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Pompeii L, Rios J, Kraft CS, Kasbaum M, Benavides E, Patlovich SJ, Ostrosky-Zeichner L, Hornbeck A, McClain C, Fernando RD, Sietsema M, Lane M. Health Care Workers' Comfort Ratings for Elastomeric Half Mask Respirators Versus N95 ® Filtering Facepiece Respirators During the COVID-19 Pandemic. Workplace Health Saf 2024:21650799241238755. [PMID: 38587354 DOI: 10.1177/21650799241238755] [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] [Indexed: 04/09/2024]
Abstract
BACKGROUND Reusable elastomeric half-mask respirators (EHMR) are an alternative to address shortages of disposable respirators. While respirator discomfort has been noted as a barrier to adherence to wearing an N95 filtering facepiece respirator (FFR) among health care personnel (HCP), few have examined EHMR comfort while providing patient care, which was the purpose of this study. METHOD Among a cohort of 183 HCP, we prospectively examined how HCP rated EHMR tolerability using the Respirator Comfort, Wearing Experience, and Function Instrument (R-COMFI) questionnaire at Study Week 2 and Week 10. At the completion of the study (Week-12), HCP compared EHMR comfort with their prior N95 FFR use. Overall R-COMFI scores and three subscales (comfort, wear experience, and function) were examined as well as individual item scores. FINDINGS The HCP reported an improved overall R-COMFI score (lower score more favorable, 30.0 vs. 28.7/47, respectively) from Week 2 to Week 10. Many individual item scores improved or remained low over this period, except difficulty communicating with patients and coworkers. The overall R-COMFI scores for the EHMR were more favorable than for the N95 FFR (33.7 vs. 37.4, respectively), with a large proportion of workers indicating their perception that EHMR fit better, provided better protection, and they preferred to wear it in pandemic conditions compared with the N95 FFR. CONCLUSION/APPLICATION TO PRACTICE Findings suggest that the EHMR is a feasible respiratory protection device with respect to tolerance. EHMRs can be considered as a possible alternative to the N95 FFR in the health care setting. Future work is needed in the EHMR design to improve communication.
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Affiliation(s)
- Lisa Pompeii
- Cincinnati Children's Hospital Medical Center
- Baylor College of Medicine
- The University of Texas Health Science Center at Houston
| | - Janelle Rios
- The University of Texas Health Science Center at Houston
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Babiker A, Karadkhele G, Bombin A, Watkins R, Robichaux C, Smith G, Beechar VB, Steed DB, Jacobs JT, Read TD, Satola S, Larsen CP, Kraft CS, Pouch SM, Woodworth MH. The Burden and Impact of Early Post-transplant Multidrug-Resistant Organism Detection Among Renal Transplant Recipients, 2005-2021. Open Forum Infect Dis 2024; 11:ofae060. [PMID: 38464488 PMCID: PMC10924447 DOI: 10.1093/ofid/ofae060] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/06/2024] [Indexed: 03/12/2024] Open
Abstract
Background Reducing the burden of multidrug-resistant organism (MDRO) colonization and infection among renal transplant recipients (RTRs) may improve patient outcomes. We aimed to assess whether the detection of an MDRO or a comparable antibiotic-susceptible organism (CSO) during the early post-transplant (EPT) period was associated with graft loss and mortality among RTRs. Methods We conducted a retrospective cohort study of RTRs transplanted between 2005 and 2021. EPT positivity was defined as a positive bacterial culture within 30 days of transplant. The incidence and prevalence of EPT MDRO detection were calculated. The primary outcome was a composite of 1-year allograft loss or mortality following transplant. Multivariable Cox hazard regression, competing risk, propensity score-weighted sensitivity, and subgroup analyses were performed. Results Among 3507 RTRs, the prevalence of EPT MDRO detection was 1.3% (95% CI, 0.91%-1.69%) with an incidence rate per 1000 EPT-days at risk of 0.42 (95% CI, 0.31-0.57). Among RTRs who met survival analysis inclusion criteria (n = 3432), 91% (3138/3432) had no positive EPT cultures and were designated as negative controls, 8% (263/3432) had a CSO detected, and 1% (31/3432) had an MDRO detected in the EPT period. EPT MDRO detection was associated with the composite outcome (adjusted hazard ratio [aHR], 3.29; 95% CI, 1.21-8.92) and death-censored allograft loss (cause-specific aHR, 7.15; 95% CI, 0.92-55.5; subdistribution aHR, 7.15; 95% CI, 0.95-53.7). A similar trend was seen in the subgroup and sensitivity analyses. Conclusions MDRO detection during the EPT period was associated with allograft loss, suggesting the need for increased strategies to optimize prevention of MDRO colonization and infection.
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Affiliation(s)
- Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Geeta Karadkhele
- Emory Transplant Center and Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrei Bombin
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Rockford Watkins
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Chad Robichaux
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gillian Smith
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Georgia Emerging Infections Program, Atlanta, Georgia, USA
- Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Vivek B Beechar
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Danielle B Steed
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jesse T Jacobs
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Timothy D Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sarah Satola
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Christian P Larsen
- Emory Transplant Center and Department of Surgery, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Stephanie M Pouch
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Michael H Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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Tarabay JA, Morgan JS, Kraft CS, Sexton ME. Validation of the STERIS Amsco 630LS steam sterilizer autoclave for inactivation of category a medical waste from patients with high-consequence infectious diseases. Infect Control Hosp Epidemiol 2024; 45:260-262. [PMID: 37675506 PMCID: PMC10877526 DOI: 10.1017/ice.2023.188] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/24/2023] [Accepted: 07/14/2023] [Indexed: 09/08/2023]
Abstract
Hospitals caring for patients with high-consequence pathogens may need to safely manage large volumes of category A waste. Using biological indicators to assess for successful sterilization, autoclave cycle parameters that would inactivate 4 categories of waste were identified and validated utilizing a STERIS Amsco 630LS Steam Sterilizer.
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Affiliation(s)
| | | | - Colleen S. Kraft
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine Emory University School of Medicine, Atlanta, Georgia
| | - Mary Elizabeth Sexton
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia
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Berenson CS, Lashner B, Korman LY, Hohmann E, Deshpande A, Louie TJ, Sims M, Pardi D, Kraft CS, Wang EEL, Cohen SH, Feuerstadt P, Oneto C, Misra B, Pullman J, De A, Memisoglu A, Lombardi DA, Hasson BR, McGovern BH, von Moltke L, Lee CH. Prevalence of Comorbid Factors in Patients With Recurrent Clostridioides difficile Infection in ECOSPOR III, a Randomized Trial of an Oral Microbiota-Based Therapeutic. Clin Infect Dis 2023; 77:1504-1510. [PMID: 37539715 PMCID: PMC10686959 DOI: 10.1093/cid/ciad448] [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: 04/14/2023] [Revised: 06/20/2023] [Accepted: 07/31/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Although comorbidities are risk factors for recurrent Clostridioides difficile infection (rCDI), many clinical trials exclude patients with medical conditions such as malignancy or immunosuppression. In a phase 3, double-blind, placebo-controlled, randomized trial (ECOSPOR III), fecal microbiota spores, live (VOWST, Seres Therapeutics; hereafter "VOS," formerly SER-109), an oral microbiota therapeutic, significantly reduced the risk of rCDI at week 8. We evaluated the efficacy of VOS compared with placebo in patients with comorbidities and other risk factors for rCDI. METHODS Adults with rCDI were randomized to receive VOS or placebo (4 capsules daily for 3 days) following standard-of-care antibiotics. In this post hoc analysis, the rate of rCDI through week 8 was assessed in VOS-treated participants compared with placebo for subgroups including (i) Charlson comorbidity index (CCI) score category (0, 1-2, 3-4, ≥5); (ii) baseline creatinine clearance (<30, 30-50, >50 to 80, or >80 mL/minute); (iii) number of CDI episodes, inclusive of the qualifying episode (3 and ≥4); (iv) exposure to non-CDI-targeted antibiotics after dosing; and (v) acid-suppressing medication use at baseline. RESULTS Of 281 participants screened, 182 were randomized (59.9% female; mean age, 65.5 years). Comorbidities were common with a mean overall baseline age-adjusted CCI score of 4.1 (4.1 in the VOS arm and 4.2 in the placebo arm). Across all subgroups analyzed, VOS-treated participants had a lower relative risk of recurrence compared with placebo. CONCLUSIONS In this post hoc analysis, VOS reduced the risk of rCDI compared with placebo, regardless of baseline characteristics, concomitant medications, or comorbidities.
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Affiliation(s)
- Charles S Berenson
- Veterans Affairs Western New York Healthcare System, University at Buffalo, New York, New York, USA
| | - Bret Lashner
- Gastroenterology Division, Cleveland Clinic, Ohio, USA
| | - Louis Y Korman
- Gastroenterology and Hepatology, Chevy Chase Clinical Research, Chevy Chase, Maryland, USA
| | - Elizabeth Hohmann
- Infectious Diseases Division, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Thomas J Louie
- Department of Microbiology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - Matthew Sims
- Section of Infectious Diseases and International Medicine, Department of Internal Medicine, Beaumont Royal Oak, Royal Oak, Michigan, USA
- Departments of Internal Medicine and Foundational Medical Studies, William Beaumont School of Medicine, Oakland University, Rochester, Michigan, USA
| | - Darrell Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - Elaine E L Wang
- Clinical Development, Seres Therapeutics, Cambridge, Massachusetts, USA
| | - Stuart H Cohen
- Division of Infectious Diseases, University of California, Davis Health, Sacramento, California, USA
| | - Paul Feuerstadt
- Division of Digestive Disease, Yale University School of Medicine, New Haven, Connecticut, USA
- Division of Gastroenterology, Yale University and PACT-Gastroenterology Center, Hamden, Connecticut, USA
| | | | - Bharat Misra
- Borland-Groover Clinic, P.A., Jacksonville, Florida, USA
| | | | - Ananya De
- Clinical Development, Seres Therapeutics, Cambridge, Massachusetts, USA
| | - Asli Memisoglu
- Clinical Development, Seres Therapeutics, Cambridge, Massachusetts, USA
| | - David A Lombardi
- Clinical Development, Seres Therapeutics, Cambridge, Massachusetts, USA
| | - Brooke R Hasson
- Clinical Development, Seres Therapeutics, Cambridge, Massachusetts, USA
| | | | - Lisa von Moltke
- Clinical Development, Seres Therapeutics, Cambridge, Massachusetts, USA
| | - Christine H Lee
- Department of Microbiology and Infectious Diseases, Island Medical Program, University of British Columbia and University of Victoria, British Columbia, Canada
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5
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Mumma JM, Weaver BW, Morgan JS, Ghassemian G, Gannon PR, Burke KB, Berryhill BA, MacKay RE, Lee L, Kraft CS. Connecting pathogen transmission and healthcare worker cognition: a cognitive task analysis of infection prevention and control practices during simulated patient care. BMJ Qual Saf 2023:bmjqs-2023-016230. [PMID: 38050151 DOI: 10.1136/bmjqs-2023-016230] [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: 04/14/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Relatively little is known about the cognitive processes of healthcare workers that mediate between performance-shaping factors (eg, workload, time pressure) and adherence to infection prevention and control (IPC) practices. We taxonomised the cognitive work involved in IPC practices and assessed its role in how pathogens spread. METHODS Forty-two registered nurses performed patient care tasks in a standardised high-fidelity simulation. Afterwards, participants watched a video of their simulation and described what they were thinking, which we analysed to obtain frequencies of macrocognitive functions (MCFs) in the context of different IPC practices. Performance in the simulation was the frequency at which participants spread harmless surrogates for pathogens (bacteriophages). Using a tertiary split, participants were categorised into a performance group: high, medium or low. To identify associations between the three variables-performance groups, MCFs and IPC practices-we used multiblock discriminant correspondence analysis (MUDICA). RESULTS MUDICA extracted two factors discriminating between performance groups. Factor 1 captured differences between high and medium performers. High performers monitored the situation for contamination events and mitigated risks by applying formal and informal rules or managing their uncertainty, particularly for sterile technique and cleaning. Medium performers engaged more in future-oriented cognition, anticipating contamination events and planning their workflow, across many IPC practices. Factor 2 distinguished the low performers from the medium and high performers who mitigated risks with informal rules and sacrificed IPC practices when managing tradeoffs, all in the context of minimising cross-contamination from physical touch. CONCLUSIONS To reduce pathogen transmission, new approaches to training IPC (eg, cognitive skills training) and system design are needed. Interventions should help nurses apply their knowledge of IPC fluidly during patient care, prioritising and monitoring situations for risks and deciding how to mitigate risks. Planning IPC into one's workflow is beneficial but may not account for the unpredictability of patient care.
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Affiliation(s)
- Joel M Mumma
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Bradley W Weaver
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Office of Quality, Emory Healthcare, Atlanta, Georgia, USA
| | - Jill S Morgan
- Clinical Research, Emory University Hospital, Atlanta, Georgia, USA
- Critical Care, Emory University Hospital, Atlanta, Georgia, USA
| | | | - Paige R Gannon
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Kylie B Burke
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Brandon A Berryhill
- Department of Biology, Emory University, Atlanta, Georgia, USA
- Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Rebecca E MacKay
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Lindsay Lee
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, USA
- Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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Woodworth MH, Conrad RE, Haldopoulos M, Pouch SM, Babiker A, Mehta AK, Sitchenko KL, Wang CH, Strudwick A, Ingersoll JM, Philippe C, Lohsen S, Kocaman K, Lindner BG, Hatt JK, Jones RM, Miller C, Neish AS, Friedman-Moraco R, Karadkhele G, Liu KH, Jones DP, Mehta CC, Ziegler TR, Weiss DS, Larsen CP, Konstantinidis KT, Kraft CS. Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement. Sci Transl Med 2023; 15:eabo2750. [PMID: 37910603 PMCID: PMC10821315 DOI: 10.1126/scitranslmed.abo2750] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 02/07/2022] [Accepted: 06/05/2023] [Indexed: 11/03/2023]
Abstract
Multidrug-resistant organism (MDRO) colonization is a fundamental challenge in antimicrobial resistance. Limited studies have shown that fecal microbiota transplantation (FMT) can reduce MDRO colonization, but its mechanisms are poorly understood. We conducted a randomized, controlled trial of FMT for MDRO decolonization in renal transplant recipients called PREMIX (NCT02922816). Eleven participants were enrolled and randomized 1:1 to FMT or an observation period followed by delayed FMT if stool cultures were MDRO positive at day 36. Participants who were MDRO positive after one FMT were treated with a second FMT. At last visit, eight of nine patients who completed all treatments were MDRO culture negative. FMT-treated participants had longer time to recurrent MDRO infection versus PREMIX-eligible controls who were not treated with FMT. Key taxa (Akkermansia muciniphila, Alistipes putredinis, Phocaeicola dorei, Phascolarctobacterium faecium, Alistipes species, Mesosutterella massiliensis, Barnesiella intestinihominis, and Faecalibacterium prausnitzii) from the single feces donor used in the study that engrafted in recipients and metabolites such as short-chain fatty acids and bile acids in FMT-responding participants uncovered leads for rational microbiome therapeutic and diagnostic development. Metagenomic analyses revealed a previously unobserved mechanism of MDRO eradication by conspecific strain competition in an FMT-treated subset. Susceptible Enterobacterales strains that replaced baseline extended-spectrum β-lactamase-producing strains were not detectable in donor microbiota manufactured as FMT doses but in one case were detectable in the recipient before FMT. These data suggest that FMT may provide a path to exploit strain competition to reduce MDRO colonization.
