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Marshall JE, Mercaldo RA, Lipner EM, Prevots DR. Correction: Nontuberculous mycobacteria testing and culture positivity in the United States. BMC Infect Dis 2024; 24:387. [PMID: 38600489 PMCID: PMC11005159 DOI: 10.1186/s12879-024-09216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024] Open
Affiliation(s)
- Julia E Marshall
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - Rachel A Mercaldo
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - Ettie M Lipner
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA.
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Dean SG, Blakney RA, Ricotta EE, Chalmers JD, Kadri SS, Olivier KN, Prevots DR. Bronchiectasis-associated infections and outcomes in a large, geographically diverse electronic health record cohort in the United States. BMC Pulm Med 2024; 24:172. [PMID: 38600466 PMCID: PMC11008033 DOI: 10.1186/s12890-024-02973-3] [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: 02/28/2023] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Bronchiectasis is a pulmonary disease characterized by irreversible dilation of the bronchi and recurring respiratory infections. Few studies have described the microbiology and prevalence of infections in large patient populations outside of specialized tertiary care centers. METHODS We used the Cerner HealthFacts Electronic Health Record database to characterize the nature, burden, and frequency of pulmonary infections among persons with bronchiectasis. Chronic infections were defined based on organism-specific guidelines. RESULTS We identified 7,749 patients who met our incident bronchiectasis case definition. In this study population, the organisms with the highest rates of isolate prevalence were Pseudomonas aeruginosa with 937 (12%) individuals, Staphylococcus aureus with 502 (6%), Mycobacterium avium complex (MAC) with 336 (4%), and Aspergillus sp. with 288 (4%). Among persons with at least one isolate of each respective pathogen, 219 (23%) met criteria for chronic P. aeruginosa colonization, 74 (15%) met criteria for S. aureus chronic colonization, 101 (30%) met criteria for MAC chronic infection, and 50 (17%) met criteria for Aspergillus sp. chronic infection. Of 5,795 persons with at least two years of observation, 1,860 (32%) had a bronchiectasis exacerbation and 3,462 (60%) were hospitalized within two years of bronchiectasis diagnoses. Among patients with chronic respiratory infections, the two-year occurrence of exacerbations was 53% and for hospitalizations was 82%. CONCLUSIONS Patients with bronchiectasis experiencing chronic respiratory infections have high rates of hospitalization.
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Affiliation(s)
- Samantha G Dean
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, USA
| | - Rebekah A Blakney
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, USA
| | - Emily E Ricotta
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, USA
| | - James D Chalmers
- University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland
| | - Sameer S Kadri
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, USA
- Department of Medicine, Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina School of Medicine, Chapel Hill, USA
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health , Bethesda, USA.
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Marshall JE, Mercaldo RA, Lipner EM, Prevots DR. Nontuberculous mycobacteria testing and culture positivity in the United States. BMC Infect Dis 2024; 24:288. [PMID: 38448840 PMCID: PMC10916245 DOI: 10.1186/s12879-024-09059-9] [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: 09/15/2023] [Accepted: 01/25/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) are environmental bacteria which may cause chronic lung disease. The prevalence of NTM pulmonary infection and disease has been increasing in the United States and globally. The predominant clinically relevant species of NTM in the United States are Mycobacterium avium complex (MAC) species and Mycobacterium abscessus. With the development of rapid species identification methods for NTM (e.g. PCR probes), more testing for NTM is being conducted through commercial labs, such as Laboratory Corporation of America (Labcorp), which provides deidentified real-time testing data to the Centers for Disease Control (CDC) pursuant to a data sharing agreement. Because NTM lung infections are not reportable in most states, other data sources are key to understanding NTM testing patterns, positivity rates, and species distributions to track infection trends and identify clinical care needs. METHODS We obtained national Labcorp data for the period January 2019 through mid-April 2022. We subset the data to only respiratory samples sent for Acid Fast Bacilli (AFB) cultures. NTM positive results were defined as those which identified an NTM species and are not Mycobacterium tuberculosis, Mycobacterium bovis, or Mycobacterium gordonae. RESULTS Overall, 112,528 respiratory samples were sent for AFB testing during the study period; 26.3% were from the Southeast U.S., identified as HSS Region IV in the Labcorp dataset, and 23.0% were from the Pacific and South Pacific region (Region IX). The culture positive prevalence ranged from 20.2% in the Southeast to 9.2% in the East North Central region (Region V). In the Southeast US, M. abscessus prevalence was 4.0%. For MAC, the highest prevalence was observed in the Mountain region (Region VII) (13.5%) and the lowest proportion was in the East South Central region (7.3%, Region III). Among positive tests, the proportion which was MAC varied from 61.8% to 88.9% and was highest in the Northeast U.S. The proportion of positive samples which were M. abscessus ranged from 3.8% to 19.7% and was highest in the Southeast. CONCLUSIONS The Southeastern region of the U.S. has the highest rate of culture positivity in Labcorp tests for total NTM and, of all positive tests, the highest proportion of M. abscessus. These estimates may underrepresent the true number of M. abscessus infections because M. absesscus-specific probes are not commercially available and not all NTM testing in the United States is done by Labcorp. Analysis of real-time testing data from commercial laboratories may provide insights into risk factors for NTM culture positivity in 'hotspot' areas.
