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Lee C, Lim Y, Saintine D, Babady NE. Analytical and clinical evaluation of the cobas Epstein-Barr virus test at a tertiary care cancer hospital. J Clin Virol 2024; 173:105680. [PMID: 38728796 DOI: 10.1016/j.jcv.2024.105680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/18/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Epstein-Barr Virus (EBV) viral loads in hematopoietic stem cell transplant (HSCT) recipients are typically monitored using quantitative molecular assays. The Cobas EBV test (Roche Molecular, Pleasanton, CA) has recently been FDA-cleared for the monitoring of EBV viral loads in plasma samples of transplant patients. In this study, we compared the viral loads obtained by a laboratory-developed test (EBV LDT) using Altona Analyte specific reagents (ASR) to those obtained on the Cobas EBV test. METHODS The analytical performance of the assay was established using the EBV verification panel from Exact Diagnostics and the EBV ATCC strain B95-8. The clinical evaluation was performed using 343 plasma samples initially tested on the EBV LDT. RESULTS The analytical sensitivity (<18.8 IU/mL), precision (SD < 0.17 log) and linear range (35.0 IU/mL to 1E + 08 IU/mL) of the Cobas EBV assay established by the manufacturers were confirmed. The strength of the qualitative agreement was substantial between the cobas EBV and the EBV LDT (85.6 %; κ = 0.71) and almost perfect when discordant results were resolved (96.4 %; κ = 0.93). The quantitative agreement was moderate (82.9 %; κ = 0.53) with the viral load obtained on the Cobas EBV test being lower across the linear range of the two tests (mean log difference of 1.0). While the absolute values of the viral loads were markedly different, the overall trends observed in patients with multiple consecutive results were similar between the two tests. CONCLUSIONS The Cobas EBV test provides an accurate and valid, in vitro diagnostic (IVD) option for monitoring of EBV viral loads in transplant patients and should provide an opportunity for increased standardization and commutability of tests results across laboratories.
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Affiliation(s)
- Cindy Lee
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Younmin Lim
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Deborah Saintine
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, United States.
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2
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Nachamkin I, Babady NE. The 2024 ASM Awards and Prize Program-recognizing excellence in the microbiological sciences. J Clin Microbiol 2024; 62:e0001224. [PMID: 38391223 PMCID: PMC10935626 DOI: 10.1128/jcm.00012-24] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
The ASM Awards and Prize Program recognizes outstanding achievements in basic and applied research, clinical microbiology, education, leadership, and service. This editorial briefly describes how the program works and highlights several awards of interest to the clinical microbiology community.
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Affiliation(s)
- Irving Nachamkin
- Member and Past Chair, Subcommittee on Awards, American Academy of Microbiology, Washington, DC, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - N. Esther Babady
- Member, Subcommittee on Awards, American Academy of Microbiology, Washington, DC, USA
- Department of Pathology and Laboratory Medicine and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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3
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Elkrief A, Waters NR, Smith N, Dai A, Slingerland J, Aleynick N, Febles B, Gogia P, Socci ND, Lumish M, Giardina PA, Chaft JE, Eng J, Motzer RJ, Mendelsohn RB, Markey KA, Zhuang M, Li Y, Yang Z, Hollmann TJ, Rudin CM, van den Brink MR, Shia J, DeWolf S, Schoenfeld AJ, Hellmann MD, Babady NE, Faleck DM, Peled JU. Immune-Related Colitis Is Associated with Fecal Microbial Dysbiosis and Can Be Mitigated by Fecal Microbiota Transplantation. Cancer Immunol Res 2024; 12:308-321. [PMID: 38108398 PMCID: PMC10932930 DOI: 10.1158/2326-6066.cir-23-0498] [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: 06/16/2023] [Revised: 09/08/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Colitis induced by treatment with immune-checkpoint inhibitors (ICI), termed irColitis, is a substantial cause of morbidity complicating cancer treatment. We hypothesized that abnormal fecal microbiome features would be present at the time of irColitis onset and that restoring the microbiome with fecal transplant from a healthy donor would mitigate disease severity. Herein, we present fecal microbiota profiles from 18 patients with irColitis from a single center, 5 of whom were treated with healthy-donor fecal microbial transplantation (FMT). Although fecal samples collected at onset of irColitis had comparable α-diversity to that of comparator groups with gastrointestinal symptoms, irColitis was characterized by fecal microbial dysbiosis. Abundances of Proteobacteria were associated with irColitis in multivariable analyses. Five patients with irColitis refractory to steroids and biologic anti-inflammatory agents received healthy-donor FMT, with initial clinical improvement in irColitis symptoms observed in four of five patients. Two subsequently exhibited recurrence of irColitis symptoms following courses of antibiotics. Both received a second "salvage" FMT that was, again, followed by clinical improvement of irColitis. In summary, we observed distinct microbial community changes that were present at the time of irColitis onset. FMT was followed by clinical improvements in several cases of steroid- and biologic-agent-refractory irColitis. Strategies to restore or prevent microbiome dysbiosis in the context of immunotherapy toxicities should be further explored in prospective clinical trials.
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Affiliation(s)
- Arielle Elkrief
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas R. Waters
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Natalie Smith
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angel Dai
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John Slingerland
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nathan Aleynick
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Binita Febles
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pooja Gogia
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nicholas D. Socci
- Bioinformatics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melissa Lumish
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul A. Giardina
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamie E. Chaft
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Juliana Eng
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Robert J. Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Robin B. Mendelsohn
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Kate A. Markey
- Fred Hutchinson Cancer Center, Seattle, Washington; Division of Medical Oncology, University of Washington, Seattle, Washington
| | - Mingqiang Zhuang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanyun Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zhifan Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Travis J. Hollmann
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Bristol Myers Squibb, Princeton, NJ, USA
| | - Charles M. Rudin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Marcel R.M. van den Brink
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Susan DeWolf
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Adam J. Schoenfeld
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Matthew D. Hellmann
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - N. Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine and the Infectious Disease Service, Department of Medicine Memorial Sloan Kettering Cancer Center, New York, NY
| | - David M. Faleck
- Gastroenterology, Hepatology & Nutrition Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Jonathan U. Peled
- Weill Cornell Medical College, New York, NY
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Babady NE, Dien Bard J. Nothing Basic About It: Guiding the Judicious Use of Diagnostic Tests. Clin Lab Med 2024; 44:xi-xiii. [PMID: 38280802 DOI: 10.1016/j.cll.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2024]
Affiliation(s)
- N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jennifer Dien Bard
- Laboratory Medicine, Clinical Microbiology and Virology, Department of Pathology and Laboratory Medicine Children's Hospital of Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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Cintron M, Jani K, Madhavappallil J, Kamboj M, Babady NE. Prevalence of astrovirus and sapovirus among adult oncology patients with acute gastroenteritis using a multiplexed gastrointestinal pathogen PCR panel. Eur J Clin Microbiol Infect Dis 2024; 43:525-531. [PMID: 38216845 DOI: 10.1007/s10096-024-04748-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
BACKGROUND Multiplex syndromic gastrointestinal panels (GIPCR) have streamlined the diagnosis of infectious diarrhea. Additionally, they have expanded the number of pathogens that can be routinely evaluated, allowing further understanding of the prevalence of enteric pathogens in various patient populations. The goal of this study was to investigate the prevalence and clinical presentation of astrovirus and sapovirus gastroenteritis in adult oncology patients as detected by the FilmArray GIPCR. METHODS All GIPCR panel results from December 2017 to June 2021 were retrospectively reviewed to determine the prevalence of astrovirus and sapovirus in adult oncology patients. Medical records were also reviewed to obtain clinical information. Repeat GIPCR positivity and symptom duration were used to estimate prolonged viral shedding. RESULTS A total of 18,014 panels were performed on samples collected from 9303 adults. Overall, astrovirus and sapovirus were detected in 0.35% (33/9303) and 0.45% (42/9303) GIPCRs respectively. At least one viral target was detected in 424 (4.4%) patients. Astrovirus accounted for 7.8% (33/424) and sapovirus 9.9% (42/424) of patients. Diarrhea was the most common symptom documented. A subset of transplant patients had protracted viral detection with a median of ~27 days (range 23-43 days) for astrovirus and 97 days (range 11-495) for sapovirus. No clusters or outbreaks were identified during the study period. CONCLUSION In oncology patients with viral gastroenteritis, astrovirus and sapovirus were the causative agents in 18% of the cases. Both viruses were associated with mild disease. Prolonged diarrhea and viral shedding were observed in a few transplant patients.
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Affiliation(s)
- Melvili Cintron
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jerin Madhavappallil
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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6
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Infante MS, Nemirovsky D, Devlin S, DeWolf S, Tamari R, Dahi PB, Lee YJ, Chung DJ, Politikos I, Barker J, Giralt SA, Babady NE, Ramanathan L, Papanicolaou GA, Seo S, Kamboj M, Perales MA, Shah GL. Outcomes and Management of the SARS-CoV2 Omicron Variant in Recipients of Hematopoietic Cell Transplantation and Chimeric Antigen Receptor T Cell Therapy. Transplant Cell Ther 2024; 30:116.e1-116.e12. [PMID: 37806446 DOI: 10.1016/j.jtct.2023.09.027] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/10/2023]
Abstract
Hematopoietic cell transplantation (HCT) and chimeric antigen receptor T cell therapy (CAR-T) recipients who develop Coronavirus disease 2019 (COVID-19) can have decreased overall survival (OS), likely due to disease-inherent and therapy-related immunodeficiency. The availability of COVID-19-directed therapies and vaccines have improved COVID-19-related outcomes, but immunocompromised individuals remain vulnerable. Specifically, the effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infections, including Omicron and its sublineages, particularly in HCT recipients, remain to be defined. The aim of this study was to compare the impact of SARS-CoV-2 Omicron infections in HCT/CAR-T recipients with outcomes previously reported for ancestral SARS-CoV-2 infections early in the pandemic (March to June 2020). This was a retrospective analysis of adult HCT/CAR-T recipients diagnosed with COVID-19 at Memorial Sloan Kettering Cancer Center between July 2021 and July 2022. We identified 353 patients (172 autologous HCT recipients [49%], 152 allogeneic HCT recipients [43%], and 29 CAR-T recipients [8%]), with a median time from HCT/CAR-T to SARS-CoV-2 infection of 1010 days (interquartile range, 300 to 2046 days). Forty-one patients (12%) were diagnosed with COVID-19 during the delta wave, and 312 patients (88%) were diagnosed during the Omicron wave. Risk factors associated with increased odds of COVID-19-related hospitalization were the presence of 2 or more comorbidities (odds ratio [OR], 4.9; 95% confidence interval [CI], 2.4 to 10.7; P < .001), CAR-T therapy compared to allogeneic HCT (OR, 7.7; 95% CI, 3.0 to 20.0; P < .001), hypogammaglobulinemia (OR, 2.71; 95% CI, 1.06 to 6.40; P = .027), and age at COVID-19 diagnosis (OR, 1.03; 95% CI, 1.0 to 1.05; P = .04). In contrast, infection during the Omicron variant BA5/BA4-dominant period compared to variant BA1 (OR, .21; 95% CI, .03 to .73; P = .037) and more than 3 years from HCT/CAR-T therapy to COVID-19 diagnosis compared to early infection at <100 days (OR, .31; 95% CI, .12 to .79; P = .011) were associated with a decreased odds for hospitalization. The OS at 12 months from COVID-19 diagnosis was 89% (95% CI, 84% to 94%), with 6 of 26 deaths attributable to COVID-19. Patients with the ancestral strain of SAR-CoV-2 had a lower OS at 12 months, with 73% (95% CI, 62% to 84%) versus 89% (95% CI, 84% to 94%; P < .001) in the Omicron cohort. Specific COVID-19 treatment was administered in 62% of patients, and 84% were vaccinated with mRNA COVID-19 vaccines. Vaccinated patients had significantly better OS than unvaccinated patients (90% [95% CI, 86% to 95%] versus 82% [95% CI, 72% to 94%] at 12 months; P = .003). No significant difference in OS was observed in patients infected with the Omicron and those infected with the Delta variant (P = .4) or treated with specific COVID-19 treatments compared with those not treated (P = .2). We observed higher OS in HCT and CAR-T recipients infected with the Omicron variants compared to those infected with the ancestral strain of SARS-CoV2. The use of COVID-19 antivirals, mAbs, and vaccines might have contributed to the improved outcomes.
