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Torres HM, Marino J, Simon MS, Singh HK, Westblade LF, Calfee DP. High touch surface bioburden associated with the use of disinfectants with and without continuously active disinfection in ambulatory care settings. Infect Control Hosp Epidemiol 2024:1-3. [PMID: 38374787 DOI: 10.1017/ice.2024.27] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
A quaternary ammonium and alcohol-based disinfectant with reported continuous activity demonstrated reduced microbial buildup on surfaces over time compared to routine disinfectants without continuous activity in in vitro and hospital studies. We compared these disinfectants in ambulatory settings and found no difference in bioburden on high-touch surfaces over time.
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Affiliation(s)
- Heidi M Torres
- Weill Cornell Medicine, New York, NY, USA
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | | | - Matthew S Simon
- Weill Cornell Medicine, New York, NY, USA
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | - Harjot K Singh
- Weill Cornell Medicine, New York, NY, USA
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | - Lars F Westblade
- Weill Cornell Medicine, New York, NY, USA
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | - David P Calfee
- Weill Cornell Medicine, New York, NY, USA
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
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2
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Zhang K, Potter RF, Marino J, Muenks CE, Lammers MG, Dien Bard J, Dingle TC, Humphries R, Westblade LF, Burnham CAD, Dantas G. Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus. mSystems 2023; 8:e0069723. [PMID: 38051037 PMCID: PMC10734486 DOI: 10.1128/msystems.00697-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCCmec configurations as well as phage elements in S. saprophyticus, which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.
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Affiliation(s)
- Kailun Zhang
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Robert F. Potter
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jamie Marino
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carol E. Muenks
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Matthew G. Lammers
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tanis C. Dingle
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Romney Humphries
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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3
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Khan I, Wu S, Hudson A, Hughes C, Stryjniak G, Westblade LF, Satlin MJ, Tedrow N, Uhlemann AC, Kraft C, Dadhania DM, Silberzweig J, De Vlaminck I, Li C, Srivatana V, Lee JR. A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients. Kidney360 2023; 4:1419-1429. [PMID: 37642987 PMCID: PMC10615377 DOI: 10.34067/kid.0000000000000249] [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] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023]
Abstract
Key Points Staphylococcus , Corynebacterium , Streptococcus , and Anaerococcus are the most common genera in the anterior nares. The nasal abundance of Staphylococcus is inversely correlated with the nasal abundance of Corynebacterium . Peritoneal dialysis patients have a distinctly diverse representation of Staphylococcus and Streptococcus in their anterior nares. Background The nasal passages harbor both commensal and pathogenic bacteria that can be associated with infectious complications. The nasal microbiome in peritoneal dialysis (PD) patients, however, has not been well characterized. In this study, we sought to characterize the anterior nasal microbiota in PD patients and assess its association with PD peritonitis. Methods In this study, we recruited 32 PD patients, 37 kidney transplant (KTx) recipients, and 22 living donor/healthy control (HC) participants and collected their anterior nasal swabs at a single point in time. We followed the PD patients for future development of peritonitis. We performed 16S ribosomal RNA (rRNA) gene sequencing of the V4–V5 hypervariable region to determine the nasal microbiota. We compared nasal abundance of common genera among the three groups using Wilcoxon rank-sum test with Benjamini–Hochberg adjustment. DESeq2 was also used to compare the groups at the amplicon sequence variant levels. Results In the entire cohort, the most abundant genera in the nasal microbiota included Staphylococcus , Corynebacterium , Streptococcus , and Anaerococcus . Correlational analyses revealed a significant inverse relationship between the nasal abundance of Staphylococcus and that of Corynebacterium . PD patients have a higher nasal abundance of Streptococcus than KTx recipients and HC participants. PD patients have a more diverse representation of Staphylococcus and Streptococcus than KTx recipients and HC participants. PD patients who concurrently have or who developed future Staphylococcus peritonitis had a numerically higher nasal abundance of Staphylococcus than PD patients who did not develop Staphylococcus peritonitis. Conclusions We find a distinct nasal microbiota signature in PD patients compared with KTx recipients and HC participants. Given the potential relationship between the nasal pathogenic bacteria and infectious complications, further studies are needed to define the nasal microbiota associated with these infectious complications and to conduct studies on the manipulation of the nasal microbiota to prevent such complications.
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Affiliation(s)
- Iman Khan
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Sylvia Wu
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Anika Hudson
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Clayton Hughes
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Gabriel Stryjniak
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Michael J. Satlin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Nicholas Tedrow
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Vagelos College of Physicians and Surgeons Columbia University, New York, New York
| | - Colleen Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, New York, New York
| | - Darshana M. Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
- Department of Transplantation Medicine, New York Presbyterian Hospital–Weill Cornell Medical Center, New York, New York
| | - Jeffrey Silberzweig
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
- The Rogosin Institute, New York, New York
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Vesh Srivatana
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
- The Rogosin Institute, New York, New York
| | - John Richard Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
- Department of Transplantation Medicine, New York Presbyterian Hospital–Weill Cornell Medical Center, New York, New York
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Gould CV, Free RJ, Bhatnagar J, Soto RA, Royer TL, Maley WR, Moss S, Berk MA, Craig-Shapiro R, Kodiyanplakkal RPL, Westblade LF, Muthukumar T, Puius YA, Raina A, Hadi A, Gyure KA, Trief D, Pereira M, Kuehnert MJ, Ballen V, Kessler DA, Dailey K, Omura C, Doan T, Miller S, Wilson MR, Lehman JA, Ritter JM, Lee E, Silva-Flannery L, Reagan-Steiner S, Velez JO, Laven JJ, Fitzpatrick KA, Panella A, Davis EH, Hughes HR, Brault AC, St George K, Dean AB, Ackelsberg J, Basavaraju SV, Chiu CY, Staples JE. Transmission of yellow fever vaccine virus through blood transfusion and organ transplantation in the USA in 2021: report of an investigation. Lancet Microbe 2023; 4:e711-e721. [PMID: 37544313 DOI: 10.1016/s2666-5247(23)00170-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND In 2021, four patients who had received solid organ transplants in the USA developed encephalitis beginning 2-6 weeks after transplantation from a common organ donor. We describe an investigation into the cause of encephalitis in these patients. METHODS From Nov 7, 2021, to Feb 24, 2022, we conducted a public health investigation involving 15 agencies and medical centres in the USA. We tested various specimens (blood, cerebrospinal fluid, intraocular fluid, serum, and tissues) from the organ donor and recipients by serology, RT-PCR, immunohistochemistry, metagenomic next-generation sequencing, and host gene expression, and conducted a traceback of blood transfusions received by the organ donor. FINDINGS We identified one read from yellow fever virus in cerebrospinal fluid from the recipient of a kidney using metagenomic next-generation sequencing. Recent infection with yellow fever virus was confirmed in all four organ recipients by identification of yellow fever virus RNA consistent with the 17D vaccine strain in brain tissue from one recipient and seroconversion after transplantation in three recipients. Two patients recovered and two patients had no neurological recovery and died. 3 days before organ procurement, the organ donor received a blood transfusion from a donor who had received a yellow fever vaccine 6 days before blood donation. INTERPRETATION This investigation substantiates the use of metagenomic next-generation sequencing for the broad-based detection of rare or unexpected pathogens. Health-care workers providing vaccinations should inform patients of the need to defer blood donation for at least 2 weeks after receiving a yellow fever vaccine. Despite mitigation strategies and safety interventions, a low risk of transfusion-transmitted infections remains. FUNDING US Centers for Disease Control and Prevention (CDC), the Biomedical Advanced Research and Development Authority, and the CDC Epidemiology and Laboratory Capacity Cooperative Agreement for Infectious Diseases.
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Affiliation(s)
- Carolyn V Gould
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA.
| | - Rebecca J Free
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Julu Bhatnagar
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Raymond A Soto
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA; Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tricia L Royer
- Division of Infectious Diseases, Department of Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Warren R Maley
- Division of Transplantation, Department of Surgery, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Sean Moss
- Division of Infectious Diseases, Department of Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Matthew A Berk
- Department of Neurology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, USA
| | - Rebecca Craig-Shapiro
- Division of Transplant Surgery, Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | | | - Lars F Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yoram A Puius
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, New York, NY, USA
| | - Amresh Raina
- Section of Advanced Heart Failure, Transplant, Mechanical Circulatory Support, and Pulmonary Hypertension, Cardiovascular Institute, Allegheny General Hospital, Allegheny Health Network, Pittsburgh, PA, USA
| | - Azam Hadi
- Section of Advanced Heart Failure, Transplant, Mechanical Circulatory Support, and Pulmonary Hypertension, Cardiovascular Institute, Allegheny General Hospital, Allegheny Health Network, Pittsburgh, PA, USA
| | - Kymberly A Gyure
- Department of Pathology and Laboratory Medicine, Allegheny General Hospital, Allegheny Health Network, Pittsburgh, PA, USA
| | - Danielle Trief
- Department of Ophthalmology, Edward S Harkness Eye Institute, Columbia University Irving Medical Center, New York, NY, USA
| | - Marcus Pereira
- Transplant Infectious Disease Program, Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Matthew J Kuehnert
- Office of the Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Hackensack Meridian School of Medicine, Hackensack, NJ, USA
| | - Vennus Ballen
- Bureau of Public Health Clinics, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Debra A Kessler
- Medical Programs and Services, New York Blood Center, New York, NY, USA
| | - Kimberly Dailey
- Division of Infectious Disease and Epidemiology, West Virginia Department of Health, Charleston, WV, USA
| | - Charles Omura
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Thuy Doan
- Department of Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer A Lehman
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Jana M Ritter
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Elizabeth Lee
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Luciana Silva-Flannery
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sarah Reagan-Steiner
- Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jason O Velez
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Janeen J Laven
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Kelly A Fitzpatrick
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Amanda Panella
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Emily H Davis
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Holly R Hughes
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Aaron C Brault
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA; Department of Biomedical Science, Graduate School of Public Health, State University of New York at Albany, Albany, NY, USA
| | - Amy B Dean
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Joel Ackelsberg
- Bureau of Communicable Diseases, New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Sridhar V Basavaraju
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - J Erin Staples
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO, USA
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5
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Potter RF, Zhang K, Reimler B, Marino J, Muenks CE, Alvarado K, Wallace MA, Westblade LF, McElvania E, Yarbrough ML, Hunstad DA, Dantas G, Burnham CAD. Uncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape. mSystems 2023; 8:e0015923. [PMID: 37341494 PMCID: PMC10469602 DOI: 10.1128/msystems.00159-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/07/2023] [Indexed: 06/22/2023] Open
Abstract
Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of P. mirabilis genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related P. mirabilis genomes, and pan-genome annotation to identify genes of interest not present in the model P. mirabilis strain HI4320. Within our cohort, Proteus is composed of 10 named species and 5 uncharacterized genomospecies. P. mirabilis can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The P. mirabilis pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain P. mirabilis HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome. IMPORTANCE Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on P. mirabilis, but similar to other Gram-negative bacteria, P. mirabilis has a mosaic genome with a linkage between phylogenetic position and accessory genome content. P. mirabilis encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection.
