stewardship can optimize the accurate diagnosis of CDI.
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20
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Keen EC, Tasoff P, Hink T, Reske KA, Burnham CAD, Dantas G, Kwon JH, Dubberke ER. Microbiome Restoration by RBX2660 Does Not Preclude Recurrence of Multidrug-Resistant Urinary Tract Infection Following Subsequent Antibiotic Exposure: A Case Report. Open Forum Infect Dis 2020; 7:ofaa042. [PMID: 32154322 PMCID: PMC7052748 DOI: 10.1093/ofid/ofaa042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 02/07/2020] [Indexed: 11/21/2022] Open
Abstract
A 62-year-old woman received RBX2660, an investigational microbiome restoration therapeutic, for recurrent multidrug-resistant (MDR) urinary tract infection (UTI). RBX2660 increased gut microbiome diversity but did not eliminate uropathogen carriage, and MDR UTI recurred after subsequent antibiotic exposure. Thus, restoration of microbiome diversity does not preclude disease recurrence by residual MDR pathogens.
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Affiliation(s)
- Eric C Keen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Preston Tasoff
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Tiffany Hink
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kimberly A Reske
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennie H Kwon
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Erik R Dubberke
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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21
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Rauseo AM, Olsen MA, Reske KA, Dubberke ER. Strategies to prevent adverse outcomes following Clostridioides difficile infection in the elderly. Expert Rev Anti Infect Ther 2020; 18:203-217. [PMID: 31976779 DOI: 10.1080/14787210.2020.1717950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: Clostridioides difficile remains the most common cause of healthcare-associated infections in the US, and it disproportionately affects the elderly. Older patients are more susceptible and have a greater risk of adverse outcomes from C. difficile infection (CDI), despite advances in treatment and prevention.Areas covered: The epidemiology and pathogenesis of CDI, as well as risk factors in the aging host, will be reviewed. The importance of antimicrobial stewardship and infection prevention in order to avoid acquisition and transmission will be discussed, as well as strategies to prevent adverse outcomes and recurrent CDI, through optimization of CDI treatment s,election.Expert opinion: Appropriate CDI-prevention strategies to avoid adverse outcomes in this susceptible population involve antimicrobial stewardship and methods to prevent C. difficile transmission in healthcare settings. Management strategies to prevent adverse outcomes include initiation of supportive therapy and proper selection of CDI specific treatments. Many patients may also benefit from adjunctive therapies or additional procedures.
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Affiliation(s)
- Adriana M Rauseo
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Margaret A Olsen
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Kimberly A Reske
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
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22
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Thänert R, Reske KA, Hink T, Wallace MA, Wang B, Schwartz DJ, Seiler S, Cass C, Burnham CA, Dubberke ER, Kwon JH, Dantas G. Comparative Genomics of Antibiotic-Resistant Uropathogens Implicates Three Routes for Recurrence of Urinary Tract Infections. mBio 2019; 10:e01977-19. [PMID: 31455657 PMCID: PMC6712402 DOI: 10.1128/mbio.01977-19] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 11/20/2022] Open
Abstract
The rise of antimicrobial resistance in uropathogens has complicated the management of urinary tract infections (UTIs), particularly in patients who are afflicted by recurrent episodes of UTIs. Antimicrobial-resistant (AR) uropathogens persistently colonizing individuals at asymptomatic time points have been implicated in the pathophysiology of UTIs. The dynamics of uropathogen persistence following the resolution of symptomatic disease are, however, mostly unclear. To further our understanding, we determined longitudinal AR uropathogen carriage and clonal persistence of uropathogenic Escherichia coli, Proteus mirabilis, and Klebsiella pneumoniae isolates in the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Clonal tracking of isolates in consecutively collected urine and fecal specimens indicated repeated transmission of uropathogens between the urinary tract and their intestinal reservoir. Our results further implicate three independent routes of recurrence of UTIs: (i) following an intestinal bloom of uropathogenic bacteria and subsequent bladder colonization, (ii) reinfection of the urinary tract from an external source, and (iii) bacterial persistence within the urinary tract. Taken together, our observation of clonal persistence following UTIs and uropathogen transmission between the intestinal and urinary tracts warrants further investigations into the connection between the intestinal microbiome and recurrent UTIs.IMPORTANCE The increasing antimicrobial resistance of uropathogens is challenging the continued efficacy of empiric antibiotic therapy for UTIs, which are among the most frequent bacterial infections worldwide. It has been suggested that drug-resistant uropathogens could persist in the intestine after the resolution of UTI and cause recurrences following periurethral contamination. A better understanding of the transmission dynamics between the intestinal and urinary tracts, combined with phenotypic characterization of the uropathogen populations in both habitats, could inform prudent therapies designed to overcome the rising resistance of uropathogens. Here, we integrate genomic surveillance with clinical microbiology to show that drug-resistant clones persist within and are readily transmitted between the intestinal and urinary tracts of patients affected by recurrent and nonrecurrent UTIs. Thus, our results advocate for understanding persistent intestinal uropathogen colonization as part of the pathophysiology of UTIs, particularly in patients affected by recurrent episodes of symptomatic disease.