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Affiliation(s)
- Maria-Stefania Infante
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; University Hospital Infanta Leonor, Madrid, Spain.
| | - David Nemirovsky
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sean Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan DeWolf
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Roni Tamari
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Parastoo B Dahi
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Yeon Joo Lee
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - David J Chung
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ioannis Politikos
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Juliet Barker
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Sergio A Giralt
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial SLoan Kettering Cancer Center, New York, New York
| | - Lakshmi Ramanathan
- Clinical Chemistry Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Genovefa A Papanicolaou
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan Seo
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mini Kamboj
- Department of Medicine, Weill Cornell Medical College, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gunjan L Shah
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
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Otto C, Babady NE. Epidemiology and Outcomes of Non-albicans Candida Bloodstream Infections in Transplant Recipients and Cancer Patients. Mycopathologia 2023; 188:863-871. [PMID: 37365379 DOI: 10.1007/s11046-023-00765-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/10/2023] [Indexed: 06/28/2023]
Abstract
We performed a retrospective survey of non-Candida albicans candidemia in patients with cancer, including those with solid tumors and those with hematological malignancies as well as transplants patients both, solid-organ transplant recipients and hematopoietic stem cell transplant recipients. The study was performed at two healthcare centers in New York City and covered the years 2018-2022. A total of 292 patients (318 isolates) were included in the study. In order of frequency, C. glabrata (38%) was the most common species recovered, followed by C. parapsilosis (19.2%), C. tropicalis (12.6%), C. krusei (10.7%), C. lusitaniae (5.7%), and C. guilliermondii (4.4%). Micafungin was the most common antifungal treatment and 18.5% of patients were on antifungal prophylaxis. The 30-day crude mortality was 40%. 4.5% of patients had more than one non-albicans species detected. In conclusion, this study represents one of the largest surveys of non-albicans species in cancer and transplant patients and provides data on the current epidemiology of these Candida species in this patient population.
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Affiliation(s)
- Caitlin Otto
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Department of Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street CLM 522, New York, NY, 10065, USA.
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8
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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9
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Hogan CA, Miller S, Piantadosi A, Gaston DC, Simner PJ, Nash S, Babady NE. Which trial do we need? Plasma metagenomic next-generation sequencing to diagnose infections in patients with haematological malignancies and febrile neutropenia: proposal for a randomized-controlled trial. Clin Microbiol Infect 2023; 29:1474-1479. [PMID: 37244468 DOI: 10.1016/j.cmi.2023.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Affiliation(s)
- Catherine A Hogan
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada; Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Miller
- Delve Bio, San Francisco, CA, USA; Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Anne Piantadosi
- Emory University Department of Medicine, Division of Infectious Diseases, Atlanta, GA, USA; Emory University Department of Pathology and Laboratory Medicine, Atlanta, GA, USA
| | - David C Gaston
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephen Nash
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Solna, Sweden
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Laracy JC, Yan J, Steiger SN, Tan CA, Cohen N, Robilotti EV, Fender J, Cohen S, Korde N, Lee-Teh M, Noy A, Oved JH, Roeker LE, Shah G, Babady NE, Kamboj M, Seo SK. Predictors of SARS-CoV-2 Omicron breakthrough infection after receipt of AZD7442 (tixagevimab-cilgavimab) for pre-exposure prophylaxis among hematologic malignancy patients. Haematologica 2023; 108:3058-3067. [PMID: 37345467 PMCID: PMC10620572 DOI: 10.3324/haematol.2023.283015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/15/2023] [Indexed: 06/23/2023] Open
Abstract
AZD7442 (tixagevimab-cilgavimab) is a combination of two human monoclonal antibodies for pre-exposure prophylaxis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection among high-risk patients who do not mount a reliable vaccine response. Foremost among these are hematologic malignancy patients with limited clinical trial or realworld experience to assess the effectiveness of this combination treatment since the emergence of Omicron and its subvariants. We performed a retrospective study of 892 high-risk hematologic malignancy patients who received AZD7442 at Memorial Sloan Kettering Cancer Center in New York City from January 1, 2022 to July 31, 2022. We evaluated demographic, clinical, and laboratory characteristics and performed regression analyses to evaluate risk factors for breakthrough infection. We also evaluated the impact of updated AZD7442 dosing regimens on the risk of breakthrough infection. Among 892 patients, 98 (10.9%) had a breakthrough infection during the study period. A majority received early outpatient treatment (82%) and eventually eight (8.2%) required hospitalization for management of Coronavirus Disease 2019 (COVID-19), with a single instance of severe COVID-19 and death. Patients who received a repeat dose or a higher firsttime dose of AZD7442 had a lower incidence of breakthrough infection. Univariate analyses did not reveal any significant predictors of breakthrough infection. While AZD7442 is effective at reducing SARS-CoV-2 breakthrough infection in patients with hematologic malignancies, no risk factors reliably predicted risk of infection. Patients who received updated dosing regimens as per Food and Drug Administration guidelines had better protection against breakthrough infection.
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Affiliation(s)
- Justin C Laracy
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY.
| | - Judy Yan
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samantha N Steiger
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carrie A Tan
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nina Cohen
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth V Robilotti
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Division of Infectious Diseases, Hospital for Special Surgery, New York, NY
| | - Jerome Fender
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sara Cohen
- Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neha Korde
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melissa Lee-Teh
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ariela Noy
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joseph H Oved
- Department of Pediatric Transplant and Cell Therapy, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lindsey E Roeker
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunjan Shah
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - N Esther Babady
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mini Kamboj
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Susan K Seo
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY
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11
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Kamboj M, Laracy JC, Usiak S, Babady NE, Yan J, Seo SK. Outcomes of hematologic malignancy patients with SARS-CoV-2 breakthrough infections after tixagevimab-cilgavimab during community transmission of monoclonal antibody resistant variants. J Infect 2023; 87:282-285. [PMID: 37451364 DOI: 10.1016/j.jinf.2023.06.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Affiliation(s)
- Mini Kamboj
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Justin C Laracy
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Shauna Usiak
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Esther Babady
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Judy Yan
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Susan K Seo
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
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12
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Algazaq J, Kamboj M, Babady NE. An infant with nasal vestibulitis and paronychia. Pediatr Dermatol 2023; 40:949-951. [PMID: 36958306 DOI: 10.1111/pde.15290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/19/2023] [Indexed: 03/25/2023]
Affiliation(s)
- Jumanah Algazaq
- Department of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mini Kamboj
- Department of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - N Esther Babady
- Clinical Microbiology Service, Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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13
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Laracy JC, Robilotti EV, Yan J, Lucca A, Aslam A, Babady NE, Kamboj M. Comparison of coronavirus disease 2019 (COVID-19) symptoms at diagnosis among healthcare personnel before and after the emergence of the omicron variant. Infect Control Hosp Epidemiol 2023; 44:821-823. [PMID: 35506167 PMCID: PMC9068496 DOI: 10.1017/ice.2022.105] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 01/06/2023]
Abstract
We used a self-reporting system to compare symptom frequency of hospital personnel with coronavirus disease 2019 before and after the emergence of the Omicron variant. Omicron was more likely to result in asymptomatic carriage (7% vs 12%; P = .009), and fewer symptoms were observed in those with booster vaccination.
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Affiliation(s)
- Justin C. Laracy
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elizabeth V. Robilotti
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Judy Yan
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anabella Lucca
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Employee Health Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anoshe Aslam
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York
| | - N. Esther Babady
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Clinical Microbiology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mini Kamboj
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York
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14
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Yan J, Steiger SN, Kodama R, Fender J, Tan C, Laracy J, Cohen N, McMillen T, Jani K, Robilotti EV, Babady NE, Seo SK, Kamboj M. Predictors of Coronavirus Disease 2019 Hospitalization After Sotrovimab in Patients With Hematologic Malignancy During the BA.1 Omicron Surge. Clin Infect Dis 2023; 76:1476-1482. [PMID: 36445792 DOI: 10.1093/cid/ciac916] [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: 08/31/2022] [Revised: 11/09/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Sotrovimab is an anti-spike neutralization monoclonal antibody developed to reduce the risk of coronavirus disease 2019 (COVID-19) progression and advancement to hospitalization in high-risk patients. Currently, there is limited research describing the association of sotrovimab treatment in patients with hematologic malignancy and the predictive factors of hospitalization. METHODS We performed an observational study of 156 consecutive cancer patients who received sotrovimab at Memorial Sloan Kettering Cancer Center in New York City during the BA.1 Omicron surge. We evaluated the demographic, clinical, and laboratory characteristics of the patients who had subsequent COVID-19-related hospitalization(s) compared to those who did not. RESULTS Among the 156 study patients, 17 (11%) were hospitalized, of whom 4 were readmitted for COVID-19-related complications; 3 deaths were attributed to COVID-19. Results from multivariable logistic regression show that significant factors associated with hospitalization include patients on anti-CD20 therapy (adjusted odds ratio [aOR], 5.59 [95% confidence interval {CI}, 1.73-18.12]; P = .004) and with relapse/refractory disease (aOR, 5.69 [95% CI, 1.69-19.16]; P = .005). Additionally, whole genome sequencing of severe acute respiratory syndrome coronavirus 2 detected high occurrences of mutations in the spike gene associated with treatment-related resistance longitudinal samples from 11 patients treated with sotrovimab. CONCLUSIONS While sotrovimab is effective at reducing COVID-19 hospitalization and disease severity in patients with hematologic malignancy when administered early, patients who received anti-CD20 antibodies showed substantial morbidity. Due to the high potential for resistance mutation to sotrovimab and increased morbidity in patients on anti-CD20 therapy, combination treatment should be explored to determine whether it provides added benefits compared to monotherapy.
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Affiliation(s)
- Judy Yan
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Samantha N Steiger
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rich Kodama
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jerome Fender
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Carrie Tan
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Justin Laracy
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
| | - Nina Cohen
- Department of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Elizabeth V Robilotti
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Susan K Seo
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
| | - Mini Kamboj
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
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15
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Clark B, Cintron M, Kamboj M, Babady NE. Effect of Non-Pharmaceutical Interventions on the Incidence of Respiratory Viruses at a Tertiary Cancer Care Center. J Clin Virol 2023; 163:105442. [PMID: 37075690 PMCID: PMC10066859 DOI: 10.1016/j.jcv.2023.105442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/04/2023]
Abstract
BACKGROUND In March 2020, nonpharmaceutical interventions (NPIs) including face coverings and social distancing were adopted to curb the spread of SARS-CoV-2. Over the course of the pandemic, adherence to these NPIs has varied and eventually became optional in most non healthcare settings. We investigated the impact of relaxation of NPI on the incidence of respiratory viruses other than SARS-CoV-2 at a tertiary cancer care hospital. METHODS This was a retrospective cohort study of respiratory viral panel results performed at between 08/01/2014-07/31/2022. Only one viral target result per patient per year was included. Poisson regression models were used to compare 2019-2020, 2020-2021, and 2021-2022 incidence of respiratory viruses to those of 2014-2019. Interrupted time series analysis was performed using autoregressive integrated moving average models in order to compare expected and observed positivity rates. RESULTS A large reduction in the odds of testing positive for a respiratory virus was observed for most respiratory viruses when comparing results from 2019 to 2020 group to the corresponding period in 2014-2019. Subsequent seasons showed ongoing reductions in the odds of testing positive while slowly increasing over time back toward pre-pandemic levels. A time interrupted series analysis showed that the monthly positivity rate for all respiratory pathogens were reduced after 03/01/2020, when compared to the expected values forecast, except for adenovirus. CONCLUSIONS This study provides valuable data that could be used to guide public health practices and support the efficacy of NPIs in curtailing the spread of novel and endemic respiratory viruses.