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Affiliation(s)
- Michael H. Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
| | - Roth E Conrad
- Ocean Science & Engineering, School of Biological Sciences, Georgia Institute of Technology; Atlanta, Georgia, 30332, USA
| | | | - Stephanie M. Pouch
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Aneesh K. Mehta
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
- Emory Transplant Center; Atlanta, Georgia, 30322, USA
| | - Kaitlin L. Sitchenko
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Charlotte H. Wang
- Emory College of Arts and Sciences, Emory University; Atlanta, Georgia, 30322, USA
| | - Amanda Strudwick
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Jessica M. Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Cécile Philippe
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Sarah Lohsen
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Kumru Kocaman
- School of Civil and Environmental Engineering, Georgia Institute of Technology; Atlanta, Georgia, 30332, USA
| | - Blake G. Lindner
- School of Civil and Environmental Engineering, Georgia Institute of Technology; Atlanta, Georgia, 30332, USA
| | - Janet K. Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology; Atlanta, Georgia, 30332, USA
| | - Rheinallt M. Jones
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Candace Miller
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - Rachel Friedman-Moraco
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | | | - Ken H. Liu
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University; Atlanta, Georgia, 30322, USA
| | - Dean P. Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University; Atlanta, Georgia, 30322, USA
| | - C. Christina Mehta
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University; Atlanta, GA, 30322, USA
| | - Thomas R. Ziegler
- Division of Endocrinology, Metabolism and Lipids, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
| | - David S. Weiss
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
| | | | | | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
- Emory Antibiotic Resistance Center; Atlanta, Georgia, 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, 30322, USA
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Martin SE, Kraft CS, Ziegler TR, Millson EC, Rishishwar L, Martin GS. The Role of Diet on the Gut Microbiome, Mood and Happiness. medRxiv 2023:2023.03.18.23287442. [PMID: 36993403 PMCID: PMC10055576 DOI: 10.1101/2023.03.18.23287442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The gut microbiome may be both helpful and harmful, and not only is it affected by diet, it has also been shown to affect mental health including personality, mood, anxiety and depression. In this clinical study we assessed dietary nutrient composition, mood, happiness, and the gut microbiome in order to understand the role of diet in the gut microbiome and how that affects mood and happiness. For this pilot study, we enrolled 20 adults to follow this protocol: recording a 2-day food log, sampling their gut microbiome, and completing five validated surveys of mental health, mood, happiness and well-being, followed by a minimum 1 week diet change and repeating the food log, microbiome sampling and the 5 surveys. The change from a predominantly Western diet to vegetarian, Mediterranean and ketogenic diets led to changes in calorie and fiber intake. After the diet change, we observed significant changes in measures of anxiety, well-being and happiness, and without changes in gut microbiome diversity. We found strong correlations between greater consumption of fat and protein to lower anxiety and depression, while consuming higher percentages of carbohydrates was associated with increased stress, anxiety, and depression. We also found strong negative correlations between total calories and total fiber intake with gut microbiome diversity without correlations to measures of mental health, mood or happiness. We have shown that changing diet affects mood and happiness, that greater fat and carbohydrate intake is directly associated with anxiety and depression and inversely correlated with gut microbiome diversity. This study is an important step towards understanding how our diet affects the gut microbiome and in turn our mood, happiness and mental health.
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Affiliation(s)
| | | | | | - Erin C Millson
- Georgia Clinical and Translational Science Alliance (CTSA)
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8
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Burke KB, Berryhill BA, Garcia R, Goldberg DA, Manuel JA, Gannon PR, Levin BR, Kraft CS, Mumma JM. A methodology for using Lambda phages as a proxy for pathogen transmission in hospitals. J Hosp Infect 2023; 133:81-88. [PMID: 36682626 PMCID: PMC10795484 DOI: 10.1016/j.jhin.2023.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/06/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/21/2023]
Abstract
BACKGROUND One major concern in hospitalized patients is acquiring infections from pathogens borne on surfaces, patients, and healthcare workers (HCWs). Fundamental to controlling healthcare-associated infections is identifying the sources of pathogens, monitoring the processes responsible for their transmission, and evaluating the efficacy of the procedures employed for restricting their transmission. AIM To present a method using the bacteriophage Lambda (λ) to achieve these ends. METHODS Defined densities of multiple genetically marked λ phages were inoculated at known hotspots for contamination on high-fidelity mannequins. HCWs then entered a pre-sanitized simulated hospital room and performed a series of patient care tasks on the mannequins. Sampling occurred on the scrubs and hands of the HCWs, as well as previously defined high-touch surfaces in hospital rooms. Following sampling, the rooms were decontaminated using procedures demonstrated to be effective. Following the conclusion of the simulation, the samples were tested for the presence, identity, and densities of these λ phages. FINDINGS The data generated enabled the determination of the sources and magnitude of contamination caused by the breakdown of established infection prevention practices by HCWs. This technique enabled the standardized tracking of multiple contaminants during a single episode of patient care. Unlike other biological surrogates, λ phages are susceptible to common hospital disinfectants, and allow for a more accurate evaluation of pathogen transmission. CONCLUSION Whereas our application of these methods focused on healthcare-associated infections and the role of HCW behaviours in their spread, these methods could be employed for identifying the sources and sites of microbial contamination in other settings.
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Affiliation(s)
- K B Burke
- Department of Biology, Emory University, Atlanta, GA, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - B A Berryhill
- Department of Biology, Emory University, Atlanta, GA, USA; Program in Microbiology and Molecular Genetics, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - R Garcia
- Department of Biology, Emory University, Atlanta, GA, USA
| | - D A Goldberg
- Department of Biology, Emory University, Atlanta, GA, USA
| | - J A Manuel
- Department of Biology, Emory University, Atlanta, GA, USA
| | - P R Gannon
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - B R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - C S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - J M Mumma
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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Sims MD, Khanna S, Feuerstadt P, Louie TJ, Kelly CR, Huang ES, Hohmann EL, Wang EEL, Oneto C, Cohen SH, Berenson CS, Korman L, Lee C, Lashner B, Kraft CS, Ramesh M, Silverman M, Pardi DS, De A, Memisoglu A, Lombardi DA, Hasson BR, McGovern BH, von Moltke L. Safety and Tolerability of SER-109 as an Investigational Microbiome Therapeutic in Adults With Recurrent Clostridioides difficile Infection: A Phase 3, Open-Label, Single-Arm Trial. JAMA Netw Open 2023; 6:e2255758. [PMID: 36780159 PMCID: PMC9926325 DOI: 10.1001/jamanetworkopen.2022.55758] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/14/2023] Open
Abstract
IMPORTANCE A safe and effective treatment for recurrent Clostridioides difficile infection (CDI) is urgently needed. Antibiotics kill toxin-producing bacteria but do not repair the disrupted microbiome, which promotes spore germination and infection recurrence. OBJECTIVES To evaluate the safety and rate of CDI recurrence after administration of investigational microbiome therapeutic SER-109 through 24 weeks. DESIGN, SETTING, AND PARTICIPANTS This phase 3, single-arm, open-label trial (ECOSPOR IV) was conducted at 72 US and Canadian outpatient sites from October 2017 to April 2022. Adults aged 18 years or older with recurrent CDI were enrolled in 2 cohorts: (1) rollover patients from the ECOSPOR III trial who had CDI recurrence diagnosed by toxin enzyme immunoassay (EIA) and (2) patients with at least 1 CDI recurrence (diagnosed by polymerase chain reaction [PCR] or toxin EIA), inclusive of their acute infection at study entry. INTERVENTIONS SER-109 given orally as 4 capsules daily for 3 days following symptom resolution after antibiotic treatment for CDI. MAIN OUTCOMES AND MEASURES The main outcomes were safety, measured as the rate of treatment-emergent adverse events (TEAEs) in all patients receiving any amount of SER-109, and cumulative rates of recurrent CDI (toxin-positive diarrhea requiring treatment) through week 24 in the intent-to-treat population. RESULTS Of 351 patients screened, 263 were enrolled (180 [68.4%] female; mean [SD] age, 64.0 [15.7] years); 29 were in cohort 1 and 234 in cohort 2. Seventy-seven patients (29.3%) were enrolled with their first CDI recurrence. Overall, 141 patients (53.6%) had TEAEs, which were mostly mild to moderate and gastrointestinal. There were 8 deaths (3.0%) and 33 patients (12.5%) with serious TEAEs; none were considered treatment related by the investigators. Overall, 23 patients (8.7%; 95% CI, 5.6%-12.8%) had recurrent CDI at week 8 (4 of 29 [13.8%; 95% CI, 3.9%-31.7%] in cohort 1 and 19 of 234 [8.1%; 95% CI, 5.0%-12.4%] in cohort 2), and recurrent CDI rates remained low through 24 weeks (36 patients [13.7%; 95% CI, 9.8%-18.4%]). At week 8, recurrent CDI rates in patients with a first recurrence were similarly low (5 of 77 [6.5%; 95% CI, 2.1%-14.5%]) as in patients with 2 or more recurrences (18 of 186 [9.7%; 95% CI, 5.8%-14.9%]). Analyses by select baseline characteristics showed consistently low recurrent CDI rates in patients younger than 65 years vs 65 years or older (5 of 126 [4.0%; 95% CI, 1.3%-9.0%] vs 18 of 137 [13.1%; 95% CI, 8.0%-20.0%]) and patients enrolled based on positive PCR results (3 of 69 [4.3%; 95% CI, 0.9%-12.2%]) vs those with positive toxin EIA results (20 of 192 [10.4%; 95% CI, 6.5%-15.6%]). CONCLUSIONS AND RELEVANCE In this trial, oral SER-109 was well tolerated in a patient population with recurrent CDI and prevalent comorbidities. The rate of recurrent CDI was low regardless of the number of prior recurrences, demographics, or diagnostic approach, supporting the beneficial impact of SER-109 for patients with CDI. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT03183141.
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Affiliation(s)
- Matthew D. Sims
- Section of Infectious Diseases and International Medicine, Department of Internal Medicine, Beaumont Hospital, Royal Oak, Michigan
- Department of Internal Medicine, Oakland University William Beaumont School of Medicine, Rochester, Michigan
- Department of Foundational Medical Studies, Oakland University William Beaumont School of Medicine, Rochester, Michigan
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Paul Feuerstadt
- Division of Digestive Disease, Yale University School of Medicine, New Haven, Connecticut
- Physicians Alliance of Connecticut–Gastroenterology Center, Hamden, Connecticut
| | - Thomas J. Louie
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Colleen R. Kelly
- Department of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Edward S. Huang
- Department of Gastroenterology, Palo Alto Medical Foundation, Sutter Health, Mountain View, California
| | | | | | | | | | | | - Louis Korman
- Gastroenterology and Hepatology, Chevy Chase Clinical Research, Chevy Chase, Maryland
| | - Christine Lee
- Island Medical Program, University of British Columbia and University of Victoria, British Columbia, Canada
| | | | - Colleen S. Kraft
- Department of Pathology and Laboratory Medicine, Division of Infectious Diseases, Emory University, Atlanta, Georgia
| | - Mayur Ramesh
- Division of Infectious Diseases, Henry Ford Health, Detroit, Michigan
| | | | - Darrell S. Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Ananya De
- Seres Therapeutics, Cambridge, Massachusetts
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10
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Matić Z, Sala MFW, Tonetto LM, Campiglia GC, Morgan J, DuBose JR, Zimring CM, Kraft CS. Understanding Experience of Patients With Highly Infectious Diseases During Extended Isolation: A Design Perspective. HERD 2023; 16:97-112. [PMID: 36164757 DOI: 10.1177/19375867221128916] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
OBJECTIVES This study aimed to develop a better understanding of the unique needs of patients with highly infectious diseases and their perceptions of being placed in isolation. We explore the subjective experiences of patients treated for Ebola in a biocontainment unit (BCU) and the healthcare personnel who cared for them. BACKGROUND The 2014 Ebola outbreak and the COVID-19 pandemic have brought to focus some major challenges of caring for patients with serious infectious diseases. Previous studies on BCU design have looked at ways to prevent self- and cross-contamination, but very few have examined how the built environment can support an improved patient experience. METHOD A qualitative study was conducted with four patients treated for Ebola and two critical care nurses who provided direct care to them at a single BCU in the U.S. Data were collected through in-depth semi-structured interviews to capture the actual patients' perception and experience of isolation. The interviews were analyzed using the thematic analysis approach. RESULTS The Ebola patients placed in source isolation perceived the BCU as an artificial environment where they lacked control, agency, autonomy, and independence. The physical separation from other patients, visitor restrictions, and staff wearing PPE contributed to feelings of social and emotional isolation, and loneliness. CONCLUSIONS The isolation can take a toll on physiological and psychological well-being. A thoughtful design of isolation units may improve patients' experience by supporting human and social interactions, empowering patients through space flexibility and personalization of space, and supporting a more holistic approach to isolation care.
