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Park SY, Lindner MS, Brick K, Noll N, Ounit R, Noa LJ, Sabzwari R, Trible R, Sniffen JC, Roth P, Khan A, Rodriguez A, Sahra S, Davis MJ, Brar IS, Balasundaram G, Nolte FS, Blauwkamp TA, Perkins BA, Bercovici S. Detection of Mpox Virus Using Microbial Cell-Free DNA: The Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens. J Infect Dis 2024; 229:S144-S155. [PMID: 37824825 DOI: 10.1093/infdis/jiad452] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND The 2022 global outbreak of Monkeypox virus (MPXV) highlighted challenges with polymerase chain reaction detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing. METHODS Fifteen plasma samples from 12 case-patients were characterized through mcfDNA sequencing. Assay performance was confirmed through in silico inclusivity and exclusivity assessments. MPXV isolates were genotyped using mcfDNA, and phylodynamic information was imputed using publicly available sequences. RESULTS MPXV mcfDNA was detected in 12 case-patients. Mpox was not suspected in 5, with 1 having documented resolution of mpox >6 months previously. Six had moderate to severe mpox, supported by high MPXV mcfDNA concentrations; 4 died. In 7 case-patients, mcfDNA sequencing detected coinfections. Genotyping by mcfDNA sequencing identified 22 MPXV mutations at 10 genomic loci in 9 case-patients. Consistent with variation observed in the 2022 outbreak, 21 of 22 variants were G > A/C > T. Phylogenetic analyses imputed isolates to sublineages arising at different time points and from different geographic locations. CONCLUSIONS We demonstrate the potential of plasma mcfDNA sequencing to detect, quantify, and, for acute infections with high sequencing coverage, subtype MPXV using a single noninvasive test. Sequencing plasma mcfDNA may augment existing mpox testing in vulnerable patient populations or in patients with atypical symptoms or unrecognized mpox. Strain type information may supplement disease surveillance and facilitate tracking emerging pathogens.
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Affiliation(s)
- Sarah Y Park
- Medical Affairs, Karius, Inc, Redwood City, California
| | | | - Kevin Brick
- Analytics, Karius, Inc., Redwood City, California
| | | | - Rachid Ounit
- Analytics, Karius, Inc., Redwood City, California
| | - Luis J Noa
- Infectious Disease Section, AdventHealth Orlando, Florida
| | - Rabeeya Sabzwari
- Infectious Diseases, Edward Hines Jr Veterans Affairs Hospital, Hines, Illinois
| | | | | | - Prerana Roth
- Infectious Diseases, Prisma Health-Upstate, Greenville, South Carolina
| | - Amir Khan
- Infectious Diseases, Carle Foundation Hospital, Urbana, Illinois
| | | | - Syeda Sahra
- Department of Infectious Diseases, Oklahoma University Medical Center, Oklahoma City
| | - Michael J Davis
- Department of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN
| | - Inderjeet S Brar
- Infectious Diseases, Baptist Memorial Health Care, Memphis, Tennessee
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McFarland LV, Hecht G, Sanders ME, Goff DA, Goldstein EJC, Hill C, Johnson S, Kashi MR, Kullar R, Marco ML, Merenstein DJ, Millette M, Preidis GA, Quigley EMM, Reid G, Salminen S, Sniffen JC, Sokol H, Szajewska H, Tancredi DJ, Woolard K. Recommendations to Improve Quality of Probiotic Systematic Reviews With Meta-Analyses. JAMA Netw Open 2023; 6:e2346872. [PMID: 38064222 DOI: 10.1001/jamanetworkopen.2023.46872] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
Importance Systematic reviews and meta-analyses often report conflicting results when assessing evidence for probiotic efficacy, partially because of the lack of understanding of the unique features of probiotic trials. As a consequence, clinical decisions on the use of probiotics have been confusing. Objective To provide recommendations to improve the quality and consistency of systematic reviews with meta-analyses on probiotics, so evidence-based clinical decisions can be made with more clarity. Evidence Review For this consensus statement, an updated literature review was conducted (January 1, 2020, to June 30, 2022) to supplement a previously published 2018 literature search to identify areas where probiotic systematic reviews with meta-analyses might be improved. An expert panel of 21 scientists and physicians with experience on writing and reviewing probiotic reviews and meta-analyses was convened and used a modified Delphi method to develop recommendations for future probiotic reviews. Findings A total of 206 systematic reviews with meta-analysis components on probiotics were screened and representative examples discussed to determine areas for improvement. The expert panel initially identified 36 items that were inconsistently reported or were considered important to consider in probiotic meta-analyses. Of these, a consensus was reached for 9 recommendations to improve the quality of future probiotic meta-analyses. Conclusions and Relevance In this study, the expert panel reached a consensus on 9 recommendations that should promote improved reporting of probiotic systematic reviews with meta-analyses and, thereby, assist in clinical decisions regarding the use of probiotics.