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Affiliation(s)
- Robert Thänert
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meghan A Wallace
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bin Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Drew J Schwartz
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sondra Seiler
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - C A Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennie H Kwon
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University, St. Louis, Missouri, USA
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23
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Robinson JI, Weir WH, Crowley JR, Hink T, Reske KA, Kwon JH, Burnham CAD, Dubberke ER, Mucha PJ, Henderson JP. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections. J Clin Invest 2019; 129:3792-3806. [PMID: 31403473 DOI: 10.1172/jci126905] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization.
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Affiliation(s)
- John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William H Weir
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jan R Crowley
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A Reske
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennie H Kwon
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Erik R Dubberke
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peter J Mucha
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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24
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Dubberke ER, Reske KA, Hink T, Kwon JH, Cass C, Bongu J, Burnham CAD, Henderson JP. Clostridium difficile colonization among patients with clinically significant diarrhea and no identifiable cause of diarrhea. Infect Control Hosp Epidemiol 2018; 39:1330-1333. [PMID: 30226126 PMCID: PMC6890223 DOI: 10.1017/ice.2018.225] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To determine the prevalence of Clostridium difficile colonization among patients who meet the 2017 IDSA/SHEA C. difficile infection (CDI) Clinical Guideline Update criteria for the preferred patient population for C. difficile testing. DESIGN Retrospective cohort. SETTING Tertiary-care hospital in St. Louis, Missouri.PatientsPatients whose diarrheal stool samples were submitted to the hospital's clinical microbiology laboratory for C. difficile testing (toxin EIA) from August 2014 to September 2016.InterventionsElectronic and manual chart review were used to determine whether patients tested for C. difficile toxin had clinically significant diarrhea and/or any alternate cause for diarrhea. Toxigenic C. difficile culture was performed on all stool specimens from patients with clinically significant diarrhea and no known alternate cause for their diarrhea. RESULTS A total of 8,931 patients with stool specimens submitted were evaluated: 570 stool specimens were EIA positive (+) and 8,361 stool specimens were EIA negative (-). Among the EIA+stool specimens, 107 (19% of total) were deemed eligible for culture. Among the EIA- stool specimens, 515 (6%) were eligible for culture. One EIA+stool specimen (1%) was toxigenic culture negative. Among the EIA- stool specimens that underwent culture, toxigenic C. difficile was isolated from 63 (12%). CONCLUSIONS Most patients tested for C. difficile do not have clinically significant diarrhea and/or potential alternate causes for diarrhea. The prevalence of toxigenic C. difficile colonization among EIA- patients who met the IDSA/SHEA CDI guideline criteria for preferred patient population for C. difficile testing was 12%.
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Affiliation(s)
- Erik R Dubberke
- 1Division of Infectious Diseases,Washington University School of Medicine,St. Louis,Missouri
| | - Kimberly A Reske
- 1Division of Infectious Diseases,Washington University School of Medicine,St. Louis,Missouri
| | - Tiffany Hink
- 1Division of Infectious Diseases,Washington University School of Medicine,St. Louis,Missouri
| | - Jennie H Kwon
- 1Division of Infectious Diseases,Washington University School of Medicine,St. Louis,Missouri
| | - Candice Cass
- 1Division of Infectious Diseases,Washington University School of Medicine,St. Louis,Missouri
| | - Jahnavi Bongu
- 1Division of Infectious Diseases,Washington University School of Medicine,St. Louis,Missouri
| | - Carey-Ann D Burnham
- 2Department of Pathology and Immunology,Department of Molecular Microbiology, andDepartment of Pediatrics,Washington University School of Medicine,St. Louis,Missouri
| | - Jeffrey P Henderson
- 1Division of Infectious Diseases,Washington University School of Medicine,St. Louis,Missouri
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25
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Dubberke ER, Reske KA, Olsen MA, Bommarito K, Cleveland AA, Silveira FP, Schuster MG, Kauffman CA, Avery RK, Pappas PG, Chiller TM. Epidemiology and outcomes of Clostridium difficile infection in allogeneic hematopoietic cell and lung transplant recipients. Transpl Infect Dis 2018; 20:e12855. [PMID: 29427356 DOI: 10.1111/tid.12855] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/29/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Clostridium difficile infection (CDI) is a common complication of lung and allogeneic hematopoietic cell (HCT) transplant, but the epidemiology and outcomes of CDI after transplant are poorly described. METHODS We performed a prospective, multicenter study of CDI within 365 days post-allogeneic HCT or lung transplantation. Data were collected via patient interviews and medical chart review. Participants were followed weekly in the 12 weeks post-transplant and while hospitalized and contacted monthly up to 18 months post-transplantation. RESULTS Six sites participated in the study with 614 total participants; 4 enrolled allogeneic HCT (385 participants) and 5 enrolled lung transplant recipients (229 participants). One hundred and fifty CDI cases occurred within 1 year of transplantation; the incidence among lung transplant recipients was 13.1% and among allogeneic HCTs was 31.2%. Median time to CDI was significantly shorter among allogeneic HCT than lung transplant recipients (27 days vs 90 days; P = .037). CDI was associated with significantly higher mortality from 31 to 180 days post-index date among the allogeneic HCT recipients (Hazard ratio [HR] = 1.80; P = .007). There was a trend towards increased mortality among lung transplant recipients from 120 to 180 days post-index date (HR = 4.7, P = .09). CONCLUSIONS The epidemiology and outcomes of CDI vary by transplant population; surveillance for CDI should continue beyond the immediate post-transplant period.