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Affiliation(s)
| | - Maria F Wong Sala
- SimTigrate Design Lab, Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | | | - Jennifer R DuBose
- SimTigrate Design Lab, Georgia Institute of Technology, Atlanta, GA, USA
| | - Craig M Zimring
- SimTigrate Design Lab, Georgia Institute of Technology, Atlanta, GA, USA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
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11
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Babiker A, Karadkhele G, Robichaux C, Page AM, Satola SW, Kraft CS, Larsen CP, Pouch SM, Woodworh MH. 81. Impact of Early Post-Transplant Multidrug-Resistant Organism Detection Among Renal Transplant Recipients, 2005–2021. Open Forum Infect Dis 2022. [PMCID: PMC9752411 DOI: 10.1093/ofid/ofac492.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background Understanding the impact of multi-drug resistant organism (MDRO) acquisition on renal transplant recipients (RTR) mortality and allograft function is paramount to mitigating deleterious outcomes. Prior studies have been limited by lack of control groups and sample sizes. We aimed to the assess whether the detection of an MDRO or a susceptible organism during the early post-transplant period was associated with increased mortality and allograft failure among RTRs. Methods We performed a retrospective cohort study of RTRs at the Emory University Transplant Center between 2005–2022. Early post-transplant culture positivity was defined as a positive culture within 30 days of renal transplant. The primary outcome was a combined composite of one year- allograft loss and/or mortality following renal transplant. A Kaplan–Meier survival analysis was performed, and differences between survival curves for RTRs with an early post-transplant positive culture (stratified by susceptibility status) and negative control RTRs were assessed using the log-rank test. Multivariable cox proportional hazard and a competing risk analysis were performed. Results Among 3,233 RTRs, 259 (8%) had a susceptible organism detected and 35 (1%) had an MDRO detected (Figure 1). Demographic and microbiology characteristics are summarized in Table 1 & 2. One hundred and forty-nine (5%) RTRs experienced the composite outcome, this was experienced more frequently among RTRs with an MDRO detected (14%, 5/35) compared to RTRs with a susceptible organism defected (8%, 21/259) and negative controls (4%, 123/2,939) (Table 3). Significant difference between time from transplantation to the composite outcome when comparing negative controls, MDRO and susceptible organisms RTRs was observed (log rank p < 0.001) (Figure 2). Early post-transplant culture positivity (aHR 1.98 [1.30, 3.04]) and MDRO detection (aHR: 3.20 [1.30, 7.84]) were significantly associated with the composite outcome (Table 4). Conclusion MDRO as well as susceptible organism acquisition during the early post-transplant period was associated with increased mortality and allograft loss highlighting the need for increased infection prevention efforts within this vulnerable population. Disclosures All Authors: No reported disclosures.
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Affiliation(s)
| | - Geeta Karadkhele
- Emory University School of Medicine, Atlanta, Georgia, Atlanta, Georgia
| | | | - Alex M Page
- Emory University School of Medicine, Atlanta, GA
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12
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Hojjatie S, Shantha JG, O’Keefe GD, Kraft CS, Voloschin A, Grossniklaus H, Yeh S. Cytopathology of Vitreous Specimens in Acute Retinal Necrosis. Ocul Immunol Inflamm 2022; 30:1609-1616. [PMID: 34242097 PMCID: PMC8742848 DOI: 10.1080/09273948.2021.1922926] [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: 02/28/2021] [Revised: 03/27/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022]
Abstract
PURPOSE To report the cytopathology of vitreous biopsy samples in patients with acute retinal necrosis (ARN) who underwent pars plana vitrectomy (PPV). We also describe two patients with unique clinical courses, cytopathologic findings, and immune response. METHODS A retrospective review of patients with ARN who developed retinal detachment (RD) and underwent PPV from 22011 to 2019 at the Emory Eye Center was performed to assess cytopathology findings of vitreous biopsy samples. Patient demographics and laboratory testing including aqueous humor PCR for viral pathogens were recorded. Additional clinical details abstracted included intravitreal injections, surgical procedures, and vitreous cytopathological reports including immunohistochemistry findings. RESULTS Fourteen eyes of 12 patients with RD were reviewed. Ten eyes showed HSV DNA (71%) and 4 demonstrated VZV DNA (29%). All eyes received intravitreal antivirals (i.e. ganciclovir or foscarnet) with a median of 8.5 intravitreal injections per eye. Diagnoses prompting PPV included tractional RD in 14 eyes (100%), rhegmatogenous RD in 8 eyes (57%), vitreous hemorrhage in 4 eyes (29%) and vitreous opacity in 4 (29%). Ophthalmic pathology reports showed lymphocyte populations in 10 eyes (71%) with a CD3 + T-cell predominance in two patients where immunohistochemistry of CD3+ and CD20+ for T- and B-cell populations was performed. Observed immune cell populations included macrophages or histiocytes (11 eyes, 79%) and polymorphonuclear cells in 4 eyes (29%). Initial median VA was 2.5 (IQR 2.0-3.0) and improved to 2.0 (IQR 1.48-3.00, p = .48) at 6-months and 1.8 (IQR 1.2-3.0, p = .45) at 12 months follow-up. CONCLUSIONS Our cohort of ARN patients undergoing PPV show a spectrum of immunologic findings with the majority demonstrating a lymphocytic response. Histiocytes, macrophages, and PMNs were also observed. Cytopathologic and immunologic studies suggest that both innate and adaptive immunity are responsible for the clinical disease findings observed in ARN. The variability of the response to treatment in patients with ARN may reflect patient-to-patient differences in their antigen-specific immune response. Understanding the immunologic response associated with ARN may provide valuable information regarding the dosing and timing of treatment.
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Affiliation(s)
- Sara Hojjatie
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | | | | | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Alfredo Voloschin
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, GA
| | - Hans Grossniklaus
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
- L.F. Montgomery Pathology Laboratory, Atlanta, GA
| | - Steven Yeh
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
- Emory Global Health Institute, Emory University, Atlanta, GA
- Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, NE
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13
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Waggoner JJ, Vos MB, Tyburski EA, Nguyen PV, Ingersoll JM, Miller C, Sullivan J, Griffiths M, Stone C, Benoit M, Benedit L, Seitter B, Jerris R, Levy JM, Kraft CS, Farmer S, Peagler A, Wood A, Westbrook AL, Morris CR, Sathian UN, Heetderks W, Li L, Roth K, Barcus M, Stenzel T, Martin GS, Lam WA. Concordance of SARS-CoV-2 Results in Self-collected Nasal Swabs vs Swabs Collected by Health Care Workers in Children and Adolescents. JAMA 2022; 328:935-940. [PMID: 36018570 PMCID: PMC9419070 DOI: 10.1001/jama.2022.14877] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Despite the expansion of SARS-CoV-2 testing, available tests have not received Emergency Use Authorization for performance with self-collected anterior nares (nasal) swabs from children younger than 14 years because the effect of pediatric self-swabbing on SARS-CoV-2 test sensitivity is unknown. OBJECTIVE To characterize the ability of school-aged children to self-collect nasal swabs for SARS-CoV-2 testing compared with collection by health care workers. DESIGN, SETTING, AND PARTICIPANTS Cross-sectional study of 197 symptomatic children and adolescents aged 4 to 14 years old. Individuals were recruited based on results of testing in the Children's Healthcare of Atlanta system from July to August 2021. EXPOSURES Children and adolescents were given instructional material consisting of a short instructional video and a handout with written and visual steps for self-swab collection. Participants first provided a self-collected nasal swab. Health care workers then collected a second specimen. MAIN OUTCOMES AND MEASURES The primary outcome was SARS-CoV-2 detection and relative quantitation by cycle threshold (Ct) in self- vs health care worker-collected nasal swabs when tested with a real-time reverse transcriptase-polymerase chain reaction test with Emergency Use Authorization. RESULTS Among the study participants, 108 of 194 (55.7%) were male and the median age was 9 years (IQR, 6-11). Of the 196 participants, 87 (44.4%) tested positive for SARS-CoV-2 and 105 (53.6%) tested negative by both self- and health care worker-collected swabs. Two children tested positive by self- or health care worker-collected swab alone; 1 child had an invalid health care worker swab. Compared with health care worker-collected swabs, self-collected swabs had 97.8% (95% CI, 94.7%-100.0%) and 98.1% (95% CI, 95.6%-100.0%) positive and negative percent agreement, respectively, and SARS-CoV-2 Ct values did not differ significantly between groups (mean [SD] Ct, self-swab: 26.7 [5.4] vs health care worker swab: 26.3 [6.0]; P = .65). CONCLUSIONS AND RELEVANCE After hearing and seeing simple instructional materials, children and adolescents aged 4 to 14 years self-collected nasal swabs that closely agreed on SARS-CoV-2 detection with swabs collected by health care workers.
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Affiliation(s)
| | - Miriam B. Vos
- Emory University School of Medicine, Atlanta, Georgia
- Children’s Healthcare of Atlanta, Atlanta, Georgia
| | | | | | | | | | | | | | - Cheryl Stone
- Children’s Healthcare of Atlanta, Atlanta, Georgia
| | | | | | | | | | | | | | | | | | - Anna Wood
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Adrianna L. Westbrook
- Pediatric Biostatistics Core, Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Claudia R. Morris
- Emory University School of Medicine, Atlanta, Georgia
- Children’s Healthcare of Atlanta, Atlanta, Georgia
| | | | - William Heetderks
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland
| | - Li Li
- Division of Microbiology, OHT7 Office of Product Evaluation and Quality, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland
| | - Kristian Roth
- Division of Microbiology, OHT7 Office of Product Evaluation and Quality, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland
| | - Mary Barcus
- Division of Microbiology, OHT7 Office of Product Evaluation and Quality, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland
| | - Timothy Stenzel
- OHT7 Office of Product Evaluation and Quality, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, Maryland
| | | | - Wilbur A. Lam
- Emory University School of Medicine, Atlanta, Georgia
- Children’s Healthcare of Atlanta, Atlanta, Georgia
- Georgia Institute of Technology, Atlanta
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14
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Mumma JM, Howard-Anderson JR, Morgan JS, Schink K, Wheatley MJ, Kraft CS, Lane MA, Kaufman NH, Ayeni O, Brownsword EA, Jacob JT. Healthcare worker mental models of patient care tasks in the context of infection prevention and control. Infect Control Hosp Epidemiol 2022; 43:1123-1128. [PMID: 34503596 PMCID: PMC10499001 DOI: 10.1017/ice.2021.368] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE Understanding the cognitive determinants of healthcare worker (HCW) behavior is important for improving the use of infection prevention and control (IPC) practices. Given a patient requiring only standard precautions, we examined the dimensions along which different populations of HCWs cognitively organize patient care tasks (ie, their mental models). DESIGN HCWs read a description of a patient and then rated the similarities of 25 patient care tasks from an infection prevention perspective. Using multidimensional scaling, we identified the dimensions (ie, characteristics of tasks) underlying these ratings and the salience of each dimension to HCWs. SETTING Adult inpatient hospitals across an academic hospital network. PARTICIPANTS In total, 40 HCWs, comprising infection preventionists and nurses from intensive care units, emergency departments, and medical-surgical floors rated the similarity of tasks. To identify the meaning of each dimension, another 6 nurses rated each task in terms of specific characteristics of tasks. RESULTS Each HCW population perceived patient care tasks to vary along 3 common dimensions; most salient was the perceived magnitude of infection risk to the patient in a task, followed by the perceived dirtiness and risk of HCW exposure to body fluids, and lastly, the relative importance of a task for preventing versus controlling an infection in a patient. CONCLUSIONS For a patient requiring only standard precautions, different populations of HCWs have similar mental models of how various patient care tasks relate to IPC. Techniques for eliciting mental models open new avenues for understanding and ultimately modifying the cognitive determinants of IPC behaviors.
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Affiliation(s)
- Joel M Mumma
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jessica R Howard-Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | | | | | | | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Morgan A Lane
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Noah H Kaufman
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Oluwateniola Ayeni
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Erik A Brownsword
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Jesse T Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia
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15
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Wang Y, Liu P, Zhang H, Ibaraki M, VanTassell J, Geith K, Cavallo M, Kann R, Saber L, Kraft CS, Lane M, Shartar S, Moe C. Early warning of a COVID-19 surge on a university campus based on wastewater surveillance for SARS-CoV-2 at residence halls. Sci Total Environ 2022; 821:153291. [PMID: 35090922 PMCID: PMC8788089 DOI: 10.1016/j.scitotenv.2022.153291] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 05/05/2023]
Abstract
As COVID-19 continues to spread globally, monitoring the disease at different scales is critical to support public health decision making. Surveillance for SARS-CoV-2 RNA in wastewater can supplement surveillance based on diagnostic testing. In this paper, we report the results of wastewater-based COVID-19 surveillance on Emory University campus that included routine sampling of sewage from a hospital building, an isolation/quarantine building, and 21 student residence halls between July 13th, 2020 and March 14th, 2021. We examined the sensitivity of wastewater surveillance for detecting COVID-19 cases at building level and the relation between Ct values from RT-qPCR results of wastewater samples and the number of COVID-19 patients residing in the building. Our results show that weekly wastewater surveillance using Moore swab samples was not sensitive enough (6 of 63 times) to reliably detect one or two sporadic cases in a residence building. The Ct values of the wastewater samples over time from the same sampling location reflected the temporal trend in the number of COVID-19 patients in the isolation/quarantine building and hospital (Pearson's r < -0.8), but there is too much uncertainty to directly estimate the number of COVID-19 cases using Ct values. After students returned for the spring 2021 semester, SARS-CoV-2 RNA was detected in the wastewater samples from most of the student residence hall monitoring sites one to two weeks before COVID-19 cases surged on campus. This finding suggests that wastewater-based surveillance can be used to provide early warning of COVID-19 outbreaks at institutions.
