1
|
Huynh DN, Shah PJ, Greenlee SB, Long SW, Alsafadi MY. Evaluation of computerized clinical decision support system to reduce unnecessary nasal methicillin-resistant Staphylococcus aureus (MRSA) polymerase chain reaction (PCR) testing. Infect Control Hosp Epidemiol 2024; 45:537-539. [PMID: 38084594 DOI: 10.1017/ice.2023.256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
Our health system implemented a novel clinical decision-support system to reduce unnecessary duplicate nasal methicillin-resistant Staphylococcus aureus (MRSA) polymerase chain reaction (PCR) orders. In an 8-month period, the rate of duplicate MRSA PCR orders within 7 days declined from 4.7% (370 of 7,861) to 1.2% (120 of 9,833).
Collapse
Affiliation(s)
- Duc N Huynh
- Department of Pharmacy, Houston Methodist Sugar Land Hospital, Sugar Land, Texas
| | - Punit J Shah
- Department of Pharmacy, Houston Methodist Sugar Land Hospital, Sugar Land, Texas
| | - Sage B Greenlee
- Department of Pharmacy, University of Utah Health, Salt Lake City, Utah
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | | |
Collapse
|
2
|
Beres SB, Olsen RJ, Long SW, Langley R, Williams T, Erlendsdottir H, Smith A, Kristinsson KG, Musser JM. Increase in invasive Streptococcus pyogenes M1 infections with close evolutionary genetic relationship, Iceland and Scotland, 2022 to 2023. Euro Surveill 2024; 29:2400129. [PMID: 38551096 PMCID: PMC10979525 DOI: 10.2807/1560-7917.es.2024.29.13.2400129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/01/2024] Open
Abstract
Group A Streptococcus isolates of the recently described M1UK clade have emerged to cause human infections in several European countries and elsewhere. Full-genome sequence analysis of M1 isolates discovered a close genomic relationship between some isolates from Scotland and the majority of isolates from Iceland causing serious infections in 2022 and 2023. Phylogenetic analysis strongly suggests that an isolate from or related to Scotland was the precursor to an M1UK variant responsible for almost all recent M1 infections in Iceland.
Collapse
Affiliation(s)
- Stephen B Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - S Wesley Long
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ross Langley
- Department of Paediatric Respiratory and Sleep Medicine, Royal Hospital for Children, Glasgow, Scotland
| | - Thomas Williams
- Department of Child Life and Health, University of Edinburgh, Edinburgh, Scotland
| | - Helga Erlendsdottir
- Department of Clinical Microbiology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Andrew Smith
- College of Medical, Veterinary and Life Sciences, Glasgow Dental Hospital and School, University of Glasgow, Glasgow, Scotland
- Scottish Microbiology Reference Laboratory, New Lister Building, Glasgow, Scotland
| | - Karl G Kristinsson
- Department of Clinical Microbiology, Landspitali - the National University Hospital of Iceland, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, United States
- Departments of Pathology and Laboratory Medicine and Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| |
Collapse
|
3
|
Kochan TJ, Nozick SH, Valdes A, Mitra SD, Cheung BH, Lebrun-Corbin M, Medernach RL, Vessely MB, Mills JO, Axline CMR, Nelson JA, VanGosen EM, Ward TJ, Ozer EA, van Duin D, Chen L, Kreiswirth BN, Long SW, Musser JM, Bulman ZP, Wunderink RG, Hauser AR. Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence. Nat Commun 2023; 14:7962. [PMID: 38042959 PMCID: PMC10693551 DOI: 10.1038/s41467-023-43802-1] [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: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Klebsiella pneumoniae has been classified into two types, classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). cKP isolates are highly diverse and important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP isolates are sensitive to most antibiotics but are highly virulent, causing community-acquired infections in healthy individuals. The virulence phenotype of hvKP is associated with pathogenicity loci responsible for siderophore and hypermucoid capsule production. Recently, convergent strains of K. pneumoniae, which possess features of both cKP and hvKP, have emerged and are cause of much concern. Here, we screen the genomes of 2,608 multidrug-resistant K. pneumoniae isolates from the United States and identify 47 convergent isolates. We perform phenotypic and genomic characterization of 12 representative isolates. These 12 convergent isolates contain a variety of antimicrobial resistance plasmids and virulence plasmids. Most convergent isolates contain aerobactin biosynthesis genes and produce more siderophores than cKP isolates but not more capsule. Unexpectedly, only 1 of the 12 tested convergent isolates has a level of virulence consistent with hvKP isolates in a murine pneumonia model. These findings suggest that additional studies should be performed to clarify whether convergent strains are indeed more virulent than cKP in mouse and human infections.
Collapse
Affiliation(s)
- Travis J Kochan
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aliki Valdes
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeleine B Vessely
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jori O Mills
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christopher M R Axline
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Julia A Nelson
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ethan M VanGosen
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Timothy J Ward
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| |
Collapse
|
4
|
Hron JD, Lehmann CU, Long SW, Pageler NM, Kannry J, Levy B, Leu MG. Creation and Evaluation of a Clinical Informatics Match: Initial Findings. Appl Clin Inform 2023; 14:973-980. [PMID: 38092359 PMCID: PMC10719044 DOI: 10.1055/s-0043-1777000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/12/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Clinical Informatics (CI) fellowship programs utilize the Electronic Residency Application Service (ERAS) to gather applications but until recently used an American Medical Informatics Association (AMIA) member-developed, simultaneous offer-acceptance process to match fellowship applicants to programs. In 2021, program directors collaborated with the AMIA to develop a new match to improve the process. OBJECTIVE Describe the results of the first 2 years of the match and address opportunities for improvement. METHODS We obtained applicant data for fellowship applicants in 2021 and 2022 from the ERAS and match data for the same years from the AMIA. We analyzed our data using descriptive statistics. RESULTS There were 159 unique applicants over the 2-year period. Applicants submitted 2,178 applications with a median of 10 per applicant (interquartile range [IQR] 3-20). One hundred and four applicants (65.4%) participated in the match and ranked a median of seven programs (2-12). Forty-two programs in 2021 and 47 programs in 2022 offered a combined total 153 positions in the match. Participating programs ranked a median of eight applicants per year (IQR 5-11). Of participating applicants, 95 (91.3%) successfully matched and of those 66 (69.5%) received their top choice. Thirty-two programs (76.2%) matched at least one candidate in 2021 and 33 programs (70.2%) matched at least one candidate in 2022. In both years, 24 programs filled all available slots (57.1% in 2021 and 51.1% in 2022). CONCLUSION Applicants were extremely successful in the new match, which successfully addressed most of the challenges of the simultaneous offer-acceptance process identified by program directors. However, applicant attrition resulted in a quarter of programs going unmatched. Although many programs still filled slots outside the match, fellowship slots may remain unfilled while the CI practice pathway remains open.
Collapse
Affiliation(s)
- Jonathan D. Hron
- Division of General Pediatrics, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States
| | - Christoph U. Lehmann
- Clinical Informatics Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, United States
| | - Natalie M. Pageler
- Division of Clinical Informatics, Department of Pediatrics, Stanford School of Medicine, Palo Alto, California, United States
| | - Joseph Kannry
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Bruce Levy
- Steele Institute for Health Innovations, Geisinger Commonwealth School of Medicine, Danville, Pennsylvania, United States
| | - Michael G. Leu
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States
- Division of Clinical Informatics, Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, Washington, United States
- IT Services, UW Medicine Information Technology Services, Seattle, Washington, United States
- Information Technology Department, Seattle Children's Hospital, Seattle, Washington, United States
| |
Collapse
|
5
|
Beres SB, Olsen RJ, Long SW, Eraso JM, Boukthir S, Faili A, Kayal S, Musser JM. Analysis of the Genomics and Mouse Virulence of an Emergent Clone of Streptococcus dysgalactiae Subspecies equisimilis. Microbiol Spectr 2023; 11:e0455022. [PMID: 36971562 PMCID: PMC10100674 DOI: 10.1128/spectrum.04550-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/04/2023] [Indexed: 03/29/2023] Open
Abstract
Streptococcus dysgalactiae subsp. equisimilis is a bacterial pathogen that is increasingly recognized as a cause of severe human infections. Much less is known about the genomics and infection pathogenesis of S. dysgalactiae subsp. equisimilis strains compared to the closely related bacterium Streptococcus pyogenes. To address these knowledge deficits, we sequenced to closure the genomes of seven S. dysgalactiae subsp. equisimilis human isolates, including six that were emm type stG62647. Recently, for unknown reasons, strains of this emm type have emerged and caused an increasing number of severe human infections in several countries. The genomes of these seven strains vary between 2.15 and 2.21 Mbp. The core chromosomes of these six S. dysgalactiae subsp. equisimilis stG62647 strains are closely related, differing on average by only 495 single-nucleotide polymorphisms, consistent with a recent descent from a common progenitor. The largest source of genetic diversity among these seven isolates is differences in putative mobile genetic elements, both chromosomal and extrachromosomal. Consistent with the epidemiological observations of increased frequency and severity of infections, both stG62647 strains studied were significantly more virulent than a strain of emm type stC74a in a mouse model of necrotizing myositis, as assessed by bacterial CFU burden, lesion size, and survival curves. Taken together, our genomic and pathogenesis data show the strains of emm type stG62647 we studied are closely genetically related and have enhanced virulence in a mouse model of severe invasive disease. Our findings underscore the need for expanded study of the genomics and molecular pathogenesis of S. dysgalactiae subsp. equisimilis strains causing human infections. IMPORTANCE Our studies addressed a critical knowledge gap in understanding the genomics and virulence of the bacterial pathogen Streptococcus dysgalactiae subsp. equisimilis. S. dysgalactiae subsp. equisimilis strains are responsible for a recent increase in severe human infections in some countries. We determined that certain S. dysgalactiae subsp. equisimilis strains are genetically descended from a common ancestor and that these strains can cause severe infections in a mouse model of necrotizing myositis. Our findings highlight the need for expanded studies on the genomics and pathogenic mechanisms of this understudied subspecies of the Streptococcus family.