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16
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Rodino KG, Babady NE, Bearman G, Binnicker MJ, Isaacs SN, Pinsky BA, Weber DJ. Laboratory Preparedness for the Current Monkeypox Outbreak. Clin Chem 2023; 69:118-124. [PMID: 36544358 DOI: 10.1093/clinchem/hvac198] [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] [Received: 10/17/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Kyle G Rodino
- Assistant Director of Clinical Microbiology, Director of the Rittenhouse Molecular Laboratory, and Assistant Professor of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N Esther Babady
- Chief of Clinical Microbiology Service and Member, Department of Pathology and Laboratory Medicine and Department of Medicine (Infectious Disease Service), Memorial Sloan Kettering Cancer Center, New York, USA
| | - Gonzalo Bearman
- Chief of Infectious Diseases, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Matthew J Binnicker
- Director of Clinical Virology and Professor of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Stuart N Isaacs
- Associate Professor of Medicine, Division of Infectious Diseases, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Pinsky
- Director of Clinical Virology at Stanford Health Care and Stanford Childrens Health and Professor, Departments of Pathology and Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David J Weber
- Director of Infection Prevention, University of North Carolina Medical Center and Professor, Division of Infectious Diseases, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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17
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Robilotti EV, Whiting K, Lucca A, Poon C, Jani K, McMillen T, Freeswick S, Korenstein D, Babady NE, Seshan VE, Kamboj M. Effectiveness of MRNA booster vaccine among healthcare workers in New York City during the Omicron surge, December 2021 to January 2022. Clin Microbiol Infect 2022; 28:1624-1628. [PMID: 35931373 PMCID: PMC9345790 DOI: 10.1016/j.cmi.2022.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/23/2022] [Accepted: 07/18/2022] [Indexed: 01/19/2023]
Abstract
OBJECTIVE To describe effectiveness of mRNA vaccines by comparing 2-dose (2D) and 3-dose (3D) healthcare worker (HCW) recipients in the setting of Omicron variant dominance. Performance of 2D and 3D vaccine series against SARS-CoV-2 variants and the clinical outcomes of HCWs may inform return-to-work guidance. METHODS In a retrospective study from December 15, 2020 to January 15, 2022, SARS-CoV-2 infections among HCWs at a large tertiary cancer centre in New York City were examined to estimate infection rates (aggregated positive tests / person-days) and 95% CIs over the Omicron period in 3D and 2D mRNA vaccinated HCWs and were compared using rate ratios. We described the clinical features of post-vaccine infections and impact of prior (pre-Omicron) COVID infection on vaccine effectiveness. RESULTS Among the 20857 HCWs in our cohort, 20,660 completed the 2D series with an mRNA vaccine during our study period and 12461 had received a third dose by January 15, 2022. The infection rate ratio for 3D versus 2D vaccinated HCWs was 0.667 (95% CI 0.623, 0.713) for an estimated 3D vaccine effectiveness of 33.3% compared to two doses only during the Omicron dominant period from December 15, 2021 to January 15, 2022. Breakthrough Omicron infections after 3D + 14 days occurred in 1,315 HCWs. Omicron infections were mild, with 16% of 3D and 11% 2D HCWs being asymptomatic. DISCUSSION Study demonstrates improved vaccine-derived protection against COVID-19 infection in 3D versus 2D mRNA vaccinees during the Omicron surge. The advantage of 3D vaccination was maintained irrespective of prior COVID-19 infection status.
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Affiliation(s)
- Elizabeth V. Robilotti
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA,Corresponding author. Elizabeth Robilotti, 1275 York Avenue, New York, NY, 10065
| | - Karissa Whiting
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anabella Lucca
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA,Employee Health Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chester Poon
- Division of Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott Freeswick
- Division of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Deborah Korenstein
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N. Esther Babady
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Venkatraman E. Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA,Division of Quality and Safety, Memorial Sloan Kettering Cancer Center, New York, NY, USA,Corresponding author. Mini Kamboj, 1275 York Avenue, New York, NY, 10065. USA
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Raible KM, Algazaq JN, Papanicolaou G, Babady NE. Acetobacter tropicalis bacteraemia in an immunocompromised patient: case report. Access Microbiol 2022; 4:acmi000374. [PMID: 36644433 PMCID: PMC9833420 DOI: 10.1099/acmi.0.000374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction. The published literature characterizing the bacterial genus Acetobacter primarily explores the role of these organisms in the fermentation industry. Reports of human infections caused by Acetobacter species are rare and are primarily associated with immunocompromised patients. Case Presentation. A young patient with refractory acute myeloid leukaemia received a peripheral blood stem cell transplant at our institution. Both pre- and post-transplant courses were complicated by polymicrobial bloodstream infections. During this time a bacterium, later identified as Acetobacter tropicalis , was isolated from blood cultures. A. tropicalis was recovered in consecutive blood cultures for approximately 1 week; during this time the patient's condition deteriorated, ending in fatal cardiorespiratory failure. Conclusion. This case provides the first report of a human infection with A. tropicalis , although the significance of this finding in a complex patient is hard to establish. This illustrates how the routine implementation of molecular identification techniques by clinical microbiology laboratories will result in the reporting of more rare or novel micro-organisms involved in human infections.
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Affiliation(s)
- Kevin M. Raible
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jumanah N. Algazaq
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Genovefa Papanicolaou
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N. Esther Babady
- Department of Pathology and Laboratory Medicine, Clinical Microbiology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Infectious Disease Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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McMillen T, Jani K, Robilotti EV, Kamboj M, Babady NE. The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants. Sci Rep 2022; 12:18968. [PMID: 36347878 PMCID: PMC9641688 DOI: 10.1038/s41598-022-21564-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 04/12/2022] [Accepted: 09/28/2022] [Indexed: 11/10/2022] Open
Abstract
The Alpha (B.1.1.7) and Omicron (B.1.1.529, BA.1, BA.4 and BA.5) variants of concern (VOC) share several mutations in their spike gene, including mutations resulting in the deletion of two amino acids at position 69 and 70 (del 69-70) in the Spike protein. Del 69-70 causes failure to detect the S gene target on a widely used, commercial test, the TaqPath SARS-CoV-2 RT-PCR (Thermo Fisher). The S gene target failure (SGTF) signature has been used to preliminarily infer the presence of Alpha and Omicron VOC. We evaluated the accuracy of the SGTF signature in identifying these two variants through analysis of all positive SARS-CoV-2 samples tested on the TaqPath RT-PCR and sequenced by next generation sequencing between December 2020 to July 2022. 2324 samples were successfully sequenced including 914 SGTF positive samples. The sensitivity and specificity of the SGTF signature was 99.6% (95% CI 96.1-99.9%) and 98.6% (95% CI 99.2-99.8%) for the Alpha variant and 99.6% (95% CI 98.9-99.9%) and 99.8% (95% CI 99.4-99.9%) for the Omicron variant. At the peak of their corresponding wave, the positive predictive value of the SGTF was 98% for Alpha and 100% for Omicron. The accuracy of the SGTF signature was high, making this genomic signature a rapid and accurate proxy for identification of these variants in real-world laboratory settings.
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Affiliation(s)
- Tracy McMillen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street, New York, NY, 10065, USA
| | - Krupa Jani
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street, New York, NY, 10065, USA
| | - Elizabeth V Robilotti
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street CLM 522, New York, NY, 10065, USA
| | - Mini Kamboj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street CLM 522, New York, NY, 10065, USA
| | - N Esther Babady
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street CLM 522, New York, NY, 10065, USA.
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20
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Abstract
The continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) necessitates that the global scientific community monitor, assess, and respond to the evolving coronavirus disease (COVID-19) pandemic. But the current reactive approach to emerging variants is ill-suited to address the quickly evolving and ever-changing pandemic. To tackle this challenge, investments in pathogen surveillance, systematic variant characterization, and data infrastructure and sharing across public and private sectors will be critical for planning proactive responses to emerging variants. Additionally, an emphasis on incorporating real-time variant identification in point-of-care diagnostics can help inform patient treatment. Active approaches to understand and identify "immunity gaps" can inform design of future vaccines, therapeutics, and diagnostics that will be more resistant to novel variants. Approaches where the scientific community actively plans for and anticipates changes to infectious diseases will result in a more resilient system, capable of adapting to evolving pathogens quickly and effectively.
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Affiliation(s)
- N. Esther Babady
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Penny L. Moore
- National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa, University of Kwazulu-Natal, Durban, South Africa
| | - Lynn W. Enquist
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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21
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Lyudovyk O, Kim JY, Qualls D, Hwee MA, Lin YH, Boutemine SR, Elhanati Y, Solovyov A, Douglas M, Chen E, Babady NE, Ramanathan L, Vedantam P, Bandlamudi C, Gouma S, Wong P, Hensley SE, Greenbaum B, Huang AC, Vardhana SA. Impaired humoral immunity is associated with prolonged COVID-19 despite robust CD8 T cell responses. Cancer Cell 2022; 40:738-753.e5. [PMID: 35679859 PMCID: PMC9149241 DOI: 10.1016/j.ccell.2022.05.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/06/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
Abstract
How immune dysregulation affects recovery from COVID-19 infection in patients with cancer remains unclear. We analyzed cellular and humoral immune responses in 103 patients with prior COVID-19 infection, more than 20% of whom had delayed viral clearance. Delayed clearance was associated with loss of antibodies to nucleocapsid and spike proteins with a compensatory increase in functional T cell responses. High-dimensional analysis of peripheral blood samples demonstrated increased CD8+ effector T cell differentiation and a broad but poorly converged COVID-specific T cell receptor (TCR) repertoire in patients with prolonged disease. Conversely, patients with a CD4+ dominant immunophenotype had a lower incidence of prolonged disease and exhibited a deep and highly select COVID-associated TCR repertoire, consistent with effective viral clearance and development of T cell memory. These results highlight the importance of B cells and CD4+ T cells in promoting durable SARS-CoV-2 clearance and the significance of coordinated cellular and humoral immunity for long-term disease control.