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Affiliation(s)
- Yuke Wang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
| | - Pengbo Liu
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Haisu Zhang
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Makoto Ibaraki
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jamie VanTassell
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Kelly Geith
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Matthew Cavallo
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Rebecca Kann
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lindsay Saber
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA; Division of Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Morgan Lane
- Division of Infectious Diseases, Emory University, Atlanta, GA, USA
| | - Samuel Shartar
- Emory University Office of Critical Event Preparedness and Response, Atlanta, GA, USA
| | - Christine Moe
- Center for Global Safe Water, Sanitation, and Hygiene, Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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16
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Johnson JA, Read TD, Petit RA, Marconi VC, Meagley KL, Rodriguez-Barradas MC, Beenhouwer DO, Brown ST, Holodniy M, Lucero-Obusan CA, Schirmer P, Ingersoll JM, Kraft CS, Neill FH, Atmar RL, Kambhampati AK, Cates JE, Mirza SA, Hall A, Cardemil CV, Lopman BA. Association of Secretor Status and Recent Norovirus Infection With Gut Microbiome Diversity Metrics in a Veterans Affairs Population. Open Forum Infect Dis 2022; 9:ofac125. [PMID: 35434176 PMCID: PMC9007923 DOI: 10.1093/ofid/ofac125] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/08/2022] [Indexed: 11/12/2022] Open
Abstract
Norovirus infection causing acute gastroenteritis could lead to adverse effects on the gut microbiome. We assessed the association of microbiome diversity with norovirus infection and secretor status in patients from Veterans Affairs medical centers. Alpha diversity metrics were lower among patients with acute gastroenteritis but were similar for other comparisons.
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Affiliation(s)
- Jordan A Johnson
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Timothy D Read
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Robert A Petit
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Vincent C Marconi
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Kathryn L Meagley
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Maria C Rodriguez-Barradas
- Infectious Diseases Section, Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - David O Beenhouwer
- Veterans Affairs Greater Los Angeles Health System, Los Angeles, California, USA
| | - Sheldon T Brown
- James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA
| | - Mark Holodniy
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
- Division of Infectious Diseases & Geographic Medicine, Stanford University, Stanford, California, USA
| | - Cynthia A Lucero-Obusan
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
| | - Patricia Schirmer
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
| | - Jessica M Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Frederick H Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Robert L Atmar
- Office of Population Health, Public Health Surveillance and Research, Veterans Health Administration, Washington, DC, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Anita K Kambhampati
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jordan E Cates
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sara A Mirza
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aron J Hall
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cristina V Cardemil
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Benjamin A Lopman
- Department of Epidemiology, Emory University Rollins School of Public Health, Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, and Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
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17
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Lane MA, Walawender M, Brownsword EA, Pu S, Saikawa E, Kraft CS, Davis RE. The impact of cold weather on respiratory morbidity at Emory Healthcare in Atlanta. Sci Total Environ 2022; 813:152612. [PMID: 34963597 DOI: 10.1016/j.scitotenv.2021.152612] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Research on temperature and respiratory hospitalizations is lacking in the southeastern U.S. where cold weather is relatively rare. This retrospective study examined the association between cold waves and pneumonia and influenza (P&I) emergency department (ED) visits and hospitalizations in three metro-Atlanta hospitals. METHODS We used a case-crossover design, restricting data to the cooler seasons of 2009-2019, to determine whether cold waves influenced ED visits and hospitalizations. This analysis considered effects by race/ethnicity, age, sex, and severity of comorbidities. We used generalized additive models and distributed lag non-linear models to examine these relationships over a 21-day lag period. RESULTS The odds of a P&I ED visit approximately one week after a cold wave were increased by as much as 11%, and odds of an ED visit resulting in hospitalization increased by 8%. For ED visits on days with minimum temperatures >20 °C, there was an increase of 10-15% in relative risk (RR) for short lags (0-2 days), and a slight decrease in RR (0-5%) one week later. For minimum temperatures <0 °C, RR decreased at short lags (5-10%) before increasing (1-5%) one week later. Hospital admissions exhibited a similar, but muted, pattern. CONCLUSION Unusually cold weather influenced P&I ED visits and admissions in this population.
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Affiliation(s)
- Morgan A Lane
- Division of Infectious Diseases, Department of Medicine Emory University, 201 Dowman Dr., Atlanta, GA 30322, USA.
| | - Maria Walawender
- Rollins School of Public Health, Emory University, 1518 Clifton Rd., Atlanta, GA 30322, USA.
| | - Erik A Brownsword
- Division of Infectious Diseases, Department of Medicine Emory University, 201 Dowman Dr., Atlanta, GA 30322, USA.
| | - Siyan Pu
- Emory College of Arts and Sciences, Emory University, 550 Asbury Cir, Atlanta, GA 30322, USA.
| | - Eri Saikawa
- Rollins School of Public Health, Emory University, 1518 Clifton Rd., Atlanta, GA 30322, USA; Emory College of Arts and Sciences, Emory University, 550 Asbury Cir, Atlanta, GA 30322, USA.
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine Emory University, 201 Dowman Dr., Atlanta, GA 30322, USA; Department of Pathology and Laboratory Medicine, Emory University, 201 Dowman Dr., Atlanta, GA 30322, USA; Emory Healthcare, 1364 Clifton Rd., Atlanta, GA 30322, USA.
| | - Robert E Davis
- Department of Environmental Sciences, University of Virginia, 291 McCormick Rd, Charlottesville, VA 22904, USA.
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18
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Malenfant JH, Joyce A, Choi MJ, Cossaboom CM, Whitesell AN, Harcourt BH, Atmar RL, Villanueva JM, Bell BP, Hahn C, Loehr J, Davey RT, Sprecher A, Kraft CS, Shoemaker T, Montgomery JM, Helfand R, Damon IK, Frey SE, Chen WH. Use of Ebola Vaccine: Expansion of Recommendations of the Advisory Committee on Immunization Practices To Include Two Additional Populations - United States, 2021. MMWR Morb Mortal Wkly Rep 2022; 71:290-292. [PMID: 35202354 DOI: 10.15585/mmwr.mm7108a2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
On December 19, 2019, the Food and Drug Administration (FDA) approved rVSVΔG-ZEBOV-GP Ebola vaccine (ERVEBO, Merck) for the prevention of Ebola virus disease (EVD) caused by infection with Ebola virus, species Zaire ebolavirus, in adults aged ≥18 years. In February 2020, the Advisory Committee on Immunization Practices (ACIP) recommended preexposure vaccination with ERVEBO for adults aged ≥18 years in the United States who are at highest risk for potential occupational exposure to Ebola virus because they are responding to an outbreak of EVD, work as health care personnel at federally designated Ebola treatment centers in the United States, or work as laboratorians or other staff members at biosafety level 4 facilities in the United States (1).
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19
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Mehta N, Wang T, Friedman-Moraco RJ, Carpentieri C, Mehta AK, Rouphael N, Dhere T, Larsen CP, Kraft CS, Woodworth MH. Fecal Microbiota Transplantation Donor Screening Updates and Research Gaps for Solid Organ Transplant Recipients. J Clin Microbiol 2022; 60:e0016121. [PMID: 34133889 PMCID: PMC8849208 DOI: 10.1128/jcm.00161-21] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In this review, we discuss stool donor screening considerations to mitigate potential risks of pathogen transmission through fecal microbiota transplant (FMT) in solid organ transplant (SOT) recipients. SOT recipients have a higher risk for Clostridioides difficile infection (CDI) and are more likely to have severe CDI. FMT has been shown to be a valuable tool in the treatment of recurrent CDI (RCDI); however, guidelines for screening for opportunistic infections transmitted through FMT are underdeveloped. We review reported adverse effects of FMT as they pertain to an immunocompromised population and discuss the current understanding and recommendations for screening found in the literature while noting gaps in research. We conclude that while FMT is being performed in the SOT population, typically with positive results, there remain many unanswered questions which may have major safety implications and warrant further study.
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Affiliation(s)
- Nirja Mehta
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Tiffany Wang
- Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Rachel J. Friedman-Moraco
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Cynthia Carpentieri
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Aneesh K. Mehta
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
- Department of Surgery, Division of Transplantation, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Nadine Rouphael
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Tanvi Dhere
- Department of Medicine, Division of Digestive Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Christian P. Larsen
- Department of Surgery, Division of Transplantation, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Colleen S. Kraft
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
| | - Michael H. Woodworth
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicinegrid.471395.d, Atlanta, Georgia, USA
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20
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Babiker A, Martin MA, Marvil C, Bellman S, Petit III RA, Bradley HL, Stittleburg VD, Ingersoll J, Kraft CS, Li Y, Zhang J, Paden CR, Read TD, Waggoner JJ, Koelle K, Piantadosi A. Unrecognized introductions of SARS-CoV-2 into the US state of Georgia shaped the early epidemic. Virus Evol 2022; 8:veac011. [PMID: 35317348 PMCID: PMC8933693 DOI: 10.1093/ve/veac011] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/15/2022] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
In early 2020, as diagnostic and surveillance responses for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ramped up, attention focused primarily on returning international travelers. Here, we build on existing studies characterizing early patterns of SARS-CoV-2 spread within the USA by analyzing detailed clinical, molecular, and viral genomic data from the state of Georgia through March 2020. We find evidence for multiple early introductions into Georgia, despite relatively sparse sampling. Most sampled sequences likely stemmed from a single or small number of introductions from Asia three weeks prior to the state's first detected infection. Our analysis of sequences from domestic travelers demonstrates widespread circulation of closely related viruses in multiple US states by the end of March 2020. Our findings indicate that the exclusive focus on identifying SARS-CoV-2 in returning international travelers early in the pandemic may have led to a failure to recognize locally circulating infections for several weeks and point toward a critical need for implementing rapid, broadly targeted surveillance efforts for future pandemics.
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Affiliation(s)
- Ahmed Babiker
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Michael A Martin
- Department of Biology, Emory University, 201 Dowman Drive, Atlanta, GA 30322, USA
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Charles Marvil
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Stephanie Bellman
- Environmental Health Sciences PhD Program, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Robert A Petit III
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Heath L Bradley
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Victoria D Stittleburg
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Jessica Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Colleen S Kraft
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Yan Li
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Jing Zhang
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Clinton R Paden
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA 30333, USA
| | - Timothy D Read
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Jesse J Waggoner
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Katia Koelle
- Department of Biology, Emory University, 201 Dowman Drive, Atlanta, GA 30322, USA
| | - Anne Piantadosi
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 201 Dowman Drive, Atlanta, GA 30322, USA
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21
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Feuerstadt P, Louie TJ, Lashner B, Wang EEL, Diao L, Bryant JA, Sims M, Kraft CS, Cohen SH, Berenson CS, Korman LY, Ford CB, Litcofsky KD, Lombardo MJ, Wortman JR, Wu H, Auniņš JG, McChalicher CWJ, Winkler JA, McGovern BH, Trucksis M, Henn MR, von Moltke L. SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection. N Engl J Med 2022; 386:220-229. [PMID: 35045228 DOI: 10.1056/nejmoa2106516] [Citation(s) in RCA: 180] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Current therapies for recurrent Clostridioides difficile infection do not address the disrupted microbiome, which supports C. difficile spore germination into toxin-producing bacteria. SER-109 is an investigational microbiome therapeutic composed of purified Firmicutes spores for the treatment of recurrent C. difficile infection. METHODS We conducted a phase 3, double-blind, randomized, placebo-controlled trial in which patients who had had three or more episodes of C. difficile infection (inclusive of the qualifying acute episode) received SER-109 or placebo (four capsules daily for 3 days) after standard-of-care antibiotic treatment. The primary efficacy objective was to show superiority of SER-109 as compared with placebo in reducing the risk of C. difficile infection recurrence up to 8 weeks after treatment. Diagnosis by toxin testing was performed at trial entry, and randomization was stratified according to age and antibiotic agent received. Analyses of safety, microbiome engraftment, and metabolites were also performed. RESULTS Among the 281 patients screened, 182 were enrolled. The percentage of patients with recurrence of C. difficile infection was 12% in the SER-109 group and 40% in the placebo group (relative risk, 0.32; 95% confidence interval [CI], 0.18 to 0.58; P<0.001 for a relative risk of <1.0; P<0.001 for a relative risk of <0.833). SER-109 led to less frequent recurrence than placebo in analyses stratified according to age stratum (relative risk, 0.24 [95% CI, 0.07 to 0.78] for patients <65 years of age and 0.36 [95% CI, 0.18 to 0.72] for those ≥65 years) and antibiotic received (relative risk, 0.41 [95% CI, 0.22 to 0.79] with vancomycin and 0.09 [95% CI, 0.01 to 0.63] with fidaxomicin). Most adverse events were mild to moderate and were gastrointestinal in nature, with similar numbers in the two groups. SER-109 dose species were detected as early as week 1 and were associated with bile-acid profiles that are known to inhibit C. difficile spore germination. CONCLUSIONS In patients with symptom resolution of C. difficile infection after treatment with standard-of-care antibiotics, oral administration of SER-109 was superior to placebo in reducing the risk of recurrent infection. The observed safety profile of SER-109 was similar to that of placebo. (Funded by Seres Therapeutics; ECOSPOR III ClinicalTrials.gov number, NCT03183128.).
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Affiliation(s)
- Paul Feuerstadt
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Thomas J Louie
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Bret Lashner
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Elaine E L Wang
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Liyang Diao
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Jessica A Bryant
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Matthew Sims
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Colleen S Kraft
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Stuart H Cohen
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Charles S Berenson
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Louis Y Korman
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Christopher B Ford
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Kevin D Litcofsky
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Mary-Jane Lombardo
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Jennifer R Wortman
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Henry Wu
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - John G Auniņš
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Christopher W J McChalicher
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Jonathan A Winkler
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Barbara H McGovern
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Michele Trucksis
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Matthew R Henn
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
| | - Lisa von Moltke
- From Yale University School of Medicine, New Haven, and PACT Gastroenterology Center, Hamden - both in Connecticut (P.F.); the University of Calgary and Foothills Medical Centre, Calgary, AB, Canada (T.J.L.); Cleveland Clinic, Cleveland (B.L.); Seres Therapeutics, Cambridge, MA (E.E.L.W., L.D., J.A.B., C.B.F., M.-J.L., K.D.L., J.R.W., H.W., J.G.A., C.W.J.M., J.A.W., B.H.M., M.T., M.R.H., L.M.); Beaumont Hospital, Royal Oak, Royal Oak, and Oakland University William Beaumont School of Medicine, Rochester - both in Michigan (M.S.); Emory University, Atlanta (C.S.K.); the University of California, Davis, Davis (S.H.C.); the University at Buffalo and Veterans Affairs Western New York Healthcare System - both in Buffalo (C.S.B.); and Capital Digestive Care, Washington, DC (L.Y.K.)