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Affiliation(s)
- Robert F. Potter
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kailun Zhang
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Ben Reimler
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jamie Marino
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Carol E. Muenks
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kelly Alvarado
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Erin McElvania
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, Illinois, USA
| | - Melanie L. Yarbrough
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - David A. Hunstad
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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6
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Khan I, Wu S, Hudson A, Hughes C, Stryjniak G, Westblade LF, Satlin MJ, Tedrow N, Uhlemann AC, Kraft C, Dadhania DM, Silberzweig J, De Vlaminck I, Li C, Srivatana V, Lee JR. A Distinct Nasal Microbiota Signature in Peritoneal Dialysis Patients. medRxiv 2023:2023.02.23.23286379. [PMID: 36865147 PMCID: PMC9980262 DOI: 10.1101/2023.02.23.23286379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Rationale & Objective The nasal passages harbor both commensal and pathogenic bacteria. In this study, we sought to characterize the anterior nasal microbiota in PD patients using 16S rRNA gene sequencing. Study Design Cross-sectional. Setting & Participants We recruited 32 PD patients, 37 kidney transplant (KTx) recipients, 22 living donor/healthy control (HC) participants and collected anterior nasal swabs at a single point in time. Predictors We performed 16S rRNA gene sequencing of the V4-V5 hypervariable region to determine the nasal microbiota. Outcomes Nasal microbiota profiles were determined at the genus level as well as the amplicon sequencing variant level. Analytical Approach We compared nasal abundance of common genera among the 3 groups using Wilcoxon rank sum testing with Benjamini-Hochberg adjustment. DESeq2 was also utilized to compare the groups at the ASV levels. Results In the entire cohort, the most abundant genera in the nasal microbiota included: Staphylococcus, Corynebacterium, Streptococcus , and Anaerococcus . Correlational analyses revealed a significant inverse relationship between the nasal abundance of Staphylococcus and that of Corynebacterium . PD patients have a higher nasal abundance of Streptococcus than KTx recipients and HC participants. PD patients have a more diverse representation of Staphylococcus and Streptococcus than KTx recipients and HC participants. PD patients who concurrently have or who developed future Staphylococcus peritonitis had a numerically higher nasal abundance of Staphylococcus than PD patients who did not develop Staphylococcus peritonitis. Limitations 16S RNA gene sequencing provides taxonomic information to the genus level. Conclusions We find a distinct nasal microbiota signature in PD patients compared to KTx recipients and HC participants. Given the potential relationship between the nasal pathogenic bacteria and infectious complications, further studies are needed to define the nasal microbiota associated with these infectious complications and to conduct studies on the manipulation of the nasal microbiota to prevent such complications.
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Affiliation(s)
- Iman Khan
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sylvia Wu
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Anika Hudson
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Clayton Hughes
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Gabriel Stryjniak
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J. Satlin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Tedrow
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Vagelos College of Physicians and Surgeons Columbia University, New York, NY
| | - Colleen Kraft
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, New York, NY
| | - Darshana M. Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital–Weill Cornell Medical Center, New York, NY, USA
| | - Jeffrey Silberzweig
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- The Rogosin Institute, New York, NY, USA
| | - Iwijn De Vlaminck
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Vesh Srivatana
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- The Rogosin Institute, New York, NY, USA
| | - John Richard Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Transplantation Medicine, New York Presbyterian Hospital–Weill Cornell Medical Center, New York, NY, USA
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7
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Satlin MJ, Chen L, Gomez-Simmonds A, Marino J, Weston G, Bhowmick T, Seo SK, Sperber SJ, Kim AC, Eilertson B, Derti S, Jenkins SG, Levi MH, Weinstein MP, Tang YW, Hong T, Juretschko S, Hoffman KL, Walsh TJ, Westblade LF, Uhlemann AC, Kreiswirth BN. Impact of a Rapid Molecular Test for Klebsiella pneumoniae Carbapenemase and Ceftazidime-Avibactam Use on Outcomes After Bacteremia Caused by Carbapenem-Resistant Enterobacterales. Clin Infect Dis 2022; 75:2066-2075. [PMID: 35522019 PMCID: PMC10200298 DOI: 10.1093/cid/ciac354] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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] [Received: 10/19/2021] [Revised: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Patients with bacteremia due to carbapenem-resistant Enterobacterales (CRE) experience delays until appropriate therapy and high mortality rates. Rapid molecular diagnostics for carbapenemases and new β-lactam/β-lactamase inhibitors may improve outcomes. METHODS We conducted an observational study of patients with CRE bacteremia from 2016 to 2018 at 8 New York and New Jersey medical centers and assessed center-specific clinical microbiology practices. We compared time to receipt of active antimicrobial therapy and mortality between patients whose positive blood cultures underwent rapid molecular testing for the Klebsiella pneumoniae carbapenemase (KPC) gene (blaKPC) and patients whose cultures did not undergo this test. CRE isolates underwent antimicrobial susceptibility testing by broth microdilution and carbapenemase profiling by whole-genome sequencing. We also assessed outcomes when ceftazidime-avibactam and polymyxins were used as targeted therapies. RESULTS Of 137 patients with CRE bacteremia, 89 (65%) had a KPC-producing organism. Patients whose blood cultures underwent blaKPC PCR testing (n = 51) had shorter time until receipt of active therapy (median: 24 vs 50 hours; P = .009) compared with other patients (n = 86) and decreased 14-day (16% vs 37%; P = .007) and 30-day (24% vs 47%; P = .007) mortality. blaKPC PCR testing was associated with decreased 30-day mortality (adjusted odds ratio: .37; 95% CI: .16-.84) in an adjusted model. The 30-day mortality rate was 10% with ceftazidime-avibactam monotherapy and 31% with polymyxin monotherapy (P = .08). CONCLUSIONS In a KPC-endemic area, blaKPC PCR testing of positive blood cultures was associated with decreased time until appropriate therapy and decreased mortality for CRE bacteremia, and ceftazidime-avibactam is a reasonable first-line therapy for these infections.
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Affiliation(s)
- Michael J Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Angela Gomez-Simmonds
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jamie Marino
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Gregory Weston
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Tanaya Bhowmick
- Division of Allergy, Immunology, and Infectious Diseases, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Susan K Seo
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Steven J Sperber
- Division of Infectious Diseases, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
- Division of Infectious Diseases, Department of Medicine, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Angela C Kim
- Division of Infectious Diseases, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA
| | - Brandon Eilertson
- Division of Infectious Diseases, Department of Medicine, State University of New York Downstate, Brooklyn, New York, USA
| | - Sierra Derti
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Stephen G Jenkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Michael H Levi
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Melvin P Weinstein
- Division of Allergy, Immunology, and Infectious Diseases, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tao Hong
- Department of Pathology, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | | | - Katherine L Hoffman
- Division of Biostatistics, Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Thomas J Walsh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
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8
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Choi JJ, McCarthy MW, Meltzer KK, Cornelius-Schecter A, Jabri A, Reshetnyak E, Banerjee S, Westblade LF, Mehta S, Simon MS, Zhao Z, Glesby MJ. The Diagnostic Accuracy Of Procalcitonin for Urinary Tract Infection in Hospitalized Older Adults: a Prospective Study. J Gen Intern Med 2022; 37:3663-3669. [PMID: 34997392 PMCID: PMC8741546 DOI: 10.1007/s11606-021-07265-8] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The diagnosis of urinary tract infection (UTI) is challenging among hospitalized older adults, particularly among those with altered mental status. OBJECTIVE To determine the diagnostic accuracy of procalcitonin (PCT) for UTI in hospitalized older adults. DESIGN We performed a prospective cohort study of older adults (≥65 years old) admitted to a single hospital with evidence of pyuria on urinalysis. PCT was tested on initial blood samples. The reference standard was a clinical definition that included the presence of a positive urine culture and any symptom or sign of infection referable to the genitourinary tract. We also surveyed the treating physicians for their clinical judgment and performed expert adjudication of cases for the determination of UTI. PARTICIPANTS Two hundred twenty-nine study participants at a major academic medical center. MAIN MEASURES We calculated the area under the receiver operating characteristic curve (AUC) of PCT for the diagnosis of UTI. KEY RESULTS In this study cohort, 61 (27%) participants met clinical criteria for UTI. The median age of the overall cohort was 82.6 (IQR 74.9-89.7) years. The AUC of PCT for the diagnosis of UTI was 0.56 (95% CI, 0.46-0.65). A series of sensitivity analyses on UTI definition, which included using a decreased threshold for bacteriuria, the treating physicians' clinical judgment, and independent infectious disease specialist adjudication, confirmed the negative result. CONCLUSIONS Our findings demonstrate that PCT has limited value in the diagnosis of UTI among hospitalized older adults. Clinicians should be cautious using PCT for the diagnosis of UTI in hospitalized older adults.
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Affiliation(s)
- Justin J Choi
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, 420 East 70th Street, LH-355, New York, NY, 10021, USA.
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA.
| | - Matthew W McCarthy
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, 420 East 70th Street, LH-355, New York, NY, 10021, USA
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | - Kerry K Meltzer
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | | | - Assem Jabri
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, 420 East 70th Street, LH-355, New York, NY, 10021, USA
| | - Evgeniya Reshetnyak
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, 420 East 70th Street, LH-355, New York, NY, 10021, USA
| | - Samprit Banerjee
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Division of Nutritional Sciences, College of Human Ecology, Cornell University, Ithaca, NY, USA
| | - Matthew S Simon
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marshall J Glesby
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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9
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Satlin MJ, Chen L, Douglass C, Hovan M, Davidson E, Soave R, La Spina M, Gomez-Arteaga A, van Besien K, Mayer S, Phillips A, Hsu JM, Malherbe R, Small CB, Jenkins SG, Westblade LF, Kreiswirth BN, Walsh TJ. Reply to Caldwell et al. Clin Infect Dis 2022; 75:180-181. [PMID: 34864913 PMCID: PMC9402634 DOI: 10.1093/cid/ciab1001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michael J Satlin
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Claire Douglass
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - Michael Hovan
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - Emily Davidson
- Cooper Medical School of Rowan University, Camden, New Jersey, USA
| | - Rosemary Soave
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Marisa La Spina
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - Alexandra Gomez-Arteaga
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USAand
| | - Koen van Besien
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USAand
| | - Sebastian Mayer
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USAand
| | - Adrienne Phillips
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USAand
| | - Jing Mei Hsu
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York, USAand
| | | | - Catherine B Small
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Stephen G Jenkins
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F Westblade
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Thomas J Walsh
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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10
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Kubiak JM, Hovan M, Davidson E, Douglass C, Burgos K, Walsh TJ, Westblade LF, Satlin MJ. Comparison between Perianal Swab and Stool Specimens for Detecting Colonization with Extended-Spectrum Beta-Lactamase-Producing and Fluoroquinolone-Resistant Enterobacterales. J Clin Microbiol 2022; 60:e0023422. [PMID: 35695506 PMCID: PMC9297816 DOI: 10.1128/jcm.00234-22] [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: 02/14/2022] [Accepted: 05/20/2022] [Indexed: 12/15/2022] Open
Abstract
Stool specimens are frequently used to detect gastrointestinal tract colonization with antimicrobial-resistant enteric bacteria, but they cannot be rapidly collected. Perianal swab specimens can be collected more quickly and efficiently, but data evaluating their suitability as a specimen type for this purpose are sparse. We performed selective culture for extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) and fluoroquinolone-resistant Enterobacterales (FQRE) using paired perianal swab and stool specimens that were collected within 1 day of each other from hematopoietic cell transplant recipients and patients with acute leukemia. Nineteen (7.6%) of 251 stool specimens yielded ESBL-E and 64 (26%) of 246 stool specimens yielded FQRE. The positive percent agreement of perianal swab specimens compared to stool specimens was 95% (18/19; 95% confidence interval [CI], 74% to 100%) for detecting ESBL-E and 95% (61/64; 95% CI, 87% to 99%) for detecting FQRE. The concordance between specimen types was 98% (95% CI, 97% to 100%). Perianal swabs are a reliable specimen type for surveillance of the gastrointestinal tract for ESBL-E and FQRE.