Collapse
Affiliation(s)
- Stephen B. Beres
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
| | - Randall J. Olsen
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - S. Wesley Long
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Jesus M. Eraso
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Sarrah Boukthir
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
| | - Ahmad Faili
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Pharmacie, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - Samer Kayal
- CHU de Rennes, Service de Bacteriologie-Hygiène Hospitalière, Rennes, France
- INSERM, CIC 1414, Rennes, France
- Université Rennes 1, Faculté de Médecine, Rennes, France
- Chemistry, Oncogenesis, Stress, and Signaling, INSERM 1242, Rennes, France
| | - James M. Musser
- Laboratory of Molecular and Translational Human Infectious Disease Research, Center for Infectious Diseases, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| |
Collapse
|
6
|
Hsu JWC, Christensen P, Ge Y, Long SW. Classification of cervical biopsy free-text diagnoses through linear-classifier based natural language processing. J Pathol Inform 2022; 13:100123. [PMID: 36268101 PMCID: PMC9577054 DOI: 10.1016/j.jpi.2022.100123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Routine cervical cancer screening has significantly decreased the incidence and mortality of cervical cancer. As selection of proper screening modalities depends on well-validated clinical decision algorithms, retrospective review correlating cytology and HPV test results with cervical biopsy diagnosis is essential for validating and revising these algorithms to changing technologies, demographics, and optimal clinical practices. However, manual categorization of the free-text biopsy diagnosis into discrete categories is extremely laborious due to the overwhelming number of specimens, which may lead to significant error and bias. Advances in machine learning and natural language processing (NLP), particularly over the last decade, have led to significant accomplishments and impressive performance in computer-based classification tasks. In this work, we apply an efficient version of an NLP framework, FastText™, to an annotated cervical biopsy dataset to create a supervised classifier that can assign accurate biopsy categories to free-text biopsy interpretations with high concordance to manually annotated data (>99.6%). We present cases where the machine-learning classifier disagrees with previous annotations and examine these discrepant cases after referee review by an expert pathologist. We also show that the classifier is robust on an untrained external dataset, achieving a concordance of 97.7%. In conclusion, we demonstrate a useful application of NLP to a real-world pathology classification task and highlight the benefits and limitations of this approach.
Collapse
Affiliation(s)
- Jim Wei-Chun Hsu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Paul Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Yimin Ge
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Corresponding author at: Houston Methodist Hospital, 6565 Fannin St, Houston, TX 77004, USA.
| |
Collapse
|
7
|
Christensen PA, Olsen RJ, Long SW, Snehal R, Davis JJ, Ojeda Saavedra M, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Mangham R, Pena S, Trinh T, Kinskey JC, Williams G, Olson R, Gollihar J, Musser JM. Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas. Am J Pathol 2022; 192:642-652. [PMID: 35123975 PMCID: PMC8812084 DOI: 10.1016/j.ajpath.2022.01.007] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 12/19/2022]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to dramatically alter the landscape of the coronavirus disease 2019 (COVID-19) pandemic. The recently described variant of concern designated Omicron (B.1.1.529) has rapidly spread worldwide and is now responsible for the majority of COVID-19 cases in many countries. Because Omicron was recognized recently, many knowledge gaps exist about its epidemiology, clinical severity, and disease course. A genome sequencing study of SARS-CoV-2 in the Houston Methodist health care system identified 4468 symptomatic patients with infections caused by Omicron from late November 2021 through January 5, 2022. Omicron rapidly increased in only 3 weeks to cause 90% of all new COVID-19 cases, and at the end of the study period caused 98% of new cases. Compared with patients infected with either Alpha or Delta variants in our health care system, Omicron patients were significantly younger, had significantly increased vaccine breakthrough rates, and were significantly less likely to be hospitalized. Omicron patients required less intense respiratory support and had a shorter length of hospital stay, consistent with on average decreased disease severity. Two patients with Omicron stealth sublineage BA.2 also were identified. The data document the unusually rapid spread and increased occurrence of COVID-19 caused by the Omicron variant in metropolitan Houston, Texas, and address the lack of information about disease character among US patients.
Collapse
Affiliation(s)
- Paul A Christensen
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Richard Snehal
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Matthew Ojeda Saavedra
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Regan Mangham
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Sindy Pena
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Trina Trinh
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Jacob C Kinskey
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Guy Williams
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Jimmy Gollihar
- Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - James M Musser
- Laboratory of Molecular and Translational Human Infectious Diseases Research, Houston Methodist Hospital, Houston, Texas; Laboratory of Antibody Discovery and Accelerated Protein Therapeutics, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
8
|
Christensen PA, Olsen RJ, Long SW, Subedi S, Davis JJ, Hodjat P, Walley DR, Kinskey JC, Ojeda Saavedra M, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Mangham R, Pena S, Trinh T, Yerramilli P, Nguyen M, Olson R, Snehal R, Gollihar J, Musser JM. Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas. Am J Pathol 2022. [PMID: 34774517 DOI: 10.1101/2021.07.19.21260808] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.
Collapse
Affiliation(s)
- Paul A Christensen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - James J Davis
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Parsa Hodjat
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Debbie R Walley
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jacob C Kinskey
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Matthew Ojeda Saavedra
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Regan Mangham
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sindy Pena
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Trina Trinh
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Prasanti Yerramilli
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Robert Olson
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Richard Snehal
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jimmy Gollihar
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; DEVCOM Army Research Laboratory-South, Austin, Texas
| | - James M Musser
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
9
|
Christensen PA, Olsen RJ, Long SW, Subedi S, Davis JJ, Hodjat P, Walley DR, Kinskey JC, Ojeda Saavedra M, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Mangham R, Pena S, Trinh T, Yerramilli P, Nguyen M, Olson R, Snehal R, Gollihar J, Musser JM. Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas. Am J Pathol 2022; 192:320-331. [PMID: 34774517 PMCID: PMC8580569 DOI: 10.1016/j.ajpath.2021.10.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022]
Abstract
Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes from samples acquired March 15, 2021, through September 20, 2021, in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.
Collapse
Affiliation(s)
- Paul A Christensen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - James J Davis
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Parsa Hodjat
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Debbie R Walley
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jacob C Kinskey
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Matthew Ojeda Saavedra
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Regan Mangham
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Sindy Pena
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Trina Trinh
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Prasanti Yerramilli
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Robert Olson
- Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Richard Snehal
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jimmy Gollihar
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; DEVCOM Army Research Laboratory-South, Austin, Texas
| | - James M Musser
- Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
10
|
Davis JJ, Long SW, Christensen PA, Olsen RJ, Olson R, Shukla M, Subedi S, Stevens R, Musser JM. Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Microbiol Spectr 2021; 9:e0180321. [PMID: 34878296 DOI: 10.1101/2021.09.27.461949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses. IMPORTANCE ARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.
Collapse
Affiliation(s)
- James J Davis
- Division of Data Science and Learning, Argonne National Laboratorygrid.187073.a, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - S Wesley Long
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A Christensen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J Olsen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Robert Olson
- Division of Data Science and Learning, Argonne National Laboratorygrid.187073.a, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Maulik Shukla
- Division of Data Science and Learning, Argonne National Laboratorygrid.187073.a, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Sishir Subedi
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rick Stevens
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratorygrid.187073.a, Argonne, Illinois, USA
- Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - James M Musser
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| |
Collapse
|
11
|
Davis JJ, Long SW, Christensen PA, Olsen RJ, Olson R, Shukla M, Subedi S, Stevens R, Musser JM. Analysis of the ARTIC Version 3 and Version 4 SARS-CoV-2 Primers and Their Impact on the Detection of the G142D Amino Acid Substitution in the Spike Protein. Microbiol Spectr 2021; 9:e0180321. [PMID: 34878296 PMCID: PMC8653831 DOI: 10.1128/spectrum.01803-21] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 10/07/2021] [Accepted: 11/05/2021] [Indexed: 12/21/2022] Open
Abstract
The ARTIC Network provides a common resource of PCR primer sequences and recommendations for amplifying SARS-CoV-2 genomes. The initial tiling strategy was developed with the reference genome Wuhan-01, and subsequent iterations have addressed areas of low amplification and sequence drop out. Recently, a new version (V4) was released, based on new variant genome sequences, in response to the realization that some V3 primers were located in regions with key mutations. Herein, we compare the performance of the ARTIC V3 and V4 primer sets with a matched set of 663 SARS-CoV-2 clinical samples sequenced with an Illumina NovaSeq 6000 instrument. We observe general improvements in sequencing depth and quality, and improved resolution of the SNP causing the D950N variation in the spike protein. Importantly, we also find nearly universal presence of spike protein substitution G142D in Delta-lineage samples. Due to the prior release and widespread use of the ARTIC V3 primers during the initial surge of the Delta variant, it is likely that the G142D amino acid substitution is substantially underrepresented among early Delta variant genomes deposited in public repositories. In addition to the improved performance of the ARTIC V4 primer set, this study also illustrates the importance of the primer scheme in downstream analyses. IMPORTANCE ARTIC Network primers are commonly used by laboratories worldwide to amplify and sequence SARS-CoV-2 present in clinical samples. As new variants have evolved and spread, it was found that the V3 primer set poorly amplified several key mutations. In this report, we compare the results of sequencing a matched set of samples with the V3 and V4 primer sets. We find that adoption of the ARTIC V4 primer set is critical for accurate sequencing of the SARS-CoV-2 spike region. The absence of metadata describing the primer scheme used will negatively impact the downstream use of publicly available SARS-Cov-2 sequencing reads and assembled genomes.