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Affiliation(s)
- Olga Lyudovyk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin Y Kim
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Qualls
- Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Madeline A Hwee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ya-Hui Lin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sawsan R Boutemine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yuval Elhanati
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Solovyov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melanie Douglas
- Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eunise Chen
- University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - N Esther Babady
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lakshmi Ramanathan
- Clinical Chemistry Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Philip Wong
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott E Hensley
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Alexander C Huang
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Santosha A Vardhana
- Lymphoma Service, Division of Hematologic Malignancies, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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22
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Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Marrero Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. J Clin Microbiol 2022; 60:e0060022. [PMID: 35582905 PMCID: PMC9199403 DOI: 10.1128/jcm.00600-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
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Affiliation(s)
- Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - David R. Peaper
- Department of Laboratory Medicine, Yale Universitygrid.47100.32, New Haven, Connecticut, USA
| | - Brendan J. Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Frederic Bushman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Andrew Marques
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Hriju Adhikari
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvaniagrid.25879.31, Philadelphia, Pennsylvania, USA
| | - Zheng Jin Tu
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Rebecca Marrero Rolon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicinegrid.471410.7, New York, New York, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicinegrid.471410.7, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicinegrid.471410.7, New York, New York, USA
| | - Daniel A. Green
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Gregory J. Berry
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Fann Wu
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Medini K. Annavajhala
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Bijal A. Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
| | - N. Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Centergrid.51462.34, New York, New York, USA
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Robert T. Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale Universitygrid.47100.32, New Haven, Connecticut, USA
| | | | - Daniel D. Rhoads
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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23
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Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Rolon RM, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. medRxiv 2022:2022.04.25.22274187. [PMID: 35547854 PMCID: PMC9094110 DOI: 10.1101/2022.04.25.22274187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
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24
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Affiliation(s)
- Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, 4650 Sunset Blvd, MS#32, Los Angeles, CA 90027, USA; Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 327 East 64th Street, CLM-522, NY 10065, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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25
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Caldararo M, Algazaq J, Schmidt E, Joanow A, Mariano A, Predmore J, Politikos I, Cho C, Stein EM, Wen X, Travis WD, Raible K, Cintron M, Babady NE, Papanicolaou G, Lee YJ. Atypical pathogens presenting with pulmonary consolidations detected by cell-free DNA next-generation sequencing in patients with hematologic malignancies. Infect Dis Clin Pract (Baltim Md) 2022; 30:e1101. [PMID: 35586753 PMCID: PMC9109825 DOI: 10.1097/ipc.0000000000001101] [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] [Indexed: 11/25/2022]
Abstract
Identification of pathogens with pulmonary presentation in patients with hematologic malignancies may be challenging due to diagnostic difficulty related to the underlying malignancy and limitations of conventional microbiologic methods. Herein, we present a case series of three patients with pulmonary consolidations due to Legionella bozemanae necrotizing pneumonia, Pneumocystis jirovecii pneumonia, and disseminated Scedosporium infection, who were diagnosed by microbial cell-free DNA next-generation sequencing. We observed that this new sequencing modality was in agreement with gold-standard diagnostics, posing a potential solution to the problem of limited capability in diagnosing infections in hematological malignancy patients.
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Affiliation(s)
- Mario Caldararo
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jumanah Algazaq
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Schmidt
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexa Joanow
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amanda Mariano
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacqueline Predmore
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ioannis Politikos
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Medical College, Cornell University, New York, NY
| | - Christina Cho
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Medical College, Cornell University, New York, NY
| | - Eytan M. Stein
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Medical College, Cornell University, New York, NY
| | - Xiaoyoun Wen
- Weill Medical College, Cornell University, New York, NY
| | - William D. Travis
- Pathology Department, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Medical College, Cornell University, New York, NY
| | - Kevin Raible
- Clinical Microbiology Service, Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melvili Cintron
- Clinical Microbiology Service, Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - N. Esther Babady
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Clinical Microbiology Service, Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Genovefa Papanicolaou
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Medical College, Cornell University, New York, NY
| | - Yeon Joo Lee
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Medical College, Cornell University, New York, NY
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26
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O’Brien CE, Zhai B, Ola M, Bergin SA, Ó Cinnéide E, O’Connor Í, Rolling T, Miranda E, Babady NE, Hohl TM, Butler G. Identification of a novel Candida metapsilosis isolate reveals multiple hybridization events. G3 (Bethesda) 2022; 12:jkab367. [PMID: 34791169 PMCID: PMC8727981 DOI: 10.1093/g3journal/jkab367] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 01/27/2023]
Abstract
Candida metapsilosis is a member of the Candida parapsilosis species complex, a group of opportunistic human pathogens. Of all the members of this complex, C. metapsilosis is the least virulent, and accounts for a small proportion of invasive Candida infections. Previous studies established that all C. metapsilosis isolates are hybrids, originating from a single hybridization event between two lineages, parent A and parent B. Here, we use MinION and Illumina sequencing to characterize a C. metapsilosis isolate that originated from a separate hybridization. One of the parents of the new isolate is very closely related to parent A. However, the other parent (parent C) is not the same as parent B. Unlike C. metapsilosis AB isolates, the C. metapsilosis AC isolate has not undergone introgression at the mating type-like locus. In addition, the A and C haplotypes are not fully collinear. The C. metapsilosis AC isolate has undergone loss of heterozygosity with a preference for haplotype A, indicating that this isolate is in the early stages of genome stabilization.
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Affiliation(s)
- Caoimhe E O’Brien
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Bing Zhai
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mihaela Ola
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sean A Bergin
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Eoin Ó Cinnéide
- School of Medicine, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Ísla O’Connor
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Thierry Rolling
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edwin Miranda
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - N Esther Babady
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tobias M Hohl
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10007, USA
| | - Geraldine Butler
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
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27
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Lee CY, Shah MK, Hoyos D, Solovyov A, Douglas M, Taur Y, Maslak P, Babady NE, Greenbaum B, Kamboj M, Vardhana SA. Prolonged SARS-CoV-2 infection in patients with lymphoid malignancies. Cancer Discov 2021; 12:62-73. [PMID: 34753749 DOI: 10.1158/2159-8290.cd-21-1033] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) infection results in both acute mortality and persistent and/or recurrent disease in patients with hematologic malignancies, but the drivers of persistent infection in this population are unknown. We found that B-cell lymphomas were at particularly high risk for persistent SARS-CoV-2 positivity. Further analysis of these patients identified discrete risk factors for initial disease severity as compared to disease chronicity. Active therapy and diminished T-cell counts were drivers of acute mortality in COVID-19 infected lymphoma patients. Conversely, B-cell-depleting therapy was the primary driver of re-hospitalization for COVID-19. In patients with persistent SARS-CoV-2 positivity, we observed high levels of viral entropy consistent with intrahost viral evolution, particularly in patients with impaired CD8+ T-cell immunity. These results suggest that persistent COVID-19 infection is likely to remain a risk in patients with impaired adaptive immunity and that additional therapeutic strategies are needed to enable viral clearance in this high-risk population.
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Affiliation(s)
- Christina Y Lee
- Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, USA
| | - Monika K Shah
- Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, USA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center
| | | | - Melanie Douglas
- Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, USA
| | - Ying Taur
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Peter Maslak
- Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | | | | | | | - Santosha A Vardhana
- Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, USA
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28
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Bolton KL, Koh Y, Foote MB, Im H, Jee J, Sun CH, Safonov A, Ptashkin R, Moon JH, Lee JY, Jung J, Kang CK, Song KH, Choe PG, Park WB, Kim HB, Oh MD, Song H, Kim S, Patel M, Derkach A, Gedvilaite E, Tkachuk KA, Wiley BJ, Chan IC, Braunstein LZ, Gao T, Papaemmanuil E, Esther Babady N, Pessin MS, Kamboj M, Diaz LA, Ladanyi M, Rauh MJ, Natarajan P, Machiela MJ, Awadalla P, Joseph V, Offit K, Norton L, Berger MF, Levine RL, Kim ES, Kim NJ, Zehir A. Clonal hematopoiesis is associated with risk of severe Covid-19. Nat Commun 2021; 12:5975. [PMID: 34645798 PMCID: PMC8514469 DOI: 10.1038/s41467-021-26138-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023] Open
Abstract
Acquired somatic mutations in hematopoietic stem and progenitor cells (clonal hematopoiesis or CH) are associated with advanced age, increased risk of cardiovascular and malignant diseases, and decreased overall survival. These adverse sequelae may be mediated by altered inflammatory profiles observed in patients with CH. A pro-inflammatory immunologic profile is also associated with worse outcomes of certain infections, including SARS-CoV-2 and its associated disease Covid-19. Whether CH predisposes to severe Covid-19 or other infections is unknown. Among 525 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, we show that CH is associated with severe Covid-19 outcomes (OR = 1.85, 95%=1.15-2.99, p = 0.01), in particular CH characterized by non-cancer driver mutations (OR = 2.01, 95% CI = 1.15-3.50, p = 0.01). We further explore the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH is significantly associated with risk of Clostridium Difficile (HR = 2.01, 95% CI: 1.22-3.30, p = 6×10-3) and Streptococcus/Enterococcus infections (HR = 1.56, 95% CI = 1.15-2.13, p = 5×10-3). These findings suggest a relationship between CH and risk of severe infections that warrants further investigation.
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Affiliation(s)
- Kelly L Bolton
- Department of Medicine, Washington University, St Louis, MO, USA.
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Genome Opinion Inc., Seoul, Korea
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Michael B Foote
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Justin Jee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Anton Safonov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joon Ho Moon
- Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Yeon Lee
- Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Jongtak Jung
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Han Song
- Genome Opinion Inc., Seoul, Korea
| | | | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andriy Derkach
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaitlyn A Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian J Wiley
- Department of Medicine, Washington University, St Louis, MO, USA
| | - Ireaneus C Chan
- Department of Medicine, Washington University, St Louis, MO, USA
| | - Lior Z Braunstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teng Gao
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Esther Babady
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa S Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Vijai Joseph
- Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eu Suk Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Robilotti EV, Whiting K, Lucca A, Poon C, Guest R, McMillen T, Jani K, Solovyov A, Kelson S, Browne K, Freeswick S, Hohl TM, Korenstein D, Ruchnewitz D, Lässig M, Łuksza M, Greenbaum B, Seshan VE, Esther Babady N, Kamboj M. Clinical and Genomic Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Infections in mRNA Vaccinated Health Care Personnel in New York City. Clin Infect Dis 2021; 75:e774-e782. [PMID: 34644393 PMCID: PMC9612794 DOI: 10.1093/cid/ciab886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Vaccine-induced clinical protection against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) variants is an evolving target. There are limited genomic level data on SARS CoV-2 breakthrough infections and vaccine effectiveness (VE) since the global spread of the B.1.617.2 (Delta) variant. METHODS In a retrospective study from 1 November 2020 to 31 August 2021, divided as pre-Delta and Delta-dominant periods, laboratory-confirmed SARS CoV-2 infections among healthcare personnel (HCP) at a large tertiary cancer center in New York City were examined to compare the weekly infection rate-ratio in vaccinated, partially vaccinated, and unvaccinated HCP. We describe the clinical and genomic epidemiologic features of post-vaccine infections to assess for selection of variants of concern (VOC)/variants of interest (VOI) in the early post-vaccine period and impact of B.1.617.2 (Delta) variant domination on VE. RESULTS Among 13658 HCP in our cohort, 12379 received at least 1 dose of a messenger RNA (mRNA) vaccine. In the pre-Delta period overall VE was 94.5%. Whole genome sequencing (WGS) of 369 isolates in the pre-Delta period did not reveal a clade bias for VOC/VOI specific to post-vaccine infections. VE in the Delta dominant phase was 75.6%. No hospitalizations occurred among vaccinated HCP in the entire study period, compared to 17 hospitalizations and 1 death among unvaccinated HCP. CONCLUSIONS Findings show high VE among HCP in New York City in the pre-Delta phase, with moderate decline in VE post-Delta emergence. SARS CoV-2 clades were similarly distributed among vaccinated and unvaccinated infected HCP without apparent clustering during the pre-Delta period of diverse clade circulation. Strong vaccine protection against hospitalization was maintained through the entire study period.