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Affiliation(s)
- Jeffrey M. Kubiak
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA
| | - Michael Hovan
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Emily Davidson
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Claire Douglass
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Kevin Burgos
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Thomas J. Walsh
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Michael J. Satlin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
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11
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Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Marrero Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. J Clin Microbiol 2022; 60:e0060022. [PMID: 35582905 PMCID: PMC9199403 DOI: 10.1128/jcm.00600-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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] [Indexed: 12/21/2022] Open
Abstract
Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
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Affiliation(s)
- Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - David R. Peaper
- Department of Laboratory Medicine, Yale Universitygrid.47100.32, New Haven, Connecticut, USA
| | - Brendan J. Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Frederic Bushman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Andrew Marques
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Hriju Adhikari
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Zheng Jin Tu
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Rebecca Marrero Rolon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicinegrid.471410.7, New York, New York, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicinegrid.471410.7, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicinegrid.471410.7, New York, New York, USA
| | - Daniel A. Green
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Gregory J. Berry
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Fann Wu
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Medini K. Annavajhala
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Bijal A. Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
| | - N. Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Robert T. Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale Universitygrid.47100.32, New Haven, Connecticut, USA
| | | | - Daniel D. Rhoads
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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12
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Wulff RT, Qiu Y, Wu C, Calfee DP, Singh HK, Hatch I, Steel PAD, Scofi JE, Westblade LF, Cushing MM. Laboratory Interventions to Eliminate Unnecessary Rapid COVID-19 Testing During a Reagent Shortage. Am J Clin Pathol 2022; 158:401-408. [PMID: 35648100 PMCID: PMC9213858 DOI: 10.1093/ajcp/aqac063] [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: 02/02/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives In the fall of 2020, US medical centers were running out of rapid coronavirus disease 2019 (COVID-19) tests. The aim of this study is to evaluate the impact of an intervention to eliminate rapid test misutilization and to quantify the effect of the countermeasures to control rapid test ordering using a test utilization dashboard. Methods Interventions were made to preserve a severely limited supply of rapid diagnostic tests based on real-time analysis of a COVID-19 test utilization dashboard. This study is a retrospective observational study evaluating pre- and postintervention rates of appropriate rapid test use, reporting times, and cost/savings of resources used. Results This study included 14,462 severe acute respiratory syndrome coronavirus 2 reverse transcriptase polymerase chain reaction tests ordered during the study period. After the intervention, there was a 27.3% decrease in nonconforming rapid tests. Rapid test reporting time from laboratory receipt decreased by 1.47 hours. The number of days of rapid test inventory on hand increased by 39 days. Conclusions Performing diagnostic test stewardship, informed by real-time review of a test utilization dashboard, was associated with significantly improved appropriate utilization of rapid diagnostic COVID-19 tests, improved reporting times, implied cost savings, and improved reagent inventory on hand, which facilitated the management of scarce resources during a pandemic.
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Affiliation(s)
- Regina T Wulff
- Department of Pathology and Laboratory Medicine , New York, NY, USA
| | - Yuqing Qiu
- Department of Population Health Sciences , New York, NY, USA
| | - Caroline Wu
- Department of Information Technology Business Solutions, NewYork-Presbyterian Hospital , New York, NY, USA
| | | | | | - Ian Hatch
- Department of Pathology and Laboratory Medicine , New York, NY, USA
| | | | - Jean E Scofi
- Department of Emergency Medicine , New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY, USA
| | - Melissa M Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine , New York, NY, USA
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13
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Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Rolon RM, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. medRxiv 2022:2022.04.25.22274187. [PMID: 35547854 PMCID: PMC9094110 DOI: 10.1101/2022.04.25.22274187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
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14
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O'Leary MK, Sundaram V, LiPuma JJ, Dörr T, Westblade LF, Alabi CA. Mechanism of Action and Resistance Evasion of an Antimicrobial Oligomer against Multidrug-Resistant Gram-Negative Bacteria. ACS Appl Bio Mater 2022; 5:1159-1168. [PMID: 35167257 DOI: 10.1021/acsabm.1c01217] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The last resort for treating multidrug-resistant (MDR) Pseudomonas aeruginosa and other MDR Gram-negative bacteria is a class of antibiotics called the polymyxins; however, polymyxin-resistant isolates have emerged. In response, antimicrobial peptides (AMPs) and their synthetic mimetics have been investigated as alternative therapeutic options. Oligothioetheramides (oligoTEAs) are a class of synthetic, sequence-defined oligomers composed of N-allylacrylamide monomers and an abiotic dithiol backbone that is resistant to serum degradation. Characteristic of other AMP mimetics, the precise balance between charge and hydrophobicity has afforded cationic oligoTEAs potent antimicrobial activity, particularly for the compound BDT-4G, which consists of a 1,4-butanedithiol backbone and guanidine pendant groups, the latter of which provides a cationic charge at physiological pH. However, the activity and mechanism of cationic oligoTEAs against MDR Gram-negative isolates have yet to be fully investigated. Herein, we demonstrated the potent antimicrobial activity of BDT-4G against clinical isolates of P. aeruginosa with a range of susceptibility profiles, assessed the kinetics of bactericidal activity, and further elucidated its mechanism of action. Activity was also evaluated against a panel of polymyxin-resistant isolates, including intrinsically-resistant species. We demonstrate that BDT-4G can evade some of the mechanisms conferring resistance to polymyxin B and thus may have therapeutic potential.
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Affiliation(s)
- Meghan K O'Leary
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Vishal Sundaram
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Tobias Dörr
- Department of Microbiology, Cornell University, Ithaca, New York 14853, United States.,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States.,Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, New York 14853, United States
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10065, United States.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York 10065, United States
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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15
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Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE. System-wide transcriptome damage and tissue identity loss in COVID-19 patients. Cell Rep Med 2022; 3:100522. [PMID: 35233546 PMCID: PMC8784611 DOI: 10.1016/j.xcrm.2022.100522] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/22/2021] [Accepted: 01/16/2022] [Indexed: 01/07/2023]
Abstract
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.
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Affiliation(s)
- Jiwoon Park
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jonathan Foox
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - David C. Danko
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | | | - Youngmi Kim
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Daniel J. Butler
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Evan E. Afshin
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - André F. Rendeiro
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Yaron Bram
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Saravia-Butler
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
- Logyx, LLC, Mountain View, CA, USA
| | - Urminder Singh
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Eve Syrkin Wurtele
- Bioinformatics and Computational Biology Program, Center for Metabolic Biology, Department of Genetics, Development and Cell Biology Iowa State University, Ames, IA, USA
| | - Jonathan Schisler
- McAllister Heart Institute at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, and Department of Pathology and Lab Medicine at The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | | | - Steven Salvatore
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Nicholas P. Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison J. Kriegel
- Department of Physiology, Cardiovascular Center, Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Olivier Elemento
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alain C. Borczuk
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Robert E. Schwartz
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christopher E. Mason
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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16
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Burnham P, Chen F, Cheng AP, Srivatana V, Zhang LT, Edusei E, Albakry S, Botticelli B, Guo X, Renaghan A, Silberzweig J, Dadhania DM, Lenz JS, Heyang M, Iliev ID, Hayden JA, Westblade LF, De Vlaminck I, Lee JR. Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis. Kidney Med 2022; 4:100383. [PMID: 35072047 PMCID: PMC8767090 DOI: 10.1016/j.xkme.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Rationale & Objective Conventional culture can be insensitive for the detection of rare infections and for the detection of common infections in the setting of recent antibiotic usage. Patients receiving peritoneal dialysis (PD) with suspected peritonitis have a significant proportion of negative conventional cultures. This study examines the utility of metagenomic sequencing of peritoneal effluent cell-free DNA (cfDNA) for evaluating the peritoneal effluent in PD patients with and without peritonitis. Study Design Prospective cohort study. Setting & Participants We prospectively characterized cfDNA in 68 peritoneal effluent samples obtained from 33 patients receiving PD at a single center from September 2016 to July 2018. Outcomes Peritoneal effluent, microbial, and human cfDNA characteristics were evaluated in culture-confirmed peritonitis and culture-negative peritonitis. Analytical Approach Descriptive statistics were analyzed and microbial cfDNA was detected in culture-confirmed peritonitis and culture-negative peritonitis. Results Metagenomic sequencing of cfDNA was able to detect and identify bacterial, viral, and eukaryotic pathogens in the peritoneal effluent from PD patients with culture-confirmed peritonitis, as well as patients with recent antibiotic usage and in cases of culture-negative peritonitis. Limitations Parallel cultures were not obtained in all the peritoneal effluent specimens. Conclusions Metagenomic cfDNA sequencing of the peritoneal effluent can identify pathogens in PD patients with peritonitis, including culture-negative peritonitis.
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17
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Magleby R, Westblade LF, Trzebucki A, Simon MS, Rajan M, Park J, Goyal P, Safford MM, Satlin MJ. Impact of Severe Acute Respiratory Syndrome Coronavirus 2 Viral Load on Risk of Intubation and Mortality Among Hospitalized Patients With Coronavirus Disease 2019. Clin Infect Dis 2021; 73:e4197-e4205. [PMID: 32603425 PMCID: PMC7337625 DOI: 10.1093/cid/ciaa851] [Citation(s) in RCA: 255] [Impact Index Per Article: 85.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Patients hospitalized with coronavirus disease 2019 (COVID-19) frequently require mechanical ventilation and have high mortality rates. However, the impact of viral burden on these outcomes is unknown. METHODS We conducted a retrospective cohort study of patients hospitalized with COVID-19 from 30 March 2020 to 30 April 2020 at 2 hospitals in New York City. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load was assessed using cycle threshold (Ct) values from a reverse transcription-polymerase chain reaction assay applied to nasopharyngeal swab samples. We compared characteristics and outcomes of patients with high, medium, and low admission viral loads and assessed whether viral load was independently associated with intubation and in-hospital mortality. RESULTS We evaluated 678 patients with COVID-19. Higher viral load was associated with increased age, comorbidities, smoking status, and recent chemotherapy. In-hospital mortality was 35.0% (Ct <25; n = 220), 17.6% (Ct 25-30; n = 216), and 6.2% (Ct >30; n = 242) with high, medium, and low viral loads, respectively (P < .001). The risk of intubation was also higher in patients with a high viral load (29.1%) compared with those with a medium (20.8%) or low viral load (14.9%; P < .001). High viral load was independently associated with mortality (adjusted odds ratio [aOR], 6.05; 95% confidence interval [CI], 2.92-12.52) and intubation (aOR, 2.73; 95% CI, 1.68-4.44). CONCLUSIONS Admission SARS-CoV-2 viral load among hospitalized patients with COVID-19 independently correlates with the risk of intubation and in-hospital mortality. Providing this information to clinicians could potentially be used to guide patient care.
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Affiliation(s)
- Reed Magleby
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - Lars F Westblade
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Alex Trzebucki
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - Matthew S Simon
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Mangala Rajan
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Joel Park
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
- Department of Emergency Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Parag Goyal
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Monika M Safford
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Michael J Satlin
- NewYork–Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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18
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Satlin MJ, Zucker J, Baer BR, Rajan M, Hupert N, Schang LM, Pinheiro LC, Shen Y, Sobieszczyk ME, Westblade LF, Goyal P, Wells MT, Sepulveda JL, Safford MM. Changes in SARS-CoV-2 viral load and mortality during the initial wave of the pandemic in New York City. PLoS One 2021; 16:e0257979. [PMID: 34797838 PMCID: PMC8604305 DOI: 10.1371/journal.pone.0257979] [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: 06/30/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Public health interventions such as social distancing and mask wearing decrease the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is unclear whether they decrease the viral load of infected patients and whether changes in viral load impact mortality from coronavirus disease 2019 (COVID-19). We evaluated 6923 patients with COVID-19 at six New York City hospitals from March 15-May 14, 2020, corresponding with the implementation of public health interventions in March. We assessed changes in cycle threshold (CT) values from reverse transcription-polymerase chain reaction tests and in-hospital mortality and modeled the impact of viral load on mortality. Mean CT values increased between March and May, with the proportion of patients with high viral load decreasing from 47.7% to 7.8%. In-hospital mortality increased from 14.9% in March to 28.4% in early April, and then decreased to 8.7% by May. Patients with high viral loads had increased mortality compared to those with low viral loads (adjusted odds ratio 2.34). If viral load had not declined, an estimated 69 additional deaths would have occurred (5.8% higher mortality). SARS-CoV-2 viral load steadily declined among hospitalized patients in the setting of public health interventions, and this correlated with decreases in mortality.