Collapse
Affiliation(s)
- James J. Davis
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - S. Wesley Long
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A. Christensen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J. Olsen
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Robert Olson
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Maulik Shukla
- Division of Data Science and Learning, Argonne National Laboratory, Lemont, Illinois, USA
- University of Chicago Consortium for Advanced Science and Engineering, Chicago, Illinois, USA
| | - Sishir Subedi
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Rick Stevens
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - James M. Musser
- Center for Infectious Diseases, Laboratory of Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Departments of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Departments of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| |
Collapse
|
12
|
Olsen RJ, Christensen PA, Long SW, Subedi S, Hodjat P, Olson R, Nguyen M, Davis JJ, Yerramilli P, Saavedra MO, Pruitt L, Reppond K, Shyer MN, Cambric J, Gadd R, Thakur RM, Batajoo A, Finkelstein IJ, Gollihar J, Musser JM. Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences. Am J Pathol 2021; 191:1754-1773. [PMID: 34303698 PMCID: PMC8299152 DOI: 10.1016/j.ajpath.2021.07.002] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022]
Abstract
Certain genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of substantial concern because they may be more transmissible or detrimentally alter the pandemic course and disease features in individual patients. SARS-CoV-2 genome sequences from 12,476 patients in the Houston Methodist health care system diagnosed from January 1 through May 31, 2021 are reported here. Prevalence of the B.1.1.7 (Alpha) variant increased rapidly and caused 63% to 90% of new cases in the latter half of May. Eleven B.1.1.7 genomes had an E484K replacement in spike protein, a change also identified in other SARS-CoV-2 lineages. Compared with non-B.1.1.7-infected patients, individuals with B.1.1.7 had a significantly lower cycle threshold (a proxy for higher virus load) and significantly higher hospitalization rate. Other variants [eg, B.1.429 and B.1.427 (Epsilon), P.1 (Gamma), P.2 (Zeta), and R.1] also increased rapidly, although the magnitude was less than that in B.1.1.7. Twenty-two patients infected with B.1.617.1 (Kappa) or B.1.617.2 (Delta) variants had a high rate of hospitalization. Breakthrough cases (n = 207) in fully vaccinated patients were caused by a heterogeneous array of virus genotypes, including many not currently designated variants of interest or concern. In the aggregate, this study delineates the trajectory of SARS-CoV-2 variants circulating in a major metropolitan area, documents B.1.1.7 as the major cause of new cases in Houston, TX, and heralds the arrival of B.1.617 variants in the metroplex.
Collapse
Affiliation(s)
- Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Parsa Hodjat
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Matthew O Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ryan Gadd
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Rashi M Thakur
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Akanksha Batajoo
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Combat Capabilities Development Command (CCDC) Army Research Laboratory-South, University of Texas, Austin, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
13
|
Long SW, Olsen RJ, Christensen PA, Subedi S, Olson R, Davis JJ, Saavedra MO, Yerramilli P, Pruitt L, Reppond K, Shyer MN, Cambric J, Finkelstein IJ, Gollihar J, Musser JM. Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern. Am J Pathol 2021; 191:983-992. [PMID: 33741335 PMCID: PMC7962948 DOI: 10.1016/j.ajpath.2021.03.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
Since the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes. In late 2020, several variants of concern emerged globally, including the UK variant (B.1.1.7), the South Africa variant (B.1.351), Brazil variants (P.1 and P.2), and two related California variants of interest (B.1.429 and B.1.427). These variants are believed to have enhanced transmissibility. For the South Africa and Brazil variants, there is evidence that mutations in spike protein permit it to escape from some vaccines and therapeutic monoclonal antibodies. On the basis of our extensive genome sequencing program involving 20,453 coronavirus disease 2019 patient samples collected from March 2020 to February 2021, we report identification of all six of these SARS-CoV-2 variants among Houston Methodist Hospital (Houston, TX) patients residing in the greater metropolitan area. Although these variants are currently at relatively low frequency (aggregate of 1.1%) in the population, they are geographically widespread. Houston is the first city in the United States in which active circulation of all six current variants of concern has been documented by genome sequencing. As vaccine deployment accelerates, increased genomic surveillance of SARS-CoV-2 is essential to understanding the presence, frequency, and medical impact of consequential variants and their patterns and trajectory of dissemination.
Collapse
Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Robert Olson
- Consortium for Advanced Science and Engineering, 22 University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - James J Davis
- Consortium for Advanced Science and Engineering, 22 University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Kristina Reppond
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Madison N Shyer
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Jessica Cambric
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas; Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, New York, New York.
| |
Collapse
|
14
|
Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, and Houston Methodist Hospital, Houston, Texas, USA.,Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA
| |
Collapse
|
15
|
Abstract
Delayed administration of active anti-infective therapy is associated with increased rates of adverse events, mortality, and costs among sepsis patients. Inherent limitations of conventional culture identification methods and the lengthy turnaround time of antimicrobial susceptibility testing are significant barriers to the timely delivery of life-saving therapy, particularly among antibiotic-resistant infections. Culture-independent diagnostic techniques that detect pathogens and antimicrobial resistance genes within clinical samples present a tremendous benefit to timely diagnosis and management of patients. Improved outcomes for rapid intervention with rapid diagnostics have been documented and include decreased mortality rates, decreased health care delivery costs, and faster delivery of appropriate therapeutics.
Collapse
Affiliation(s)
- Taryn A Eubank
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - S W Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Katherine K Perez
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA.,Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| |
Collapse
|
16
|
Salazar E, Kuchipudi SV, Christensen PA, Eagar T, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers D, Lavinder J, Gollihar J, Cardona J, Ippolito G, Nissly R, Bird I, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary I, Cattadori IM, Hudson PJ, Josleyn NM, Prugar L, Huie K, Herbert A, Bernard DW, Dye JM, Kapur V, Musser JM. Convalescent plasma anti-SARS-CoV-2 spike protein ectodomain and receptor-binding domain IgG correlate with virus neutralization. J Clin Invest 2020; 130:6728-6738. [PMID: 32910806 PMCID: PMC7685744 DOI: 10.1172/jci141206] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [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: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the urgent need for assays that detect protective levels of neutralizing antibodies. We studied the relationship among anti-spike ectodomain (anti-ECD), anti-receptor-binding domain (anti-RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by 2 in vitro assays using convalescent plasma samples from 68 patients with COVID-19. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers and in vitro VN titers. The probability of a VN titer of ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment, was ≥80% when anti-RBD or anti-ECD titers were ≥1:1350. Of all donors, 37% lacked VN titers of ≥160. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease VN or IgG titers. Analysis of 2814 asymptomatic adults found 73 individuals with anti-ECD IgG titers of ≥1:50 and strong positive correlation with anti-RBD and VN titers. Fourteen of these individuals had VN titers of ≥1:160, and all of them had anti-RBD titers of ≥1:1350. We conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titers of ≥1:1350 may provide critical information about protection against COVID-19 disease.
Collapse
Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Todd Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Dalton Towers
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Jimmy Gollihar
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Jose Cardona
- Combat Capabilities Development Command Army Research Laboratory — South, University of Texas, Austin, Texas, USA
| | - Gregory Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas, USA
| | - Ruth Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Ian Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | - Abhinay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, and
| | | | | | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Nicole M. Josleyn
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Laura Prugar
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Kathleen Huie
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Andrew Herbert
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - John M. Dye
- US Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences and
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania, USA
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas, USA
| |
Collapse
|
17
|
Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. mBio 2020; 11:e02707-20. [PMID: 33127862 PMCID: PMC7642679 DOI: 10.1128/mbio.02707-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [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: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 01/18/2023] Open
Abstract
We sequenced the genomes of 5,085 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains causing two coronavirus disease 2019 (COVID-19) disease waves in metropolitan Houston, TX, an ethnically diverse region with 7 million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston and from viruses recovered in an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotype and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein-the primary target of global vaccine efforts-are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR3022. Our report represents the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.IMPORTANCE There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population of 7 million, is experiencing a massive second disease wave that began in late May 2020. To understand SARS-CoV-2 molecular population genomic architecture and evolution and the relationship between virus genotypes and patient features, we sequenced the genomes of 5,085 SARS-CoV-2 strains from these two waves. Our report provides the first molecular characterization of SARS-CoV-2 strains causing two distinct COVID-19 disease waves.
Collapse
MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Antibodies, Neutralizing/immunology
- Base Sequence
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- COVID-19
- COVID-19 Testing
- Clinical Laboratory Techniques
- Coronavirus Infections/diagnosis
- Coronavirus Infections/epidemiology
- Coronavirus Infections/immunology
- Coronavirus Infections/virology
- Coronavirus RNA-Dependent RNA Polymerase
- Genome, Viral
- Genotype
- Humans
- Machine Learning
- Models, Molecular
- Molecular Diagnostic Techniques
- Pandemics
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/virology
- RNA-Dependent RNA Polymerase/chemistry
- RNA-Dependent RNA Polymerase/genetics
- SARS-CoV-2
- Sequence Analysis, Protein
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Texas/epidemiology
- Viral Nonstructural Proteins/chemistry
- Viral Nonstructural Proteins/genetics
Collapse
Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Paul A Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - David W Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - James J Davis
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois, USA
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hung-Che Kuo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Hoang A T Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - J Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Jule Goike
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chia-Wei Chou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Kamyab Javanmardi
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| |
Collapse
|
18
|
Long SW, Olsen RJ, Christensen PA, Bernard DW, Davis JJ, Shukla M, Nguyen M, Saavedra MO, Yerramilli P, Pruitt L, Subedi S, Kuo HC, Hendrickson H, Eskandari G, Nguyen HAT, Long JH, Kumaraswami M, Goike J, Boutz D, Gollihar J, McLellan JS, Chou CW, Javanmardi K, Finkelstein IJ, Musser JM. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area. medRxiv 2020:2020.09.22.20199125. [PMID: 33024977 PMCID: PMC7536878 DOI: 10.1101/2020.09.22.20199125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that has been linked to increased transmission and infectivity. Patients infected with the Gly614 variant strains had significantly higher virus loads in the nasopharynx on initial diagnosis. We found little evidence of a significant relationship between virus genotypes and altered virulence, stressing the linkage between disease severity, underlying medical conditions, and host genetics. Some regions of the spike protein - the primary target of global vaccine efforts - are replete with amino acid replacements, perhaps indicating the action of selection. We exploited the genomic data to generate defined single amino acid replacements in the receptor binding domain of spike protein that, importantly, produced decreased recognition by the neutralizing monoclonal antibody CR30022. Our study is the first analysis of the molecular architecture of SARS-CoV-2 in two infection waves in a major metropolitan region. The findings will help us to understand the origin, composition, and trajectory of future infection waves, and the potential effect of the host immune response and therapeutic maneuvers on SARS-CoV-2 evolution.