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Affiliation(s)
- Julia E Marshall
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - Rachel A Mercaldo
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - Ettie M Lipner
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA.
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Loria V, Aparicio A, Hildesheim A, Cortés B, Barrientos G, Retana D, Sun K, Ocampo R, Prevots DR, Zúñiga M, Waterboer T, Wong-McClure R, Morera M, Butt J, Binder M, Abdelnour A, Calderón A, Gail MH, Pfeiffer RM, Solís CB, Fantin R, Vanegas JC, Mercado R, Ávila C, Porras C, Herrero R. Cohort profile: evaluation of immune response and household transmission of SARS-CoV-2 in Costa Rica: the RESPIRA study. BMJ Open 2023; 13:e071284. [PMID: 38070892 PMCID: PMC10729140 DOI: 10.1136/bmjopen-2022-071284] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/19/2023] [Indexed: 12/18/2023] Open
Abstract
PURPOSE The RESPIRA cohort aims to describe the nature, magnitude, time course and efficacy of the immune response to SARS-CoV-2 infection and vaccination, population prevalence, and household transmission of COVID-19. PARTICIPANTS From November 2020, we selected age-stratified random samples of COVID-19 cases from Costa Rica confirmed by PCR. For each case, two population-based controls, matched on age, sex and census tract were recruited, supplemented with hospitalised cases and household contacts. Participants were interviewed and blood and saliva collected for antibodies and PCR tests. Participants will be followed for 2 years to assess antibody response and infection incidence. FINDINGS TO DATE Recruitment included 3860 individuals: 1150 COVID-19 cases, 1999 population controls and 719 household contacts from 304 index cases. The age and regional distribution of cases was as planned, including four age strata, 30% rural and 70% urban. The control cohort had similar sex, age and regional distribution as the cases according to the study design. Among the 1999 controls recruited, 6.8% reported at enrolment having had COVID-19 and an additional 12.5% had antibodies against SARS-CoV-2. Compliance with visits and specimens has been close to 70% during the first 18 months of follow-up. During the study, national vaccination was implemented and nearly 90% of our cohort participants were vaccinated during follow-up. FUTURE PLANS RESPIRA will enable multiple analyses, including population prevalence of infection, clinical, behavioural, immunological and genetic risk factors for SARS-CoV-2 acquisition and severity, and determinants of household transmission. We are conducting retrospective and prospective assessment of antibody levels, their determinants and their protective efficacy after infection and vaccination, the impact of long-COVID and a series of ancillary studies. Follow-up continues with bimonthly saliva collection for PCR testing and biannual blood collection for immune response analyses. Follow-up will be completed in early 2024. TRIAL REGISTRATION NUMBER NCT04537338.