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Affiliation(s)
- Michael J. Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
- * E-mail:
| | - Jason Zucker
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Benjamin R. Baer
- Department of Statistics and Data Science, Cornell University, Ithaca, New York, United States of America
| | - Mangala Rajan
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Nathaniel Hupert
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, United States of America
- Cornell Institute for Disease and Disaster Preparedness, New York, New York, United States of America
| | - Luis M. Schang
- College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Laura C. Pinheiro
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Epidemiology and Biostatistics, CUNY Graduate School of Public Health and Health Policy, New York, New York, United States of America
| | - Magdalena E. Sobieszczyk
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Parag Goyal
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Division of Cardiology, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Martin T. Wells
- Department of Statistics and Data Science, Cornell University, Ithaca, New York, United States of America
- Division of Biostatistics and Epidemiology, Weill Cornell Medicine, New York, New York, United States of America
| | - Jorge L. Sepulveda
- Department of Pathology, George Washington University, Washington, DC, United States of America
| | - Monika M. Safford
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
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19
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Choi JJ, Westblade LF, Gottesdiener LS, Liang K, Li HA, Wehmeyer GT, Glesby MJ, Simon MS. Impact of a Multiplex Polymerase Chain Reaction Panel on Duration of Empiric Antibiotic Therapy in Suspected Bacterial Meningitis. Open Forum Infect Dis 2021; 8:ofab467. [PMID: 34646911 PMCID: PMC8500300 DOI: 10.1093/ofid/ofab467] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/13/2021] [Indexed: 01/20/2023] Open
Abstract
Background Multiplex polymerase chain reaction (PCR) panels allow for rapid detection or exclusion of pathogens causing meningitis and encephalitis (ME). The clinical impact of rapid multiplex PCR ME panel results on the duration of empiric antibiotic therapy is not well characterized. Methods We performed a retrospective prepost study at our institution that evaluated the clinical impact of a multiplex PCR ME panel among adults with suspected bacterial meningitis who received empiric antibiotic therapy and underwent lumbar puncture in the emergency department. The primary outcome was the duration of empiric antibiotic therapy. Results The positive pathogen detection rates were similar between pre- and post-multiplex PCR ME panel periods (17.5%, 24 of 137 vs 20.3%, 14 of 69, respectively). The median duration of empiric antibiotic therapy was significantly reduced in the post-multiplex PCR ME panel period compared with the pre-multiplex PCR ME panel period (34.7 vs 12.3 hours, P = .01). At any point in time, 46% more patients in the post-multiplex PCR ME panel period had empiric antibiotic therapy discontinued or de-escalated compared with the pre-multiplex PCR ME panel period (sex- and immunosuppressant use-adjusted hazard ratio 1.46, P = .01). The median hospital length of stay was shorter in the post-multiplex PCR ME panel period (3 vs 4 days, P = .03). Conclusions The implementation of the multiplex PCR ME panel for bacterial meningitis reduced the duration of empiric antibiotic therapy and possibly hospital length of stay compared with traditional microbiological testing methods.
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Affiliation(s)
- Justin J Choi
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lee S Gottesdiener
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kyle Liang
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Han A Li
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Graham T Wehmeyer
- Division of General Internal Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Marshall J Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Matthew S Simon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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20
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Affiliation(s)
- Lars F Westblade
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Reed Magleby
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA
| | - Alex Trzebucki
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA
| | - Matthew S Simon
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Mangala Rajan
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Joel Park
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA.,Department of Emergency Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Parag Goyal
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Monika M Safford
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Michael J Satlin
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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21
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Yang HS, Hou Y, Zhang H, Chadburn A, Westblade LF, Fedeli R, Steel PAD, Racine-Brzostek SE, Velu P, Sepulveda JL, Satlin MJ, Cushing MM, Kaushal R, Zhao Z, Wang F. Machine Learning Highlights Downtrending of COVID-19 Patients with a Distinct Laboratory Profile. Health Data Sci 2021; 2021:7574903. [PMID: 36405356 PMCID: PMC9629663 DOI: 10.34133/2021/7574903] [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] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/07/2021] [Indexed: 06/16/2023]
Abstract
BACKGROUND New York City (NYC) experienced an initial surge and gradual decline in the number of SARS-CoV-2-confirmed cases in 2020. A change in the pattern of laboratory test results in COVID-19 patients over this time has not been reported or correlated with patient outcome. METHODS We performed a retrospective study of routine laboratory and SARS-CoV-2 RT-PCR test results from 5,785 patients evaluated in a NYC hospital emergency department from March to June employing machine learning analysis. RESULTS A COVID-19 high-risk laboratory test result profile (COVID19-HRP), consisting of 21 routine blood tests, was identified to characterize the SARS-CoV-2 patients. Approximately half of the SARS-CoV-2 positive patients had the distinct COVID19-HRP that separated them from SARS-CoV-2 negative patients. SARS-CoV-2 patients with the COVID19-HRP had higher SARS-CoV-2 viral loads, determined by cycle threshold values from the RT-PCR, and poorer clinical outcome compared to other positive patients without the COVID12-HRP. Furthermore, the percentage of SARS-CoV-2 patients with the COVID19-HRP has significantly decreased from March/April to May/June. Notably, viral load in the SARS-CoV-2 patients declined, and their laboratory profile became less distinguishable from SARS-CoV-2 negative patients in the later phase. CONCLUSIONS Our longitudinal analysis illustrates the temporal change of laboratory test result profile in SARS-CoV-2 patients and the COVID-19 evolvement in a US epicenter. This analysis could become an important tool in COVID-19 population disease severity tracking and prediction. In addition, this analysis may play an important role in prioritizing high-risk patients, assisting in patient triaging and optimizing the usage of resources.
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Affiliation(s)
- He S. Yang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Yu Hou
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Hao Zhang
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Richard Fedeli
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Peter A. D. Steel
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sabrina E. Racine-Brzostek
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Jorge L. Sepulveda
- Department of Pathology, School of Medicine and Health Sciences, George Washington University, Washington DC, USA
| | - Michael J. Satlin
- Division of Infectious Disease, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa M. Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Rainu Kaushal
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Zhen Zhao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York-Presbyterian Hospital/Weill Cornell Medical Campus, New York, NY, USA
| | - Fei Wang
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
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22
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Kubiak J, Davidson E, Soave R, Kodiyanplakkal RP, Robertson A, Besien KV, Shore TB, Lee JR, Westblade LF, Satlin MJ. Colonization with Gastrointestinal Pathogens Prior to Hematopoietic Cell Transplantation and Associated Clinical Implications. Transplant Cell Ther 2021; 27:499.e1-499.e6. [PMID: 33811020 DOI: 10.1016/j.jtct.2021.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/14/2021] [Indexed: 11/29/2022]
Abstract
Infectious diarrhea following hematopoietic cell transplantation (HCT) significantly contributes to morbidity and mortality. Most HCT recipients experience diarrhea in the post-transplantation period, and infectious pathogens are frequently detected during diarrheal episodes. However, little is known about how frequently these patients are colonized with gastrointestinal (GI) pathogens before their transplantation and whether colonization predicts future diarrheal illness. We sought to determine how frequently HCT recipients are colonized with GI pathogens before HCT and the degree to which pre-HCT colonization predicts post-transplantation infectious diarrheal illness. We conducted a prospective cohort study of allogeneic and autologous HCT recipients at a single center between December 2016 and January 2019. Stool samples were collected during the week before HCT, and formed samples were evaluated for the presence of 22 diarrheal pathogens using the BioFire FilmArray GI panel. We determined the frequency with which participants were colonized with each pathogen and identified factors associated with colonization. We then determined how frequently pretransplantation colonization led to post-transplantation diarrheal infections due to the colonizing pathogen and whether colonization was associated with increased number of days of post-transplantation diarrhea during the transplant hospitalization. We enrolled 112 asymptomatic patients (allogeneic, 61%; autologous, 39%) who had a formed stool specimen before HCT, of whom 41 (37%) had a GI pathogen detected. The most commonly detected organisms were Clostridioides difficile (n = 21; 19%), Yersinia enterocolitica (n = 9; 8%), enteropathogenic Escherichia coli (EPEC) (n = 6; 6%), and norovirus (n = 5; 4%). Female sex and previous C. difficile infection were associated with C. difficile colonization, and having non-Hodgkin lymphoma was associated with being colonized with a diarrheal pathogen other than C. difficile. Thirteen of 21 patients (62%) with pretransplantation C. difficile colonization developed a clinical C. difficile infection post-transplantation, and 8 of 10 patients (80%) colonized with EPEC or enteroaggregative E. coli developed post-transplantation infections due to their colonizing pathogen. Pretransplantation C. difficile colonization was also associated with an increased duration of post-transplantation diarrhea (P = .048). Conversely, none of the 9 patients with pretransplantation Yersinia enterocolitica colonization developed a post-transplantation Y. enterocolitica infection. Patients admitted for HCT are frequently colonized with a diverse range of GI pathogens. Colonization with C. difficile colonization and diarrheagenic E. coli is frequently associated with post-transplantation diarrheal infections caused by these organisms, but the clinical significance of colonization with other GI pathogens is not clear.
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Affiliation(s)
- Jeffrey Kubiak
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Emily Davidson
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Rosemary Soave
- Department of Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Rosy Priya Kodiyanplakkal
- Department of Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Amy Robertson
- New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Koen van Besien
- Department of Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Tsiporah B Shore
- Department of Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - John R Lee
- Department of Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Department of Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York
| | - Michael J Satlin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Department of Medicine, Weill Cornell Medicine, New York, New York; New York-Presbyterian Hospital, Weill Cornell Medical Center, New York, New York.
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23
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Satlin MJ, Chen L, Douglass C, Hovan M, Davidson E, Soave R, La Spina M, Gomez-Arteaga A, van Besien K, Mayer S, Phillips A, Hsu JM, Malherbe R, Small CB, Jenkins SG, Westblade LF, Kreiswirth BN, Walsh TJ. Colonization with Fluoroquinolone-Resistant Enterobacterales Decreases the Effectiveness of Fluoroquinolone Prophylaxis in Hematopoietic Cell Transplant Recipients. Clin Infect Dis 2021; 73:1257-1265. [PMID: 33956965 DOI: 10.1093/cid/ciab404] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Levofloxacin prophylaxis is recommended to prevent Gram-negative bloodstream infections (BSIs) in patients with prolonged chemotherapy-induced neutropenia. However, increasing fluoroquinolone resistance may decrease the effectiveness of this approach. METHODS We assessed the prevalence of colonization with fluoroquinolone-resistant Enterobacterales (FQRE) among patients admitted for hematopoietic cell transplantation (HCT) from November 2016-August 2019 and compared the risk of Gram-negative BSI between FQRE-colonized and non-colonized patients. All patients received levofloxacin prophylaxis during neutropenia. Stool samples were collected upon admission for HCT and weekly thereafter until recovery from neutropenia, and underwent selective culture for FQRE. All isolates were identified and underwent antimicrobial susceptibility testing by broth microdilution. FQRE isolates also underwent whole-genome sequencing. RESULTS Fifty-four (23%) of 234 patients were colonized with FQRE prior to HCT, including 30 (25%) of 119 allogeneic and 24 (21%) of 115 autologous HCT recipients. Recent antibacterial use was associated with FQRE colonization (P=0.048). Ninety-one percent of colonizing FQRE isolates were Escherichia coli and 29% produced extended-spectrum ß-lactamases. Seventeen (31%) FQRE-colonized patients developed Gram-negative BSI despite levofloxacin prophylaxis, compared to only two (1.1%) of 180 patients who were not colonized with FQRE on admission (P<0.001). Of the 17 Gram-negative BSIs in FQRE-colonized patients, 15 (88%) were caused by FQRE isolates that were genetically identical to the colonizing strain. CONCLUSIONS Nearly one-third of HCT recipients with pre-transplant FQRE colonization developed Gram-negative BSI while receiving levofloxacin prophylaxis and infections were typically caused by their colonizing strains. In contrast, levofloxacin prophylaxis was highly effective in patients not initially colonized with FQRE.