Collapse
Affiliation(s)
- S. Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - Randall J. Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - Paul A. Christensen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - David W. Bernard
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| | - James J. Davis
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, 5801 South Ellis Avenue, Chicago, Illinois, 60637
- Computing, Environment and Life Sciences, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439
| | - Matthew Ojeda Saavedra
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Sishir Subedi
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Hung-Che Kuo
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Heather Hendrickson
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Ghazaleh Eskandari
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Hoang A. T. Nguyen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - J. Hunter Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Muthiah Kumaraswami
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
| | - Jule Goike
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Daniel Boutz
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712
| | - Jimmy Gollihar
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas 78712
| | - Jason S. McLellan
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Chia-Wei Chou
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Kamyab Javanmardi
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
| | - Ilya J. Finkelstein
- Department of Molecular Biosciences and Institute of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712
| | - James M. Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030
- Departments of Pathology and Laboratory Medicine, and Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065
| |
Collapse
|
19
|
Salazar E, Perez KK, Ashraf M, Chen J, Castillo B, Christensen PA, Eubank T, Bernard DW, Eagar TN, Long SW, Subedi S, Olsen RJ, Leveque C, Schwartz MR, Dey M, Chavez-East C, Rogers J, Shehabeldin A, Joseph D, Williams G, Thomas K, Masud F, Talley C, Dlouhy KG, Lopez BV, Hampton C, Lavinder J, Gollihar JD, Maranhao AC, Ippolito GC, Saavedra MO, Cantu CC, Yerramilli P, Pruitt L, Musser JM. Treatment of Coronavirus Disease 2019 (COVID-19) Patients with Convalescent Plasma. Am J Pathol 2020; 190:1680-1690. [PMID: 32473109 PMCID: PMC7251400 DOI: 10.1016/j.ajpath.2020.05.014] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2, has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for >100 years. Patients (n = 25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28, 2020, to April 14, 2020. Patients were transfused with convalescent plasma, obtained from donors with confirmed severe acute respiratory syndrome coronavirus 2 infection who had recovered. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 after transfusion. Clinical improvement was assessed on the basis of a modified World Health Organization six-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains. At day 7 after transfusion with convalescent plasma, nine patients had at least a one-point improvement in clinical scale, and seven of those were discharged. By day 14 after transfusion, 19 (76%) patients had at least a one-point improvement in clinical status, and 11 were discharged. No adverse events as a result of plasma transfusion were observed. Whole genome sequencing data did not identify a strain genotype-disease severity correlation. The data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease.
Collapse
Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Katherine K Perez
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pharmacy, Houston Methodist Hospital, Houston, Texas
| | - Madiha Ashraf
- Division of Infectious Diseases, Department of Clinical Medicine, Houston Methodist Hospital, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Taryn Eubank
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas
| | - David W Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Todd N Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Mary R Schwartz
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Monisha Dey
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Cheryl Chavez-East
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - John Rogers
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Ahmed Shehabeldin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - David Joseph
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Guy Williams
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Karen Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Faisal Masud
- Division of Infectious Diseases, Department of Clinical Medicine, Houston Methodist Hospital, Houston, Texas; Department of Anesthesiology and Critical Care, Houston Methodist Hospital, Houston, Texas
| | - Christina Talley
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Katharine G Dlouhy
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Bevin V Lopez
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Curt Hampton
- Academic Office of Clinical Trials, Houston Methodist Research Institute, Houston, Texas
| | - Jason Lavinder
- Department of Molecular Biosciences, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Jimmy D Gollihar
- Combat Capabilities Development Command (CCDC) Army Research Laboratory-South, University of Texas at Austin, Austin, Texas
| | - Andre C Maranhao
- Department of Molecular Biosciences, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Gregory C Ippolito
- Department of Molecular Biosciences, Dell Medical School, University of Texas at Austin, Austin, Texas; Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Matthew O Saavedra
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Concepcion C Cantu
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Prasanti Yerramilli
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Layne Pruitt
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York; Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas.
| |
Collapse
|
20
|
Hujer AM, Long SW, Olsen RJ, Taracila MA, Rojas LJ, Musser JM, Bonomo RA. Predicting β-lactam resistance using whole genome sequencing in Klebsiella pneumoniae: the challenge of β-lactamase inhibitors. Diagn Microbiol Infect Dis 2020; 98:115149. [PMID: 32858260 DOI: 10.1016/j.diagmicrobio.2020.115149] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/01/2020] [Accepted: 07/18/2020] [Indexed: 11/25/2022]
Abstract
Although multiple antimicrobial resistance (AMR) determinants can confer the same in vitro antimicrobial susceptibility testing (AST) phenotype, their differing effect on optimal therapeutic choices is uncertain. Using a large population-based collection of clinical strains spanning a 3.5-year period, we applied WGS to detect inhibitor resistant (IR), extended-spectrum β-lactamase (ESBL), and carbapenem resistant (CR) β-lactamase (bla) genes and compared the genotype to the AST phenotype in select isolates. All blaNDM-1 (9/9) and the majority of blaNDM-1/OXA-48 (3/4) containing isolates were resistant to CAZ/AVI as predicted by WGS. The combination of ATM and CAZ/AVI restored susceptibility by disk diffusion assay. Unexpectedly, clinical Kp isolates bearing blaKPC-8 (V240G) and blaKPC-14 (G242 and T243 deletion) did not test fully resistant to CAZ/AVI. Lastly, despite the complexity of the β-lactamase background, CAZ/AVI retained potency. Presumed phenotypes conferred by AMR determinants need to be tested if therapeutic decisions are being guided by their presence or absence.
Collapse
Affiliation(s)
- Andrea M Hujer
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Magdalena A Taracila
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - Laura J Rojas
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, TX; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University, Cleveland, OH; Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH; Department of Molecular Biology and Microbiology, Pharmacology, Biochemistry, and the Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH; CWRU-Cleveland VAMC, Center, for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH.
| |
Collapse
|
21
|
Salazar E, Kuchipudi SV, Christensen PA, Eagar TN, Yi X, Zhao P, Jin Z, Long SW, Olsen RJ, Chen J, Castillo B, Leveque C, Towers DM, Lavinder J, Gollihar JD, Cardona J, Ippolito GC, Nissly RH, Bird IM, Greenawalt D, Rossi RM, Gontu A, Srinivasan S, Poojary IB, Cattadori IM, Hudson PJ, Joselyn N, Prugar L, Huie K, Herbert A, Bernard DW, Dye J, Kapur V, Musser JM. Relationship between Anti-Spike Protein Antibody Titers and SARS-CoV-2 In Vitro Virus Neutralization in Convalescent Plasma. bioRxiv 2020:2020.06.08.138990. [PMID: 32577662 PMCID: PMC7302218 DOI: 10.1101/2020.06.08.138990] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ectodomain (ECD) and anti-receptor binding domain (RBD) IgG titers, and SARS-CoV-2 virus neutralization (VN) titers generated by two different in vitro assays using convalescent plasma samples obtained from 68 COVID-19 patients, including 13 who donated plasma multiple times. Only 23% (16/68) of donors had been hospitalized. We also studied 16 samples from subjects found to have anti-spike protein IgG during surveillance screening of asymptomatic individuals. We report a strong positive correlation between both plasma anti-RBD and anti-ECD IgG titers, and in vitro VN titer. Anti-RBD plasma IgG correlated slightly better than anti-ECD IgG titer with VN titer. The probability of a VN titer ≥160 was 80% or greater with anti-RBD or anti-ECD titers of ≥1:1350. Thirty-seven percent (25/68) of convalescent plasma donors lacked VN titers ≥160, the FDA-recommended level for convalescent plasma used for COVID-19 treatment. Dyspnea, hospitalization, and disease severity were significantly associated with higher VN titer. Frequent donation of convalescent plasma did not significantly decrease either VN or IgG titers. Analysis of 2,814 asymptomatic adults found 27 individuals with anti-RBD or anti-ECD IgG titers of ≥1:1350, and evidence of VN ≥1:160. Taken together, we conclude that anti-RBD or anti-ECD IgG titers can serve as a surrogate for VN titers to identify suitable plasma donors. Plasma anti-RBD or anti-ECD titer of ≥1:1350 may provide critical information about protection against COVID-19 disease.