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Affiliation(s)
- Lynne V McFarland
- McFarland Consulting, Seattle, Washington
- Public Health Reserve Corp, Seattle Washington
| | - Gail Hecht
- Division of Gastroenterology and Nutrition, Loyola University Chicago, Maywood, Illinois
| | - Mary E Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, Colorado
| | - Debra A Goff
- Ohio State University Wexner Medical Center, Ohio State University College of Pharmacy, Columbus
| | | | - Colin Hill
- International Scientific Association for Probiotics and Prebiotics, University College Cork, Ireland
| | - Stuart Johnson
- Stritch School of Medicine, Loyola University Medical Center, Chicago, Illinois
- Departments of Medicine and Research, Edward Hines Jr Veterans Affairs Hospital, Hines, Illinois
| | - Maryam R Kashi
- Department of Gastroenterology, AdventHealth Medical Group, Orlando, Florida
| | | | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis
| | - Daniel J Merenstein
- Research Programs Family Medicine, Department of Human Science, Georgetown University School of Health, Washington, DC
| | - Mathieu Millette
- Bio-K Plus, a Kerry Company, Laval, Quebec, Canada
- INRS-Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
| | - Geoffrey A Preidis
- Department of Pediatrics, Division of Gastroenterology, Hepatology, and Nutrition, Baylor College of Medicine and Texas Children's Hospital, Houston
| | - Eamonn M M Quigley
- Lynda K and David M. Underwood Center for Digestive Disorders, Houston Methodist Hospital and Weill Cornell Medical College, Houston, Texas
| | - Gregor Reid
- St Joseph's Hospital, Lawson Health Research Institute, London, Ontario, Canada
| | - Seppo Salminen
- Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Jason C Sniffen
- Infectious Disease Consultants, Altamonte Springs, Florida
- Department of Internal Medicine, Infectious Diseases and Tropical Medicine Section, University of South Florida, Tampa
| | - Harry Sokol
- Gastroenterology Department, Centre de Recherche Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Sorbonne University, INSERM, Paris, France
- Paris Centre for Microbiome Medicine FHU, Paris, France
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche, Micalis & AgroParisTech, Jouy en Josas, France
| | - Hania Szajewska
- Department of Paediatrics, Medical University of Warsaw, Warsaw, Poland
| | - Daniel J Tancredi
- Department of Pediatrics, University of California, Davis School of Medicine, Sacramento
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Maziade PJ, Ship N, Sniffen JC, Goldstein EJC. Enhanced Clostridioides difficile infection prevention with a pharmacy-controlled policy that adds a three-strain Lactobacillus probiotic concomitantly to antibiotic therapy. Clin Infect Dis 2021; 73:1524-1527. [PMID: 33966076 PMCID: PMC8528394 DOI: 10.1093/cid/ciab414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Indexed: 01/13/2023] Open
Abstract
When 70% of antibiotic users took a 3-strain Lactobacillus probiotic preparation the hospital-wide rate of healthcare-associated Clostridioides difficile infection improved significantly. The incidence of C. difficile infection for those taking the probiotic along with multiple antibiotics or a single high-risk antibiotic was decreased by at least half.
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Affiliation(s)
- Pierre-Jean Maziade
- Microbiology and Infectious Diseases, Centre Intégré de Santé et de Services Sociaux de Lanaudière, Terrebonne, Canada
| | - Noam Ship
- Research and Development, Bio-K Plus International Inc., Laval, Canada
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Sniffen JC, McFarland LV, Evans CT, Goldstein EJC. Choosing an appropriate probiotic product for your patient: An evidence-based practical guide. PLoS One 2018; 13:e0209205. [PMID: 30586435 PMCID: PMC6306248 DOI: 10.1371/journal.pone.0209205] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [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: 08/02/2018] [Accepted: 11/30/2018] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Clinicians and patients face a daunting task when choosing the most appropriate probiotic for their specific needs. Available preparations encompass a diverse and continuously expanding product base, with most available products lacking evidence-based trials that support their use. Even when evidence exists, not all probiotic products are equally effective for all disease prevention or treatment indications. At this point in time, drug regulatory agencies offer limited assistance with regard to guidance and oversight in most countries, including the U.S. METHODS We reviewed the current medical literature and sources on the internet to survey the types of available probiotic products and to determine which probiotics had evidence-based efficacy data. Standard medical databases from inception to June 2018 were searched and discussions with experts in the field were conducted. We graded the strength of the evidence for probiotics having multiple, randomized controlled trials and developed a guide for the practical selection of current probiotic products for specific uses. RESULTS We found the efficacy of probiotic products is both strain-specific and disease-specific. Important factors involved in choosing the appropriate probiotic include matching the strain(s) with the targeted disease or condition, type of formulation, dose used and the source (manufacturing quality control and shelf-life). While we found many probiotic products lacked confirmatory trials, we found sufficient evidence for 22 different types of probiotics from 249 trials to be included. For example, several types of probiotics had strong evidence for the prevention of antibiotic-associated diarrhea [Saccharomyces boulardii I-745, a three-strain mixture (Lactobacillus acidophilus CL1285, L. casei Lbc80r, L. rhamnosus CLR2) and L. casei DN114001]. Strong evidence was also found for four types of probiotics for the prevention of a variety of other diseases/conditions (enteral-feed associated diarrhea, travellers' diarrhea, necrotizing enterocolits and side-effects associated with H. pylori treatments. The evidence was most robust for the treatment of pediatric acute diarrhea based on 59 trials (7 types of probiotics have strong efficacy), while an eight-strain multi-strain mixture showed strong efficacy for inflammatory bowel disease and two types of probiotics had strong efficacy for irritable bowel disease. Of the 22 types of probiotics reviewed, 15 (68%) had strong-moderate evidence for efficacy for at least one type of disease. CONCLUSION The choice of an appropriate probiotic is multi-factored, based on the mode and type of disease indication and the specific efficacy of probiotic strain(s), as well as product quality and formulation. TRIAL REGISTRATION This review was registered with PROSPERO: CRD42018103979.