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Affiliation(s)
- Michael J Satlin
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ; Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Claire Douglass
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,DeSales University Physician Assistant Program, Center Valley, PA, USA
| | - Michael Hovan
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Emily Davidson
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Rosemary Soave
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Marisa La Spina
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, USA
| | - Alexandra Gomez-Arteaga
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Koen van Besien
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sebastian Mayer
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Adrienne Phillips
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jing-Mei Hsu
- Department of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Catherine B Small
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephen G Jenkins
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ; Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Thomas J Walsh
- Transplantation-Oncology Infectious Diseases Program, Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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24
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Kondo M, Simon MS, Westblade LF, Jenkins SG, Babady NE, Loo AS, Calfee DP. Implementation of infectious diseases rapid molecular diagnostic tests and antimicrobial stewardship program involvement in acute-care hospitals. Infect Control Hosp Epidemiol 2021; 42:609-611. [PMID: 33059776 PMCID: PMC8050139 DOI: 10.1017/ice.2020.1230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 01/03/2023]
Abstract
A survey of acute-care hospitals found that rapid molecular diagnostic tests (RMDTs) have been widely adopted. Although many hospitals use their antimicrobial stewardship team and/or guidelines to help clinicians interpret results and optimize treatment, opportunities to more fully achieve the potential benefits of RMDTs remain.
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Affiliation(s)
- Maiko Kondo
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew S Simon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephen G Jenkins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela S Loo
- Department of Pharmacy, NewYork-Presbyterian Hospital, New York, NY, USA
| | - David P Calfee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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25
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Rogers WS, Westblade LF, Soave R, Jenkins SG, van Besien K, Singh HK, Walsh TJ, Small CB, Shore T, Crawford CV, Satlin MJ. Impact of a Multiplexed Polymerase Chain Reaction Panel on Identifying Diarrheal Pathogens in Hematopoietic Cell Transplant Recipients. Clin Infect Dis 2021; 71:1693-1700. [PMID: 31687767 DOI: 10.1093/cid/ciz1068] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 03/23/2019] [Accepted: 11/01/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Diarrhea is common and associated with substantial morbidity among hematopoietic cell transplant (HCT) recipients, but the etiology is often not identified. Multiplexed polymerase chain reaction (PCR) assays increase the detection of diarrheal pathogens, but the impact of this technology in this population has not been evaluated. METHODS Our center replaced stool cultures and other conventional microbiologic methods with the FilmArray Gastrointestinal Panel (GI PCR) in June 2016. We reviewed all adult patients who received an HCT from June 2014-May 2015 (pre-GI PCR, n = 163) and from June 2016-May 2017 (post-GI PCR, n = 182) and followed them for 1 year after transplantation. Clostridioides difficile infection was diagnosed by an independent PCR test in both cohorts. RESULTS The proportion of patients with ≥1 identified infectious diarrheal pathogen increased from 25% to 37% after implementation of GI PCR (P = .01). Eight patients (5%) in the pre-GI PCR cohort tested positive for a pathogen other than C. difficile versus 49 patients (27%) in the post-GI PCR cohort (P < .001). The most common non-C. difficile diarrheal pathogens in the post-GI PCR cohort were enteropathogenic Escherichia coli (n = 14, 8%), norovirus (n = 14, 8%), and Yersinia enterocolitica (n = 7, 4%). The percentage of diarrheal episodes with an identified infectious etiology increased from 14% to 23% (P = .001). Median total costs of stool testing per patient did not increase (pre: $473; post: $425; P = .25). CONCLUSIONS Infectious etiologies of diarrhea were identified in a higher proportion of HCT recipients after replacing conventional stool testing with a multiplexed PCR assay, without an increase in testing costs.
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Affiliation(s)
- Wesley S Rogers
- NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA.,Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Rosemary Soave
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA.,Transplantation-Oncology Infectious Diseases Program, Weill Cornell Medicine, New York, New York, USA
| | - Stephen G Jenkins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA.,Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Koen van Besien
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York, USA
| | - Harjot K Singh
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA.,Transplantation-Oncology Infectious Diseases Program, Weill Cornell Medicine, New York, New York, USA
| | - Thomas J Walsh
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA.,Transplantation-Oncology Infectious Diseases Program, Weill Cornell Medicine, New York, New York, USA
| | - Catherine B Small
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA.,Transplantation-Oncology Infectious Diseases Program, Weill Cornell Medicine, New York, New York, USA
| | - Tsiporah Shore
- Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, New York, USA
| | - Carl V Crawford
- Division of Gastroenterology, Weill Cornell Medicine, New York, New York, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA.,Transplantation-Oncology Infectious Diseases Program, Weill Cornell Medicine, New York, New York, USA
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26
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Westblade LF, Simon MS, Satlin MJ. Bacterial coinfections in coronavirus disease 2019. Trends Microbiol 2021; 29:930-941. [PMID: 33934980 PMCID: PMC8026275 DOI: 10.1016/j.tim.2021.03.018] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 02/07/2023]
Abstract
Bacterial coinfections increase the severity of respiratory viral infections and were frequent causes of mortality in influenza pandemics but have not been well characterized in patients with coronavirus disease 2019 (COVID-19). The aim of this review was to identify the frequency and microbial etiologies of bacterial coinfections that are present upon admission to the hospital and that occur during hospitalization for COVID-19. We found that bacterial coinfections were present in <4% of patients upon admission and the yield of routine diagnostic tests for pneumonia was low. When bacterial coinfections did occur, Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae were the most common pathogens and atypical bacteria were rare. Although uncommon upon admission, bacterial infections frequently occurred in patients with prolonged hospitalization, and Pseudomonas aeruginosa, Klebsiella spp., and S. aureus were common pathogens. Antibacterial therapy and diagnostic testing for bacterial infections are unnecessary upon admission in most patients hospitalized with COVID-19, but clinicians should be vigilant for nosocomial bacterial infections.
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Affiliation(s)
- Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew S Simon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Satlin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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27
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Cazer CL, Westblade LF, Simon MS, Magleby R, Castanheira M, Booth JG, Jenkins SG, Gröhn YT. Analysis of Multidrug Resistance in Staphylococcus aureus with a Machine Learning-Generated Antibiogram. Antimicrob Agents Chemother 2021; 65:e02132-20. [PMID: 33431415 PMCID: PMC8097487 DOI: 10.1128/aac.02132-20] [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: 10/06/2020] [Accepted: 12/24/2020] [Indexed: 01/12/2023] Open
Abstract
Multidrug resistance (MDR) surveillance consists of reporting MDR prevalence and MDR phenotypes. Detailed knowledge of the specific associations underlying MDR patterns can allow antimicrobial stewardship programs to accurately identify clinically relevant resistance patterns. We applied machine learning and graphical networks to quantify and visualize associations between resistance traits in a set of 1,091 Staphylococcus aureus isolates collected from one New York hospital between 2008 and 2018. Antimicrobial susceptibility testing was performed using reference broth microdilution. The isolates were analyzed by year, methicillin susceptibility, and infection site. Association mining was used to identify resistance patterns that consisted of two or more individual antimicrobial resistance (AMR) traits and quantify the association among the individual resistance traits in each pattern. The resistance patterns captured the majority of the most common MDR phenotypes and reflected previously identified pairwise relationships between AMR traits in S. aureus Associations between β-lactams and other antimicrobial classes (macrolides, lincosamides, and fluoroquinolones) were common, although the strength of the association among these antimicrobial classes varied by infection site and by methicillin susceptibility. Association mining identified associations between clinically important AMR traits, which could be further investigated for evidence of resistance coselection. For example, in skin and skin structure infections, clindamycin and tetracycline resistance occurred together 1.5 times more often than would be expected if they were independent from one another. Association mining efficiently discovered and quantified associations among resistance traits, allowing these associations to be compared between relevant subsets of isolates to identify and track clinically relevant MDR.
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Affiliation(s)
- Casey L Cazer
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Matthew S Simon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Reed Magleby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | - James G Booth
- Department of Statistics and Data Science, Cornell University, Ithaca, New York, USA
| | - Stephen G Jenkins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Yrjö T Gröhn
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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28
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Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun 2021; 12:1660. [PMID: 33712587 PMCID: PMC7954844 DOI: 10.1038/s41467-021-21361-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [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: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, Columbia, NY, USA
| | - Evan T Sholle
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Craig D Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ciaran Hassan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | | | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | | | | | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | - Jeffrey A Rosenfeld
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
- Department of Pathology, Robert Wood Johnson Medical School, New York, NJ, USA
| | - Ying Chen
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
| | - Peter A D Steel
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amos J Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Thomas R Campion
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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29
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Zhang LT, Westblade LF, Iqbal F, Taylor MR, Chung A, Satlin MJ, Magruder M, Edusei E, Albakry S, Botticelli B, Robertson A, Alston T, Dadhania DM, Lubetzky M, Hirota SA, Greenway SC, Lee JR. Gut microbiota profiles and fecal beta-glucuronidase activity in kidney transplant recipients with and without post-transplant diarrhea. Clin Transplant 2021; 35:e14260. [PMID: 33605497 DOI: 10.1111/ctr.14260] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 11/08/2020] [Revised: 02/01/2021] [Accepted: 02/13/2021] [Indexed: 12/18/2022]
Abstract
Post-transplant diarrhea is a common complication after solid organ transplantation and is frequently attributed to the widely prescribed immunosuppressant mycophenolate mofetil (MMF). Given recent work identifying the relationship between MMF toxicity and gut bacterial β-glucuronidase activity, we evaluated the relationship between gut microbiota composition, fecal β-glucuronidase activity, and post-transplant diarrhea. We recruited 97 kidney transplant recipients and profiled the gut microbiota in 273 fecal specimens using 16S rRNA gene sequencing. We further characterized fecal β-glucuronidase activity in a subset of this cohort. Kidney transplant recipients with post-transplant diarrhea had decreased gut microbial diversity and decreased relative gut abundances of 12 genera when compared to those without post-transplant diarrhea (adjusted p value < .15, Wilcoxon rank sum test). Among the kidney transplant recipients with post-transplant diarrhea, those with higher fecal β-glucuronidase activity had a more prolonged course of diarrhea (≥7 days) compared to patients with lower fecal β-glucuronidase activity (91% vs 40%, p = .02, Fisher's exact test). Our data reveal post-transplant diarrhea as a complex phenomenon with decreased gut microbial diversity and commensal gut organisms. This study further links commensal bacterial metabolism with an important clinical outcome measure, suggesting fecal β-glucuronidase activity could be a novel biomarker for gastrointestinal-related MMF toxicity.
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Affiliation(s)
- Lisa T Zhang
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Fatima Iqbal
- Departments of Pediatrics and Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael R Taylor
- Departments of Pediatrics and Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Alice Chung
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Satlin
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Matthew Magruder
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA
| | - Emmanuel Edusei
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA
| | - Shady Albakry
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA
| | - Brittany Botticelli
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA
| | - Amy Robertson
- New York Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Tricia Alston
- New York Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Darshana M Dadhania
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA.,Department of Transplantation Medicine, NewYork-Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Michelle Lubetzky
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA.,Department of Transplantation Medicine, NewYork-Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Simon A Hirota
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Steven C Greenway
- Departments of Pediatrics and Biochemistry and Molecular Biology, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Cardiac Sciences, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - John R Lee
- Department of Medicine, Division of Nephrology and Hypertension, Weill Cornell Medicine, New York, NY, USA.,Department of Transplantation Medicine, NewYork-Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
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30
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Park J, Foox J, Hether T, Danko D, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu S, Tatonetti N, Shapira S, Salvatore M, Loda M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Borczuk AC, Meydan C, Schwartz RE, Mason CE. Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps. bioRxiv 2021. [PMID: 33758858 DOI: 10.1101/2021.03.08.434433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus has infected over 115 million people and caused over 2.5 million deaths worldwide. Yet, the molecular mechanisms underlying the clinical manifestations of COVID-19, as well as what distinguishes them from common seasonal influenza virus and other lung injury states such as Acute Respiratory Distress Syndrome (ARDS), remains poorly understood. To address these challenges, we combined transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues, matched with spatial protein and expression profiling (GeoMx) across 357 tissue sections. These results define both body-wide and tissue-specific (heart, liver, lung, kidney, and lymph nodes) damage wrought by the SARS-CoV-2 infection, evident as a function of varying viral load (high vs. low) during the course of infection and specific, transcriptional dysregulation in splicing isoforms, T cell receptor expression, and cellular expression states. In particular, cardiac and lung tissues revealed the largest degree of splicing isoform switching and cell expression state loss. Overall, these findings reveal a systemic disruption of cellular and transcriptional pathways from COVID-19 across all tissues, which can inform subsequent studies to combat the mortality of COVID-19, as well to better understand the molecular dynamics of lethal SARS-CoV-2 infection and other viruses.