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Affiliation(s)
- E R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - K A Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - M A Olsen
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - K Bommarito
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - A A Cleveland
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - F P Silveira
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, USA
| | - M G Schuster
- University of Pennsylvania, Philadelphia, PA, USA
| | - C A Kauffman
- VA Ann Arbor Healthcare System, University of Michigan Medical School, Ann Arbor, MI, USA
| | - R K Avery
- Johns Hopkins University, Baltimore, MD, USA
| | - P G Pappas
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - T M Chiller
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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26
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Olsen MA, Yan Y, Reske KA, Zilberberg M, Dubberke ER. Impact of Clostridium difficile recurrence on hospital readmissions. Am J Infect Control 2015; 43:318-22. [PMID: 25690876 DOI: 10.1016/j.ajic.2014.12.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/16/2014] [Accepted: 12/16/2014] [Indexed: 11/25/2022]
Abstract
BACKGROUND The impact of recurrent Clostridium difficile infections (CDIs) on hospital readmissions is unknown. The objective of this study was to determine whether recurrent CDI was independently associated with the number of hospital readmissions and days readmitted. METHODS We performed a retrospective cohort study at an academic, urban, tertiary care hospital. Data were collected from electronic medical records and supplemented with chart review. CDI patients were followed for 180 days to ascertain the number of hospital readmissions and total days readmitted. Univariate and multivariable negative binomial regression models were used to evaluate factors, including CDI recurrence, associated with hospital readmissions. RESULTS The study included 3,950 patients with CDI from 2003-2009, including 413 patients with recurrent CDI. Recurrent CDI patients were significantly more likely to have at least 1 readmission (85% vs 41%; P < .001) and had more days readmitted (mean = 18.6 vs 7.6; P < .001) than patients without recurrent CDI. In multivariable analysis, recurrent CDI was independently associated with number of readmissions (rate ratio = 2.54; 95% confidence interval [CI], 2.21-2.91) and days readmitted (rate ratio = 3.97; 95% CI, 3.11-5.08) after adjustment for demographics, comorbidities, and medications. CONCLUSION Recurrent CDI patients are significantly more likely than patients without a recurrence to be readmitted and spend increased time readmitted to the hospital.
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27
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Dubberke ER, Sadhu J, Gatti R, Reske KA, DiPersio JF, Devine SM, Fraser VJ. Severity of Clostridium difficile–Associated Disease (CDAD) in Allogeneic Stem Cell Transplant Recipients: Evaluation of a CDAD Severity Grading System. Infect Control Hosp Epidemiol 2015; 28:208-11. [PMID: 17265405 DOI: 10.1086/511792] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 05/03/2006] [Indexed: 11/03/2022]
Abstract
The purpose of this study was to develop and test a Clostridium difficile-associated disease (CDAD) grading system based on presenting symptoms in allogeneic stem cell transplant recipients. Patients with severe CDAD had significantly shorter median survival times and more adverse outcomes than patients with mild or moderate CDAD.
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Affiliation(s)
- Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Olsen MA, Yan Y, Reske KA, Zilberberg MD, Dubberke ER. Recurrent Clostridium difficile infection is associated with increased mortality. Clin Microbiol Infect 2014; 21:164-70. [PMID: 25658560 DOI: 10.1016/j.cmi.2014.08.017] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 02/06/2023]
Abstract
Clostridium difficile infections (CDI) are associated with decreased survival, and up to 30% of CDI patients may experience a recurrence. Data on the impact of recurrent CDI on mortality are scarce. The purpose of this study was to determine whether recurrent CDI was independently associated with decreased 6-month survival compared with patients with CDI who did not develop a recurrence. We performed a retrospective cohort study at an academic, urban, tertiary care hospital. Data were collected from the electronic medical record and chart review. CDI patients were followed for 180 days from the end of their index hospital discharge or end of index CDI antibiotic treatment, whichever was later, to determine mortality. Kaplan-Meier analysis was used to compare patient mortality by recurrent CDI status. Cox proportional hazards models were used to determine independent risk factors for death within 180 days. In all, 3958 patients aged ≥ 18 years who developed an initial CDI episode from 2003 to 2009, including 421 patients with recurrent CDI, were included in the study. Thirty-six per cent of persons with recurrent CDI died within 180 days, compared with 26% of persons without CDI recurrence (log-rank p <0.001). Recurrent CDI was associated with significantly higher hazards of death within 180 days, adjusting for demographics, comorbidities and medications received during the index CDI hospitalization (hazard ratio 1.33; 95% CI 1.12-1.58). Recurrent CDI is associated with significantly increased risk of death within 6 months after completion of their initial CDI treatment compared with CDI patients who do not develop a recurrence.