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22
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Damhorst GL, Broder KJ, Overton EC, Rara R, Busch LM, Burd EM, Webster AS, Kraft CS, Babiker A. Clinical Utilization of DiaSorin Molecular Polymerase Chain Reaction in Pneumocystis Pneumonia. Open Forum Infect Dis 2022; 9:ofab634. [PMID: 35036467 PMCID: PMC8754379 DOI: 10.1093/ofid/ofab634] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/08/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pneumocystis jirovecii polymerase chain reaction (PCR) testing is a sensitive diagnostic tool but does not distinguish infection from colonization. Cycle threshold (CT) may correlate with fungal burden and could be considered in clinical decision making. Clinical use of PCR and significance of CT values have not previously been examined with the DiaSorin Molecular platform. METHODS Retrospective review of P jirovecii PCR, CT values and clinical data from 18 months in a multihospital academic health system. The diagnostic performance of PCR with respect to pathology and correlation of CT with severity were examined. RESULTS Ninety-nine of 1006 (9.8%) assays from 786 patients in 919 encounters were positive. Among 91 (9.9%) encounters in which P jirovecii pneumonia (PJP) was treated, 41 (45%) were influenced by positive PCR. Negative PCR influenced discontinuation of therapy in 35 cases. Sensitivity and specificity of PCR were 93% (95% CI, 68%-100%) and 94% (95% CI, 91%-96%) with respect to pathology. CT values from deep respiratory specimens were significantly different among treated patients (P = .04) and those with positive pathology results (P < .0001) compared to patients not treated and those with negative pathology, respectively, and was highly predictive of positive pathology results (area under the curve = 0.92). No significant difference was observed in comparisons based on indicators of disease severity. CONCLUSIONS Pneumocystis jirovecii PCR was a highly impactful tool in the diagnosis and management of PJP, and use of CT values may have value in the treatment decision process in select cases. Further investigation in a prospective manner is needed.
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Affiliation(s)
- Gregory L Damhorst
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kari J Broder
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | - Lindsay M Busch
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eileen M Burd
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrew S Webster
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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23
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Kelley CF, Pollack I, Yacoub R, Zhu Z, Van Doren VE, Gumber S, Amara RR, Fedirko V, Kraft CS, de Man TJB, Hu YJ, Grimsley Ackerley C, Sullivan PS, Bostick RM. Condomless receptive anal intercourse is associated with markers of mucosal inflammation in a cohort of men who have sex with men in Atlanta, Georgia. J Int AIDS Soc 2021; 24:e25859. [PMID: 34911162 PMCID: PMC8673926 DOI: 10.1002/jia2.25859] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction We previously showed that the rectal mucosal immune environment among men who have sex with men (MSM) engaging in condomless receptive anal intercourse (CRAI) is immunologically distinct from that of men who do not engage in anal intercourse (AI). Here, we further examined these differences with quantitative immunohistochemistry to better understand the geographic distribution of immune markers of interest. Methods We enrolled a cohort of MSM engaging in CRAI (n = 41) and men who do not engage in AI (n = 21) between October 2013 and April 2015. Participants were healthy, HIV‐negative men aged 18–45 from the metro Atlanta area. We performed rectal mucosal sampling via rigid sigmoidoscopy during two study visits separated by a median of nine weeks and timed with sexual activity for MSM engaging in CRAI. We used standardized, automated immunohistochemistry and quantitative image analysis to investigate the rectal mucosal distribution of neutrophils (MPO), IL‐17‐producing cells (IL‐17) and Tregs (FOXP3) in the lamina propria, and cellular proliferation (Ki67) and adherens junction protein (E‐cadherin) in the epithelium. We examined associations between biomarker expression and the rectal mucosal microbiota composition by 16s rRNA sequencing. Results Relative to the colonic crypt base, IL‐17, FOXP3, and MPO expression increased towards the rectal lumen, while Ki67 decreased and E‐cadherin was more uniformly distributed. Throughout the rectal mucosa distribution examined, MSM engaging in CRAI had higher mean lamina propria MPO expression (p = 0.04) and epithelial Ki67 (p = 0.04) compared to controls. There were no significant differences in IL‐17, FOXP3 or E‐cadherin expression. We found no significant associations of the five biomarkers with the global rectal microbiota composition or the individual taxa examined. Conclusions Understanding the mucosal distribution of inflammatory mediators can enhance our knowledge of the earliest events in HIV transmission. Neutrophil enrichment and crypt epithelial cell proliferation likely represent sub‐clinical inflammation in response to CRAI in the rectal mucosa of MSM, which could increase the risk for HIV acquisition. However, the contributory role of the microbiota in mucosal inflammation among MSM remains unclear. HIV prevention may be enhanced by interventions that reduce inflammation or capitalize on the presence of specific inflammatory mechanisms during HIV exposure.
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Affiliation(s)
- Colleen F Kelley
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, The Hope Clinic, Atlanta, Georgia, USA.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Ilana Pollack
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, The Hope Clinic, Atlanta, Georgia, USA
| | - Rami Yacoub
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Zhengyi Zhu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Vanessa E Van Doren
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, The Hope Clinic, Atlanta, Georgia, USA
| | - Sanjeev Gumber
- Division of Pathology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Rama R Amara
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Veronika Fedirko
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA.,Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, The Hope Clinic, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Cassie Grimsley Ackerley
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, The Hope Clinic, Atlanta, Georgia, USA
| | - Patrick S Sullivan
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Roberd M Bostick
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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24
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Su M, Immergluck KS, Stampfer S, Rao A, Bassitt L, Nguyen V, Stittleburg VD, Ingersoll JM, Kraft CS, Martin GS, Piantadosi A, Lam WA, Waggoner J, Babiker A. 148. Single-amplicon, Multiplex Real-time RT-PCR with Tiled Probes to Detect SARS-CoV-2 spike Mutations Associated with Variants of Concern. Open Forum Infect Dis 2021. [PMCID: PMC8644603 DOI: 10.1093/ofid/ofab466.148] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/14/2022] Open
Abstract
Background Detection and surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is of great public health importance. Broadly accessible and inexpensive assays are needed to enhance variant surveillance and detection globally. We developed and validated a single-reaction multiplex real-time RT-PCR (the Spike SNP assay) to detect specific mutations associated with variants of concern (VOC). Methods A single primer pair was designed to amplify a 348 bp region of spike. Probes were initially designed with locked nucleic acids (LNAs) to increase probe melting temperature, shorten probe length, and specifically detect 417K, E484K, and N501Y (Figure). The assay was optimized and evaluated using characterized variant sample pools. Clinical evaluation was performed on a convenience set of residual nasopharyngeal swabs, and variant calls were confirmed by SARS-CoV-2 genomic sequencing in a subset of samples. Following the initial evaluation, unmodified probes (without LNAs) were designed to detect L452R, L452Q, and E484Q. Figure. Spike SNP distinguishes mutations occurring in different lineages (A-C). ![]()
Representative results of variant detection a single Spike SNP run are shown for mutations in the codons for 4177K (A) and mutations that encode 484K (B) and 501Y (C). Curves show dilutions of the following variants: blue, BEI 52286 (wild type); pink B.1.1.7; purple, B1.525; and green, P.1. Variant pools were used for B.1.17, B.1.525, and P.1 strains. Curves are displayed for a given dilution in each channel and result interpretation is shown (D). Results The lower limit of 95% detection was 2.46 to 2.48 log10 GE/mL for the three targets (~1-2 GE/reaction). Among 253 nasopharyngeal swabs with detectable SARS-CoV-2 RNA, the Spike SNP assay was positive in 238 (94.1%), including all samples with Ct values < 30 (220/220) for the N2 target and 18/33 samples with N2 Ct values ≥ 30. Results were confirmed by SARS-CoV-2 genomic sequencing in 50/50 samples (100%). Subsequent addition of the 452R probe did not affect performance for the original targets, and probes for 452Q and 484Q performed similarly to LNA-modified probes. Conclusion The Spike SNP assay provides fast, inexpensive and sensitive detection of specific mutations associated with SARS-CoV-2 VOCs, and the assay can be quickly modified to detect new mutations in the receptor binding domain. Similar analytical performance of LNA-modified and unmodified probes presents options for future assay customization that balance the shorter probe length (LNAs) and increased accessibility (unmodified). The Spike SNP assay, if implemented across laboratories offering SARS-CoV-2 testing, could greatly increase capacity for variant detection and surveillance globally. Disclosures Colleen S. Kraft, MD, MSc, Rebiotix (Individual(s) Involved: Self): Advisor or Review Panel member
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Affiliation(s)
- Maxwell Su
- Emory University School of Medicine, Atlanta, GA
| | | | | | - Anuradha Rao
- Emory University School of Medicine, Atlanta, Georgia
| | - Leda Bassitt
- Emory University School of Medicine, Atlanta, GA
| | - Vi Nguyen
- Emory University School of Medicine, Atlanta, GA
| | | | | | | | | | | | - Wilbur A Lam
- Emory University School of Medicine, Atlanta, GA
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25
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Straub TJ, Diao L, Ford C, Sims M, Louie TJ, Berenson C, Kraft CS, Cohen SH, Cohen SH, Paskovaty A, Lombardo MJ, McGovern B, von Moltke L, Henn M. LB15. SER-109, an Investigational Microbiome Therapeutic, Reduces Abundance of Antimicrobial Resistance Genes in Patients with Recurrent Clostridioides difficile Infection (rCDI) after Standard-of-Care Antibiotics. Open Forum Infect Dis 2021. [DOI: 10.1093/ofid/ofab466.1651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
The gastrointestinal microbiota is the first line of defense against colonization with antimicrobial resistant (AR) bacteria, particularly in vulnerable hosts with frequent antibiotic exposure. In a double-blind Phase 3 trial of rCDI patients, SER-109, an orally formulated consortia of purified Firmicutes spores, was superior to placebo in reducing CDI recurrence at week 8 post clinical resolution on standard-of-care (SoC) antibiotics. Overall recurrence rates were lower in SER-109 vs placebo (12.4% vs 39.8%, respectively) relative risk, 0.32 [95% CI, 0.18–0.58; p< 0.001 for RR< 1.0; p< 0.001 for RR< 0.833]. This is a post-hoc analysis examining the impact of SER-109 on antimicrobial resistance genes (ARGs) abundance in the intestinal microbiota compared to placebo.
Methods
Subjects with rCDI received SoC antibiotics, then were randomized 1:1 to SER-109 or placebo at baseline. Of 182 subjects, 140 who had paired stool samples at baseline and 1-week post-treatment were included in this analysis. ARG abundances and taxonomic profiles were generated from whole metagenomic shotgun sequencing. t-tests were used to compare changes in ARG abundance from baseline; mixed linear models were used to associate ARG and taxon abundances across time points.
Results
ARG abundance was reduced overall by week 1, with a significantly greater decrease in SER-109 subjects vs. placebo at week 1 (Fig. 1). Proteobacteria relative abundance were positively correlated with ARG abundance across all samples (Fig. 2), with the Enterobacteriaceae family associated with the abundance of 95 ARGs (all p < 0.05). Enterococcaceae relative abundance was associated with glycopeptide AR abundance (p < 0.001). At week 1, Proteobacteria relative abundance was significantly decreased from baseline in SER-109 subjects vs. placebo (p < 0.001). Enterobacteriaceae and Enterococcaceae relative abundances were also decreased from baseline in SER-109 subjects vs. placebo (p < 0.001 and p = 0.007, respectively).
Figure 1. Significant reduction in ARG abundance at week 1 from baseline in SER-109 treatment compared to placebo.
Figure 2. Total ARG abundance is associated with the relative abundance of Proteobacteria in SER-109 and placebo subjects at baseline and week 1.
Conclusion
SER-109 was associated with significantly greater reduction of ARGs and AR bacteria abundances compared to placebo at 1 week post treatment. These findings support a potential role of microbiome therapeutics in rapid decolonization of AR bacteria with implications for infection prevention.