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31
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Huang J, Salinas T, Westblade LF, Lee JR. The Potential Role of the Gut Microbiota in Kidney Transplantation. Kidney360 2021; 2:890-893. [PMID: 35373069 PMCID: PMC8791346 DOI: 10.34067/kid.0006912020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/05/2021] [Indexed: 02/04/2023]
Affiliation(s)
- Jennifer Huang
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Thalia Salinas
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - John R. Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, New York,Department of Transplantation Medicine, New York Presbyterian Hospital Weill Cornell Medical Center, New York, New York
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32
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Shin J, Choe D, Ransegnola B, Hong H, Onyekwere I, Cross T, Shi Q, Cho B, Westblade LF, Brito IL, Dörr T. A multifaceted cellular damage repair and prevention pathway promotes high-level tolerance to β-lactam antibiotics. EMBO Rep 2021; 22:e51790. [PMID: 33463026 PMCID: PMC7857431 DOI: 10.15252/embr.202051790] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 09/25/2020] [Revised: 11/17/2020] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
Bactericidal antibiotics are powerful agents due to their ability to convert essential bacterial functions into lethal processes. However, many important bacterial pathogens are remarkably tolerant against bactericidal antibiotics due to inducible damage repair responses. The cell wall damage response two-component system VxrAB of the gastrointestinal pathogen Vibrio cholerae promotes high-level β-lactam tolerance and controls a gene network encoding highly diverse functions, including negative control over multiple iron uptake systems. How this system contributes to tolerance is poorly understood. Here, we show that β-lactam antibiotics cause an increase in intracellular free iron levels and collateral oxidative damage, which is exacerbated in the ∆vxrAB mutant. Mutating major iron uptake systems dramatically increases ∆vxrAB tolerance to β-lactams. We propose that VxrAB reduces antibiotic-induced toxic iron and concomitant metabolic perturbations by downregulating iron uptake transporters and show that iron sequestration enhances tolerance against β-lactam therapy in a mouse model of cholera infection. Our results suggest that a microorganism's ability to counteract diverse antibiotic-induced stresses promotes high-level antibiotic tolerance and highlights the complex secondary responses elicited by antibiotics.
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Affiliation(s)
- Jung‐Ho Shin
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Donghui Choe
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
- KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonKorea
| | - Brett Ransegnola
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Hye‐Rim Hong
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Ikenna Onyekwere
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Trevor Cross
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
| | - Qiaojuan Shi
- Meinig School of Biomedical EngineeringCornell UniversityIthacaNYUSA
| | - Byung‐Kwan Cho
- Department of Biological SciencesKorea Advanced Institute of Science and TechnologyDaejeonKorea
- KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonKorea
- Intelligent Synthetic Biology CenterDaejeonKorea
| | - Lars F Westblade
- Department of Pathology and Laboratory MedicineWeill Cornell MedicineNew YorkNYUSA
- Division of Infectious DiseasesDepartment of MedicineWeill Cornell MedicineNew YorkNYUSA
| | - Ilana L Brito
- Meinig School of Biomedical EngineeringCornell UniversityIthacaNYUSA
| | - Tobias Dörr
- Weill Institute for Cell and Molecular BiologyCornell, UniversityIthacaNYUSA
- Department of MicrobiologyCornell UniversityIthacaNYUSA
- Cornell Institute of Host‐Microbe Interactions and DiseaseCornell UniversityIthacaNYUSA
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33
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O'Leary MK, Chen SS, Westblade LF, Alabi CA. Design of a PEGylated Antimicrobial Prodrug with Species-Specific Activation. Biomacromolecules 2021; 22:984-992. [PMID: 33428376 DOI: 10.1021/acs.biomac.0c01695] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The rise of multidrug-resistant (MDR) "superbugs" has created an urgent need to develop new classes of antimicrobial agents to target these organisms. Oligothioetheramides (oligoTEAs) are a unique class of antimicrobial peptide (AMP) mimetics with one promising compound, BDT-4G, displaying potent activity against MDR Pseudomonas aeruginosa clinical isolates. Despite widely demonstrated potency, BDT-4G and other AMP mimetics have yet to enjoy broad preclinical success against systemic infections, primarily due to their cytotoxicity. In this work, we explore a prodrug strategy to render BDT-4G inactive until it is exposed to an enzyme secreted by the targeted bacteria. The prodrug consists of polyethylene glycol (PEG) conjugated to BDT-4G by a peptide substrate. PEG serves to inactivate and reduce the toxicity of BDT-4G by masking its cationic charge and antimicrobial activity is recovered following site-specific cleavage of the short peptide linker by LasA, a virulence factor secreted by P. aeruginosa. This approach concurrently reduces cytotoxicity by greater than 1 order of magnitude in vitro and provides species specificity through the identity of the cleavable linker.
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Affiliation(s)
- Meghan K O'Leary
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Sabrina S Chen
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York 10065-4805, United States.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York 10065-4805, United States
| | - Christopher A Alabi
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
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34
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Velu P, Craney A, Ruggiero P, Sipley J, Cong L, Hissong EM, Loda M, Westblade LF, Cushing M, Rennert H. Rapid Implementation of Severe Acute Respiratory Syndrome Coronavirus 2 Emergency Use Authorization RT-PCR Testing and Experience at an Academic Medical Institution. J Mol Diagn 2020; 23:149-158. [PMID: 33285285 PMCID: PMC7718583 DOI: 10.1016/j.jmoldx.2020.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/11/2020] [Accepted: 10/21/2020] [Indexed: 01/19/2023] Open
Abstract
An epidemic caused by an outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in December 2019 has since rapidly spread internationally, requiring urgent response from the clinical diagnostics community. We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time RT-PCR test offered in the NewYork-Presbyterian Hospital system following the Emergency Use Authorization issued by the US Food and Drug Administration. Nasopharyngeal and sputum specimens (n = 174) were validated using newly designed dual-target real-time RT-PCR (altona RealStar SARS-CoV-2 Reagent) for detecting SARS-CoV-2 in upper respiratory tract and lower respiratory tract specimens. Accuracy testing demonstrated excellent assay agreement between expected and observed values and comparable diagnostic performance to reference tests. The limit of detection was 2.7 and 23.0 gene copies per reaction for nasopharyngeal and sputum specimens, respectively. Retrospective analysis of 1694 upper respiratory tract specimens from 1571 patients revealed increased positivity in older patients and males compared with females, and an increasing positivity rate from approximately 20% at the start of testing to 50% at the end of testing 3 weeks later. Herein, we demonstrate that the assay accurately and sensitively identifies SARS-CoV-2 in multiple specimen types in the clinical setting and summarize clinical data from early in the epidemic in New York City.
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Affiliation(s)
- Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - John Sipley
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - Erika M Hissong
- Department of Pathology and Laboratory Medicine, NewYork-Presbyterian Hospital-Weill Cornell Medicine, New York, New York
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.
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35
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Yang HS, Racine-Brzostek SE, Karbaschi M, Yee J, Dillard A, Steel PAD, Lee WS, McDonough KA, Qiu Y, Ketas TJ, Francomano E, Klasse PJ, Hatem L, Westblade LF, Wu H, Chen H, Zuk R, Tan H, Girardin R, Dupuis AP, Payne AF, Moore JP, Cushing MM, Chadburn A, Zhao Z. Testing-on-a-probe biosensors reveal association of early SARS-CoV-2 total antibodies and surrogate neutralizing antibodies with mortality in COVID-19 patients. medRxiv 2020. [PMID: 33236020 DOI: 10.1101/2020.11.19.20235044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The association of mortality with early humoral response to SARS-CoV-2 infection within the first few days after onset of symptoms (DAOS) has not been thoroughly investigated partly due to a lack of sufficiently sensitive antibody testing methods. Here we report two sensitive and automated testing-on-a-probe (TOP) biosensor assays for SARS-CoV-2 viral specific total antibodies (TAb) and surrogate neutralizing antibodies (SNAb), which are suitable for clinical use. The TOP assays employ an RBD-coated quartz probe using a Cy5-Streptavidin-polysacharide conjugate to improved sensitivity and minimize interference. Disposable cartridge containing pre-dispensed reagents requires no liquid manipulation or fluidics during testing. The TOP-TAb assay exhibited higher sensitivity in the 0-7 DAOS window than a widely used FDA-EUA assay. The rapid (18 min) and automated TOP-SNAb correlated well with two well-established SARS-CoV-2 virus neutralization tests. The clinical utility of the TOP assays was demonstrated by evaluating early antibody responses in 120 SARS-CoV-2 RT-PCR positive adult hospitalized patients. Higher baseline TAb and SNAb positivity rates and more robust antibody responses were seen in patients who survived COVID-19 than those who died in the hospital. Survival analysis using the Cox Proportional Hazards Model showed that patients who were TAb and SNAb negative at initial hospital presentation were at a higher risk of in-hospital mortality. Furthermore, TAb and SNAb levels at presentation were inversely associated with SARS-CoV-2 viral load based on concurrent RT-PCR testing. Overall, the sensitive and automated TAb and SNAb assays allow detection of early SARS-CoV-2 antibodies which associate with mortality.
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Westblade LF, Brar G, Pinheiro LC, Paidoussis D, Rajan M, Martin P, Goyal P, Sepulveda JL, Zhang L, George G, Liu D, Whittier S, Plate M, Small CB, Rand JH, Cushing MM, Walsh TJ, Cooke J, Safford MM, Loda M, Satlin MJ. SARS-CoV-2 Viral Load Predicts Mortality in Patients with and without Cancer Who Are Hospitalized with COVID-19. Cancer Cell 2020; 38:661-671.e2. [PMID: 32997958 PMCID: PMC7492074 DOI: 10.1016/j.ccell.2020.09.007] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022]
Abstract
Patients with cancer may be at increased risk of severe coronavirus disease 2019 (COVID-19), but the role of viral load on this risk is unknown. We measured SARS-CoV-2 viral load using cycle threshold (CT) values from reverse-transcription polymerase chain reaction assays applied to nasopharyngeal swab specimens in 100 patients with cancer and 2,914 without cancer who were admitted to three New York City hospitals. Overall, the in-hospital mortality rate was 38.8% among patients with a high viral load, 24.1% among patients with a medium viral load, and 15.3% among patients with a low viral load (p < 0.001). Similar findings were observed in patients with cancer (high, 45.2% mortality; medium, 28.0%; low, 12.1%; p = 0.008). Patients with hematologic malignancies had higher median viral loads (CT = 25.0) than patients without cancer (CT = 29.2; p = 0.0039). SARS-CoV-2 viral load results may offer vital prognostic information for patients with and without cancer who are hospitalized with COVID-19.
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Affiliation(s)
- Lars F Westblade
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Gagandeep Brar
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Laura C Pinheiro
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Mangala Rajan
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Peter Martin
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Parag Goyal
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Jorge L Sepulveda
- Department of Pathology, George Washington University, Washington, DC 20037, USA
| | - Lisa Zhang
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gary George
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Dakai Liu
- NewYork-Presbyterian Hospital Queens, Queens, NY 11355, USA
| | - Susan Whittier
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA; NewYork-Presbyterian Hospital, Columbia University Medical Center, New York, NY 10032, USA
| | - Markus Plate
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Catherine B Small
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Jacob H Rand
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Melissa M Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Thomas J Walsh
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Joseph Cooke
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital Queens, Queens, NY 11355, USA
| | - Monika M Safford
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA
| | - Michael J Satlin
- Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; NewYork-Presbyterian Hospital, Weill Cornell Medical Center, New York, NY 10065, USA.