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Affiliation(s)
- M A Olsen
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA; Division of Public Health Sciences, Washington University School of Medicine, St Louis, MO, USA.
| | - Y Yan
- Division of Public Health Sciences, Washington University School of Medicine, St Louis, MO, USA; Department of General Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - K A Reske
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
| | - M D Zilberberg
- EviMed Research Group, LLC, Goshen, MA, USA; University of Massachusetts, Amherst, MA, USA
| | - E R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
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Dubberke ER, Schaefer E, Reske KA, Zilberberg M, Hollenbeak CS, Olsen MA. Attributable inpatient costs of recurrent Clostridium difficile infections. Infect Control Hosp Epidemiol 2014; 35:1400-7. [PMID: 25333435 DOI: 10.1086/678428] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To determine the attributable inpatient costs of recurrent Clostridium difficile infections (CDIs). DESIGN Retrospective cohort study. SETTING Academic, urban, tertiary care hospital. PATIENTS A total of 3,958 patients aged 18 years or more who developed an initial CDI episode from 2003 through 2009. METHODS Data were collected electronically from hospital administrative databases and were supplemented with chart review. Patients with an index CDI episode during the study period were followed up for 180 days from the end of their index hospitalization or the end of their index CDI antibiotic treatment (whichever occurred later). Total hospital costs during the outcome period for patients with recurrent versus a single episode of CDI were analyzed using zero-inflated lognormal models. RESULTS There were 421 persons with recurrent CDI (recurrence rate, 10.6%). Recurrent CDI case patients were significantly more likely than persons without recurrence to have any hospital costs during the outcome period (P < .001). The estimated attributable cost of recurrent CDI was $11,631 (95% confidence interval, $8,937-$14,588). CONCLUSIONS The attributable costs of recurrent CDI are considerable. Patients with recurrent CDI are significantly more likely to have inpatient hospital costs than patients who do not develop recurrences. Better strategies to predict and prevent CDI recurrences are needed.
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Affiliation(s)
- Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri
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Lanzas C, Dubberke ER, Lu Z, Reske KA, Gröhn YT. Epidemiological model for Clostridium difficile transmission in healthcare settings. Infect Control Hosp Epidemiol 2011; 32:553-61. [PMID: 21558767 DOI: 10.1086/660013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Recent outbreaks of Clostridium difficile infection (CDI) have been difficult to control, and data indicate that the importance of different sources of transmission may have changed. Our objectives were to evaluate the contributions of asymptomatic and symptomatic C. difficile carriers to new colonizations and to determine the most important epidemiological factors influencing C. difficile transmission. DESIGN, SETTING, AND PATIENTS Retrospective cohort study of all patients admitted to medical wards at a large tertiary care hospital in the United States in the calendar year 2008. METHODS Data from six medical wards and published literature were used to develop a compartmental model of C. difficile transmission. Patients could be in one of five transition states in the model: resistant to colonization (R), susceptible to colonization (S), asymptomatically colonized without protection against CDI (C(-)), asymptomatically colonized with protection against CDI (C(+)), and diseased (ie, with CDI; D). RESULTS The contributions of C(-), C(+), and D patients to new colonizations were similar. The simulated basic reproduction number ranged from 0.55 to 1.99, with a median of 1.04. These values suggest that transmission within the ward alone from patients with CDI cannot sustain new C. difficile colonizations and therefore that the admission of colonized patients plays an important role in sustaining transmission in the ward. The epidemiological parameters that ranked as the most influential were the proportion of admitted C(-) patients and the transmission coefficient for asymptomatic carriers. CONCLUSION Our study underscores the need to further evaluate the role of asymptomatically colonized patients in C. difficile transmission in healthcare settings.
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Affiliation(s)
- C Lanzas
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.
