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Baghdadi JD, Tung CC, Johnson JK, Morgan DJ, Harris AD. Changes in use of multiplex respiratory panel testing during the COVID-19 pandemic. Infect Control Hosp Epidemiol 2024:1-6. [PMID: 39387187 DOI: 10.1017/ice.2024.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
BACKGROUND COVID-19 changed the epidemiology of community-acquired respiratory viruses. We explored patterns of respiratory viral testing to understand which tests are most clinically useful in the postpandemic era. METHODS We conducted a retrospective observational study of discharge data from PINC-AI (formerly Premier), a large administrative database. Use of multiplex nucleic acid amplification respiratory panels in acute care, including small (2-5 targets), medium (6-11), and large panels (>11), were compared between the early pandemic (03/2020-10/2020), late pandemic (11/2020-4/2021), and prepandemic respiratory season (11/2019 - 02/2020) using ANOVA. RESULTS A median of 160.5 facilities contributed testing data per quarter (IQR 155.5-169.5). Prepandemic, facilities averaged 103 respiratory panels monthly (sd 138), including 79 large (sd 126), 7 medium (sd 31), and 16 small panels (sd 73). Relative to prepandemic, utilization decreased during the early pandemic (62 panels monthly/facility; sd 112) but returned to the prepandemic baseline by the late pandemic (107 panels monthly/facility; sd 211). Relative to prepandemic, late pandemic testing involved more small panel use (58 monthly/facility, sd 156) and less large panel use (47 monthly/facility, sd 116). Comparisons among periods demonstrated significant differences in overall testing (P < 0.0001), large panel use (P < 0.0001), and small panel use (P < 0.0001). CONCLUSIONS Postpandemic, clinical use of respiratory panel testing shifted from predominantly large panels to predominantly small panels. Factors driving this change may include resource availability, costs, and the clinical utility of targeting important pathogenic viruses instead of testing "for everything."
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Affiliation(s)
- Jonathan D Baghdadi
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
- University of Maryland - Institute for Health Computing, North Bethesda, MD, USA
| | - Chih Chun Tung
- Pharmacy Research Computing, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | - J Kristie Johnson
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Daniel J Morgan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
- Maryland VA Health Care System, Baltimore, MD, USA
| | - Anthony D Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
- University of Maryland - Institute for Health Computing, North Bethesda, MD, USA
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Paniz-Mondolfi AE, Ramírez JD. FDA's proposed rule and its regulatory impact on emerging and reemerging neglected tropical diseases in the United States. PLoS Negl Trop Dis 2024; 18:e0012116. [PMID: 38722919 PMCID: PMC11081280 DOI: 10.1371/journal.pntd.0012116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024] Open
Abstract
Diagnosing infectious diseases significantly influences patient care, aiding in outbreak identification, response, and public health monitoring. However, the range of FDA-approved molecular tests remains notably limited, especially concerning neglected tropical diseases (NTDs). Drawing upon our experience as one of the largest healthcare networks in the greater New York metropolitan area, this viewpoint manuscript aims to spotlight the existing diagnostic landscape and unmet clinical needs for 4 emerging NTDs increasingly prevalent in the United States, additionally, it delves into the possible adverse effects of the FDA's Proposed Rule on Laboratory-Developed Tests for these clinical conditions and the broader spectrum of NTDs.