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Magruder M, Edusei E, Zhang L, Albakry S, Satlin MJ, Westblade LF, Malha L, Sze C, Lubetzky M, Dadhania DM, Lee JR. Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection. Gut Microbes 2020; 12:1805281. [PMID: 32865119 PMCID: PMC7524266 DOI: 10.1080/19490976.2020.1805281] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Urinary tract infection (UTI) is a common complication in kidney transplant recipients and can lead to significant morbidity and mortality. Recent evidence supports a role for the gut as a source for UTIs but little is known about the relationship between gut commensal bacteria and UTI development. We hypothesized that the abundance of gut commensal bacteria is associated with a lower risk of developing bacteriuria and UTIs. We performed gut microbiome profiling using 16S rRNA gene sequencing of the V4-V5 hypervariable region on 510 fecal specimens in 168 kidney transplant recipients. Fifty-one kidney transplant recipients (30%) developed Enterobacteriaceae bacteriuria within the first 6 months after transplantation (Enterobacteriaceae Bacteriuria Group) and 117 did not (No Enterobacteriaceae Bacteriuria Group). The relative abundances of Faecalibacterium and Romboutsia were significantly higher in the fecal specimens from the No Enterobacteriaceae Bacteriuria Group than those from the Enterobacteriaceae Bacteriuria Group (Adjusted P value<.01). The combined relative abundance of Faecalibacterium and Romboutsia was inversely correlated with the relative abundance of Enterobacteriaceae (r = -0.13, P = .003). In a multivariable Cox Regression, a top tercile cutoff of the combined relative abundance of Faecalibacterium and Romboutsia of ≥13.7% was independently associated with a decreased risk for Enterobacteriaceae bacteriuria (hazard ratio 0.3, P = .02) and Enterobacteriaceae UTI (hazard ratio 0.4, P = .09). In conclusion, we identify bacterial taxa associated with decreased risk for Enterobacteriaceae bacteriuria and Enterobacteriaceae UTI in kidney transplant recipients, which supports future studies on modulating the gut microbiota as a novel treatment for preventing UTIs.
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Affiliation(s)
- Matthew Magruder
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Emmanuel Edusei
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lisa Zhang
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shady Albakry
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J. Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Line Malha
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Christina Sze
- Department of Urology, NewYork Presbyterian Hospital – Weill Cornell Medical Center, New York, NY, USA
| | - Michelle Lubetzky
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Transplantation Medicine, New York Presbyterian Hospital – Weill Cornell Medical Center, New York, NY, USA
| | - Darshana M. Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Transplantation Medicine, New York Presbyterian Hospital – Weill Cornell Medical Center, New York, NY, USA
| | - John R. Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA,Department of Transplantation Medicine, New York Presbyterian Hospital – Weill Cornell Medical Center, New York, NY, USA,CONTACT John Richard Lee Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, 525 E. 68th Street Box #3, New York, NY 10065, USA
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Bushman D, Alroy KA, Greene SK, Keating P, Wahnich A, Weiss D, Pathela P, Harrison C, Rakeman J, Langley G, Tong S, Tao Y, Uehara A, Queen K, Paden CR, Szymczak W, Orner EP, Nori P, Lai PA, Jacobson JL, Singh HK, Calfee DP, Westblade LF, Vasovic LV, Rand JH, Liu D, Singh V, Burns J, Prasad N, Sell J. Detection and genetic characterization of community‐based SARS‐CoV‐2 infections – New York City, March 2020. Am J Transplant 2020. [DOI: 10.1111/ajt.16377] [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: 11/28/2022]
Affiliation(s)
- Dena Bushman
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
- Epidemic Intelligence Service CDC
| | - Karen A. Alroy
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
- Epidemic Intelligence Service CDC
| | - Sharon K. Greene
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
| | - Page Keating
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
| | - Amanda Wahnich
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
| | - Don Weiss
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
| | - Preeti Pathela
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
| | - Christy Harrison
- Public Health Laboratory New York City Department of Health and Mental Hygiene
| | - Jennifer Rakeman
- Public Health Laboratory New York City Department of Health and Mental Hygiene
| | - Gayle Langley
- Division of Viral Diseases National Center for Immunization and Respiratory Diseases CDC
| | - Suxiang Tong
- Division of Viral Diseases National Center for Immunization and Respiratory Diseases CDC
| | - Ying Tao
- Division of Viral Diseases National Center for Immunization and Respiratory Diseases CDC
| | - Anna Uehara
- Division of Viral Diseases National Center for Immunization and Respiratory Diseases CDC
| | - Krista Queen
- Division of Viral Diseases National Center for Immunization and Respiratory Diseases CDC
| | - Clinton R. Paden
- Division of Viral Diseases National Center for Immunization and Respiratory Diseases CDC
| | - Wendy Szymczak
- Department of Pathology Montefiore Medical Center Albert Einstein College of Medicine Bronx New York
| | - Erika P. Orner
- Department of Pathology Montefiore Medical Center Albert Einstein College of Medicine Bronx New York
| | - Priya Nori
- Department of Pathology Montefiore Medical Center Albert Einstein College of Medicine Bronx New York
- Division of Infectious Diseases Department of Medicine Montefiore Medical Center Albert Einstein College of Medicine Bronx New York
| | - Phi A. Lai
- Department of Pathology and Laboratory Medicine NYU Langone Hospital Brooklyn New York
| | | | - Harjot K. Singh
- Division of Infectious Diseases Department of Medicine Weill Cornell Medicine New York New York
| | - David P. Calfee
- Division of Infectious Diseases Department of Medicine Weill Cornell Medicine New York New York
| | - Lars F. Westblade
- Division of Infectious Diseases Department of Medicine Weill Cornell Medicine New York New York
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York New York
| | - Ljiljana V. Vasovic
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York New York
| | - Jacob H. Rand
- Department of Pathology and Laboratory Medicine Weill Cornell Medicine New York New York
| | - Dakai Liu
- New York‐Presbyterian Queens Flushing New York
| | | | | | | | - Jessica Sell
- Incident Command System Surveillance and Epidemiology Section New York City Department of Health and Mental Hygiene
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Affiliation(s)
- Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, United States of America
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, United States of America
| | - Jeff Errington
- The Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Tobias Dörr
- Weill Institute for Cell and Molecular Biology and Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
- Cornell Institute of Host-Pathogen Interactions and Disease, Cornell University, Ithaca, New York, United States of America
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40
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. Lab Chip 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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Cheleuitte-Nieves C, Heselpoth RD, Westblade LF, Lipman NS, Fischetti VA. Searching for a Bacteriophage Lysin to Treat Corynebacterium bovis in Immunocompromised Mice. Comp Med 2020; 70:328-335. [PMID: 32471521 PMCID: PMC7446641 DOI: 10.30802/aalas-cm-19-000096] [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: 09/13/2019] [Revised: 10/23/2019] [Accepted: 12/22/2019] [Indexed: 01/21/2023]
Abstract
Corynebacterium bovis is the causative agent of Corynebacterium-associated hyperkeratosis in immunocompromised mice. The resulting skin pathology can be profound and can be associated with severe wasting, making the animals unsuitable for research. Although the administration of antibiotics is effective in resolving clinical symptoms, antibiotics do not eradicate the offending bacterium. Furthermore, antibiotic use may be contraindicated as it can affect tumor growth and is associated with Clostridioides difficile enterotoxemia in highly immunocompromised murine strains. Lysins, which are lytic enzymes obtained from bacteriophages, are novel antimicrobial agents for treating bacterial diseases. The advantage of lysins are its target specificity, with minimal off-target complications that could affect the host or the biology of the engrafted tumor. The aim of this study was to identify lysins active against C. bovis. Chemical activation of latent prophages by using mitomycin C in 3 C. bovis isolates did not cause bacteriophage induction as determined through plaque assays and transmission electron microscopy. As an alternative approach, 8 lysins associated with other bacterial species, including those from the closely related species C. falsenii, were tested for their lytic action against C. bovis but were unsuccessful. These findings were congruent with the previously reported genomic analysis of 21 C. bovis isolates, which failed to reveal bacteriophage sequences by using the PHAST and PHASTER web server tools. From these results, we suggest C. bovis is among those rare bacterial species devoid of lysogenic bacteriophages, thus making the identification of C. bovis-specific lysins more challenging. However, C. bovis may be a useful model organism for studying the effects of antiphage systems.
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Affiliation(s)
- Christopher Cheleuitte-Nieves
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York; Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, New York;,
| | - Ryan D Heselpoth
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York; Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
| | - Neil S Lipman
- Tri-Institutional Training Program in Laboratory Animal Medicine and Science, Memorial Sloan Kettering Cancer Center, Weill Cornell Medicine, and The Rockefeller University, New York, New York; Center of Comparative Medicine and Pathology, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, New York
| | - Vincent A Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York
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Bushman D, Alroy KA, Greene SK, Keating P, Wahnich A, Weiss D, Pathela P, Harrison C, Rakeman J, Langley G, Tong S, Tao Y, Uehara A, Queen K, Paden CR, Szymczak W, Orner EP, Nori P, Lai PA, Jacobson JL, Singh HK, Calfee DP, Westblade LF, Vasovic LV, Rand JH, Liu D, Singh V, Burns J, Prasad N, Sell J. Detection and Genetic Characterization of Community-Based SARS-CoV-2 Infections - New York City, March 2020. MMWR Morb Mortal Wkly Rep 2020; 69:918-922. [PMID: 32678072 PMCID: PMC7366849 DOI: 10.15585/mmwr.mm6928a5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Jenkins S, Ledeboer NA, Westblade LF, Burnham CA, Faron ML, Bergman Y, Yee R, Mesich B, Gerstbrein D, Wallace MA, Robertson A, Fauntleroy KA, Klavins AS, Malherbe R, Hsiung A, Simner PJ. Evaluation of NG-Test Carba 5 for Rapid Phenotypic Detection and Differentiation of Five Common Carbapenemase Families: Results of a Multicenter Clinical Evaluation. J Clin Microbiol 2020; 58:e00344-20. [PMID: 32376668 PMCID: PMC7315033 DOI: 10.1128/jcm.00344-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/28/2020] [Indexed: 12/24/2022] Open
Abstract
NG-Test Carba 5 is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of five common carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM) directly from bacterial colonies. The assay is simple to perform and has recently received U.S. Food and Drug Administration clearance. A method comparison study was performed at geographically diverse medical centers (n = 3) in the United States, where 309 Enterobacterales and Pseudomonas aeruginosa isolates were evaluated by NG-Test Carba 5 (NG Biotech, Guipry, France), the Xpert Carba-R assay (Cepheid, Inc., Sunnyvale, CA), the modified carbapenem inactivation method (mCIM), the EDTA-modified carbapenem inactivation method, and disk diffusion with carbapenems. Colonies from tryptic soy agar with 5% sheep blood (blood agar) and MacConkey agar were tested, and the results were compared to those obtained by a composite reference method. Additionally, a fourth medical center performed a medium comparison study by evaluating the performance characteristics of NG-Test Carba 5 from blood, MacConkey, and Mueller-Hinton agars with 110 isolates of Enterobacterales and P. aeruginosa These results were compared to the expected genotypic and mCIM results. For the multicenter method comparison study, the overall positive percent agreement (PPA) and the overall negative percent agreement (NPA) of NG-Test Carba 5 with the composite reference method were 100% for both blood and MacConkey agars. The medium comparison study at the fourth site showed that the PPA ranged from 98.9% to 100% and that the NPA ranged from 95.2% to 100% for blood, MacConkey, and Mueller-Hinton agars. NG-Test Carba 5 accurately detected and differentiated five common carbapenemase families from Enterobacterales and P. aeruginosa colonies on commonly used agar media. The results of this test will support a streamlined laboratory work flow and will expedite therapeutic and infection control decisions.
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Affiliation(s)
| | | | | | - C A Burnham
- Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | | | - Yehudit Bergman
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebecca Yee
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brian Mesich
- Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | | | - Meghan A Wallace
- Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | | | | | | | | | | | - Patricia J Simner
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Butler DJ, Mozsary C, Meydan C, Danko D, Foox J, Rosiene J, Shaiber A, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Westover CD, Ryon K, Young B, Bhattacharya C, Ruggiero P, Langhorst BW, Tanner N, Gawrys J, Meleshko D, Xu D, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Schwartz RE, Iftner A, Bezdan D, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Hajirasouliha I, Horner SM, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Levy S, Wu S, Tatonetti N, Imielinski M, Rennert H, Mason CE. Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions. bioRxiv 2020:2020.04.20.048066. [PMID: 32511352 PMCID: PMC7255793 DOI: 10.1101/2020.04.20.048066] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.