Collapse
Affiliation(s)
- Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Suresh V. Kuchipudi
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
| | - Paul A. Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Todd N. Eagar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Xin Yi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Picheng Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Zhicheng Jin
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - S. Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Randall J. Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| | - Jian Chen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Brian Castillo
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Christopher Leveque
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - Dalton M. Towers
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas at Austin
| | - Jimmy D. Gollihar
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Jose Cardona
- CCDC Army Research Laboratory-South, University of Texas, Austin, Texas
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, University of Texas at Austin
- Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, Texas
| | - Ruth H. Nissly
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Ian M. Bird
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Denver Greenawalt
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Randall M. Rossi
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Abinhay Gontu
- Penn State Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Sreenidhi Srinivasan
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Indira B. Poojary
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - Isabella M. Cattadori
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Peter J. Hudson
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Nicole Joselyn
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Laura Prugar
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Kathleen Huie
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Andrew Herbert
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - David W. Bernard
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
| | - John Dye
- USAMRIID (United States Army Medical Research Institute of Infectious Diseases), Frederick, Maryland
| | - Vivek Kapur
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
- Department of Animal Science, Pennsylvania State University, University Park, Pennsylvania
| | - James M. Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York
- Center for Molecular and Translational Human Infectious Diseases, Houston Methodist Research Institute, Houston, Texas
| |
Collapse
|
22
|
Salazar E, Perez KK, Ashraf M, Chen J, Castillo B, Christensen PA, Eubank T, Bernard DW, Eagar TN, Long SW, Subedi S, Olsen RJ, Leveque C, Schwartz MR, Dey M, Chavez-East C, Rogers J, Shehabeldin A, Joseph D, Williams G, Thomas K, Masud F, Talley C, Dlouhy KG, Lopez BV, Hampton C, Lavinder J, Gollihar JD, Maranhao AC, Ippolito GC, Saavedra MO, Cantu CC, Yerramilli P, Pruitt L, Musser JM. Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas. medRxiv 2020:2020.05.08.20095471. [PMID: 32511574 PMCID: PMC7274255 DOI: 10.1101/2020.05.08.20095471] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for more than 100 years. METHODS Patients (n=25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28 to April 14, 2020. Patients were transfused with convalescent plasma obtained from donors with confirmed SARS-CoV-2 infection and had been symptom free for 14 days. The primary study outcome was safety, and the secondary outcome was clinical status at day 14 post-transfusion. Clinical improvement was assessed based on a modified World Health Organization 6-point ordinal scale and laboratory parameters. Viral genome sequencing was performed on donor and recipient strains. RESULTS At baseline, all patients were receiving supportive care, including anti-inflammatory and anti-viral treatments, and all patients were on oxygen support. At day 7 post-transfusion with convalescent plasma, nine patients had at least a 1-point improvement in clinical scale, and seven of those were discharged. By day 14 post-transfusion, 19 (76%) patients had at least a 1-point improvement in clinical status and 11 were discharged. No adverse events as a result of plasma transfusion were observed. The whole genome sequencing data did not identify a strain genotype-disease severity correlation. CONCLUSIONS The data indicate that administration of convalescent plasma is a safe treatment option for those with severe COVID-19 disease. Randomized, controlled trials are needed to determine its efficacy.
Collapse
|
23
|
Smith KP, Wang H, Durant TJ, Mathison BA, Sharp SE, Kirby JE, Long SW, Rhoads DD. Applications of Artificial Intelligence in Clinical Microbiology Diagnostic Testing. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.clinmicnews.2020.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
24
|
Christensen PA, Subedi S, Pepper K, Hendrickson HL, Li Z, Thomas JS, Long SW, Olsen RJ. Development and validation of Houston Methodist Variant Viewer version 3: updates to our application for interpretation of next-generation sequencing data. JAMIA Open 2020; 3:299-305. [PMID: 32734171 PMCID: PMC7382636 DOI: 10.1093/jamiaopen/ooaa004] [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: 11/18/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 11/13/2022] Open
Abstract
Objectives Informatics tools that support next-generation sequencing workflows are essential to deliver timely interpretation of somatic variants in cancer. Here, we describe significant updates to our laboratory developed bioinformatics pipelines and data management application termed Houston Methodist Variant Viewer (HMVV). Materials and Methods We collected feature requests and workflow improvement suggestions from the end-users of HMVV version 1. Over 1.5 years, we iteratively implemented these features in five sequential updates to HMVV version 3. Results We improved the performance and data throughput of the application while reducing the opportunity for manual data entry errors. We enabled end-user workflows for pipeline monitoring, variant interpretation and annotation, and integration with our laboratory information system. System maintenance was improved through enhanced defect reporting, heightened data security, and improved modularity in the code and system environments. Discussion and Conclusion Validation of each HMVV update was performed according to expert guidelines. We enabled an 8× reduction in the bioinformatics pipeline computation time for our longest running assay. Our molecular pathologists can interpret the assay results at least 2 days sooner than was previously possible. The application and pipeline code are publicly available at https://github.com/hmvv.
Collapse
Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Sishir Subedi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Kristi Pepper
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Zejuan Li
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| |
Collapse
|
25
|
Lu S, Soeung V, Nguyen HAT, Long SW, Musser JM, Palzkill T. Development and Evaluation of a Novel Protein-Based Assay for Specific Detection of KPC β-Lactamases from Klebsiella pneumoniae Clinical Isolates. mSphere 2020; 5:e00918-19. [PMID: 31915233 PMCID: PMC6952207 DOI: 10.1128/msphere.00918-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 12/12/2019] [Indexed: 11/20/2022] Open
Abstract
Carbapenemases confer resistance to nearly all β-lactam antibiotics. The extensive spread of carbapenemase-producing multidrug-resistant bacteria contributes significantly to hospital-acquired infections. We have developed a novel protein-based binding assay that identifies KPC β-lactamases from clinical isolates. We used the protein-protein interaction between KPCs and a soluble β-lactamase inhibitory protein (BLIP) variant, BLIPK74T/W112D, which specifically inhibits KPCs but not other β-lactamases. In this assay, BLIPK74T/W112D was allowed to form complexes with KPC-2 in bacterial cell lysates and then extracted using His tag binding resins. We demonstrated the presence of KPC-2 by monitoring the hydrolysis of a colorimetric β-lactam substrate. Also, to further increase the accuracy of the method, a BLIPK74T/W112D-mediated inhibition assay was developed. The binding and inhibition assays were validated by testing 127 Klebsiella pneumoniae clinical isolates with known genome sequences for the presence of KPC. Our assays identified a total of 32 strains as KPC-2 producers, a result in 100% concordance with genome sequencing predictions. To further simplify the assay and decrease the time to obtain results, the BLIPK74T/W112D protein was tested in combination with the widely used Carba-NP assay. For this purpose, the genome-sequenced K. pneumoniae strains were tested for the presence of carbapenemases with the Carba-NP test with and without the addition of BLIPK74T/W122D The test accurately identified carbapenemase-producing strains and the addition of BLIPK74T/W112D allowed a further determination that the strains contain KPC carbapenemase. Thus, the BLIPK74T/W112D protein is an effective sensor to specifically detect KPC β-lactamases produced by clinical isolates.IMPORTANCE Infections caused by carbapenem-resistant Enterobacteriaceae are associated with high therapeutic failure and mortality rates. Thus, it is critical to rapidly identify clinical isolates expressing KPC β-lactamases to facilitate administration of the correct antibiotic treatment and initiate infection control strategies. To address this problem, we developed a protein-based, KPC-specific binding assay in combination with a cell lysate inhibition assay that provided a 100% identification rate of KPC from clinical isolates of known genomic sequence. In addition, this protein sensor was adapted to the Carba-NP assay to provide a rapid strategy to detect KPC-producing isolates that will facilitate informed treatment of critically ill patients.
Collapse
Affiliation(s)
- Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Victoria Soeung
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Hoang A T Nguyen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
26
|
Nguyen M, Long SW, McDermott PF, Olsen RJ, Olson R, Stevens RL, Tyson GH, Zhao S, Davis JJ. Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella. J Clin Microbiol 2019; 57:e01260-18. [PMID: 30333126 PMCID: PMC6355527 DOI: 10.1128/jcm.01260-18] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/25/2018] [Indexed: 11/20/2022] Open
Abstract
Nontyphoidal Salmonella species are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available for Salmonella strains because of surveillance efforts from public health agencies. In this study, a collection of 5,278 nontyphoidal Salmonella genomes, collected over 15 years in the United States, was used to generate extreme gradient boosting (XGBoost)-based machine learning models for predicting MICs for 15 antibiotics. The MIC prediction models had an overall average accuracy of 95% within ±1 2-fold dilution step (confidence interval, 95% to 95%), an average very major error rate of 2.7% (confidence interval, 2.4% to 3.0%), and an average major error rate of 0.1% (confidence interval, 0.1% to 0.2%). The model predicted MICs with no a priori information about the underlying gene content or resistance phenotypes of the strains. By selecting diverse genomes for the training sets, we show that highly accurate MIC prediction models can be generated with less than 500 genomes. We also show that our approach for predicting MICs is stable over time, despite annual fluctuations in antimicrobial resistance gene content in the sampled genomes. Finally, using feature selection, we explore the important genomic regions identified by the models for predicting MICs. To date, this is one of the largest MIC modeling studies to be published. Our strategy for developing whole-genome sequence-based models for surveillance and clinical diagnostics can be readily applied to other important human pathogens.
Collapse
Affiliation(s)
- Marcus Nguyen
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Patrick F McDermott
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Robert Olson
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA
| | - Rick L Stevens
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA
- Department of Computer Science, University of Chicago, Chicago, Illinois, USA
| | - Gregory H Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, Maryland, USA
| | - James J Davis
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA
- Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, Illinois, USA
| |
Collapse
|
27
|
Christensen PA, Olsen RJ, Perez KK, Cernoch PL, Long SW. Real-time Communication With Health Care Providers Through an Online Respiratory Pathogen Laboratory Report. Open Forum Infect Dis 2019; 5:ofy322. [PMID: 30619910 PMCID: PMC6306568 DOI: 10.1093/ofid/ofy322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 10/04/2018] [Accepted: 11/27/2018] [Indexed: 11/24/2022] Open
Abstract
We implemented a real-time report to distribute respiratory pathogen data for our 8-hospital system to anyone with an Internet connection and a web browser. Real-time access to accurate regional laboratory observation data during an epidemic influenza season can guide diagnostic and therapeutic strategies.
Collapse
Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - Katherine K Perez
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.,Department of Pharmacy, Houston Methodist Hospital, Houston, Texas
| | - Patricia L Cernoch
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| |
Collapse
|
28
|
|
29
|
Christensen P, Long SW, Olsen R, Davis J, Musser J. A Web-Based Respiratory Pathogen Laboratory Report for Summarizing Key Metrics to Stakeholders. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqy112.360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Nguyen M, Brettin T, Long SW, Musser JM, Olsen RJ, Olson R, Shukla M, Stevens RL, Xia F, Yoo H, Davis JJ. Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae. Sci Rep 2018; 8:421. [PMID: 29323230 PMCID: PMC5765115 DOI: 10.1038/s41598-017-18972-w] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [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: 09/27/2017] [Accepted: 12/12/2017] [Indexed: 12/20/2022] Open
Abstract
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics. The overall accuracy of the model, within ±1 two-fold dilution factor, is 92%. Individual accuracies are ≥90% for 15/20 antibiotics. We show that the MICs predicted by the model correlate with known antimicrobial resistance genes. Importantly, the genome-wide approach described in this study offers a way to predict MICs for isolates without knowledge of the underlying gene content. This study shows that machine learning can be used to build a complete in silico MIC prediction panel for K. pneumoniae and provides a framework for building MIC prediction models for other pathogenic bacteria.