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Affiliation(s)
| | | | - Anabella Lucca
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Employee Health Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
| | - Chester Poon
- Division of Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rebecca Guest
- Employee Health Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexander Solovyov
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Suzanne Kelson
- Division of Digital Products and Informatics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kevin Browne
- Department of Nursing, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Scott Freeswick
- Division of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tobias M Hohl
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
| | - Deborah Korenstein
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Marta Łuksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin Greenbaum
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - N Esther Babady
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mini Kamboj
- Correspondence: M. Kamboj, 1275 York Ave, New York, NY 10065 ()
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Cintrón M, Sumner R, McMillen T, Mead PA, Babady NE. Evaluation of a Commercial Multiplexed Molecular Lower Respiratory Panel at a Tertiary Care Cancer Center. J Mol Diagn 2021; 23:1741-1748. [PMID: 34438100 DOI: 10.1016/j.jmoldx.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/22/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022] Open
Abstract
Diagnosis and management of bacterial pneumonia still relies on bacterial culture and antimicrobial susceptibility testing. The Unyvero Lower Respiratory Tract panel (LRT) is a multiplex molecular assay that provides results within approximately 4.5 hours. This study evaluated the analytical performance of the LRT on bronchoalveolar lavage (BAL) fluids and bronchial washings (BW) in a cancer patient population and retrospectively determined clinical impact on therapy. Sensitivity and specificity of LRT on BAL and BW compared with bacterial culture and susceptibilities were calculated. Chart reviews were performed to determine whether antibiotic management would have changed based on the LRT results. A total of 113 BAL and 123 BW respiratory samples from 191 patients were included. The overall sensitivity and specificity were 91.7% (95% CI, 77.5%-98.3%) and 92.0% (95% CI, 87.3%-95.4%), respectively. Staphylococcus aureus was the most common target detected (n = 21) with 89.5% (95% CI, 66.8%-98.7%) sensitivity and 98.2% (95% CI, 95.4%-99.5%) specificity. Based on availability of LRT results, 4.8% of patients could have been de-escalated faster. The LRT demonstrated an overall high accuracy for the detection of common bacteria associated with pneumonia. In this cancer inpatient cohort, treatment adjustment based on LRT results would have occurred in a small number of cases. Larger studies are necessary to understand the real-world impact within specific high-risk populations.
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Affiliation(s)
- Melvilí Cintrón
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rawlica Sumner
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hunter College, New York, New York
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter A Mead
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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Chow K, Aslam A, McClure T, Singh J, Burns J, McMillen T, Jani K, Lucca A, Bubb T, Robilotti EV, Babady NE, Kamboj M. Risk of Healthcare-Associated Transmission of SARS-CoV-2 in Hospitalized Cancer Patients. Clin Infect Dis 2021; 74:1579-1585. [PMID: 34329418 PMCID: PMC8385815 DOI: 10.1093/cid/ciab670] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 06/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background There is limited information on the risk of hospital-acquired coronavirus disease 2019 (COVID-19) among high-risk hospitalized patients after exposure to an infected patient or healthcare worker (HCW) in a nonoutbreak setting. Methods This study was conducted at a tertiary care cancer center in New York City from 10 March 2020 until 28 February 2021. In early April 2020, the study institution implemented universal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing at admission and retesting every 3 days through the hospital stay. Contact tracing records were reviewed for all exposures to SARS-CoV-2 positive patients and HCWs. Results From 10 March 2020 to 28 February 2021, 11 348 unique patients who were SARS-CoV-2 polymerase chain reaction (PCR) negative at the time of admission underwent 31 662 postadmission tests during their hospitalization, and 112 tested positive (0.98%). Among these, 49 patients housed in semiprivate rooms during admission resulted in 74 close contacts and 14 secondary infections within 14 days, for an overall attack rate of 18.9%. Among those exposed to a roommate undergoing an aerosol-generating procedure (AGP), the attack rate was 35.7%. Whole genome sequencing (WGS) corroborated transmission in 6/8 evaluated pairs. In addition, three transmission events occurred in 214 patients with significant exposure to 105 COVID-19 positive healthcare workers (1.4%). Conclusions The overall risk of hospital-acquired COVID-19 is low for hospitalized cancer patients, even during periods of high community prevalence. However, shared occupancy with an unrecognized case is associated with a high secondary attack rate in exposed roommates.
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Affiliation(s)
- Karin Chow
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anoshe Aslam
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tara McClure
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Singh
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacquelyn Burns
- Hospital Administration, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anabella Lucca
- Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Employee Health and Wellness Services, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tania Bubb
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth V Robilotti
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Esther Babady
- Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Bange EM, Han NA, Wileyto P, Kim JY, Gouma S, Robinson J, Greenplate AR, Hwee MA, Porterfield F, Owoyemi O, Naik K, Zheng C, Galantino M, Weisman AR, Ittner CAG, Kugler EM, Baxter AE, Oniyide O, Agyekum RS, Dunn TG, Jones TK, Giannini HM, Weirick ME, McAllister CM, Babady NE, Kumar A, Widman AJ, DeWolf S, Boutemine SR, Roberts C, Budzik KR, Tollett S, Wright C, Perloff T, Sun L, Mathew D, Giles JR, Oldridge DA, Wu JE, Alanio C, Adamski S, Garfall AL, Vella LA, Kerr SJ, Cohen JV, Oyer RA, Massa R, Maillard IP, Maxwell KN, Reilly JP, Maslak PG, Vonderheide RH, Wolchok JD, Hensley SE, Wherry EJ, Meyer NJ, DeMichele AM, Vardhana SA, Mamtani R, Huang AC. CD8 + T cells contribute to survival in patients with COVID-19 and hematologic cancer. Nat Med 2021; 27:1280-1289. [PMID: 34017137 PMCID: PMC8291091 DOI: 10.1038/s41591-021-01386-7] [Citation(s) in RCA: 305] [Impact Index Per Article: 101.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
Patients with cancer have high mortality from coronavirus disease 2019 (COVID-19), and the immune parameters that dictate clinical outcomes remain unknown. In a cohort of 100 patients with cancer who were hospitalized for COVID-19, patients with hematologic cancer had higher mortality relative to patients with solid cancer. In two additional cohorts, flow cytometric and serologic analyses demonstrated that patients with solid cancer and patients without cancer had a similar immune phenotype during acute COVID-19, whereas patients with hematologic cancer had impairment of B cells and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibody responses. Despite the impaired humoral immunity and high mortality in patients with hematologic cancer who also have COVID-19, those with a greater number of CD8 T cells had improved survival, including those treated with anti-CD20 therapy. Furthermore, 77% of patients with hematologic cancer had detectable SARS-CoV-2-specific T cell responses. Thus, CD8 T cells might influence recovery from COVID-19 when humoral immunity is deficient. These observations suggest that CD8 T cell responses to vaccination might provide protection in patients with hematologic cancer even in the setting of limited humoral responses.
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Affiliation(s)
- Erin M Bange
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Nicholas A Han
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul Wileyto
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Justin Y Kim
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James Robinson
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Allison R Greenplate
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Madeline A Hwee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florence Porterfield
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Olutosin Owoyemi
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Karan Naik
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cathy Zheng
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Galantino
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Ariel R Weisman
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Caroline A G Ittner
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily M Kugler
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Baxter
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Olutwatosin Oniyide
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Presbyterian Hospital, Philadelphia, PA, USA
| | - Roseline S Agyekum
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Presbyterian Hospital, Philadelphia, PA, USA
| | - Thomas G Dunn
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Presbyterian Hospital, Philadelphia, PA, USA
| | - Tiffanie K Jones
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Presbyterian Hospital, Philadelphia, PA, USA
| | - Heather M Giannini
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Madison E Weirick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher M McAllister
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - N Esther Babady
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita Kumar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adam J Widman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Susan DeWolf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sawsan R Boutemine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Roberts
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Krista R Budzik
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan Tollett
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Carla Wright
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Tara Perloff
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Pennsylvania Hospital, Philadelphia, NY, USA
| | - Lova Sun
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Divij Mathew
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josephine R Giles
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA
| | - Derek A Oldridge
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer E Wu
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA
| | - Cécile Alanio
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA
| | - Sharon Adamski
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alfred L Garfall
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura A Vella
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Samuel J Kerr
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Lancaster General Hospital, Philadelphia, PA, USA
| | - Justine V Cohen
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Pennsylvania Hospital, Philadelphia, NY, USA
| | - Randall A Oyer
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Lancaster General Hospital, Philadelphia, PA, USA
| | - Ryan Massa
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Presbyterian Hospital, Philadelphia, PA, USA
| | - Ivan P Maillard
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - John P Reilly
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter G Maslak
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert H Vonderheide
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA
| | - Jedd D Wolchok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA
| | - Scott E Hensley
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA
| | - Nuala J Meyer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Angela M DeMichele
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Santosha A Vardhana
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA.
| | - Ronac Mamtani
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - Alexander C Huang
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Parker Institute for Cancer Immunotherapy, Philadelphia, PA, USA.
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Wilcox JA, Remsik J, Babady NE, McMillen TA, Vachha BA, Halpern NA, Dhawan V, Rosenblum M, Iacobuzio-Donahue CA, Avila EK, Santomasso B, Boire A. Abstract 703: An inflammatory leptomeningeal signature in cancer patients with neurologic manifestations of COVID-19. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: COVID-19 is associated with a wide spectrum of neurologic manifestations, which can emerge weeks to months after the initial infection. Cancer patients are at a heightened risk of severe infections due to their immunocompromised status. Leading hypotheses predict that SARS-CoV-2 neuroinvasion or neurologic toxicity from the systemic cytokine storm may account for neurologic dysfunction.
Methods: We prospectively evaluated cancer patients with confirmed SARS-CoV-2 infection and subsequent neurologic manifestations at an NCI-designated cancer center. Evaluations included neurologic examinations, brain imaging, electroencephalogram, and cerebrospinal fluid (CSF) analysis for SARS-CoV-2 detection by RT-PCR for viral RNA and ELISA for nucleocapsid (N) and spike (S2) proteins. Additional proteomic analysis compared the CSF of patients with COVID-19 (CoV+) to cancer- and brain metastasis-matched COVID-19-negative controls (CoV-), and to patients with other cancer-associated neuroinflammatory conditions, including immune effector cell-associated neurotoxicity syndrome (ICANS) and autoimmune encephalitis.
Results: Between May and July 2020, we evaluated 18 COVID-19-positive cancer patients with a wide range of solid tumor and hematologic malignancies. Thirteen (72.2%) of our patients received tumor-directed treatment within 30 days of SARS-CoV-2 infection. Neurologic diagnoses include protracted critical care delirium (N=10), limbic encephalitis (N=4), refractory headaches (N=2), rhombencephalitis (N=1), and large-territory infarctions (N=1). A median delay of 19 days (range 0-77) existed between onset of respiratory symptoms and neurologic manifestations. Among 13 patients who underwent CSF analysis, there was no evidence of SARS-CoV-2 neuroinvasion by RT-PCR in the CSF (N=13) or by N and S2 protein detection (N=10). Targeted proteomic analysis detected a significant accumulation of IL-6 and -8, IFN-gamma, CXCL-1, -6, -9, -10, and -11, CCL-8 and -20, MMP-10 and 4E-BP1 in the CSF of CoV+ patients (N=10) relative to matched CoV- controls (pooled, p=0.029). Combined analysis of these 12 inflammatory mediators revealed CoV+ cytokine levels approaching that of ICANS. CSF MMP-10, a marker of neurodegeneration, correlated with neurologic dysfunction by Karnofsky performance status (p=0.011) and by disability rating scale (p=0.086) at the time of lumbar puncture.