Disclosures
Timothy J. Straub, MS, Seres Therapeutics (Employee) Liyang Diao, PhD, Seres Therapeutics (Employee) Christopher Ford, PhD, Seres Therapeutics (Employee, Shareholder) Matthew Sims, MD, PhD, Astra Zeneca (Independent Contractor)Diasorin Molecular (Independent Contractor)Epigenomics Inc (Independent Contractor)Finch (Independent Contractor)Genentech (Independent Contractor)Janssen Pharmaceuticals NV (Independent Contractor)Kinevant Sciences gmBH (Independent Contractor)Leonard-Meron Biosciences (Independent Contractor)Merck and Co (Independent Contractor)OpGen (Independent Contractor)Prenosis (Independent Contractor)Regeneron Pharmaceuticals Inc (Independent Contractor)Seres Therapeutics Inc (Independent Contractor)Shire (Independent Contractor)Summit Therapeutics (Independent Contractor) Thomas J. Louie, MD, Artugen (Advisor or Review Panel member)Crestone (Consultant, Grant/Research Support)Da Volterra (Advisor or Review Panel member)Finch Therapeutics (Grant/Research Support, Advisor or Review Panel member)MGB Biopharma (Grant/Research Support, Advisor or Review Panel member)Rebiotix (Consultant, Grant/Research Support)Seres Therapeutics (Consultant, Grant/Research Support)Summit PLC (Grant/Research Support)Vedanta (Grant/Research Support, Advisor or Review Panel member) Colleen S. Kraft, MD, MSc, Rebiotix (Individual(s) Involved: Self): Advisor or Review Panel member Stuart H. Cohen, MD, Seres (Research Grant or Support) Stuart H. Cohen, MD, Nothing to disclose Mary-Jane Lombardo, PhD, Seres Therapeutics (Employee, Shareholder) Barbara McGovern, MD, Seres Therapeutics (Employee, Shareholder) Lisa von Moltke, MD, Seres Therapeutics (Employee, Shareholder) Matt Henn, PhD, Seres Therapeutics (Employee, Shareholder)
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Affiliation(s)
| | | | | | | | - Thomas J Louie
- Cumming School of Medicine, University of Calgary, Calgary, Canada, Calgary, Alberta, Canada
| | | | | | | | | | | | | | | | | | - Matt Henn
- Seres Therapeutics, Inc., Cambridge, MA
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26
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Liu KH, Owens JA, Saeedi B, Cohen CE, Bellissimo MP, Naudin C, Darby T, Druzak S, Maner-Smith K, Orr M, Hu X, Fernandes J, Camacho MC, Hunter-Chang S, VanInsberghe D, Ma C, Ganesh T, Yeligar SM, Uppal K, Go YM, Alvarez JA, Vos MB, Ziegler TR, Woodworth MH, Kraft CS, Jones RM, Ortlund E, Neish AS, Jones DP. Microbial metabolite delta-valerobetaine is a diet-dependent obesogen. Nat Metab 2021; 3:1694-1705. [PMID: 34931082 PMCID: PMC8711632 DOI: 10.1038/s42255-021-00502-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/04/2021] [Indexed: 12/17/2022]
Abstract
Obesity and obesity-related metabolic disorders are linked to the intestinal microbiome. However, the causality of changes in the microbiome-host interaction affecting energy metabolism remains controversial. Here, we show the microbiome-derived metabolite δ-valerobetaine (VB) is a diet-dependent obesogen that is increased with phenotypic obesity and is correlated with visceral adipose tissue mass in humans. VB is absent in germ-free mice and their mitochondria but present in ex-germ-free conventionalized mice and their mitochondria. Mechanistic studies in vivo and in vitro show VB is produced by diverse bacterial species and inhibits mitochondrial fatty acid oxidation through decreasing cellular carnitine and mitochondrial long-chain acyl-coenzyme As. VB administration to germ-free and conventional mice increases visceral fat mass and exacerbates hepatic steatosis with a western diet but not control diet. Thus, VB provides a molecular target to understand and potentially manage microbiome-host symbiosis or dysbiosis in diet-dependent obesity.
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Affiliation(s)
- Ken H Liu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Joshua A Owens
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Bejan Saeedi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Catherine E Cohen
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Moriah P Bellissimo
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Crystal Naudin
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Trevor Darby
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Samuel Druzak
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Kristal Maner-Smith
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael Orr
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jolyn Fernandes
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Mary Catherine Camacho
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Sarah Hunter-Chang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - David VanInsberghe
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Chunyu Ma
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Thota Ganesh
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Samantha M Yeligar
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Atlanta Veterans Affairs Health Care System, Decatur, GA, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jessica A Alvarez
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Miriam B Vos
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas R Ziegler
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael H Woodworth
- Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Rheinallt M Jones
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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Lane MA, Walawender M, Webster AS, Brownsword EA, Ingersoll JM, Miller C, Waggoner J, Uyeki TM, Lindsley WG, Kraft CS. Sampling for SARS-CoV-2 Aerosols in Hospital Patient Rooms. Viruses 2021; 13:2347. [PMID: 34960615 PMCID: PMC8703426 DOI: 10.3390/v13122347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/21/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 12/21/2022] Open
Abstract
Evidence varies as to how far aerosols spread from individuals infected with SARS-CoV-2 in hospital rooms. We investigated the presence of aerosols containing SARS-CoV-2 inside of dedicated COVID-19 patient rooms. Three National Institute for Occupational Safety and Health BC 251 two-stage cyclone samplers were set up in each patient room for a six-hour sampling period. Samplers were place on tripods, which each held two samplers at various heights above the floor. Extracted samples underwent reverse transcription polymerase chain reaction for selected gene regions of the SARS-CoV-2 virus nucleocapsid. Patient medical data were compared between participants in rooms where virus-containing aerosols were detected and those where they were not. Of 576 aerosols samples collected from 19 different rooms across 32 participants, 3% (19) were positive for SARS-CoV-2, the majority from near the head and foot of the bed. Seven of the positive samples were collected inside a single patient room. No significant differences in participant clinical characteristics were found between patients in rooms with positive and negative aerosol samples. SARS-CoV-2 viral aerosols were detected from the patient rooms of nine participants (28%). These findings provide reassurance that personal protective equipment that was recommended for this virus is appropriate given its spread in hospital rooms.
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Affiliation(s)
- Morgan A. Lane
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (A.S.W.); (E.A.B.); (J.W.); (C.S.K.)
| | - Maria Walawender
- Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA;
| | - Andrew S. Webster
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (A.S.W.); (E.A.B.); (J.W.); (C.S.K.)
- Department of Infectious Diseases, Atlanta VA Health Care System, Decatur, GA 30033, USA
| | - Erik A. Brownsword
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (A.S.W.); (E.A.B.); (J.W.); (C.S.K.)
| | - Jessica M. Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA; (J.M.I.); (C.M.)
| | - Candace Miller
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA; (J.M.I.); (C.M.)
| | - Jesse Waggoner
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (A.S.W.); (E.A.B.); (J.W.); (C.S.K.)
- Emory Healthcare, Atlanta, GA 30322, USA
| | - Timothy M. Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30322, USA;
| | - William G. Lindsley
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV 26508, USA;
| | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (A.S.W.); (E.A.B.); (J.W.); (C.S.K.)
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA 30322, USA; (J.M.I.); (C.M.)
- Emory Healthcare, Atlanta, GA 30322, USA
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28
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Kyu S, Ramonell RP, Kuruvilla M, Kraft CS, Wang YF, Falsey AR, Walsh EE, Daiss JL, Paulos S, Rajam G, Wu H, Velusamy S, Lee FEH. Diagnosis of Streptococcus pneumoniae infection using circulating antibody secreting cells. PLoS One 2021; 16:e0259644. [PMID: 34767590 PMCID: PMC8589192 DOI: 10.1371/journal.pone.0259644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 10/22/2021] [Indexed: 11/18/2022] Open
Abstract
Background Streptococcus pneumoniae infections cause morbidity and mortality worldwide. A rapid, simple diagnostic method could reduce the time needed to introduce definitive therapy potentially improving patient outcomes. Methods We introduce two new methods for diagnosing S. pneumoniae infections by measuring the presence of newly activated, pathogen-specific, circulating Antibody Secreting Cells (ASC). First, ASC were detected by ELISpot assays that measure cells secreting antibodies specific for signature antigens. Second, the antibodies secreted by isolated ASC were collected in vitro in a novel matrix, MENSA (media enriched with newly synthesized antibodies) and antibodies against S. pneumoniae antigens were measured using Luminex immunoassays. Each assay was evaluated using blood from S. pneumoniae and non-S. pneumoniae-infected adult patients. Results We enrolled 23 patients with culture-confirmed S. pneumoniae infections and 24 controls consisting of 12 non-S. pneumoniae infections, 10 healthy donors and two colonized with S. pneumoniae. By ELISpot assays, twenty-one of 23 infected patients were positive, and all 24 controls were negative. Using MENSA samples, four of five S. pneumoniae-infected patients were positive by Luminex immunoassays while all five non-S. pneumoniae-infected patients were negative. Conclusion Specific antibodies produced by activated ASC may provide a simple diagnostic for ongoing S. pneumoniae infections. This method has the potential to diagnose acute bacterial infections.
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Affiliation(s)
- Shuya Kyu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Richard P. Ramonell
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Merin Kuruvilla
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Yun F. Wang
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Ann R. Falsey
- Division of Infectious Diseases, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- Rochester General Hospital, Rochester, New York, United States of America
| | - Edward E. Walsh
- Division of Infectious Diseases, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- Rochester General Hospital, Rochester, New York, United States of America
| | - John L. Daiss
- Center for Musculoskeletal Research and Department of Orthopaedics, University of Rochester Medical Center, Rochester, New York, United States of America
- MicroB-plex, Inc., Atlanta, Georgia, United States of America
| | - Simon Paulos
- Merck & Co., Inc., Kenilworth, New Jersey, United States of America
| | | | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, United States of America
| | - Srinivasan Velusamy
- Division of Bacterial Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - F. Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail:
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29
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Liu KH, Lee CM, Singer G, Bais P, Castellanos F, Woodworth MH, Ziegler TR, Kraft CS, Miller GW, Li S, Go YM, Morgan ET, Jones DP. Large scale enzyme based xenobiotic identification for exposomics. Nat Commun 2021; 12:5418. [PMID: 34521839 PMCID: PMC8440538 DOI: 10.1038/s41467-021-25698-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 09/14/2020] [Accepted: 08/18/2021] [Indexed: 01/14/2023] Open
Abstract
Advances in genomics have revealed many of the genetic underpinnings of human disease, but exposomics methods are currently inadequate to obtain a similar level of understanding of environmental contributions to human disease. Exposomics methods are limited by low abundance of xenobiotic metabolites and lack of authentic standards, which precludes identification using solely mass spectrometry-based criteria. Here, we develop and validate a method for enzymatic generation of xenobiotic metabolites for use with high-resolution mass spectrometry (HRMS) for chemical identification. Generated xenobiotic metabolites were used to confirm identities of respective metabolites in mice and human samples based upon accurate mass, retention time and co-occurrence with related xenobiotic metabolites. The results establish a generally applicable enzyme-based identification (EBI) for mass spectrometry identification of xenobiotic metabolites and could complement existing criteria for chemical identification.
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Affiliation(s)
- Ken H. Liu
- grid.189967.80000 0001 0941 6502Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia USA
| | - Choon M. Lee
- grid.189967.80000 0001 0941 6502Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Grant Singer
- grid.189967.80000 0001 0941 6502Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Preeti Bais
- The Jackson Laboratory for Genomic Medicine, Atlanta, Connecticut USA
| | | | - Michael H. Woodworth
- grid.189967.80000 0001 0941 6502Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia USA
| | - Thomas R. Ziegler
- grid.189967.80000 0001 0941 6502Division of Endocrinology, Metabolism and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia USA
| | - Colleen S. Kraft
- grid.189967.80000 0001 0941 6502Division of Infectious Disease, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia USA ,grid.189967.80000 0001 0941 6502Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, Georgia USA
| | - Gary W. Miller
- grid.21729.3f0000000419368729Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York USA
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, Atlanta, Connecticut USA
| | - Young-Mi Go
- grid.189967.80000 0001 0941 6502Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia USA
| | - Edward T. Morgan
- grid.189967.80000 0001 0941 6502Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia USA
| | - Dean P. Jones
- grid.189967.80000 0001 0941 6502Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia USA
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30
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Woodworth MH, Kwon JH, Kraft CS. An Ounce of Prevention Is Equivalent to How Much Decolonization Exactly? Clin Infect Dis 2021; 72:e924. [PMID: 33029623 DOI: 10.1093/cid/ciaa1524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael H Woodworth
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jennie H Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Colleen S Kraft
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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31
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Affiliation(s)
- Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA.,Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
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32
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Babiker A, Ingersoll JM, Adelman MW, Webster AS, Broder KJ, Stittleburg V, Waggoner JJ, Kraft CS, Woodworth MH. Validation of High-Sensitivity Severe Acute Respiratory Syndrome Coronavirus 2 Testing for Stool-Toward the New Normal for Fecal Microbiota Transplantation. Clin Transl Gastroenterol 2021; 12:e00363. [PMID: 34106090 PMCID: PMC8189625 DOI: 10.14309/ctg.0000000000000363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/08/2021] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Mounting evidence demonstrates potential for fecal-oral transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The US Food and Drug Administration now requires SARS-CoV-2 testing of potential feces donors before the use of stool manufactured for fecal microbiota transplantation. We sought to develop and validate a high-sensitivity SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) procedure for testing stool specimens. METHODS A modified extraction method was used with an RT-PCR assay adapted from the Centers for Disease Control and Prevention PCR protocol for respiratory specimens. Contrived specimens were created using pre-COVID-19 banked stool specimens and spiking in known concentrations of SARS-CoV-2-specific nucleic acid. The highest transcript concentration at which 2/2 or 1/2 SARS-CoV-2 targets were detected in 9/10 replicates was defined as the dual-target limit and single-target limit of detection, respectively. The clinical performance of the assay was evaluated with stool samples collected from 17 nasopharyngeal swab RT-PCR-positive patients and 14 nasopharyngeal RT-PCR-negative patients. RESULTS The dual-target and single-target limit of detection were 56 copies/μL and 3 copies/μL, respectively. SARS-CoV-2 was detected at concentrations as low as 0.6 copies/μL. Clinical stool samples from known COVID-19-positive patients demonstrated the detection of SARS-CoV-2 in stool up to 29 days from symptom onset with a high agreement with nasopharyngeal swab tests (kappa statistic of 0.95, P value < 0.001). DISCUSSION The described RT-PCR test is a sensitive and flexible approach for the detection of SARS-CoV-2 in stool specimens. We propose an integrated screening approach that incorporates this stool test to support continuation of fecal microbiota transplantation programs.