Collapse
Affiliation(s)
- Marcus Nguyen
- Northern Illinois University, Computation Science, DeKalb, IL, 60115, USA.,University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Thomas Brettin
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute and Houston Methodist Hospital, Houston, Texas, 77030, USA.,Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Robert Olson
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Maulik Shukla
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Rick L Stevens
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA.,University of Chicago, Department of Computer Science, Chicago, IL, 60439, USA
| | - Fangfang Xia
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - Hyunseung Yoo
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA.,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA
| | - James J Davis
- University of Chicago, Computation Institute, Chicago, IL, 60637, USA. .,Argonne National Laboratory, Computing Environment and Life Sciences, Argonne, IL, 60439, USA.
| |
Collapse
|
31
|
Christensen PA, Ni Y, Bao F, Hendrickson HL, Greenwood M, Thomas JS, Long SW, Olsen RJ. Houston Methodist Variant Viewer: An Application to Support Clinical Laboratory Interpretation of Next-generation Sequencing Data for Cancer. J Pathol Inform 2017; 8:44. [PMID: 29226007 PMCID: PMC5719586 DOI: 10.4103/jpi.jpi_48_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 06/27/2017] [Accepted: 10/12/2017] [Indexed: 01/17/2023] Open
Abstract
Introduction Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist. Although commercial tools for NGS data analysis and interpretation are available, they are often costly, lack key functionality or cannot be customized by the end user. Methods To facilitate NGS data analysis in our clinical molecular diagnostics laboratory, we created a custom bioinformatics tool termed Houston Methodist Variant Viewer (HMVV). HMVV is a Java-based solution that integrates sequencing instrument output, bioinformatics analysis, storage resources and end user interface. Results Compared to the predicate method used in our clinical laboratory, HMVV markedly simplifies the bioinformatics workflow for the molecular technologist and facilitates the variant review by the molecular pathologist. Importantly, HMVV reduces time spent researching the biological significance of the variants detected, standardizes the online resources used to perform the variant investigation and assists generation of the annotated report for the electronic medical record. HMVV also maintains a searchable variant database, including the variant annotations generated by the pathologist, which is useful for downstream quality improvement and research projects. Conclusions HMVV is a clinical grade, low-cost, feature-rich, highly customizable platform that we have made available for continued development by the pathology informatics community.
Collapse
Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Yunyun Ni
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA.,Helix, San Carlos, California 94070, USA
| | - Feifei Bao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Heather L Hendrickson
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Michael Greenwood
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Jessica S Thomas
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| | - Randall J Olsen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, Texas, USA
| |
Collapse
|
32
|
Christensen PA, Lee NE, Thrall MJ, Powell SZ, Chevez-Barrios P, Long SW. RecutClub.com: An Open Source, Whole Slide Image-based Pathology Education System. J Pathol Inform 2017; 8:10. [PMID: 28382224 PMCID: PMC5364738 DOI: 10.4103/jpi.jpi_72_16] [Citation(s) in RCA: 2] [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: 09/23/2016] [Accepted: 01/18/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Our institution's pathology unknown conferences provide educational cases for our residents. However, the cases have not been previously available digitally, have not been collated for postconference review, and were not accessible to a wider audience. Our objective was to create an inexpensive whole slide image (WSI) education suite to address these limitations and improve the education of pathology trainees. MATERIALS AND METHODS We surveyed residents regarding their preference between four unique WSI systems. We then scanned weekly unknown conference cases and study set cases and uploaded them to our custom built WSI viewer located at RecutClub.com. We measured site utilization and conference participation. RESULTS Residents preferred our OpenLayers WSI implementation to Ventana Virtuoso, Google Maps API, and OpenSlide. Over 16 months, we uploaded 1366 cases from 77 conferences and ten study sets, occupying 793.5 GB of cloud storage. Based on resident evaluations, the interface was easy to use and demonstrated minimal latency. Residents are able to review cases from home and from their mobile devices. Worldwide, 955 unique IP addresses from 52 countries have viewed cases in our site. CONCLUSIONS We implemented a low-cost, publicly available repository of WSI slides for resident education. Our trainees are very satisfied with the freedom to preview either the glass slides or WSI and review the WSI postconference. Both local users and worldwide users actively and repeatedly view cases in our study set.
Collapse
Affiliation(s)
- Paul A Christensen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, TX 77030, USA
| | - Nathan E Lee
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, TX 77030, USA
| | - Michael J Thrall
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, TX 77030, USA
| | - Suzanne Z Powell
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, TX 77030, USA
| | - Patricia Chevez-Barrios
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, TX 77030, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Weill Cornell Medical College of Cornell University, Houston, TX 77030, USA
| |
Collapse
|
33
|
Lee GC, Long SW, Musser JM, Beres SB, Olsen RJ, Dallas SD, Nunez YO, Frei CR. Comparative Whole Genome Sequencing of Community-Associated Methicillin-Resistant Staphylococcus aureus
Sequence Type 8 from Primary Care Clinics in a Texas Community. Pharmacotherapy 2015; 35:220-8. [DOI: 10.1002/phar.1536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Grace C. Lee
- College of Pharmacy; The University of Texas at Austin; Austin Texas
- School of Medicine; The University of Texas Health Science Center; San Antonio Texas
| | - S. Wesley Long
- Center for Molecular and Translational Infectious Diseases; Houston Methodist Research Institute; Houston Methodist Hospital; Houston Texas
- Department of Pathology and Genomic Medicine; Houston Methodist Hospital; Houston Texas
| | - James M. Musser
- Center for Molecular and Translational Infectious Diseases; Houston Methodist Research Institute; Houston Methodist Hospital; Houston Texas
- Department of Pathology and Genomic Medicine; Houston Methodist Hospital; Houston Texas
| | - Stephen B. Beres
- Center for Molecular and Translational Infectious Diseases; Houston Methodist Research Institute; Houston Methodist Hospital; Houston Texas
- Department of Pathology and Genomic Medicine; Houston Methodist Hospital; Houston Texas
| | - Randall J. Olsen
- Center for Molecular and Translational Infectious Diseases; Houston Methodist Research Institute; Houston Methodist Hospital; Houston Texas
- Department of Pathology and Genomic Medicine; Houston Methodist Hospital; Houston Texas
| | - Steven D. Dallas
- School of Medicine; The University of Texas Health Science Center; San Antonio Texas
| | - Yury O. Nunez
- College of Pharmacy; The University of Texas at Austin; Austin Texas
- School of Medicine; The University of Texas Health Science Center; San Antonio Texas
| | - Christopher R. Frei
- College of Pharmacy; The University of Texas at Austin; Austin Texas
- School of Medicine; The University of Texas Health Science Center; San Antonio Texas
| |
Collapse
|
34
|
Long SW, Olsen RJ, Mehta SC, Palzkill T, Cernoch PL, Perez KK, Musick WL, Rosato AE, Musser JM. PBP2a mutations causing high-level Ceftaroline resistance in clinical methicillin-resistant Staphylococcus aureus isolates. Antimicrob Agents Chemother 2014; 58:6668-74. [PMID: 25155594 PMCID: PMC4249384 DOI: 10.1128/aac.03622-14] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/16/2014] [Indexed: 12/25/2022] Open
Abstract
Ceftaroline is the first member of a novel class of cephalosporins approved for use in the United States. Although prior studies have identified eight ceftaroline-resistant methicillin-resistant Staphylococcus aureus (MRSA) isolates in Europe and Asia with MICs ranging from 4 to 8 mg/liter, high-level resistance to ceftaroline (>32 mg/liter) has not been described in MRSA strains isolated in the United States. We isolated a ceftaroline-resistant (MIC > 32 mg/liter) MRSA strain from the blood of a cystic fibrosis patient and five MRSA strains from the respiratory tract of this patient. Whole-genome sequencing identified two amino acid-altering mutations uniquely present in the ceftaroline-binding pocket of the transpeptidase region of penicillin-binding protein 2a (PBP2a) in ceftaroline-resistant isolates. Biochemical analyses and the study of isogenic mutant strains confirmed that these changes caused ceftaroline resistance. Thus, we identified the molecular mechanism of ceftaroline resistance in the first MRSA strain with high-level ceftaroline resistance isolated in the United States.
Collapse
Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Shrenik C Mehta
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Patricia L Cernoch
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Katherine K Perez
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - William L Musick
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - Adriana E Rosato
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| |
Collapse
|
35
|
Salazar E, Divatia M, Cernoch PL, Olsen RJ, Long SW, Land GA, Davis JR, Musser JM. Improving positive blood culture removal time significantly decreases total processing time. Arch Pathol Lab Med 2014; 139:199-203. [PMID: 24806519 DOI: 10.5858/arpa.2013-0681-oa] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Timely processing of blood cultures with positive results, including Gram staining and notification of clinicians, is a critical function of the clinical microbiology laboratory. Analysis of processing time in our laboratory revealed opportunities to enhance workflow efficiency. We found that the average time from positive blood culture result to removal of the bottle for processing (positive-to-removal [PR] time) was inadequate for our rapid pathogen identification program. OBJECTIVE To determine whether increased vigilance about PR time and prioritization of laboratory resources would decrease PR time and total processing time. DESIGN We performed a retrospective analysis of blood culture PR time 7 months before and 7 months after an in-service meeting during which the importance of PR time was emphasized, and corrective measures were implemented. RESULTS Before the in-service meeting, the average PR time for 5057 samples was 38 minutes, with an aggregate time of 192,251 minutes. Unexpectedly, we discovered that only 51.8% (2617 of 5057) of the positive blood cultures were removed in less than 10 minutes. After the in-service meeting, for 5293 samples, the average PR time improved to 8 minutes, the aggregate time improved to 44,630 minutes, and 84.5% (4470 of 5293) of the positive blood cultures were removed in less than 10 minutes. These improvements reduced the time to telephone notification of the Gram stain results to a caregiver by 46.7% (from 105 minutes to 56 minutes). CONCLUSIONS Increased awareness of barriers to rapid pathogen identification and interventions for improving performance time significantly enhanced care of patients with bloodstream infections.