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Affiliation(s)
- Jason C. Sniffen
- Department of Internal Medicine, Infectious Disease Section, Florida Hospital Orlando, Orlando, FL, United States of America
| | - Lynne V. McFarland
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington Medical Center, Seattle, Washington United States of America
| | - Charlesnika T. Evans
- Department of Preventive Medicine and Center for Healthcare Studies, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States of America
- Department of Veterans Affairs (VA), Center of Innovation of Complex Chronic Healthcare (CINCCH), Edward Hines, Jr. VA Hospital, Hines, IL, United States of America
| | - Ellie J. C. Goldstein
- RM Alden Research Laboratory and David Geffen School of Medicine at UCLA, Los Angeles, CA, United States of America
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Goldstein EJC, Johnson SJ, Maziade PJ, Evans CT, Sniffen JC, Millette M, McFarland LV. Probiotics and prevention of Clostridium difficile infection. Anaerobe 2016; 45:114-119. [PMID: 27988389 DOI: 10.1016/j.anaerobe.2016.12.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 10/30/2016] [Revised: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 12/16/2022]
Abstract
The role of probiotics as adjunctive measures in the prevention of Clostridium difficile infection (CDI) has been controversial. However, a growing body of evidence has suggested that they have a role in primary prevention of CDI. Elements of this controversy are reviewed and the proposed mechanisms of action, the value and cost effectiveness of probiotics are addressed with a focus on three agents, Saccharomyces boulardii, Lactobacillus rhamnosus GG and the combination of Lactobacillus acidophilus CL1285, Lactobacillus casei LBC80R, Lactobacillus rhamnosus CLR2 (Bio-K+).
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Affiliation(s)
- E J C Goldstein
- R M Alden Research Laboratory, Santa Monica, CA, USA; UCLA School of Medicine, Los Angeles, CA, USA.
| | | | | | - C T Evans
- Department of Preventive Medicine and Center for Healthcare Studies, Northwestern University, Chicago, IL, USA; Edward Hines Jr VA Hospital, Chicago, IL, USA
| | | | - M Millette
- Bio-K Plus International Inc., Laval, Canada
| | - L V McFarland
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
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Sniffen JC. Treatment of Helicobacter pylori infection in peptic ulcer disease. N Engl J Med 1996; 334:473-4. [PMID: 8552164 DOI: 10.1056/nejm199602153340717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Abstract
1. The effect of extracellularly applied pentachlorophenol (PCP) was studied on the membrane potential (Vm) and Ca2+ uptake in isolated single skeletal muscle cells of Balanus nubilus. 2. When compared with the controls, 0.1 mM PCP induced a significant (P < 0.05) increase in Ca2+ uptake accompanied by membrane depolarization (9 mV at 45 min incubation). This depolarization was reduced by 11% of extracellular Ca2+ (Cao2+) was replaced by Tris+ and by 50% if extracellular Na+ was also replaced by Tris+. 3. The Ca2+ channel blocker, verapamil (0.1 mM), completely inhibited the PCP-induced Ca2+ uptake as well as the membrane depolarization either in the absence or presence of Cao2+. Experiments on voltage-clamped cells show that the PCP-induced Ca2+ uptake was independent of the PCP-induced depolarization. 4. The results indicate that PCP induces activation of a verapamil-sensitive Ca2+ influx pathway (presumably L-type Ca2+ channels) independent of Vm. The permeation of Ca2+, Na+ and Tris+ through this pathway produces membrane depolarization in the following order of effectiveness: Ca2+ > Na+ > Tris+.
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Affiliation(s)
- J C Nwoga
- Department of Biology, Florida A & M University, Tallahassee 32307, USA
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