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Dubberke ER, Butler AM, Nyazee HA, Reske KA, Yokoe DS, Mayer J, Mangino JE, Khan YM, Fraser VJ. The impact of ICD-9-CM code rank order on the estimated prevalence of Clostridium difficile infections. Clin Infect Dis 2011; 53:20-5. [PMID: 21653298 DOI: 10.1093/cid/cir246] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND US estimates of the Clostridium difficile infection (CDI) burden have utilized International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) diagnosis codes. Whether ICD-9-CM code rank order affects CDI prevalence estimates is important because the National Hospital Discharge Survey (NHDS) and the Nationwide Inpatient Sample (NIS) have varying limits on the number of ICD-9-CM codes collected. METHODS ICD-9-CM codes for CDI (008.45), C. difficile toxin assay results, and dates of admission and discharge were collected from electronic hospital databases for adult patients admitted to 4 hospitals in the United States from July 2000 through June 2006. CDI prevalence per 1000 discharges was calculated and compared for NHDS and NIS limits and toxin assay results from the same hospitals. CDI prevalence estimates were compared using the χ(2) test, and the test of equality was used to compare slopes. RESULTS CDI prevalence measured by NIS criteria was significantly higher than that measured using NHDS criteria (10.7 cases per 1000 discharges versus 9.4 cases per 1000 discharges; P<.001) in the 4 hospitals. CDI prevalence measured by toxin assay results was 9.4 cases per 1000 discharges (P=.57 versus NHDS). However, the CDI prevalence increased more rapidly over time when measured according to the NHDS criteria than when measured according to toxin assay results (β=1.09 versus 0.84; P=.008). CONCLUSIONS Compared with the NHDS definition, the NIS definition captured 12% more CDI cases and reported significantly higher CDI rates. Rates calculated using toxin assay results were not different from rates calculated using NHDS criteria, but CDI prevalence appeared to increase more rapidly when measured by NHDS criteria than when measured by toxin assay results.
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Affiliation(s)
- Erik R Dubberke
- Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA.
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Dubberke ER, Yan Y, Reske KA, Butler AM, Doherty J, Pham V, Fraser VJ. Development and validation of a Clostridium difficile infection risk prediction model. Infect Control Hosp Epidemiol 2011; 32:360-6. [PMID: 21460487 DOI: 10.1086/658944] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To develop and validate a risk prediction model that could identify patients at high risk for Clostridium difficile infection (CDI) before they develop disease. DESIGN AND SETTING Retrospective cohort study in a tertiary care medical center. PATIENTS Patients admitted to the hospital for at least 48 hours during the calendar year 2003. METHODS Data were collected electronically from the hospital's Medical Informatics database and analyzed with logistic regression to determine variables that best predicted patients' risk for development of CDI. Model discrimination and calibration were calculated. The model was bootstrapped 500 times to validate the predictive accuracy. A receiver operating characteristic curve was calculated to evaluate potential risk cutoffs. RESULTS A total of 35,350 admitted patients, including 329 with CDI, were studied. Variables in the risk prediction model were age, CDI pressure, times admitted to hospital in the previous 60 days, modified Acute Physiology Score, days of treatment with high-risk antibiotics, whether albumin level was low, admission to an intensive care unit, and receipt of laxatives, gastric acid suppressors, or antimotility drugs. The calibration and discrimination of the model were very good to excellent (C index, 0.88; Brier score, 0.009). CONCLUSIONS The CDI risk prediction model performed well. Further study is needed to determine whether it could be used in a clinical setting to prevent CDI-associated outcomes and reduce costs.
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Affiliation(s)
- Erik R Dubberke
- Washington University School of Medicine, St. Louis, Missouri, USA.
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Litvin M, Reske KA, Mayfield J, McMullen KM, Georgantopoulos P, Copper S, Hoppe-Bauer JE, Fraser VJ, Warren DK, Dubberke ER. Identification of a pseudo-outbreak of Clostridium difficile infection (CDI) and the effect of repeated testing, sensitivity, and specificity on perceived prevalence of CDI. Infect Control Hosp Epidemiol 2010; 30:1166-71. [PMID: 19848606 DOI: 10.1086/648089] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To describe a pseudo-outbreak of Clostridium difficile infection (CDI) caused by a faulty toxin assay lot and to determine the effect of sensitivity, specificity, and repeated testing for C. difficile on perceived CDI burden, positive predictive value, and false-positive results. DESIGN Outbreak investigation and criterion standard. PATIENTS Patients hospitalized at a tertiary care hospital who had at least 1 toxin assay for detection of C. difficile performed during the period from July 1, 2004, through June 30, 2006. METHODS The run control chart method and the chi(2) test were used to compare CDI rates and the proportion of positive test results before, during, and after the pseudo-outbreak. The effect of repeated testing was evaluated by using 3 hypothetical models with a sample of 10,000 patients and various assay sensitivity and specificity estimates. RESULTS In November of 2005, the CDI rate at the hospital increased from 1.5 to 2.6 cases per 1,000 patient-days (P < .01), and the proportion of positive test results increased from 13.6% to 22.1% (P < .01). An investigation revealed a pseudo-outbreak caused by a faulty toxin assay lot. A decrease of only 1.2% in the specificity of the toxin assay would result in a 32% increase in perceived incidence of CDI at this institution. When calculated by use of the manufacturer's stated specificity and sensitivity and this institution's testing practices, the positive predictive value of the test decreased from 80.6% to 4.1% for patients who received 3 tests. CONCLUSION Specificity is as important as sensitivity when testing for CDI. False-positive CDI cases can drain hospital resources and adversely affect patients. Repeated testing for C. difficile should be performed with caution.