Collapse
Affiliation(s)
- Eric Salazar
- From the Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Long SW, Wright AM, Beres SB, Consamus EN, Flores AR, Barrios R, Richter GS, Oh SY, Garufi G, Maier H, Drews AL, Stockbauer KE, Cernoch P, Schneewind O, Olsen RJ, Musser JM. Whole Genome Sequence Analysis of a
B. cereus
Strain Causing a Fatal Anthrax‐Like Pulmonary Infection. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.1034.5] [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: 11/11/2022]
Affiliation(s)
- S. Wesley Long
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - Angela M Wright
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - Stephen B Beres
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - Erin N Consamus
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - Anthony R Flores
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - Roberto Barrios
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - G. Stefan Richter
- Howard Taylor Ricketts LaboratoryArgonne National LaboratoryArgonneIL
| | - So-Young Oh
- Howard Taylor Ricketts LaboratoryArgonne National LaboratoryArgonneIL
| | - Gabriella Garufi
- Howard Taylor Ricketts LaboratoryArgonne National LaboratoryArgonneIL
| | - Hannah Maier
- Howard Taylor Ricketts LaboratoryArgonne National LaboratoryArgonneIL
| | - Ashley L Drews
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | | | - Patricia Cernoch
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - Olaf Schneewind
- Howard Taylor Ricketts LaboratoryArgonne National LaboratoryArgonneIL
| | - Randall J Olsen
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| | - James M Musser
- Department of Pathology & Genomic MedicineThe Methodist HospitalHoustonTX
| |
Collapse
|
37
|
Abstract
CONTEXT Throughout history, technologic advancements have fueled the engine of innovation, which, in turn, has driven discovery. Accordingly, recent advancements in DNA sequencing technology are revolutionizing bacterial genomics. OBJECTIVE To review important developments from the literature. The current state of bacterial genomics, with an emphasis on human pathogens and the clinical pathology laboratory, will be discussed. DATA SOURCES A comprehensive review was performed of the relevant literature indexed in PubMed (National Library of Medicine) and referenced medical texts. CONCLUSIONS Many important discoveries bearing on infectious disease research and pathology laboratory practice have been achieved through whole-genome sequencing strategies. Bacterial genomics has improved our understanding of molecular pathogenesis, host-pathogen interactions, and antibiotic-resistance mechanisms. Bacterial genomics has also facilitated the study of population structures, epidemics and outbreaks, and newly identified pathogens. Many opportunities now exist for clinical pathologists to contribute to bacterial genomics, including in the design of new diagnostic tests, therapeutic agents, and vaccines.
Collapse
Affiliation(s)
- Randall J Olsen
- Department of Pathology and Genomic Medicine, The Methodist Hospital System, Houston, TX 77030, USA.
| | | | | |
Collapse
|
38
|
Wright AM, Beres SB, Consamus EN, Long SW, Flores AR, Barrios R, Richter GS, Oh SY, Garufi G, Maier H, Drews AL, Stockbauer KE, Cernoch P, Schneewind O, Olsen RJ, Musser JM. Rapidly progressive, fatal, inhalation anthrax-like infection in a human: case report, pathogen genome sequencing, pathology, and coordinated response. Arch Pathol Lab Med 2011; 135:1447-59. [PMID: 21882964 DOI: 10.5858/2011-0362-sair.1] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Ten years ago a bioterrorism event involving Bacillus anthracis spores captured the nation's interest, stimulated extensive new research on this pathogen, and heightened concern about illegitimate release of infectious agents. Sporadic reports have described rare, fulminant, and sometimes fatal cases of pneumonia in humans and nonhuman primates caused by strains of Bacillus cereus , a species closely related to Bacillus anthracis. OBJECTIVES To describe and investigate a case of rapidly progressive, fatal, anthrax-like pneumonia and the overwhelming infection caused by a Bacillus species of uncertain provenance in a patient residing in rural Texas. DESIGN We characterized the genome of the causative strain within days of its recovery from antemortem cultures using next-generation sequencing and performed immunohistochemistry on tissues obtained at autopsy with antibodies directed against virulence proteins of B anthracis and B cereus. RESULTS We discovered that the infection was caused by a previously unknown strain of B cereus that was closely related to, but genetically distinct from, B anthracis . The strain contains a plasmid similar to pXO1, a genetic element encoding anthrax toxin and other known virulence factors. Immunohistochemistry demonstrated that several homologs of B anthracis virulence proteins were made in infected tissues, likely contributing to the patient's death. CONCLUSIONS Rapid genome sequence analysis permitted us to genetically define this strain, rule out the likelihood of bioterrorism, and contribute effectively to the institutional response to this event. Our experience strongly reinforced the critical value of deploying a well-integrated, anatomic, clinical, and genomic strategy to respond rapidly to a potential emerging, infectious threat to public health.
Collapse
Affiliation(s)
- Angela M Wright
- Department of Pathology and Laboratory Medicine, The Methodist Hospital System, Houston, Texas, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Labruna MB, McBride JW, Camargo LMA, Aguiar DM, Yabsley MJ, Davidson WR, Stromdahl EY, Williamson PC, Stich RW, Long SW, Camargo EP, Walker DH. A preliminary investigation of Ehrlichia species in ticks, humans, dogs, and capybaras from Brazil. Vet Parasitol 2006; 143:189-95. [PMID: 16962245 DOI: 10.1016/j.vetpar.2006.08.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Revised: 07/01/2006] [Accepted: 08/01/2006] [Indexed: 10/24/2022]
Abstract
A molecular epidemiologic investigation in two Brazilian states (Rondônia and São Paulo) was undertaken to determine if Ehrlichia species responsible for human and animal ehrlichioses in North America could be found in Brazilian vectors, potential natural mammalian reservoirs and febrile human patients with a tick bite history. Samples, including 376 ticks comprising 9 Amblyomma species, 29 capybara (Hydrochaeris hydrochaeris) spleens, 5 canine blood, and 75 human blood samples from febrile patients with history of tick bites were tested by a real-time PCR assay targeting a fragment of the Ehrlichia dsb gene. Ehrlichia DNA was not detected in any tick, capybara or human samples. In contrast, 4 out of 5 dogs contained Ehrlichia canis DNA in their blood, which were sequenced, representing the first report of E. canis infecting dogs in the Amazon region of Brazil. Further studies are needed to evaluate the presence of other agents of human and animal ehrlichioses in Brazil.
Collapse
Affiliation(s)
- Marcelo B Labruna
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 7755-0609, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Abstract
While bacterial transformation has evolved since the early 20th century to allow for the genetic manipulation of a variety of microbial agents, rickettsial organisms have proved resistant to such advances until only recently. The Ehrlichia are small, gram-negative, obligately intracellular bacterial parasites, which belong to the family Anaplasmataceae and cause a variety of infections in human and animal hosts. E. chaffeensis is the causative agent of human monocytotropic ehrlichiosis and is transmitted by Amblyomma americanum, the Lone Star tick. In this work, we describe the first report of successful transformation of a closely related ehrlichial species, the murine monocytotropic species E. muris. Application of these techniques should allow for a wide variety of molecular studies to be performed that were previously impossible. This heralds the beginning of a new era in ehrlichial research.
Collapse
Affiliation(s)
- S Wesley Long
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-0609, USA.
| | | | | | | |
Collapse
|
41
|
Abstract
A canine model for human monocytic ehrlichiosis was used to assess persistent infection and antigenic variation of Ehrlichia chaffeensis. Two beagle dogs were infected subcutaneously with E. chaffeensis Arkansas strain. The dogs were observed for 6 months after inoculation for clinical signs, blood chemistry changes, antibodies to E. chaffeensis and presence of E. chaffeensis in the blood. Both dogs developed thrombocytopenia, but exhibited normal body temperatures during the entire course of infection. In one dog, E. chaffeensis was cultivated for up to 74 days post-inoculation and E. chaffeensis DNA was detected in the dog's blood for up to 81 days. In the other dog, E. chaffeensis was cultured for up to 102 days and E. chaffeensis DNA was detected in the blood for up to 117 days. PCR amplification and DNA sequence analysis indicated that there was no genetic variation in the 120 kDa outer-membrane glycoprotein gene of E. chaffeensis during infection of the dogs. The dogs developed antibodies to the immunodominant proteins of E. chaffeensis, including the 175, 140, 120, 80, 50 and 28 kDa proteins, starting in the fifth week post-inoculation. The dogs maintained high antibody titres throughout the 6-month study period. These results indicate that dogs become carriers of E. chaffeensis for 2-4 months after infection without exhibiting signs of clinical disease, suggesting that dogs may serve as a natural host for E. chaffeensis.