Conclusion: A durable accumulation of IFN-gamma-mediated cytokines is detected in the CSF of cancer patients with neurologic manifestations of COVID-19, in the absence of detectable neuroinvasion. We hypothesize that cytokine-mediated neuroinflammation is responsible for the prolonged neurologic sequela of COVID-19. Our findings suggest a potential role for anti-inflammatory treatments in the management of such patients.
Citation Format: Jessica A. Wilcox, Jan Remsik, N. Esther Babady, Tracy A. McMillen, Behroze A. Vachha, Neil A. Halpern, Vikram Dhawan, Marc Rosenblum, Christine A. Iacobuzio-Donahue, Edward K. Avila, Bianca Santomasso, Adrienne Boire. An inflammatory leptomeningeal signature in cancer patients with neurologic manifestations of COVID-19 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 703.
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Affiliation(s)
| | - Jan Remsik
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Vikram Dhawan
- Memorial Sloan Kettering Cancer Center, New York, NY
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Rubinstein ML, Wolk DM, Babady NE, Johnson JK, Atkinson B, Makim R, Parrott JS. Mapping the Evidence on Rapid Diagnosis of Bloodstream Infections: A Scoping Review. J Appl Lab Med 2021; 6:1012-1024. [PMID: 34125211 DOI: 10.1093/jalm/jfab041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/05/2021] [Indexed: 01/12/2023]
Abstract
BACKGROUND Laboratory and other healthcare professionals participate in developing clinical practice guidelines through systematic review of the evidence. A significant challenge is the identification of areas for analytic focus when the evidence consists of several categories of interventions and outcomes that span both laboratory and clinical processes. The challenge increases when these interventions present as sets of combined interventions. A scoping review may provide a transparent and defensible analytic route forward for systematic reviews challenged in this manner. CONTENT A scoping review was carried out to characterize the evidence on rapid identification of bloodstream infections. Fifty-five studies previously identified by the supported systematic review were charted in duplicate. Charted records were analyzed using descriptive content analysis and evidence mapping with a 5-step process. SUMMARY The 5-step analysis culminated in the characterization of 9 different intervention chain configurations that will facilitate the comparison of complex intervention practices across studies. Furthermore, our evidence map indicates that the current evidence base is strongly centered on 3 specific clinical outcomes, and it links these outcomes to the most represented intervention chain configurations. The scoping review effort generated a route forward for the supported systematic review and meta-analysis.
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Affiliation(s)
- Matthew L Rubinstein
- Department of Clinical Laboratory and Medical Imaging Sciences, Department of Interdisciplinary Studies, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Donna M Wolk
- Molecular and Microbial Diagnostics and Development, Geisinger Medical Laboratories, Diagnostic Medicine Institute, Danville, PA, USA
| | - N Esther Babady
- Department of Laboratory Medicine, Clinical Microbiology Services, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Bridgette Atkinson
- Department of Rehabilitation and Movement Science, School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Roshni Makim
- Department of Rehabilitation and Movement Science, School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - J Scott Parrott
- Department of Interdisciplinary Studies, Department of Biostatistics and Epidemiology, School of Health Professions, School of Public Health, Rutgers, The State University of New Jersey, NJ, USA
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Hata J, Madej R, Babady NE. What Every Clinical Virologist Should Know About The VALID Act On Behalf of the Pan-American Society for Clinical Virology Clinical Practice Com. J Clin Virol 2021; 141:104875. [PMID: 34243115 DOI: 10.1016/j.jcv.2021.104875] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/26/2022]
Abstract
In 2018, a bi-partisan proposed draft legislation called the Verifying Accurate, Leading-edge IVCT Development (VALID) Act was released by Representative Larry Bucshon (Republican-Indiana) and Diana DeGette, (Democrat-Colorado). The VALID Act attempts to create a new framework for the oversight and regulations of both laboratory-developed testing procedures (commonly known as laboratory-developed tests) and In vitro diagnostic tests by the U.S. Food and Drug Administration. The potential impact of this new law if passed may be significant for clinical laboratories in terms of diagnostic test development and implementation. In this report, we review the background and key information that every clinical virologist should know about the VALID Act.
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Affiliation(s)
- Jane Hata
- Mayo Clinic, Jacksonville, FL, U.S.A
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Kondo M, Simon MS, Westblade LF, Jenkins SG, Babady NE, Loo AS, Calfee DP. Implementation of infectious diseases rapid molecular diagnostic tests and antimicrobial stewardship program involvement in acute-care hospitals. Infect Control Hosp Epidemiol 2021; 42:609-611. [PMID: 33059776 PMCID: PMC8050139 DOI: 10.1017/ice.2020.1230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A survey of acute-care hospitals found that rapid molecular diagnostic tests (RMDTs) have been widely adopted. Although many hospitals use their antimicrobial stewardship team and/or guidelines to help clinicians interpret results and optimize treatment, opportunities to more fully achieve the potential benefits of RMDTs remain.
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Affiliation(s)
- Maiko Kondo
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew S Simon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephen G Jenkins
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela S Loo
- Department of Pharmacy, NewYork-Presbyterian Hospital, New York, NY, USA
| | - David P Calfee
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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Babady NE. Clinical Metagenomics for Bloodstream Infections: Is the Juice Worth the Squeeze? Clin Infect Dis 2021; 72:246-248. [PMID: 31942942 DOI: 10.1093/cid/ciaa041] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Affiliation(s)
- N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Remsik J, Wilcox JA, Babady NE, McMillen TA, Vachha BA, Halpern NA, Dhawan V, Rosenblum M, Iacobuzio-Donahue CA, Avila EK, Santomasso B, Boire A. Inflammatory Leptomeningeal Cytokines Mediate COVID-19 Neurologic Symptoms in Cancer Patients. Cancer Cell 2021; 39:276-283.e3. [PMID: 33508216 PMCID: PMC7833316 DOI: 10.1016/j.ccell.2021.01.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2 infection induces a wide spectrum of neurologic dysfunction that emerges weeks after the acute respiratory infection. To better understand this pathology, we prospectively analyzed of a cohort of cancer patients with neurologic manifestations of COVID-19, including a targeted proteomics analysis of the cerebrospinal fluid. We find that cancer patients with neurologic sequelae of COVID-19 harbor leptomeningeal inflammatory cytokines in the absence of viral neuroinvasion. The majority of these inflammatory mediators are driven by type II interferon and are known to induce neuronal injury in other disease states. In these patients, levels of matrix metalloproteinase-10 within the spinal fluid correlate with the degree of neurologic dysfunction. Furthermore, this neuroinflammatory process persists weeks after convalescence from acute respiratory infection. These prolonged neurologic sequelae following systemic cytokine release syndrome lead to long-term neurocognitive dysfunction. Our findings suggest a role for anti-inflammatory treatment(s) in the management of neurologic complications of COVID-19 infection.
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Affiliation(s)
- Jan Remsik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jessica A Wilcox
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - N Esther Babady
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tracy A McMillen
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Behroze A Vachha
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neil A Halpern
- Department of Critical Care, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vikram Dhawan
- Department of Critical Care, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marc Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edward K Avila
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bianca Santomasso
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Adrienne Boire
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Bange EM, Han NA, Wileyto P, Kim JY, Gouma S, Robinson J, Greenplate AR, Porterfield F, Owoyemi O, Naik K, Zheng C, Galantino M, Weisman AR, Ittner CA, Kugler EM, Baxter AE, Oniyide O, Agyekum RS, Dunn TG, Jones TK, Giannini HM, Weirick ME, McAllister CM, Babady NE, Kumar A, Widman AJ, DeWolf S, Boutemine SR, Roberts C, Budzik KR, Tollett S, Wright C, Perloff T, Sun L, Mathew D, Giles JR, Oldridge DA, Wu JE, Alanio C, Adamski S, Garfall AL, Vella L, Kerr SJ, Cohen JV, Oyer RA, Massa R, Maillard IP, Maxwell KN, Reilly JP, Maslak PG, Vonderheide RH, Wolchok JD, Hensley SE, Wherry EJ, Meyer N, DeMichele AM, Vardhana SA, Mamtani R, Huang AC. CD8 T cells compensate for impaired humoral immunity in COVID-19 patients with hematologic cancer. Res Sq 2021:rs.3.rs-162289. [PMID: 33564756 PMCID: PMC7872363 DOI: 10.21203/rs.3.rs-162289/v1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer patients have increased morbidity and mortality from Coronavirus Disease 2019 (COVID-19), but the underlying immune mechanisms are unknown. In a cohort of 100 cancer patients hospitalized for COVID-19 at the University of Pennsylvania Health System, we found that patients with hematologic cancers had a significantly higher mortality relative to patients with solid cancers after accounting for confounders including ECOG performance status and active cancer status. We performed flow cytometric and serologic analyses of 106 cancer patients and 113 non-cancer controls from two additional cohorts at Penn and Memorial Sloan Kettering Cancer Center. Patients with solid cancers exhibited an immune phenotype similar to non-cancer patients during acute COVID-19 whereas patients with hematologic cancers had significant impairment of B cells and SARS-CoV-2-specific antibody responses. High dimensional analysis of flow cytometric data revealed 5 distinct immune phenotypes. An immune phenotype characterized by CD8 T cell depletion was associated with a high viral load and the highest mortality of 71%, among all cancer patients. In contrast, despite impaired B cell responses, patients with hematologic cancers and preserved CD8 T cells had a lower viral load and mortality. These data highlight the importance of CD8 T cells in acute COVID-19, particularly in the setting of impaired humoral immunity. Further, depletion of B cells with anti-CD20 therapy resulted in almost complete abrogation of SARS-CoV-2-specific IgG and IgM antibodies, but was not associated with increased mortality compared to other hematologic cancers, when adequate CD8 T cells were present. Finally, higher CD8 T cell counts were associated with improved overall survival in patients with hematologic cancers. Thus, CD8 T cells likely compensate for deficient humoral immunity and influence clinical recovery of COVID-19. These observations have important implications for cancer and COVID-19-directed treatments, immunosuppressive therapies, and for understanding the role of B and T cells in acute COVID-19.