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Affiliation(s)
- Alberto E. Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Juan David Ramírez
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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3
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Moss SF, Shah SC, Tan MC, El-Serag HB. Evolving Concepts in Helicobacter pylori Management. Gastroenterology 2024; 166:267-283. [PMID: 37806461 PMCID: PMC10843279 DOI: 10.1053/j.gastro.2023.09.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/10/2023] [Accepted: 09/18/2023] [Indexed: 10/10/2023]
Abstract
Helicobacter pylori is the most common chronic bacterial infection worldwide and the most significant risk factor for gastric cancer, which remains a leading cause of cancer-related death globally. H pylori and gastric cancer continue to disproportionately impact racial and ethnic minority and immigrant groups in the United States. The approach to H pylori case-finding thus far has relied on opportunistic testing based on symptoms or high-risk indicators, such as racial or ethnic background and family history. However, this approach misses a substantial proportion of individuals infected with H pylori who remain at risk for gastric cancer because most infections remain clinically silent. Moreover, individuals with chronic H pylori infection are at risk for gastric preneoplastic lesions, which are also asymptomatic and only reliably diagnosed using endoscopy and biopsy. Thus, to make a significant impact in gastric cancer prevention, a systematic approach is needed to better identify individuals at highest risk of both H pylori infection and its complications, including gastric preneoplasia and cancer. The approach to H pylori eradication must also be optimized given sharply decreasing rates of successful eradication with commonly used therapies and increasing antimicrobial resistance. With growing acceptance that H pylori should be managed as an infectious disease and the increasing availability of susceptibility testing, we now have the momentum to abandon empirical therapies demonstrated to have inadequate eradication rates. Molecular-based susceptibility profiling facilitates selection of a personalized eradication regimen without necessitating an invasive procedure. An improved approach to H pylori eradication coupled with population-level programs for screening and treatment could be an effective and efficient strategy to prevent gastric cancer, especially in minority and potentially marginalized populations that bear the heaviest burden of H pylori infection and its complications.
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Affiliation(s)
- Steven F Moss
- Brown University, Providence, Rhode Island; Providence VA Medical Center, Providence, Rhode Island
| | - Shailja C Shah
- University of California at San Diego, San Diego, California; VA San Diego Healthcare System, San Diego, California
| | - Mimi C Tan
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Hashem B El-Serag
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas.
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4
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Hare D, Dembicka KM, Brennan C, Campbell C, Sutton-Fitzpatrick U, Stapleton PJ, De Gascun CF, Dunne CP. Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review. J Hosp Infect 2023; 140:139-155. [PMID: 37562592 DOI: 10.1016/j.jhin.2023.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses. AIM To systematically appraise available literature, published between January 1st, 2020 and June 30th, 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission. METHODS Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31st, 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. FINDINGS In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS. CONCLUSION WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks.
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Affiliation(s)
- D Hare
- UCD National Virus Reference Laboratory, University College Dublin, Ireland; School of Medicine, University of Limerick, Limerick, Ireland.
| | - K M Dembicka
- School of Medicine, University of Limerick, Limerick, Ireland
| | - C Brennan
- UCD National Virus Reference Laboratory, University College Dublin, Ireland
| | - C Campbell
- UCD National Virus Reference Laboratory, University College Dublin, Ireland
| | | | | | - C F De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Ireland
| | - C P Dunne
- School of Medicine, University of Limerick, Limerick, Ireland; Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
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Barberia LG, Boing A, Gusmão J, Miyajima F, Abud A, Kemp B, Zamudio M, Moraes de Sousa TC. An assessment of the public health surveillance strategy based on molecular testing during three major pandemic waves of COVID-19 in Brazil. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002164. [PMID: 37594920 PMCID: PMC10437824 DOI: 10.1371/journal.pgph.0002164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/20/2023] [Indexed: 08/20/2023]
Abstract
A national laboratory-based surveillance system was adapted to monitor the situation of SARS-CoV-2 in Brazil. The objective of the study was to compare the challenges in implementing COVID-19 surveillance strategies based on the Ministry of Health's (MoH) distribution of RT-PCR tests to different types of laboratories. This retrospective study analyzed the MoH's testing policies and distribution of RT-PCR tests to laboratories during the first, second, and third waves. Recipient laboratories were divided into groups: public health laboratories that belonged to the national network of public health laboratories (Group 1); public laboratories granted authorization during the pandemic (Group 2); and High-Capacity Testing Centers (Group 3). We analyzed the timing and duration of COVID-19 testing policies and the allocation of tests to laboratories by group and wave. Using t-tests, we analyzed the difference in the weekly average of tests distributed to labs by group and using Pearson's correlation coefficient, analyzed the test distribution according to infection and death rates. Between epiweek 9, 2020, and epiweek 22, 2022, the MoH distributed an average of 263,004 RT-PCR tests per week. The weekly average of tests distributed was highest in the second wave (310,327 tests), followed by the first (218,005 tests) and third waves (201,226 tests). There was a significant increase in the mean weekly tests distributed in the second wave compared to the first and third waves (p = 0.047; IC 8.29-1110.71). We found a significant difference between the weekly average of tests distributed in the first and second wave (p < 0.001; IC -209.83-76.20) to Group 2. Group 3 received the second-highest number of tests from the MoH overall, with a reduction during the third wave to first-wave levels. The distribution of RT-PCR tests was not correlated with the case and death incidence.