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Affiliation(s)
- Marina Litvin
- Department of Medicine, Washington University School of Medicine, Barnes-Jewish Hospital, St Louis, Missouri 63110, USA
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Dubberke ER, McMullen KM, Mayfield JL, Reske KA, Georgantopoulos P, Warren DK, Fraser VJ. Hospital-associated Clostridium difficile infection: is it necessary to track community-onset disease? Infect Control Hosp Epidemiol 2009; 30:332-7. [PMID: 19239377 DOI: 10.1086/596604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
OBJECTIVES To compare Clostridium difficile infection (CDI) rates determined with use of a traditional definition (ie, with healthcare-onset CDI defined as diagnosis of CDI more than 48 hours after hospital admission) with rates determined with use of expanded definitions, including both healthcare-onset CDI and community-onset CDI, diagnosed within 48 hours after hospital admission in patients who were hospitalized in the previous 30 or 60 days, and to determine whether differences exist between patients with CDI onset in the community and those with CDI onset in a healthcare setting. DESIGN Prospective cohort. SETTING Tertiary acute care facility. PATIENTS General medicine patients who received a diagnosis of CDI during the period January 1, 2004, through December 31, 2005. METHODS CDI was classified as healthcare-onset CDI, healthcare facility-associated CDI after hospitalization within the previous 30 days, and/or healthcare facility-associated CDI after hospitalization within the previous 60 days. Patient demographic characteristics and medication exposures were obtained. The CDI incidence with use of each definition, CDI rate variability, patient demographic characteristics, and medication exposures were compared. RESULTS The healthcare-onset CDI rate (1.6 cases per 1,000 patient-days) was significantly lower than the 30-day healthcare facility-associated CDI rate (2.4 cases per 1,000 patient-days; P< .01) and the 60-day healthcare facility-associated CDI rate (2.6 cases per 1,000 patient-days; P< .01). There was good correlation between the healthcare-onset CDI rate and both the 30-day (correlation, 0.69; P< .01) and 60-day (correlation, 0.70; P< .01) healthcare facility-associated CDI rates. There were no months in which the CDI rate was more than 3 standard deviations from the mean. Compared with patients with healthcare-onset CDI, patients with community-onset CDI were less likely to have received a fourth-generation cephalosporin (P= .02) or intravenous vancomycin (P+ .01) during hospitalization. CONCLUSIONS Compared with the traditional definition, expanded definitions identify more patients with CDI. There is good correlation between traditional and expanded CDI definitions; therefore, it is unclear whether expanded surveillance is necessary to identify an abnormal change in CDI rates. Cases that met the expanded definitions were less likely to have occurred in patients with fourth-generation cephalosporin and vancomycin exposure.
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Affiliation(s)
- Erik R Dubberke
- Washington University School of Medicine, St. Louis, Missouri, USA.
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Dubberke ER, Butler AM, Reske KA, Agniel D, Olsen MA, D'Angelo G, McDonald LC, Fraser VJ. Attributable outcomes of endemic Clostridium difficile-associated disease in nonsurgical patients. Emerg Infect Dis 2008; 14:1031-8. [PMID: 18598621 PMCID: PMC2600322 DOI: 10.3201/eid1407.070867] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
CDAD led to significantly worse outcomes in these patients. Data are limited on the attributable outcomes of Clostridium difficile–associated disease (CDAD), particularly in CDAD-endemic settings. We conducted a retrospective cohort study of nonsurgical inpatients admitted for >48 hours in 2003 (N = 18,050). The adjusted hazard ratios for readmission (hazard ratio 2.19, 95% confidence interval [CI] 1.87–2.55) and deaths within 180 days (hazard ratio 1.23, 95% CI 1.03–1.46) were significantly different among CDAD case-patients and noncase patients. In a propensity score matched-pairs analysis that used a nested subset of the cohort (N = 706), attributable length of stay attributable to CDAD was 2.8 days, attributable readmission at 180 days was 19.3%, and attributable death at 180 days was 5.7%. CDAD patients were significantly more likely than controls to be discharged to a long-term-care facility or outside hospital. Even in a nonoutbreak setting, CDAD had a statistically significant negative impact on patient illness and death, and the impact of CDAD persisted beyond hospital discharge.