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Affiliation(s)
- Ahmed Babiker
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jessica M. Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Max W. Adelman
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Andrew S. Webster
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Kari J. Broder
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Victoria Stittleburg
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jesse J. Waggoner
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S. Kraft
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Michael H. Woodworth
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
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Shantha JG, Auld SC, Anthony C, Ward L, Adelman MW, Maier CL, Price KW, Jacob J, Fashina T, Randleman C, Xu LT, Barnett J, Sadan O, Kandiah PA, Varkey JB, Kraft CS, Rouphael N, Linderman S, Ahmed R, Drews-Botsch C, Waggoner JJ, Weinmann M, Murphy DJ, Yeh S. Retinopathy and Systemic Disease Morbidity in Severe COVID-19. Ocul Immunol Inflamm 2021; 29:743-750. [PMID: 34464544 PMCID: PMC8562588 DOI: 10.1080/09273948.2021.1952278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/29/2021] [Revised: 06/17/2021] [Accepted: 06/30/2021] [Indexed: 01/08/2023]
Abstract
PURPOSE To assess the prevalence of retinopathy and its association with systemic morbidity and laboratory indices of coagulation and inflammatory dysfunction in severe COVID-19. DESIGN Retrospective, observational cohort study. METHODS Adult patients hospitalized with severe COVID-19 who underwent ophthalmic examination from April to July 2020 were reviewed. Retinopathy was defined as one of the following: 1) Retinal hemorrhage; 2) Cotton wool spots; 3) Retinal vascular occlusion. We analyzed medical comorbidities, sequential organ failure assessment (SOFA) scores, clinical outcomes, and laboratory values for their association with retinopathy. RESULTS Thirty-seven patients with severe COVID-19 were reviewed, the majority of whom were female (n = 23, 62%), Black (n = 26, 69%), and admitted to the intensive care unit (n = 35, 95%). Fourteen patients had retinopathy (38%) with retinal hemorrhage in 7 (19%), cotton wool spots in 8 (22%), and a branch retinal artery occlusion in 1 (3%) patient. Patients with retinopathy had higher SOFA scores than those without retinopathy (8.0 vs. 5.3, p = .03), higher rates of respiratory failure requiring invasive mechanical ventilation and shock requiring vasopressors (p < .01). Peak D-dimer levels were 28,971 ng/mL in patients with retinopathy compared to 12,575 ng/mL in those without retinopathy (p = .03). Peak CRP was higher in patients with cotton wool spots versus those without cotton wool spots (354 mg/dL vs. 268 mg/dL, p = .03). Multivariate logistic regression modeling showed an increased risk of retinopathy with higher peak D-dimers (aOR 1.32, 95% CI 1.01-1.73, p = .04) and male sex (aOR 9.6, 95% CI 1.2-75.5, p = .04). CONCLUSION Retinopathy in severe COVID-19 was associated with greater systemic disease morbidity involving multiple organs. Given its association with coagulopathy and inflammation, retinopathy may offer insight into disease pathogenesis in patients with severe COVID-19.
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Affiliation(s)
| | - Sara C Auld
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University School of Medicine, Atlanta, GA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Casey Anthony
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
| | - Laura Ward
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA
| | - Max W. Adelman
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA
| | - Cheryl L. Maier
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Kenneth W. Price
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
| | - Jesse Jacob
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA
| | - Tolu Fashina
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
| | - Casey Randleman
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
| | - Lucy T. Xu
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
| | - Joshua Barnett
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
| | - Ofer Sadan
- Department of Neurology and Neurosurgery, Division of Neurocritical Care, Emory University School of Medicine, Atlanta, GA
| | - Prem A. Kandiah
- Department of Neurology and Neurosurgery, Division of Neurocritical Care, Emory University School of Medicine, Atlanta, GA
| | - Jay B. Varkey
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA
| | - Colleen S. Kraft
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Nadine Rouphael
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA
| | - Susanne Linderman
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA
| | - Carolyn Drews-Botsch
- Department of Global and Community Health, College of Health and Human Services, George Mason University, Fairfax, VA
| | - Jesse J. Waggoner
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA
| | - Max Weinmann
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University School of Medicine, Atlanta, GA
| | - David J. Murphy
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University School of Medicine, Atlanta, GA
| | - Steven Yeh
- Emory Eye Center, Emory University School of Medicine, Atlanta, GA
- Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, NE
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Abstract
The COVID-19 pandemic has changed the way we practice medicine and lead our lives. In addition to pulmonary symptoms; COVID-19 as a syndrome has multisystemic involvement including frequent gastrointestinal symptoms such as diarrhea. Due to microbiome alterations with COVID-19 and frequent antibiotic exposure, COVID-19 can be complicated by Clostridioides difficile infection. Co-infection with these two can be associated with a high risk of complications. Infection control measures in hospitals is enhanced due to the COVID-19 pandemic which in turn appears to reduce the incidence of hospital-acquired infections such as C. difficile infection. Another implication of COVID-19 and its potential transmissibility by stool is microbiome-based therapies. Potential stool donors should be screened COVID-19 symptoms and be tested for COVID-19. #Clostridioides difficile complicating #COVID-19 can be associated with high mortality. COVID-19 patients with diarrhea, especially those who received antibiotics recently should be tested for C. difficile.
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Affiliation(s)
- Sahil Khanna
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Colleen S Kraft
- Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA 30322, USA.,Division of Infectious Diseases, Emory University, Atlanta, GA 30322, USA
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Lane M, Kraft CS, Ayers M, Love K, Brownsword E, Sexton ME. Novel approach to deployment of crisis situation supply of N95 respirator models in a healthcare system. Am J Infect Control 2021; 49:500-502. [PMID: 33159996 PMCID: PMC8800390 DOI: 10.1016/j.ajic.2020.11.001] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/02/2020] [Indexed: 12/01/2022]
Abstract
Given supply constraints of N95s in the United States during the COVID-19 pandemic, healthcare facilities have turned to extended use protocols and new sources of N95s. Because fit testing every employee for every new mask is not feasible, our Infection Prevention Department developed a method for rapid deployment of new N95s.
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Affiliation(s)
- Morgan Lane
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA.
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA; Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA
| | - Marie Ayers
- Department of Infection Prevention , Emory Healthcare, Atlanta, GA
| | - Kari Love
- Department of Infection Prevention , Emory Healthcare, Atlanta, GA
| | - Erik Brownsword
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
| | - Mary Elizabeth Sexton
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA
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Sherman AC, Babiker A, Sieben AJ, Pyden A, Steinberg J, Kraft CS, Koelle K, Kanjilal S. The Effect of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Mitigation Strategies on Seasonal Respiratory Viruses: A Tale of 2 Large Metropolitan Centers in the United States. Clin Infect Dis 2021; 72:e154-e157. [PMID: 33161424 PMCID: PMC7717225 DOI: 10.1093/cid/ciaa1704] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 11/04/2020] [Indexed: 12/22/2022] Open
Abstract
To assess the impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic on seasonal respiratory viruses, absolute case counts and viral reproductive rates from 2019-2020 were compared against previous seasons. Our findings suggest that the public health measures implemented to reduce SARS-CoV-2 transmission significantly reduced the transmission of other respiratory viruses.
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Affiliation(s)
- Amy C Sherman
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Alexander Pyden
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - James Steinberg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, USA
| | - Sanjat Kanjilal
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Healthcare Institute, Boston, Massachusetts, USA
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Sam SS, Rogers R, Gillani FS, Tsongalis GJ, Kraft CS, Caliendo AM. Evaluation of a Next-Generation Sequencing Metagenomics Assay to Detect and Quantify DNA Viruses in Plasma from Transplant Recipients. J Mol Diagn 2021; 23:719-731. [PMID: 33706010 PMCID: PMC8279015 DOI: 10.1016/j.jmoldx.2021.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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] [Received: 08/19/2020] [Revised: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 11/24/2022] Open
Abstract
Viral infections are major causes of morbidity and mortality in solid-organ and hematopoietic stem cell transplant recipients. This study evaluated the performance of the Galileo Pathogen Solution metagenomics Next-Generation sequencing assay to detect and quantify 11 DNA viruses (cytomegalovirus, Epstein-Barr virus, BK virus, human adenovirus, JC virus, herpes simplex virus 1 and 2, varicella zoster virus, human herpesvirus 6A and 6B, and parvovirus B19) and to qualitatively detect torque teno virus. DNA extracted from 47 plasma samples of viremic transplant recipients were subjected to DNA library preparation with pathogen enrichment/human background depletion, sequencing, and automated data analysis. The viral loads were determined with the Galileo assay using a standard curve generated from a calibration panel. All of the samples tested had a 100% agreement with the real-time quantitative PCR (qPCR) assays in detecting the primary virus targets and the majority of the quantified samples had a viral load difference within 0.46 log10 IU/mL or copies/mL. The mean difference for cytomegalovirus between the Galileo and qPCR assays was 0.21 log10 IU/mL (SD, ±0.43 log10 IU/mL). The mean difference for BK virus between the Galileo and qPCR assays was 0.17 log10 cp/mL (SD, ±0.67 log10 cp/mL). Additionally, 75 co-infections were detected in 31 samples by the Galileo assay. The study findings show that the Galileo assay can simultaneously detect and quantify multiple viruses in transplant recipients with results that are comparable with standard-of-care qPCR assays.
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Affiliation(s)
- Soya S Sam
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island; Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island.
| | - Ralph Rogers
- Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
| | - Fizza S Gillani
- Division of Infectious Diseases, The Miriam Hospital, Providence, Rhode Island; Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
| | - Gregory J Tsongalis
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Angela M Caliendo
- Division of Infectious Diseases, Warren Alpert School of Medicine, Brown University, Providence, Rhode Island
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38
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Lane MA, Brownsword EA, Babiker A, Ingersoll JM, Waggoner J, Ayers M, Klopman M, Uyeki TM, Lindsley WG, Kraft CS. Bioaerosol sampling for SARS-CoV-2 in a referral center with critically ill COVID-19 patients March-May 2020. Clin Infect Dis 2021; 73:e1790-e1794. [PMID: 33506256 PMCID: PMC7953966 DOI: 10.1093/cid/ciaa1880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Indexed: 12/23/2022] Open
Abstract
Background Previous research has shown that rooms of patients with coronavirus disease 2019 (COVID-19) present the potential for healthcare-associated transmission through aerosols containing severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). However, data on the presence of these aerosols outside of patient rooms are limited. We investigated whether virus-containing aerosols were present in nursing stations and patient room hallways in a referral center with critically ill COVID-19 patients. Methods Eight National Institute for Occupational Safety and Health BC 251 2-stage cyclone samplers were set up throughout 6 units, including nursing stations and visitor corridors in intensive care units and general medical units, for 6 h each sampling period. Samplers were placed on tripods which held 2 samplers positioned 102 cm and 152 cm above the floor. Units were sampled for 3 days. Extracted samples underwent reverse transcription polymerase chain reaction for selected gene regions of the SARS-CoV-2 virus nucleocapsid and the housekeeping gene human RNase P as an internal control. Results The units sampled varied in the number of laboratory-confirmed COVID-19 patients present on the days of sampling. Some of the units included patient rooms under negative pressure, while most were maintained at a neutral pressure. Of 528 aerosol samples collected, none were positive for SARS-CoV-2 RNA by the estimated limit of detection of 8 viral copies/m3 of air. Conclusions Aerosolized SARS-CoV-2 outside of patient rooms was undetectable. While healthcare personnel should avoid unmasked close contact with each other, these findings may provide reassurance for the use of alternatives to tight-fitting respirators in areas outside of patient rooms during the current pandemic.
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Affiliation(s)
- Morgan A Lane
- Division of Infectious Diseases, Department of Medicine Emory University, Atlanta, GA, USA
| | - Erik A Brownsword
- Division of Infectious Diseases, Department of Medicine Emory University, Atlanta, GA, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Jessica M Ingersoll
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Jesse Waggoner
- Division of Infectious Diseases, Department of Medicine Emory University, Atlanta, GA, USA.,Emory Healthcare, Atlanta, GA
| | | | - Matthew Klopman
- Emory Healthcare, Atlanta, GA.,Department of Anesthesiology, Emory University, Atlanta, GA, USA
| | - Timothy M Uyeki
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine Emory University, Atlanta, GA, USA.,Emory Healthcare, Atlanta, GA.,Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
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Abstract
OBJECTIVES To review published clinical evidence on management of Clostridioides difficile infection in critically ill patients. DATA SOURCES We obtained relevant studies from a PubMed literature review and bibliographies of reviewed articles. STUDY SELECTION We selected English-language studies addressing aspects of C. difficile infection relevant to critical care clinicians including epidemiology, risk factors, diagnosis, treatment, and prevention, with a focus on high-quality clinical evidence. DATA EXTRACTION We reviewed potentially relevant studies and abstracted information on study design, methods, patient selection, and results of relevant studies. This is a synthetic (i.e., not systematic) review. DATA SYNTHESIS C. difficile infection is the most common healthcare-associated infection in the United States. Antibiotics are the most significant C. difficile infection risk factor, and among antibiotics, cephalosporins, clindamycin, carbapenems, fluoroquinolones, and piperacillin-tazobactam confer the highest risk. Age, diabetes mellitus, inflammatory bowel disease, and end-stage renal disease are risk factors for C. difficile infection development and mortality. C. difficile infection diagnosis is based on testing appropriately selected patients with diarrhea or on clinical suspicion for patients with ileus. Patients with fulminant disease (C. difficile infection with hypotension, shock, ileus, or megacolon) should be treated with oral vancomycin and IV metronidazole, as well as rectal vancomycin in case of ileus. Patients who do not respond to initial therapy should be considered for fecal microbiota transplant or surgery. Proper infection prevention practices decrease C. difficile infection risk. CONCLUSIONS Strong clinical evidence supports limiting antibiotics when possible to decrease C. difficile infection risk. For patients with fulminant C. difficile infection, oral vancomycin reduces mortality, and adjunctive therapies (including IV metronidazole) and interventions (including fecal microbiota transplant) may benefit select patients. Several important questions remain regarding fulminant C. difficile infection management, including which patients benefit from fecal microbiota transplant or surgery.
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Affiliation(s)
- Max W. Adelman
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael H. Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Virginia O. Shaffer
- Department of Surgery, Emory University School of Medicine, Atlanta, GA, USA
| | - Greg S. Martin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Emory Critical Care Center, Atlanta, GA, USA
| | - Colleen S. Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
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Damhorst GL, Adelman MW, Woodworth MH, Kraft CS. Current Capabilities of Gut Microbiome-Based Diagnostics and the Promise of Clinical Application. J Infect Dis 2020; 223:S270-S275. [PMID: 33330938 DOI: 10.1093/infdis/jiaa689] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is increasing evidence for the importance of the gut microbiome in human health and disease. Traditional and modern technologies - from cell culture to next generation sequencing - have facilitated these advances in knowledge. Each of the tools employed in measuring the microbiome exhibits unique capabilities that may be leveraged for clinical diagnostics. However, much still needs to be done to standardize the language and metrics by which a microbiome is characterized. Here we review the capabilities of gut microbiome-based diagnostics, review selected examples, and discuss the outlook towards clinical application.