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Affiliation(s)
- Lorena G. Barberia
- Department of Political Science, University of Sao Paulo, Avenida Professor Luciano Gualberto, Cidade Universitária, Sao Paulo, SP, Brazil
| | - Alexandra Boing
- Departamento de Saúde Pública, Programa de Pós-graduação em Saúde Coletiva, Universidade Federal de Santa Catarina, Campus Universitário Reitor João David Ferreira Lima, Centro de Ciências da Saúde, Trindade, Florianópolis, Santa Catarina, Brazil
| | - João Gusmão
- Multiprofessional Residency Program in Public Health Policy Management, School of Government, Fiocruz, Gleba A, Brasília, DF, Brazil
| | - Fabio Miyajima
- Analytical Competence Molecular Epidemiology Laboratories, Genomic Surveillance Network, Oswaldo Cruz Foundation (FIOCRUZ), Ceara Branch–Eusebio, Rio de Janeiro, Brazil
- Faculty of Medicine, Postgraduate Programmes in Medical Sciences/Pharmacology/Pathology, Federal University of Ceara, Fortaleza, Brazil
| | - Adriano Abud
- Instituto Adolfo Lutz, Prédio Central, Centro de Respostas Rápidas, Cerqueira Cesar, Sao Paulo, SP, Brazil
| | - Brigina Kemp
- Conselho de Secretários Municipais de Saúde—SP, Sao Paulo, SP, Brazil
| | - Marcela Zamudio
- Department of Political Science, University of Sao Paulo, Cidade Universitária, Sao Paulo, SP, Brazil
| | - Tatiane C. Moraes de Sousa
- Department of Political Science, University of Sao Paulo, Avenida Professor Luciano Gualberto, Cidade Universitária, Sao Paulo, SP, Brazil
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Hijano DR, Ferrolino JA, Hidinger J, Brazelton JN, Gu Z, Suganda S, Glasgow HL, Allison KJ, Peterson M, Dallas RH, Maron G, Hayden RT. Clinical Correlation of Adenoviral Load in the Respiratory Tract Measured by Digital PCR in Immunocompromised Children. Open Forum Infect Dis 2023; 10:ofad030. [PMID: 36776777 PMCID: PMC9907548 DOI: 10.1093/ofid/ofad030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/19/2023] [Indexed: 01/25/2023] Open
Abstract
Immunocompromised patients can have life-threatening adenoviral infection. Viral load in blood and stool is commonly used to guide antiviral therapy. We developed and evaluated a digital polymerase chain reaction assay to quantify human adenovirus in the respiratory tract and showed that higher peak load correlates with disseminated infection, mechanical ventilation, and death.
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Affiliation(s)
- Diego R Hijano
- Correspondence: Randall T. Hayden, MD, Department of Pathology, Mail Stop 250, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 (); or Diego R. Hijano, MD, MSc, Department of Infectious Diseases, Mail Stop 230, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 ()
| | | | - Jennifer Hidinger
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Jessica N Brazelton
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Zhengming Gu
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Sri Suganda
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Heather L Glasgow
- Department of Pathology, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Kim J Allison
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Megan Peterson
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Ronald H Dallas
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Gabriela Maron
- Department of Infectious Diseases, St. Jude Children Research Hospital, Memphis, Tennessee, USA
| | - Randall T Hayden
- Correspondence: Randall T. Hayden, MD, Department of Pathology, Mail Stop 250, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 (); or Diego R. Hijano, MD, MSc, Department of Infectious Diseases, Mail Stop 230, St Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105 ()
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7
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Babady NE, Burckhardt RM, Krammer F, Moore PL, Enquist LW. Building a Resilient Scientific Network for COVID-19 and Beyond. mBio 2022; 13:e0222322. [PMID: 36125317 PMCID: PMC9600431 DOI: 10.1128/mbio.02223-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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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