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Affiliation(s)
- Erin M. Bange
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
| | - Nicholas A. Han
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
| | - Paul Wileyto
- Abramson Cancer Center, University of Pennsylvania
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania
| | - Justin Y. Kim
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
| | - Sigrid Gouma
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | | | - Allison R. Greenplate
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Florence Porterfield
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Olutosin Owoyemi
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Karan Naik
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Cathy Zheng
- Abramson Cancer Center, University of Pennsylvania
| | | | - Ariel R. Weisman
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Caroline A.G. Ittner
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Emily M. Kugler
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Amy E. Baxter
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Olutwatosin Oniyide
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Roseline S. Agyekum
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Thomas G. Dunn
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Tiffanie K. Jones
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Heather M. Giannini
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Madison E. Weirick
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | | | - N. Esther Babady
- Department of Medicine, Memorial Sloan Kettering Cancer Center
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Anita Kumar
- Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Adam J Widman
- Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Susan DeWolf
- Department of Medicine, Memorial Sloan Kettering Cancer Center
| | | | | | | | | | - Carla Wright
- Abramson Cancer Center, University of Pennsylvania
| | - Tara Perloff
- Abramson Cancer Center, University of Pennsylvania
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Pennsylvania Hospital
| | - Lova Sun
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
| | - Divij Mathew
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Josephine R. Giles
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Parker Institute for Cancer Immunotherapy
| | - Derek A. Oldridge
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Jennifer E. Wu
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Parker Institute for Cancer Immunotherapy
| | - Cécile Alanio
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Parker Institute for Cancer Immunotherapy
| | - Sharon Adamski
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
| | - Alfred L. Garfall
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
| | - Laura Vella
- Department of Pediatrics, Perelman School of Medicine, Children’s Hospital of Philadelphia
| | - Samuel J. Kerr
- Abramson Cancer Center, University of Pennsylvania
- Division of Hematology/Oncology, Department of Medicine, Lancaster General Hospital
| | - Justine V. Cohen
- Abramson Cancer Center, University of Pennsylvania
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Pennsylvania Hospital
| | - Randall A. Oyer
- Abramson Cancer Center, University of Pennsylvania
- Division of Hematology/Oncology, Department of Medicine, Lancaster General Hospital
| | - Ryan Massa
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, Presbyterian Hospital
| | - Ivan P. Maillard
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
| | | | - Kara N. Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
| | - John P. Reilly
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Peter G. Maslak
- Department of Medicine, Memorial Sloan Kettering Cancer Center
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Robert H. Vonderheide
- Abramson Cancer Center, University of Pennsylvania
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Parker Institute for Cancer Immunotherapy
| | - Jedd D. Wolchok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center
- Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Scott E. Hensley
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - E. John Wherry
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania
- Parker Institute for Cancer Immunotherapy
| | - Nuala Meyer
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Division of Pulmonary and Critical Care, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
| | - Angela M. DeMichele
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
| | - Santosha A. Vardhana
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center
- Department of Medicine, Memorial Sloan Kettering Cancer Center
- Parker Institute for Cancer Immunotherapy
| | - Ronac Mamtani
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
| | - Alexander C. Huang
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania
- Abramson Cancer Center, University of Pennsylvania
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania
- Parker Institute for Cancer Immunotherapy
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Aydillo T, Gonzalez-Reiche AS, Aslam S, van de Guchte A, Khan Z, Obla A, Dutta J, van Bakel H, Aberg J, García-Sastre A, Shah G, Hohl T, Papanicolaou G, Perales MA, Sepkowitz K, Babady NE, Kamboj M. Shedding of Viable SARS-CoV-2 after Immunosuppressive Therapy for Cancer. N Engl J Med 2020; 383:2586-2588. [PMID: 33259154 PMCID: PMC7722690 DOI: 10.1056/nejmc2031670] [Citation(s) in RCA: 310] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
| | | | - Sadaf Aslam
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Zenab Khan
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ajay Obla
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Jayeeta Dutta
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Judith Aberg
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Gunjan Shah
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tobias Hohl
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Mini Kamboj
- Memorial Sloan Kettering Cancer Center, New York, NY
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Shah GL, DeWolf S, Lee YJ, Tamari R, Dahi PB, Lavery JA, Ruiz J, Devlin SM, Cho C, Peled JU, Politikos I, Scordo M, Babady NE, Jain T, Vardhana S, Daniyan A, Sauter CS, Barker JN, Giralt SA, Goss C, Maslak P, Hohl TM, Kamboj M, Ramanathan L, van den Brink MR, Papadopoulos E, Papanicolaou G, Perales MA. Favorable outcomes of COVID-19 in recipients of hematopoietic cell transplantation. J Clin Invest 2020; 130:6656-6667. [PMID: 32897885 PMCID: PMC7685738 DOI: 10.1172/jci141777] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUNDUnderstanding outcomes and immunologic characteristics of cellular therapy recipients with SARS-CoV-2 is critical to performing these potentially life-saving therapies in the COVID-19 era. In this study of recipients of allogeneic (Allo) and autologous (Auto) hematopoietic cell transplant and CD19-directed chimeric antigen receptor T cell (CAR T) therapy at Memorial Sloan Kettering Cancer Center, we aimed to identify clinical variables associated with COVID-19 severity and assess lymphocyte populations.METHODSWe retrospectively investigated patients diagnosed between March 15, 2020, and May 7, 2020. In a subset of patients, lymphocyte immunophenotyping, quantitative real-time PCR from nasopharyngeal swabs, and SARS-CoV-2 antibody status were available.RESULTSWe identified 77 patients with SARS-CoV-2 who were recipients of cellular therapy (Allo, 35; Auto, 37; CAR T, 5; median time from cellular therapy, 782 days; IQR, 354-1611 days). Overall survival at 30 days was 78%. Clinical variables significantly associated with the composite endpoint of nonrebreather or higher oxygen requirement and death (n events = 25 of 77) included number of comorbidities (HR 5.41, P = 0.004), infiltrates (HR 3.08, P = 0.032), and neutropenia (HR 1.15, P = 0.04). Worsening graft-versus-host disease was not identified among Allo recipients. Immune profiling revealed reductions and rapid recovery in lymphocyte populations across lymphocyte subsets. Antibody responses were seen in a subset of patients.CONCLUSIONIn this series of Allo, Auto, and CAR T recipients, we report overall favorable clinical outcomes for patients with COVID-19 without active malignancy and provide preliminary insights into the lymphocyte populations that are key for the antiviral response and immune reconstitution.FUNDINGNIH grant P01 CA23766 and NIH/National Cancer Institute grant P30 CA008748.
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Affiliation(s)
- Gunjan L. Shah
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Susan DeWolf
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yeon Joo Lee
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Infectious Disease Service, Department of Medicine
| | - Roni Tamari
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Parastoo B. Dahi
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | | | - Josel Ruiz
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Christina Cho
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Jonathan U. Peled
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Ioannis Politikos
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Michael Scordo
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - N. Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine
| | - Tania Jain
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Santosha Vardhana
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Lymphoma Service and
| | - Anthony Daniyan
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Leukemia Service, Department of Medicine; and
| | - Craig S. Sauter
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Juliet N. Barker
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Sergio A. Giralt
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | | | | | - Tobias M. Hohl
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Infectious Disease Service, Department of Medicine
| | - Mini Kamboj
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Infectious Disease Service, Department of Medicine
| | - Lakshmi Ramanathan
- Clinical Chemistry Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marcel R.M. van den Brink
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Esperanza Papadopoulos
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Genovefa Papanicolaou
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
- Infectious Disease Service, Department of Medicine
| | - Miguel-Angel Perales
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
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Bolton KL, Koh Y, Foote MB, Im H, Jee J, Sun CH, Safonov A, Ptashkin R, Moon JH, Lee JY, Jung J, Kang CK, Song KH, Choe PG, Park WB, Kim HB, Oh MD, Song H, Kim S, Patel M, Derkach A, Gedvilaite E, Tkachuk KA, Braunstein LZ, Gao T, Papaemmanuil E, Babady NE, Pessin MS, Kamboj M, Diaz LA, Ladanyi M, Rauh MJ, Natarajan P, Machiela MJ, Awadalla P, Joseph V, Offit K, Norton L, Berger MF, Levine RL, Kim ES, Kim NJ, Zehir A. Clonal hematopoiesis is associated with risk of severe Covid-19. medRxiv 2020:2020.11.25.20233163. [PMID: 33269365 PMCID: PMC7709186 DOI: 10.1101/2020.11.25.20233163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Acquired somatic mutations in hematopoietic stem and progenitor cells (clonal hematopoiesis or CH) are associated with advanced age, increased risk of cardiovascular and malignant diseases, and decreased overall survival. 1-4 These adverse sequelae may be mediated by altered inflammatory profiles observed in patients with CH. 2,5,6 A pro-inflammatory immunologic profile is also associated with worse outcomes of certain infections, including SARS-CoV-2 and its associated disease Covid-19. 7,8 Whether CH predisposes to severe Covid-19 or other infections is unknown. Among 515 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, we found that CH was associated with severe Covid-19 outcomes (OR=1.9, 95%=1.2-2.9, p=0.01). We further explored the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH was significantly associated with risk of Clostridium Difficile (HR=2.0, 95% CI: 1.2-3.3, p=6×10 -3 ) and Streptococcus/Enterococcus infections (HR=1.5, 95% CI=1.1-2.1, p=5×10 -3 ). These findings suggest a relationship between CH and risk of severe infections that warrants further investigation.
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Babady NE, Aslam A, McMillen T, Syed M, Zehir A, Kamboj M. Genotypic correlation between post discharge Clostridiodes difficle infection (CDI) and previous unit-based contacts. J Hosp Infect 2020; 109:96-100. [PMID: 33171187 DOI: 10.1016/j.jhin.2020.10.028] [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: 01/20/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 11/18/2022]
Abstract
BACKGROUND Cases of Clostridiodes difficile infection (CDI) diagnosed after hospital discharge account for a substantial proportion of new infections. It is unclear whether post-discharge infections originate from hospital-based transmission. METHODS This was a Retrospective cohort study at a tertiary-care cancer center (non-outbreak setting). For all laboratory-identified cases of CDI in 2015-2016, patients with post-discharge (PD) CDI within eight weeks of their hospital stay were included in the study. Isolates from PD-CDI cases and their CDI-positive unit-based contacts were first genotyped by multilocus sequence typing (MLST). Common strains were further examined by core genome sequencing (CGS) to evaluate transmission links. RESULTS Of 173 cases examined by MLST, 50% of PD cases matched previous unit contacts. Next, 34 isolates, including 16 PD cases and their 18-unit contacts were examined by CGS. None were ≤3 single-nucleotide variants apart. Seventy percent of PD cases had in-hospital antibiotic exposure before CDI onset in the community. CONCLUSION Our study results suggest that symptomatic CDI cases are not a substantial source of transmission to PD cases. Frequent antibiotic exposure in post-discharge CDI cases is an important target for surveillance and stewardship efforts.
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Affiliation(s)
- N E Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Aslam
- Infection Control and Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - T McMillen
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kamboj
- Infection Control and Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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44
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Aslam A, Singh J, Robilotti E, Chow K, Bist T, Reidy-Lagunes D, Shah M, Korenstein D, Babady NE, Kamboj M. SARS CoV-2 Surveillance and Exposure in the Perioperative Setting with Universal testing and Personal Protective Equipment (PPE) Policies. Clin Infect Dis 2020; 73:e3013-e3018. [PMID: 33090210 PMCID: PMC7665395 DOI: 10.1093/cid/ciaa1607] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Indexed: 12/23/2022] Open
Abstract
Background New York City (NYC) experienced a surge of COVID-19 cases in March and April 2020. Since then, universal PCR based surveillance testing and PPE measures are in wide use in procedural settings. There is limited published experience on the utility and sustainability of PCR based surveillance testing in areas with receding and consistently low community COVID-19 rates. Methods The study was conducted at a tertiary care cancer center in NYC from March 22, 2020, until August 22, 2020. Asymptomatic patients underwent SARS CoV-2 testing before surgeries, interventional radiology procedures, and endoscopy. Contact tracing in procedural areas was done if a patient with an initial negative screen re-tested positive within 48 hours of the procedure. Results From March 22 until August 22, 2020, 11,540 unique patients underwent 14,233 tests before surgeries or procedures at MSKCC. Overall, 65 patients were positive, with a peak rate of 4.3% that fell below 0.3 % after April 2020. For the 65 positive cases, three were pre-symptomatic, and 38 were asymptomatic. Among asymptomatic test-positive patients, 76 % had PCR cycle threshold (Ct) > 30 at first detection. Five patients tested newly positive in the immediate post-operative period, exposing 82 employees with one case of probable transmission (1.2%). Conclusion The prevalence of SARS-CoV-2 infection identified on pre-procedural surveillance was low in our study, which was conducted in an area with limited community spread at the later stage of the study Universal PPE is protective in procedural settings. Optimal and flexible diagnostic strategies are needed to accomplish and sustain the goals of comprehensive pre-procedure surveillance testing.