Collapse
Affiliation(s)
- Xiao-Feng Zhang
- Departments of Pathology and Microbiology and Immunology, Center for Biodefense and Emerging Infectious Diseases1 and Animal Resource Center2, University of Texas Medical Branch, Galveston, Texas 77555-0609, USA
| | - Jian-Zhi Zhang
- Departments of Pathology and Microbiology and Immunology, Center for Biodefense and Emerging Infectious Diseases1 and Animal Resource Center2, University of Texas Medical Branch, Galveston, Texas 77555-0609, USA
| | - S Wesley Long
- Departments of Pathology and Microbiology and Immunology, Center for Biodefense and Emerging Infectious Diseases1 and Animal Resource Center2, University of Texas Medical Branch, Galveston, Texas 77555-0609, USA
| | - Randall P Ruble
- Departments of Pathology and Microbiology and Immunology, Center for Biodefense and Emerging Infectious Diseases1 and Animal Resource Center2, University of Texas Medical Branch, Galveston, Texas 77555-0609, USA
| | - Xue-Jie Yu
- Departments of Pathology and Microbiology and Immunology, Center for Biodefense and Emerging Infectious Diseases1 and Animal Resource Center2, University of Texas Medical Branch, Galveston, Texas 77555-0609, USA
| |
Collapse
|
42
|
Long SW, Zhang X, Zhang J, Ruble RP, Teel P, Yu XJ. Evaluation of transovarial transmission and transmissibility of Ehrlichia chaffeensis (Rickettsiales: Anaplasmataceae) in Amblyomma americanum (Acari: Ixodidae). J Med Entomol 2003; 40:1000-1004. [PMID: 14765684 DOI: 10.1603/0022-2585-40.6.1000] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
It has long been assumed that Ehrlichia chaffeensis (Anderson, Dawson & Wilson), is not transmitted transovarially in the lone star tick vector Amblyomma americanum (L.). To test this hypothesis, three beagle dogs, Canis familiaris (L.) (Carnivora: Canidae), were subcutaneously infected with E. chaffeensis (Arkansas strain). Uninfected nymphal lone star ticks were placed on the infected dogs and allowed to feed to repletion. These nymphal ticks were allowed to molt, and five of five adult female ticks sampled were confirmed to be infected by polymerase chain reaction (PCR). Forty infected adult ticks, the majority of which were female with several males included to stimulate feeding, were then placed on two uninfected dogs. Fourteen females were removed early and the rest were allowed to feed to repletion. After feeding to repletion, the six remaining females detached and two of these females were tested preoviposition, whereas the remaining four were allowed to lay eggs. All six of these fully engorged females tested negative by PCR. The egg clutches laid by four engorged adult females, and the larvae that hatched from these eggs along with larvae from a previously untested egg clutch, were shown to be uninfected by PCR. This seems to support the long-held assumption of lack of transovarial transmission. Also of interest, we found that these PCR-confirmed infected adult ticks reared in the laboratory did not transmit E. chaffeensis to uninfected dogs.
Collapse
Affiliation(s)
- S Wesley Long
- Department of Pathology, WHO Collaborating Center for Tropical Disease, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | | | | | | | | | | |
Collapse
|
43
|
Long SW, Zhang XF, Qi H, Standaert S, Walker DH, Yu XJ. Antigenic variation of Ehrlichia chaffeensis resulting from differential expression of the 28-kilodalton protein gene family. Infect Immun 2002; 70:1824-31. [PMID: 11895944 PMCID: PMC127871 DOI: 10.1128/iai.70.4.1824-1831.2002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The transcriptional activity and allele variation of the 28-kDa outer membrane protein gene (p28) of Ehrlichia chaffeensis were analyzed to determine the mechanism of the antigenic variation of the 28-kDa outer membrane proteins. Reverse transcriptase PCR amplification of mRNA indicated that 16 of the 22 members of the p28 multigene family were transcribed. Amino acid sequence analysis indicated that the p28-19 protein was produced in vitro in the Arkansas strain. The p28-19 gene and its promoter region were sequenced and compared in 12 clinical isolates of E. chaffeensis to determine allele variation. The variation of the p28-19 gene among the isolates is limited to three types represented by strains Arkansas, 91HE17, and Sapulpa, respectively. These results indicate that the majority of the p28 genes are active genes and that antigenic variation of the E. chaffeensis 28-kDa proteins may result from differential expression of the p28 gene family members rather than gene conversion.
Collapse
Affiliation(s)
- S Wesley Long
- Department of Pathology and WHO Collaborating Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas 77555-0609, USA
| | | | | | | | | | | |
Collapse
|
44
|
Schulenberg J, Maggs JL, Long SW, Sher KJ, Gotham HJ, Baer JS, Kivlahan DR, Marlatt GA, Zucker RA. The problem of college drinking: insights from a developmental perspective. Alcohol Clin Exp Res 2001; 25:473-7. [PMID: 11290861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
This article represents the proceedings of a symposium at the 2000 RSA Meeting in Denver, Colorado. John Schulenberg and Jennifer L. Maggs were Organizers. Stephen W. Long was Chair and provided opening remarks. The presentations were: (1) I'm not a drunk, just a college student: Binge drinking during college as a developmental disturbance, by John Schulenberg; (2) Course of alcohol use disorders during college, by Kenneth J. Sher; (3) How do students experience alcohol and its effects? Positive versus negative expectancies and consequences, by Jennifer L. Maggs; and (4) Brief intervention in the context of developmental trends in college drinking, by G. Alan Marlatt. Critique and commentary were provided by Robert A. Zucker.
Collapse
Affiliation(s)
- J Schulenberg
- Institute for Social Research, University of Michigan, Ann Arbor 48106-1248, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Davis TC, Long SW, Jackson RH, Mayeaux EJ, George RB, Murphy PW, Crouch MA. Rapid estimate of adult literacy in medicine: a shortened screening instrument. Fam Med 1993; 25:391-5. [PMID: 8349060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND This study was conducted to validate a shortened version of the Rapid Estimate of Adult Literacy in Medicine (REALM). This screening instrument is designed to be used in public health and primary care settings to identify patients with low reading levels. It provides reading grade estimates for patients who read below a ninth-grade level. The REALM can be administered in one to two minutes by personnel with minimal training. METHODS Two hundred and three patients in four university hospital clinics (internal medicine, family practice, ambulatory care, and obstetrics/gynecology) were given the REALM and three other standardized reading tests: the reading recognition section of the Peabody Individual Achievement Test-Revised (PIAT-R), the Wide Range Achievement Test-Revised (WRAT-R), and the Slosson Oral Reading Test-Revised (SORT-R). One hundred inmates at a state prison were also given the REALM twice, one week apart, to determine test-retest reliability. RESULTS The REALM correlated well with the three other tests. (Correlation coefficients were 0.97 [PIAT-R], 0.96 [SORT-R], and 0.88 [WRAT-R].) All correlations were significant at P < .0001. Test-retest reliability was 0.99 (P < .001). CONCLUSIONS The REALM provides an estimate of patient reading ability, displays excellent concurrent validity with standardized reading tests, and is a practical instrument for busy primary care settings.
Collapse
Affiliation(s)
- T C Davis
- Department of Internal Medicine, Louisiana State University Medical Center School of Medicine, Shreveport
| | | | | | | | | | | | | |
Collapse
|
46
|
Davis TC, Jackson RH, George RB, Long SW, Talley D, Murphy PW, Mayeaux EJ, Truong T. Reading ability in patients in substance misuse treatment centers. Int J Addict 1993; 28:571-82. [PMID: 8098019 DOI: 10.3109/10826089309039648] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Adult inpatients in state-supported (public) and private substance misuse treatment settings were tested for reading ability. Patient education materials and consent forms were assessed for readability levels. Public patients' mean reading levels were significantly lower than those of private patients, and were 4 to 5 years below the level needed to read and understand standard treatment materials. More than half of the public and almost one-third of the private patients tested were reading below a 9th grade level. Standard treatment materials were written on 11th to 12th grade reading levels; admission and consent forms were written on 12th to 18th grade levels. Patients in substance misuse settings should be tested for literacy levels upon admission and provided with materials commensurate with their reading ability.
Collapse
Affiliation(s)
- T C Davis
- Department of Medicine, Louisiana State University Medical Center School of Medicine, Shreveport 71130-3932
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Davis TC, Crouch MA, Long SW, Jackson RH, Bates P, George RB, Bairnsfather LE. Rapid assessment of literacy levels of adult primary care patients. Fam Med 1991; 23:433-5. [PMID: 1936717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Health education materials, medical instructions, consent forms, and self-report questionnaires are often given to patients with little regard for their ability to read them. Reading ability is rarely tested in medical settings. The Rapid Estimate of Adult Literacy in Medicine (REALM) was developed as a quick screening tool to assist physicians in identifying patients with limited reading skills and in estimating patient reading levels. This information can be used to tailor materials and instructions to patients' abilities. The REALM and the reading sections of the Peabody Individual Achievement Test-Revised and the Slosson Oral Reading Test were used to test reading ability in 207 adults in six public and private primary care clinics. REALM scores correlated highly with those of the standardized reading tests. The REALM, which takes three to five minutes to administer and score, appears to be a practical instrument to estimate patient literacy in primary care, patient education, and medical research.
Collapse
Affiliation(s)
- T C Davis
- Department of Family Medicine, Louisiana State University Medical Center, School of Medicine, Shreveport 71130-3932
| | | | | | | | | | | | | |
Collapse
|
48
|
Abstract
This article introduces the neuroclinician to the Kaufman Assessment Battery for Children (K-ABC), a new test of intelligence and achievement with a strong theoretical base supported by diverse cognitive and neuropsychological research. The K-ABC global scales and their subtests are described in some detail, followed by a discussion of the neuropsychological relevance of the K-ABC subtests. The article also provides discussions of research in the following areas: psychometric properties of the K-ABC and a comparison to the Wechsler scales; interpretation and remediation of sequential-simultaneous processing differences; the value of the K-ABC in the assessment of minority children; and controversy surrounding the K-ABC.
Collapse
|
49
|
Abstract
This article will familiarize neuroclinicians with the WISC-R and with the results of countless research studies on this popular test of the intelligence of children and adolescents. In addition to a description of the WISC-R and its subtests, and a discussion of the WISC-R from a historical context, the article reviews research in the following areas: relationship of the WISC-R to Wechsler's preschool and adult scales; interpretation of verbal-performance IQ differences; clinical implications of scatter; relationship of an IQ score to present and future functioning; and comparison of IQs on the WISC-R with scores on other tests for children and adolescents.
Collapse
|
50
|
Long SW. Treatment of Abortion. Tex Med J (Austin) 1896; 12:62-64. [PMID: 36955906 PMCID: PMC9621894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Affiliation(s)
- S W Long
- Professor of Diseases of Women and Children, Medical College of Virginia, Richmond, Va
| |
Collapse
|