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Affiliation(s)
- Gregory L Damhorst
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Max W Adelman
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Michael H Woodworth
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Department of Medicine, Division of Infectious Diseases, Emory School of Medicine, Atlanta, Georgia, USA.,Department of Pathology and Laboratory Medicine; Department of Medicine; Division of Infectious Diseases, Emory University, Atlanta, Georgia, USA
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41
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Lane MA, Brownsword EA, Morgan JS, Babiker A, Vanairsdale SA, Lyon GM, Mehta AK, Ingersoll JM, Lindsley WG, Kraft CS. Bioaerosol sampling of a ventilated patient with COVID-19. Am J Infect Control 2020; 48:1540-1542. [PMID: 32763347 PMCID: PMC7402277 DOI: 10.1016/j.ajic.2020.07.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/02/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022]
Abstract
Bioaerosol samples were collected in an airborne infection isolation room, bathroom, and anteroom of a ventilated patient with coronavirus disease 2019. Twenty-eight samples were negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid, possibly due to the patient being on a closed-circuit ventilator or the efficiency of the air exchanges in the room.
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Howard-Anderson J, Webster A, Goyal A, Vadnais DS, Kraft CS, Steinberg JP, Jacob JT. COVID-19 or common coronavirus? A cautionary tale in advanced diagnostics. ACTA ACUST UNITED AC 2020; 7:345-346. [PMID: 32710717 DOI: 10.1515/dx-2020-0093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jessica Howard-Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Andrew Webster
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Abhinav Goyal
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - David S Vadnais
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - James P Steinberg
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Jesse T Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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43
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Ransom EM, Burnham CAD, Jones L, Kraft CS, McDonald LC, Reinink AR, Young VB. Fecal Microbiota Transplantations: Where Are We, Where Are We Going, and What Is the Role of the Clinical Laboratory? Clin Chem 2020; 66:512-517. [PMID: 32232453 DOI: 10.1093/clinchem/hvaa021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 01/13/2020] [Indexed: 11/14/2022]
Affiliation(s)
- Eric M Ransom
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Lee Jones
- President and CEO, Rebiotix, A Ferring Company, Roseville, MN
| | - Colleen S Kraft
- Associate Professor, Department of Pathology and Laboratory Medicine, Department of Medicine, Division of Infectious Diseases, Emory University, Atlanta, GA
| | - L Clifford McDonald
- Associate Director for Science, Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, Atlanta, GA
| | - Andrew R Reinink
- Assistant Professor, Minneapolis VA Medical Center and University of Minnesota School of Medicine, Division of Gastroenterology, Hepatology, & Nutrition, Minneapolis, MN
| | - Vincent B Young
- Professor, Department of Internal Medicine/Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI
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Almulhim AM, Vellozzi-Averhoff CM, Howard-Anderson J, Babiker A, Kraft CS. Answer to November 2020 Photo Quiz. J Clin Microbiol 2020; 58:e00454-20. [PMID: 33087545 PMCID: PMC7587088 DOI: 10.1128/jcm.00454-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Abdulaziz M Almulhim
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | | | - Jessica Howard-Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
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45
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Steed DB, Wang T, Raheja D, Waldman AD, Babiker A, Dhere T, Kraft CS, Woodworth MH. Gram-Negative Taxa and Antimicrobial Susceptibility after Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection. mSphere 2020; 5:e00853-20. [PMID: 33055258 PMCID: PMC7565895 DOI: 10.1128/msphere.00853-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/08/2020] [Accepted: 09/20/2020] [Indexed: 12/15/2022] Open
Abstract
Fecal microbiota transplantation (FMT) has promising applications in reducing multidrug-resistant organism (MDRO) colonization and antibiotic resistance (AR) gene abundance. However, data on clinical microbiology results after FMT are limited. We examined the changes in antimicrobial susceptibility profiles in patients with Gram-negative infections in the year before and the year after treatment with FMT for recurrent Clostridioides difficile infection (RCDI). We also examined whether a history of FMT changed health care provider behavior with respect to culture ordering and antibiotic prescription. Medical records for RCDI patients who underwent FMT at Emory University between July 2012 and March 2017 were reviewed retrospectively. FMT-treated patients with Gram-negative culture data in the 1-year period preceding and the 1-year period following FMT were included. Demographic and clinical data were abstracted, including CDI history, frequency of Gram-negative cultures, microbiological results, and antibiotic prescription in response to positive cultures in the period following FMT. Twelve patients were included in this case series. We pooled data from infections at all body sites and found a decrease in the number of total and Gram-negative cultures post-FMT. We compared susceptibility profiles across taxa given the potential for horizontal transmission of AR elements and observed increased susceptibility to nitrofurantoin, trimethoprim-sulfamethoxazole, and the aminoglycosides. FMT did not drastically influence health care provider ordering of bacterial cultures or antibiotic prescribing practices. We observed a reduction in Gram-negative cultures and a trend toward increased antimicrobial susceptibility. This study supports further investigation of FMT as a means of improving antimicrobial susceptibility.IMPORTANCE Fecal microbiota transplantation (FMT), which is highly efficacious in treating recurrent C. difficile infection (RCDI), has a promising application in decolonization of multidrug-resistant organisms, reduction of antibiotic resistance gene abundance, and restoration of healthy intestinal microbiota. However, data representing clinical microbiology results after FMT are limited. We sought to characterize the differences in culture positivity and antimicrobial susceptibility profiles in patients with Gram-negative infections in the year before and the year after FMT for RCDI. Drawing on prior studies that had demonstrated the success of FMT in eradicating extraintestinal infections and the occurrence of patient-level interspecies transfer of resistance elements, we employed an agnostic analytic approach of reviewing the data irrespective of body site or species. In a small RCDI population, we observed an improvement in the antimicrobial susceptibility profile of Gram-negative bacteria following FMT, which supports further study of FMT as a strategy to combat antibiotic resistance.
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Affiliation(s)
| | - Tiffany Wang
- Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Alex D Waldman
- Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, Georgia, USA
| | - Tanvi Dhere
- Emory University School of Medicine, Department of Medicine, Division of Digestive Diseases, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Atlanta, Georgia, USA
- Emory University School of Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, Georgia, USA
| | - Michael H Woodworth
- Emory University School of Medicine, Department of Medicine, Division of Infectious Diseases, Atlanta, Georgia, USA
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46
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Wong MF, Matić Z, Campiglia GC, Zimring CM, Mumma JM, Kraft CS, Casanova LM, Durso FT, Walsh VL, Shah PY, Shane AL, Jacob JT, Dubose JR. Design Strategies for Biocontainment Units to Reduce Risk During Doffing of High-level Personal Protective Equipment. Clin Infect Dis 2020; 69:S241-S247. [PMID: 31517982 PMCID: PMC6743504 DOI: 10.1093/cid/ciz617] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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] [Indexed: 12/31/2022] Open
Abstract
Background Few data exist to guide the physical design of biocontainment units, particularly the doffing area. This can impact the contamination risk of healthcare workers (HCWs) during doffing of personal protective equipment (PPE). Methods In phase I of our study, we analyzed simulations of a standard patient care task with 56 trained HCWs focusing on doffing of high-level PPE. In phase II, using a rapid cycle improvement approach, we tested different balance aids and redesigned doffing area layouts with 38 students. In phase III, we tested 1 redesigned layout with an additional 10 trained HCWs. We assessed the effectiveness of design changes on improving the HCW performance (measured by occurrence and number of risky behaviors) and reducing the physical and cognitive load by comparing the results from phase I and phase III. Results The physical load was highest when participants were removing their shoe covers without any balance aid; the use of a chair required the lowest physical effort, followed by horizontal and vertical grab bars. In the revised design (phase III), the overall performance of participants improved. There was a significant decrease in the number of HCW risky behaviors (P = .004); 5 risky behaviors were eliminated and 2 others increased. There was a significant decrease in physical load when removing disposable shoe covers (P = .04), and participants reported a similar workload in the redesigned doffing layout (P = .43). Conclusions Through optimizing the design and layout of the doffing space, we reduced risky behaviors of HCWs during doffing of high-level PPE.
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Affiliation(s)
- Maria F Wong
- SimTigrate Design Lab, Georgia State University, and College of Design
| | - Zorana Matić
- SimTigrate Design Lab, Georgia State University, and College of Design
| | | | - Craig M Zimring
- SimTigrate Design Lab, Georgia State University, and College of Design
| | - Joel M Mumma
- School of Psychology, Georgia State University, and Georgia Institute of Technology
| | - Colleen S Kraft
- Division of Infectious Diseases, Georgia State University, and Department of Medicine.,Department of Pathology and Laboratory Medicine, Georgia State University, and Emory University School of Medicine
| | | | - Francis T Durso
- School of Psychology, Georgia State University, and Georgia Institute of Technology
| | - Victoria L Walsh
- Division of Infectious Diseases, Georgia State University, and Department of Medicine
| | - Puja Y Shah
- Division of Infectious Diseases, Georgia State University, and Department of Medicine
| | - Andi L Shane
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Georgia
| | - Jesse T Jacob
- Division of Infectious Diseases, Georgia State University, and Department of Medicine
| | - Jennifer R Dubose
- SimTigrate Design Lab, Georgia State University, and College of Design
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Mumma JM, Durso FT, Casanova LM, Erukunuakpor K, Kraft CS, Ray SM, Shane AL, Walsh VL, Shah PY, Zimring C, DuBose J, Jacob JT. Variability in the Duration and Thoroughness of Hand Hygiene. Clin Infect Dis 2020; 69:S221-S223. [PMID: 31517981 PMCID: PMC6743505 DOI: 10.1093/cid/ciz612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Indexed: 12/25/2022] Open
Abstract
We observed 354 hand hygiene instances across 41 healthcare workers doffing personal protective equipment at 4 hospital-based biocontainment units. We measured the duration and thoroughness of each hand hygiene instance. Both parameters varied substantially, with systematic differences between hospitals and differences between healthcare workers accounting for much of the variance.
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Affiliation(s)
- Joel M Mumma
- School of Psychology, Georgia Institute of Technology, Atlanta
| | - Francis T Durso
- School of Psychology, Georgia Institute of Technology, Atlanta
| | | | | | - Colleen S Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta.,Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta
| | - Susan M Ray
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta
| | - Andi L Shane
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta
| | - Victoria L Walsh
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta
| | - Puja Y Shah
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta
| | - Craig Zimring
- School of Architecture, Georgia Institute of Technology, Atlanta
| | - Jennifer DuBose
- School of Architecture, Georgia Institute of Technology, Atlanta
| | - Jesse T Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta
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Mumma JM, Durso FT, Casanova LM, Erukunuakpor K, Kraft CS, Ray SM, Shane AL, Walsh VL, Shah PY, Zimring C, DuBose J, Jacob JT. Common Behaviors and Faults When Doffing Personal Protective Equipment for Patients With Serious Communicable Diseases. Clin Infect Dis 2020; 69:S214-S220. [PMID: 31517977 PMCID: PMC6743503 DOI: 10.1093/cid/ciz614] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background The safe removal of personal protective equipment (PPE) can limit transmission of serious communicable diseases, but this process poses challenges to healthcare workers (HCWs). Methods We observed 41 HCWs across 4 Ebola treatment centers in Georgia doffing PPE for simulated patients with serious communicable diseases. Using human factors methodologies, we obtained the details, sequences, and durations of doffing steps; identified the ways each step can fail (failure modes [FMs]); quantified the riskiness of FMs; and characterized the workload of doffing steps. Results Eight doffing steps were common to all hospitals—removal of boot covers, gloves (outer and inner pairs), the outermost garment, the powered air purifying respirator (PAPR) hood, and the PAPR helmet assembly; repeated hand hygiene (eg, with hand sanitizer); and a final handwashing with soap and water. Across hospitals, we identified 256 FMs during the common doffing steps, 61 of which comprised 19 common FMs. Most of these common FMs were above average in their riskiness at each hospital. At all hospitals, hand hygiene, removal of the outermost garment, and removal of boot covers were above average in their overall riskiness. Measurements of workload revealed that doffing steps were often mentally demanding, and this facet of workload correlated most strongly with the effortfulness of a doffing step. Conclusions We systematically identified common points of concern in protocols for doffing high-level PPE. Addressing FMs related to hand hygiene and the removal of the outermost garment, boot covers, and PAPR hood could improve HCW safety when doffing high-level PPE. We identified ways that doffing protocols for high-level personal protective equipment may fail to protect healthcare workers. Hand hygiene, removing the outermost garment, boot covers, and respirator hood harbored the greatest risk and failed in similar ways across different hospitals.
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Affiliation(s)
- Joel M Mumma
- School of Psychology, Georgia Institute of Technology, Atlanta
| | - Francis T Durso
- School of Psychology, Georgia Institute of Technology, Atlanta
| | | | | | - Colleen S Kraft
- Division of Infectious Diseases, Atlanta Department of Medicine.,Department of Pathology and Laboratory Medicine, Atlanta Emory University School of Medicine
| | - Susan M Ray
- Division of Infectious Diseases, Atlanta Department of Medicine
| | - Andi L Shane
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta
| | | | - Puja Y Shah
- Division of Infectious Diseases, Atlanta Department of Medicine
| | - Craig Zimring
- School of Architecture, Georgia Institute of Technology, Atlanta
| | - Jennifer DuBose
- School of Architecture, Georgia Institute of Technology, Atlanta
| | - Jesse T Jacob
- Division of Infectious Diseases, Atlanta Department of Medicine
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Affiliation(s)
- Kari Broder
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Charles Myers
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Terri White
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Heather Jones
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - John Cardella
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eileen M Burd
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Charles E Hill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Colleen S Kraft
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
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Wells JR, Crozier I, Kraft CS, Sexton ME, Hill CE, Ribner BS, Bavari S, Palacios G, Pearce WA, Van Gelder R, Grossniklaus H, Cazares L, Zeng X, Shantha JG, Yeh S. Approach to Cataract Surgery in an Ebola Virus Disease Survivor with Prior Ocular Viral Persistence. Emerg Infect Dis 2020; 26:1553-1556. [PMID: 32568043 PMCID: PMC7323527 DOI: 10.3201/eid2607.191559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A 46-year-old patient with previously documented Ebola virus persistence in his ocular fluid, associated with severe panuveitis, developed a visually significant cataract. A multidisciplinary approach was taken to prevent and control infection. Ebola virus persistence was assessed before and during the operation to provide safe, vision-restorative phacoemulsification surgery.
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