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Affiliation(s)
- Daniel J. Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | | | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- Tri-Institutional Computational Biol. & Medicine Program, Weill Cornell Medicine, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
| | - Joel Rosiene
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Alon Shaiber
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A. Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, NY, USA
| | - Craig D. Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
| | | | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- Tri-Institutional Computational Biol. & Medicine Program, Weill Cornell Medicine, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, NY, USA
| | | | - Amos J. Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institute of Health, MD, USA
| | | | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | | | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Stacy M. Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, NC, USA
- Department of Medicine, Duke University Medical Center, NC, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Mirella Salvatore
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, NY, USA
| | - Marcin Imielinski
- New York Genome Center, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, NY, USA
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, NY, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, NY, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, NY, USA
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Wang R, Vemulapati S, Westblade LF, Glesby MJ, Mehta S, Erickson D. cAST: Capillary-Based Platform for Real-Time Phenotypic Antimicrobial Susceptibility Testing. Anal Chem 2020; 92:2731-2738. [PMID: 31944675 DOI: 10.1021/acs.analchem.9b04991] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance is recognized as one of the greatest emerging threats to public health. Antimicrobial resistant (AMR) microorganisms affect nearly 2 million people a year in the United States alone and place an estimated $20 billion burden on the healthcare system. The rise of AMR microorganisms can be attributed to a combination of overprescription of antimicrobials and a lack of accessible diagnostic methods. Delayed diagnosis is one of the primary reasons for empiric therapy, and diagnostic methods that enable rapid and accurate results are highly desirable to facilitate evidence-based treatment. This is particularly true for clinical situations at the point-of-care where access to state-of-the-art diagnostic equipment is scarce. Here, we present a capillary-based antimicrobial susceptibility testing platform (cAST), a unique approach that offers accelerated assessment of antimicrobial susceptibility in a low-cost and simple testing format. cAST delivers an expedited time-to-readout by means of optical assessment of bacteria incubated in a small capillary form factor along with a resazurin dye. cAST was designed using a combination of off-the-shelf and custom 3D-printed parts, making it extremely suitable for use in resource-limited settings. We demonstrate that growth of bacteria in cAST is approximately 25% faster than in a conventional microplate, further validate the diagnostic performance with clinical isolates, and show that cAST can deliver accurate antimicrobial susceptibility test results within 4-8 h.
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Affiliation(s)
- Ruisheng Wang
- Meinig School of Biomedical Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Sasank Vemulapati
- Sibley School of Mechanical and Aerospace Engineering , Cornell University , Ithaca , New York 14853 , United States
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine , Weill Cornell Medicine , New York , New York 10065 , United States.,Division of Infectious Diseases, Department of Medicine , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Marshall J Glesby
- Division of Infectious Diseases, Department of Medicine , Weill Cornell Medicine , New York , New York 10065 , United States
| | - Saurabh Mehta
- Division of Nutritional Sciences , Cornell University , Ithaca , New York 14853 , United States
| | - David Erickson
- Meinig School of Biomedical Engineering , Cornell University , Ithaca , New York 14853 , United States.,Division of Nutritional Sciences , Cornell University , Ithaca , New York 14853 , United States
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Satlin MJ, Westblade LF, Lee JR. Avoiding infections in transplant recipients: does the gut microbiota have a key role? Expert Rev Clin Immunol 2020; 16:113-115. [PMID: 31851851 DOI: 10.1080/1744666x.2019.1706485] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Michael J Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - John R Lee
- Division of Nephrology and Hypertension, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
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Kodiyanplakkal RPL, Laplante JM, Westblade LF, van Besien K, Salvatore M, St George K. Detection and Characterization of Influenza B Virus With Reduced Neuraminidase Susceptibility in a Stem Cell Transplant Recipient. Open Forum Infect Dis 2019; 6:ofz493. [PMID: 32128335 PMCID: PMC7047943 DOI: 10.1093/ofid/ofz493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 10/08/2019] [Accepted: 11/12/2019] [Indexed: 12/30/2022] Open
Abstract
Antiviral-resistant influenza viruses in the clinical environment, especially type B, are reported rarely. A stem cell transplant recipient remained influenza B positive for 2 months, despite repeated antiviral treatments. Laboratory tests demonstrated the evolution and persistence of neuraminidase inhibitor-resistant influenza B virus with a substitution at codon 119.
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Affiliation(s)
| | - Jennifer M Laplante
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Lars F Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Koen van Besien
- Division of Hematology Oncology, Weill Cornell Medicine, New York, New York, USA
| | - Mirella Salvatore
- Division of Public Health Programs, Weill Cornell Medicine, New York, New York, USA
| | - Kirsten St George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, USA
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Satlin MJ, Chavda KD, Baker TM, Chen L, Shashkina E, Soave R, Small CB, Jacobs SE, Shore TB, van Besien K, Westblade LF, Schuetz AN, Fowler VG, Jenkins SG, Walsh TJ, Kreiswirth BN. Colonization With Levofloxacin-resistant Extended-spectrum β-Lactamase-producing Enterobacteriaceae and Risk of Bacteremia in Hematopoietic Stem Cell Transplant Recipients. Clin Infect Dis 2019; 67:1720-1728. [PMID: 29701766 DOI: 10.1093/cid/ciy363] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/24/2018] [Indexed: 11/13/2022] Open
Abstract
Background Bacteremia caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) is associated with inadequate empirical therapy and substantial mortality in neutropenic patients. Strategies are needed to identify neutropenic patients at high risk of these infections. Methods From April 2014 to September 2016, we collected perianal swabs, both at admission and weekly thereafter, from patients undergoing hematopoietic stem cell transplantation (HSCT). Patients received prophylactic levofloxacin while neutropenic. Swabs were plated onto selective agar, colonies were identified and underwent antimicrobial susceptibility testing, and phenotypic ESBL testing and polymerase chain reaction for β-lactamase genes were performed on ceftriaxone-resistant Enterobacteriaceae. We then determined the prevalence of pre-transplant ESBL-E colonization and risk of ESBL-E bacteremia. Colonizing and bloodstream isolates from patients with ESBL-E bacteremia underwent multilocus sequence typing and pulsed-field gel electrophoresis. Results We analyzed 312 patients, including 212 allogeneic and 100 autologous HSCT recipients. Ten percent (31/312) of patients had pre-transplant ESBL-E colonization. Susceptibility rates of colonizing ESBL-E were: levofloxacin, 25%; cefepime, 9%; piperacillin-tazobactam, 84%; and meropenem, 97%. Of 31 patients colonized with ESBL-E pre-transplant, 10 (32%) developed ESBL-E bacteremia during their transplant admission, compared to 1 (0.4%) of 281 patients not colonized with ESBL-E (P < .001). All bloodstream ESBL-E were levofloxacin-resistant and colonizing and bloodstream isolates from individual patients had identical genotypic profiles. Conclusions HSCT recipients who are colonized with levofloxacin-resistant ESBL-E pre-transplant and receive levofloxacin prophylaxis have high rates of bacteremia from their colonizing strain during neutropenia. Assessing for ESBL-E colonization in neutropenic patients could lead to optimization of empirical antibacterial therapy.
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Affiliation(s)
- Michael J Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
| | - Kalyan D Chavda
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark
| | - Thomas M Baker
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Clinical Immunology, Janssen Research & Development, Spring House, Pennsylvania
| | - Liang Chen
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark
| | - Elena Shashkina
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark
| | - Rosemary Soave
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
| | - Catherine B Small
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York
| | - Samantha E Jacobs
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Tsiporah B Shore
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Koen van Besien
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, New York
| | - Lars F Westblade
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Audrey N Schuetz
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York.,Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Vance G Fowler
- Division of Infectious Diseases, Duke University Medical Center, Durham, North Carolina
| | - Stephen G Jenkins
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Thomas J Walsh
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York.,Departments of Pediatrics and Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Barry N Kreiswirth
- Public Health Research Institute, Rutgers New Jersey Medical School, Newark
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49
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Westblade LF, Satlin MJ, Albakry S, Botticelli B, Robertson A, Alston T, Magruder M, Zhang LT, Edusei E, Chan K, Lubetzky M, Dadhania DM, Pamer EG, Suthanthiran M, Lee JR. Gastrointestinal pathogen colonization and the microbiome in asymptomatic kidney transplant recipients. Transpl Infect Dis 2019; 21:e13167. [PMID: 31502737 DOI: 10.1111/tid.13167] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/07/2019] [Accepted: 09/01/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND In kidney transplant recipients, gastrointestinal (GI) pathogens in feces are only evaluated during diarrheal episodes. Little is known about the prevalence of GI pathogens in asymptomatic individuals in this population. METHODS We recruited 142 kidney transplant recipients who provided a non-diarrheal fecal sample within the first 10 days after transplantation. The specimens were evaluated for GI pathogens using the BioFire® FilmArray® GI Panel (BioFire Diagnostics, LLC), which tests for 22 pathogens. The fecal microbiome was also characterized using 16S rRNA gene sequencing of the V4-V5 hypervariable region. We evaluated whether detection of Clostridioides difficile and other GI pathogens was associated with post-transplant diarrhea within the first 3 months after transplantation. RESULTS Among the 142 subjects, a potential pathogen was detected in 43 (30%) using the GI Panel. The most common organisms detected were C difficile (n = 24, 17%), enteropathogenic Escherichia coli (n = 8, 6%), and norovirus (n = 5, 4%). Detection of a pathogen on the GI panel or detection of C difficile alone was not associated with future post-transplant diarrhea (P > .05). The estimated number of gut bacterial species was significantly lower in subjects colonized with C difficile than those not colonized with a GI pathogen (P = .01). CONCLUSION Colonization with GI pathogens, particularly C difficile, is common at the time of kidney transplantation but does not predict subsequent diarrhea. Detection of C difficile carriage was associated with decreased microbial diversity and may be a biomarker of gut dysbiosis.
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Affiliation(s)
- Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Satlin
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shady Albakry
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Brittany Botticelli
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Amy Robertson
- NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Tricia Alston
- NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Matthew Magruder
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Lisa T Zhang
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Emmanuel Edusei
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Kevin Chan
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA
| | - Michelle Lubetzky
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA.,Department of Transplantation Medicine, Weill Cornell Medical Center, NewYork-Presbyterian Hospital, New York, NY, USA
| | - Darshana M Dadhania
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA.,Department of Transplantation Medicine, Weill Cornell Medical Center, NewYork-Presbyterian Hospital, New York, NY, USA
| | - Eric G Pamer
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA.,Department of Transplantation Medicine, Weill Cornell Medical Center, NewYork-Presbyterian Hospital, New York, NY, USA
| | - John R Lee
- Division of Nephrology and Hypertension, NewYork Presbyterian Hospital - Weill Cornell Medical Center, New York, NY, USA.,Department of Transplantation Medicine, Weill Cornell Medical Center, NewYork-Presbyterian Hospital, New York, NY, USA
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50
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Morales A, Mathur-Wagh U, Tran A, Cui I, DeSimone RA, Jenkins SG, Westblade LF, Jones S. Cavitary Pulmonary Nodules in an Immunocompromised Patient With Urothelial Carcinoma of the Bladder. Clin Infect Dis 2019; 67:1631-1634. [PMID: 30376101 PMCID: PMC7448926 DOI: 10.1093/cid/ciy270] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Ayana Morales
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York
| | - Usha Mathur-Wagh
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York
| | - Anthony Tran
- New York City Department of Health and Mental Hygiene, New York
| | - Isabelle Cui
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York
| | - Robert A DeSimone
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York
| | - Stephen G Jenkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York
| | - Lars F Westblade
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York.,Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York
| | - Sian Jones
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York
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