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Affiliation(s)
- Erik R Dubberke
- Washington University School of Medicine, St. Louis, Missouri, USA
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Dubberke ER, Reske KA, Olsen MA, McDonald LC, Fraser VJ. Short- and long-term attributable costs of Clostridium difficile-associated disease in nonsurgical inpatients. Clin Infect Dis 2008; 46:497-504. [PMID: 18197759 DOI: 10.1086/526530] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND The incidence of Clostridium difficile-associated disease (CDAD) is increasing. There are few data on the short-term and long-term attributable costs of CDAD. The objective of this study was to determine the acute and 180-day attributable inpatient costs of CDAD. METHODS We performed a retrospective cohort study of all patients without operating room costs who were admitted for > or =48 h to Barnes-Jewish Hospital, a tertiary care hospital in St. Louis, Missouri, 1 January 2003-31 December 2003 (n = 24,691). Attributable costs of CDAD were determined by multivariable linear regression and propensity-score matched-pairs analyses (n = 684) for the hospitalization in which CDAD occurred and per patient over a 180-day period, including the initial hospitalization. RESULTS CDAD was associated with $2454 (95% confidence interval, $2380-$2950; increase in cost, 41%) attributable costs per CDAD episode by linear regression and with $3240 attributable costs (P < .001; increase in cost, 33%) by propensity-score matched-pairs analysis. CDAD was associated with $5042 (95% confidence interval, $3797-$6481; increase in cost, 53%) attributable inpatient costs over 180 days by linear regression and with $7179 attributable costs for inpatient care (P < .001; 48% increase in costs) by propensity-score matched-pairs analysis. CONCLUSIONS CDAD was associated with a significant increase in costs for inpatient care and increased costs at 180 days after the initial hospitalization when the CDAD episode occurred.
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Affiliation(s)
- Erik R Dubberke
- Washington University School of Medicine, Saint Louis, Missouri, USA.
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Dubberke ER, Sadhu J, Gatti R, Reske KA, DiPersio JF, Devine SM, Fraser VJ. Reply to Jaber et al. Infect Control Hosp Epidemiol 2008. [DOI: 10.1086/527273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Dubberke ER, Reske KA, Olsen MA, McMullen KM, Mayfield JL, McDonald LC, Fraser VJ. Evaluation of Clostridium difficile-associated disease pressure as a risk factor for C difficile-associated disease. Arch Intern Med 2007. [PMID: 17533213 DOI: 10.1086/52582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Colonization pressure has been identified as an important risk factor in the transmission of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus species, but the role of colonization pressure in the transmission of Clostridium difficile-associated disease (CDAD) is unclear. The purpose of this study was to evaluate CDAD pressure, a modified form of colonization pressure based on symptomatic CDAD cases, as a risk factor for CDAD. METHODS Retrospective cohort and nested case-control studies of patients admitted to Barnes-Jewish Hospital from January 1, 2003, through December 31, 2003. Univariate analysis and multivariate logistic regression models were used to evaluate the role of CDAD pressure as a risk factor for CDAD. RESULTS A total of 36 275 patients were included in the cohort, of which 382 had CDAD. The median CDAD pressure was higher for case patients than noncase patients (1.4 vs 0.3; P<.001), and only 1 patient with CDAD had a CDAD pressure of 0. In the nested case-control study, CDAD pressure remained an independent risk factor for CDAD after adjustment for demographics, severity of illness, medications received (chemotherapy, gastric acid suppressors, antidiarrheals or narcotics, and antibiotics), and abdominal procedures or surgery performed. CONCLUSIONS The results of this study suggest that CDAD pressure may be an independent risk factor for CDAD. Future studies that evaluate risk of CDAD should control for CDAD pressure.
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Affiliation(s)
- Erik R Dubberke
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Dubberke ER, Reske KA, Olsen MA, McMullen KM, Mayfield JL, McDonald LC, Fraser VJ. Evaluation of Clostridium difficile-associated disease pressure as a risk factor for C difficile-associated disease. ACTA ACUST UNITED AC 2007; 167:1092-7. [PMID: 17533213 DOI: 10.1001/archinte.167.10.1092] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Colonization pressure has been identified as an important risk factor in the transmission of methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus species, but the role of colonization pressure in the transmission of Clostridium difficile-associated disease (CDAD) is unclear. The purpose of this study was to evaluate CDAD pressure, a modified form of colonization pressure based on symptomatic CDAD cases, as a risk factor for CDAD. METHODS Retrospective cohort and nested case-control studies of patients admitted to Barnes-Jewish Hospital from January 1, 2003, through December 31, 2003. Univariate analysis and multivariate logistic regression models were used to evaluate the role of CDAD pressure as a risk factor for CDAD. RESULTS A total of 36 275 patients were included in the cohort, of which 382 had CDAD. The median CDAD pressure was higher for case patients than noncase patients (1.4 vs 0.3; P<.001), and only 1 patient with CDAD had a CDAD pressure of 0. In the nested case-control study, CDAD pressure remained an independent risk factor for CDAD after adjustment for demographics, severity of illness, medications received (chemotherapy, gastric acid suppressors, antidiarrheals or narcotics, and antibiotics), and abdominal procedures or surgery performed. CONCLUSIONS The results of this study suggest that CDAD pressure may be an independent risk factor for CDAD. Future studies that evaluate risk of CDAD should control for CDAD pressure.