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Affiliation(s)
- Anoshe Aslam
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jessica Singh
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Robilotti
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY.,Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karin Chow
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tarun Bist
- Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diane Reidy-Lagunes
- Gastrointestinal Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Monika Shah
- Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Deborah Korenstein
- General Medicine, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - N Esther Babady
- Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY.,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mini Kamboj
- Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY.,Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, NY
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Remsik J, Wilcox JA, Babady NE, McMillen T, Vachha BA, Halpern NA, Dhawan V, Rosenblum M, Iacobuzio-Donahue CA, Avila EK, Santomasso B, Boire A. Inflammatory leptomeningeal cytokines mediate delayed COVID-19 encephalopathy. medRxiv 2020:2020.09.15.20195511. [PMID: 32995805 PMCID: PMC7523144 DOI: 10.1101/2020.09.15.20195511] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 infection induces a wide spectrum of neurologic dysfunction. Here we show that a particularly vulnerable population with neurologic manifestations of COVID-19 harbor an influx of inflammatory cytokines within the cerebrospinal fluid in the absence of viral neuro-invasion. The majority of these inflammatory mediators are driven by type 2 interferon and are known to induce neuronal injury in other disease models. Levels of matrix metalloproteinase-10 within the spinal fluid correlate with the degree of neurologic dysfunction. Furthermore, this neuroinflammatory process persists weeks following convalescence from the acute respiratory infection. These prolonged neurologic sequelae following a systemic cytokine release syndrome lead to long-term neurocognitive dysfunction with a wide range of phenotypes.
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46
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Morjaria S, Frame J, Franco-Garcia A, Geyer A, Kamboj M, Babady NE. Clinical Performance of (1,3) Beta-D Glucan for the Diagnosis of Pneumocystis Pneumonia (PCP) in Cancer Patients Tested With PCP Polymerase Chain Reaction. Clin Infect Dis 2020; 69:1303-1309. [PMID: 30561560 DOI: 10.1093/cid/ciy1072] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/13/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Serum (1,3)-beta-D glucan (BDG) is increasingly used to guide the management of suspected Pneumocystis pneumonia (PCP). BDG lacks specificity for PCP, and its clinical performance in high-risk cancer patients has not been fully assessed. Polymerase chain reaction (PCR) for PCP detection is highly sensitive, but cannot differentiate between colonization and infection. We evaluated the diagnostic performance of serum BDG in conjunction with PCP PCR on respiratory samples in patients with cancer and unexplained lung infiltrates. METHODS We performed a retrospective analysis of adult patients evaluated for PCP at our institution from 2012 to 2015, using serum BDG and PCP PCR. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the serum BDG at different thresholds were evaluated using PCP PCR alone or in conjunction with clinical presentation in PCP PCR-positive patients. RESULTS With PCP PCR alone as the reference method, BDG (≥80 pg/mL) had a sensitivity of 69.8%, specificity of 81.2%, PPV of 34.6%, and NPV of 95.2% for PCP. At ≥200 pg/mL in patients with a positive PCR and a compatible PCP clinical syndrome, BDG had a sensitivity of 70%, specificity of 100%, PPV of 100%, and NPV of 52.0% for PCP. CONCLUSIONS Patients negative by both BDG and PCR were unlikely to have PCP. In patients with a compatible clinical syndrome for PCP, higher BDG values (>200 pg/mL) were consistently associated with clinically-significant PCP infections among PCP PCR-positive oncology patients.
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Affiliation(s)
- Sejal Morjaria
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - John Frame
- Department of Quality and Safety, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexandra Franco-Garcia
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Geyer
- Weill Cornell Medical College, New York, New York.,Pulmonary Service, Department of Medicine, New York, New York
| | - Mini Kamboj
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - N Esther Babady
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Robilotti EV, Babady NE, Mead PA, Rolling T, Perez-Johnston R, Bernardes M, Bogler Y, Caldararo M, Figueroa CJ, Glickman MS, Joanow A, Kaltsas A, Lee YJ, Lucca A, Mariano A, Morjaria S, Nawar T, Papanicolaou GA, Predmore J, Redelman-Sidi G, Schmidt E, Seo SK, Sepkowitz K, Shah MK, Wolchok JD, Hohl TM, Taur Y, Kamboj M. Determinants of COVID-19 disease severity in patients with cancer. Nat Med 2020; 26:1218-1223. [PMID: 32581323 DOI: 10.1038/s41591-020-0979-0] [Citation(s) in RCA: 422] [Impact Index Per Article: 105.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/11/2020] [Indexed: 12/23/2022]
Abstract
As of 10 April 2020, New York State had 180,458 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and 9,385 reported deaths. Patients with cancer comprised 8.4% of deceased individuals1. Population-based studies from China and Italy suggested a higher coronavirus disease 2019 (COVID-19) death rate in patients with cancer2,3, although there is a knowledge gap as to which aspects of cancer and its treatment confer risk of severe COVID-194. This information is critical to balance the competing safety considerations of reducing SARS-CoV-2 exposure and cancer treatment continuation. From 10 March to 7 April 2020, 423 cases of symptomatic COVID-19 were diagnosed at Memorial Sloan Kettering Cancer Center (from a total of 2,035 patients with cancer tested). Of these, 40% were hospitalized for COVID-19, 20% developed severe respiratory illness (including 9% who required mechanical ventilation) and 12% died within 30 d. Age older than 65 years and treatment with immune checkpoint inhibitors (ICIs) were predictors for hospitalization and severe disease, whereas receipt of chemotherapy and major surgery were not. Overall, COVID-19 in patients with cancer is marked by substantial rates of hospitalization and severe outcomes. The association observed between ICI and COVID-19 outcomes in our study will need further interrogation in tumor-specific cohorts.
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Affiliation(s)
- Elizabeth V Robilotti
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - N Esther Babady
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Mead
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Thierry Rolling
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Perez-Johnston
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marilia Bernardes
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yael Bogler
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mario Caldararo
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cesar J Figueroa
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Michael S Glickman
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Alexa Joanow
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Kaltsas
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Yeon Joo Lee
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Anabella Lucca
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Employee Health and Wellness Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amanda Mariano
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sejal Morjaria
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Tamara Nawar
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Genovefa A Papanicolaou
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Jacqueline Predmore
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gil Redelman-Sidi
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Elizabeth Schmidt
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Susan K Seo
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Kent Sepkowitz
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Monika K Shah
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Jedd D Wolchok
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA.,Human Oncology and Pathogenesis Program, Department of Medicine, Ludwig Center and Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias M Hohl
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Ying Taur
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA
| | - Mini Kamboj
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Infection Control, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, NY, USA.
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Nolte FS, Babady NE, Buchan BW, Capraro GA, Graf EH, Leber AL, McElvania E, Yao JDC. Responding to the Challenges of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Perspectives from the Association for Molecular Pathology Infectious Disease Subdivision Leadership. J Mol Diagn 2020; 22:968-974. [PMID: 32565306 PMCID: PMC7303040 DOI: 10.1016/j.jmoldx.2020.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/29/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023] Open
Abstract
Clinical molecular laboratory professionals are at the frontline of the response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing accurate, high-quality laboratory results to aid in diagnosis, treatment, and epidemiology. In this role, we have encountered numerous regulatory, reimbursement, supply-chain, logistical, and systems challenges that we have struggled to overcome to fulfill our calling to provide patient care. In this Perspective from the Association for Molecular Pathology Infectious Disease Subdivision Leadership team, we review how our members have risen to these challenges, provide recommendations for managing the current pandemic, and outline the steps we can take as a community to better prepare for future pandemics.
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Affiliation(s)
- Frederick S Nolte
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina.
| | - N Esther Babady
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Blake W Buchan
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Gerald A Capraro
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; Carolinas Pathology Group, Atrium Health, Charlotte, North Carolina
| | - Erin H Graf
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Amy L Leber
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Erin McElvania
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; NorthShore University HealthSystem, University of Chicago, Pritzker School of Medicine, Chicago, Illinois
| | - Joseph D C Yao
- The Infectious Disease Subdivision Leadership of the Association for Molecular Pathology, Rockville, Maryland; Yao Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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Kajon AE, Lamson DM, Spiridakis E, Cardenas AM, Babady NE, Fisher BT, St George K. Isolation of a novel intertypic recombinant human mastadenovirus B2 from two unrelated bone marrow transplant recipients. New Microbes New Infect 2020; 35:100677. [PMID: 32405419 PMCID: PMC7210458 DOI: 10.1016/j.nmni.2020.100677] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/19/2020] [Accepted: 04/03/2020] [Indexed: 12/17/2022] Open
Abstract
Human adenoviruses (HAdV) are well-known opportunistic pathogens of immunocompromised adult and pediatric patients but specific associations between HAdV species or individual HAdV types and disease are poorly understood. In this study we report the isolation of a novel HAdV-B2 genotype from two unrelated immunocompromised patients, both recipients of a hematopoietic cell transplant. In both patients, the course of HAdV infection is consistent with a scenario of reactivation of a latent virus rather than a primary opportunistic infection. Archived HAdV PCR-positive plasma, urine, and stool specimens were processed for virus isolation and detailed molecular characterization. Virus isolates were recovered from patient 1 from PCR-positive urine specimens obtained at days 103 and 116 after transplant in association with gross hematuria, and from a stool specimen obtained 138 days after transplant in association with diarrhea. An isolate was recovered from patient 2 from a PCR-positive urine specimen. Hexon and fiber gene amplification and sequencing were carried out for initial molecular typing, identifying the isolates as an intertypic recombinant with a HAdV-11-like hexon gene and a HAdV-77-like fiber gene. Comprehensive restriction fragment length polymorphism (RFLP) analysis was performed on viral DNA purified from urine and stool isolates, and next generation whole genome sequencing was carried out on purified viral genomic DNA. The genomes of the two isolated strains are 99.5% identical and represent the same RFLP genomic variant. The identified virus is a novel HAdV-B2 genotype designated HAdV-78 exhibiting a HAdV-11-like penton base, a HAdV-11-like hexon and a HAdV-77-like fiber (P11H11F77). A novel HAdV-B2 type was isolated from 2 unrelated stem cell transplant recipients. The two isolated strains are 99.5% identical and represent the same genomic variant. The virus is an intertypic recombinant P11H11F77 designated HAdV-78. Genotype HAdV-78 is closely related to HAdV-77 with a 99% sequence similarity.
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Affiliation(s)
- A E Kajon
- Lovelace Respiratory Research Institute (LRRI), Albuquerque, NM, USA
| | - D M Lamson
- Virology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - E Spiridakis
- Division of Infectious Diseases, The Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - A M Cardenas
- Infectious Disease Diagnostics Laboratory, Children's Hospital of Philadelphia, Philadelphia, PA
| | - N E Babady
- Department of Laboratory Medicine and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B T Fisher
- Division of Infectious Diseases, The Center for Pediatric Clinical Effectiveness, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - K St George
- Virology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
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50
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Cintrón M, O'Sullivan B, Babady NE, Tang YW. Vibrio cholera and V. parahaemolyticus coinfection in an oncology patient with gastroenteritis. Diagn Microbiol Infect Dis 2019; 96:114927. [PMID: 31740171 DOI: 10.1016/j.diagmicrobio.2019.114927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
Abstract
Vibrio-related gastroenteritis in the United States is mostly associated with the consumption of raw or improperly cooked seafood. We describe a case of a stage IV lung adenocarcinoma patient who became ill after eating crab while visiting Upstate New York. Molecular testing and culture confirmed a coinfection with V. parahaemolyticus and a nontoxigenic strain V. cholera.
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Affiliation(s)
- Melvilí Cintrón
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Barbara O'Sullivan
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Rockefeller University Hospital, New York, New York, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Infectious Diseases Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Yi-Wei Tang
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Infectious Diseases Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA; Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York, USA.
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