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Affiliation(s)
- Erik R Dubberke
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Dubberke ER, Reske KA, Noble-Wang J, Thompson A, Killgore G, Mayfield J, Camins B, Woeltje K, McDonald JR, McDonald LC, Fraser VJ. Prevalence of Clostridium difficile environmental contamination and strain variability in multiple health care facilities. Am J Infect Control 2007; 35:315-8. [PMID: 17577478 DOI: 10.1016/j.ajic.2006.12.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 12/06/2006] [Accepted: 12/06/2006] [Indexed: 11/16/2022]
Abstract
BACKGROUND Clostridium difficile spores can contaminate the hospital environment. Little is known about the prevalence and strain variability of C. difficile environmental contamination in health care facilities. The objective of this study was to assess C. difficile environmental contamination at various health care facilities in a metropolitan area and determine if the North American pulsed field gel electrophoresis type 1 (NAP1) strain was present. METHODS A cross-sectional pilot survey was conducted. Forty-eight environmental samples were collected from six health care facilities. Samples were cultured for the presence of C. difficile, and positive samples underwent pulsed field gel electrophoresis, toxinotyping, and detection of binary toxin and/or tcdC deletion. RESULTS C. difficile was cultured from 13 of 48 (27%) samples. Rooms housing a patient with C. difficile-associated disease (CDAD) were more likely to be culture positive than non-CDAD patient rooms (100% vs. 33%; P < 0.01); C. difficile was not isolated outside of patient rooms (0 of 12 samples). The NAP1 epidemic strain was found in 5 out of 6 facilities. CONCLUSION C. difficile spores frequently contaminated the hospital environment. Rooms with a CDAD patient were more likely to be contaminated than rooms without a CDAD patient. The NAP1 strain was prevalent throughout the metropolitan area.
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Affiliation(s)
- Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Reske KA, Jenkins T, Fernandez C, VanAmber D, Hedberg CW. Beneficial effects of implementing an announced restaurant inspection program. J Environ Health 2007; 69:27-34, 76; quiz 79-80. [PMID: 17506354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Announced inspections are being incorporated into restaurant inspection programs to support active managerial control; however, their effectiveness is unknown. The study reported here examined the results of 1314 inspections conducted from June 2001 through August 2003 in Minneapolis, Minnesota. Of these, 343 were routine inspections that preceded and 157 were routine inspections that followed an announced inspection, and 501 were routine inspections of restaurants that did not undergo an announced inspection. Significant reductions in frequency of citations for critical violations in two food safety categories--(1) the person-in-charge demonstrates knowledge of foodborne-disease prevention and (2) prevention of cross-contamination--were seen in establishments that had undergone an announced inspection (relative risk [RR] of 0.7, p = .007, and RR of 0.4, p = .001, respectively). The frequency of citation for these critical violations did not decline in establishments that did not undergo an announced inspection. Announced inspections appear to be effective in supporting active managerial control and represent a promising approach to improving food safety in restaurants.
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Affiliation(s)
- Kimberly A Reske
- University of Minnesota, School of Public Health, Minneapolis, MN 55440, USA
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Abstract
BACKGROUND & AIMS Clostridium difficile-associated disease (CDAD) rates have been increasing. We sought to determine whether CDAD incidence has increased specifically in hospitalized patients with IBD. We also explored possible differences in the risk for and time to presentation of CDAD between IBD and non-IBD patients. METHODS We analyzed hospital admissions from 1998-2004 for demographics, length of stay, C difficile infections, and time from admission to a positive C difficile test. We calculated CDAD incidence for non-IBD, all IBD, CD, and UC admissions and used logistic regression to estimate the risk for CDAD. RESULTS CDAD incidence increased in each group and was higher in all IBD than non-IBD groups. During the observation period, CDAD rates approximately doubled in CD (9.5 to 22.3/1000 admissions) and tripled in UC (18.4 to 57.6/1000). Length of stay was similar among the groups. For all years combined, the adjusted odds ratios for CDAD in all IBD, CD, and UC admissions were 2.9 (95% confidence interval, 2.1-4.1), 2.1 (1.3-3.4), and 4.0 (2.4-6.6), respectively. The median times from admission to a positive C difficile test result for non-IBD, CD, and UC were 4.0, 0.8, and 0.5 days, respectively. CONCLUSIONS CDAD incidence in IBD has increased and is higher than in the non-IBD population. IBD and UC patients in particular have a higher risk for CDAD. C difficile infections in IBD are confirmed predominantly within 48 hours of admission, suggesting most were acquired before hospitalization.
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Affiliation(s)
- Joseph F Rodemann
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St Louis, Missouri 63110, USA
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Abstract
We conducted a retrospective cohort study to compare Clostridium difficile–associated disease rates determined by C. difficile–toxin assays and International Classification of Diseases, 9th Revision (ICD-9) codes. The correlation between toxin assay results and ICD-9 codes was good (κ = 0.72, p<0.01). The sensitivity of the ICD-9 codes was 78% and the specificity was 99.7%.
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Affiliation(s)
- Erik R Dubberke
- Washington University in St. Louis-School of Medicine, Saint Louis, Missouri, USA.
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