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Affiliation(s)
- Viviana Loria
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Amada Aparicio
- Caja Costarricense de Seguro Social, San Jose, Costa Rica
| | - Allan Hildesheim
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Bernal Cortés
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Gloriana Barrientos
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Daniela Retana
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda, Maryland, USA
| | - Rebeca Ocampo
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael Zúñiga
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Tim Waterboer
- Infections and Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Melvin Morera
- Caja Costarricense de Seguro Social, San Jose, Costa Rica
| | - Julia Butt
- Infections and Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Marco Binder
- Virus-Associated Carcinogenesis, German Cancer Research Center, Heidelberg, Germany
| | - Arturo Abdelnour
- Hospital Nacional de Niños, Caja Costarricense de Seguro Social, San Jose, Costa Rica
| | | | - Mitchell H Gail
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ruth M Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Cristina Barboza Solís
- Public Health Dental Department, Universidad de Costa Rica, Sabanilla de Montes de Oca, Costa Rica
| | - Romain Fantin
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Juan Carlos Vanegas
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Rachel Mercado
- Department of Laboratory Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Carlos Ávila
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomedicas-Fundacion Inciensa, San Jose, Costa Rica
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Prevots DR, Marshall JE, Wagner D, Morimoto K. Global Epidemiology of Nontuberculous Mycobacterial Pulmonary Disease: A Review. Clin Chest Med 2023; 44:675-721. [PMID: 37890910 PMCID: PMC10625169 DOI: 10.1016/j.ccm.2023.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
Nontuberculous mycobacterial (NTM) isolation and pulmonary disease (NTM-PD) have continued to increase in most regions of the world, driven mainly by Mycobacterium avium. Single-center studies also support increasing trends as well as a persistent burden of undiagnosed NTM among persons suspected of having tuberculosis (TB), in countries with moderate-to-high TB prevalence. Cumulative exposure to water and soil presents an increased risk to susceptible hosts, and trace metals in water supply are recently recognized risk factors. Establishing standard case definitions for subnational and national surveillance systems with mandatory notification of NTM-PD are needed to allow comparisons within and across countries and regions.
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Affiliation(s)
- D Rebecca Prevots
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, Bethesda, MD 20852, USA.
| | - Julia E Marshall
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Lane, Bethesda, MD 20852, USA
| | - Dirk Wagner
- Division of Infectious Diseases, Department of Internal Medicine II, Medical Center- University of Freiburg, Faculty of Medicine, Hugstetter Street. 55, Freiburg b106, Germany
| | - Kozo Morimoto
- Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), 3-1-24, Matsuyama, Kiyose, Tokyo, Japan
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Fantin R, Agarwala N, Aparicio A, Pfeiffer R, Waterboer T, Abdelnour A, Butt J, Flock J, Remans K, Prevots DR, Porras C, Hildesheim A, Loria V, Gail MH, Herrero R. Estimating the cumulative incidence of SARS-CoV-2 infection in Costa Rica: modelling seroprevalence data in a population-based cohort. Lancet Reg Health Am 2023; 27:100616. [PMID: 37868648 PMCID: PMC10589740 DOI: 10.1016/j.lana.2023.100616] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023]
Abstract
Background The true incidence of SARS-CoV-2 infection in Costa Rica was likely much higher than officially reported, because infection is often associated with mild symptoms and testing was limited by official guidelines and socio-economic factors. Methods Using serology to define natural infection, we developed a statistical model to estimate the true cumulative incidence of SARS-CoV-2 in Costa Rica early in the pandemic. We estimated seroprevalence from 2223 blood samples collected from November 2020 to October 2021 from 1976 population-based controls from the RESPIRA study. Samples were tested for antibodies against SARS-CoV-2 nucleocapsid and the receptor-binding-domain of the spike proteins. Using a generalized linear model, we estimated the ratio of true infections to officially reported cases. Applying these ratios to officially reported totals by age, sex, and geographic area, we estimated the true number of infections in the study area, where 70% of Costa Ricans reside. We adjusted the seroprevalence estimates for antibody decay over time, estimated from 1562 blood samples from 996 PCR-confirmed COVID-19 cases. Findings The estimated total proportion infected (ETPI) was 4.0 times higher than the officially reported total proportion infected (OTPI). By December 16th, 2021, the ETPI was 47% [42-52] while the OTPI was 12%. In children and adolescents, the ETPI was 11.0 times higher than the OTPI. Interpretation Our findings suggest that nearly half the population had been infected by the end of 2021. By the end of 2022, it is likely that a large majority of the population had been infected. Funding This work was sponsored and funded by the National Institute of Allergy and Infectious Diseases through the National Cancer Institute, the Science, Innovation, Technology and Telecommunications Ministry of Costa Rica, and Costa Rican Biomedical Research Agency-Fundacion INCIENSA (grant N/A).
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Affiliation(s)
- Romain Fantin
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, San José, Costa Rica
| | - Neha Agarwala
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Amada Aparicio
- Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Ruth Pfeiffer
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Tim Waterboer
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Julia Butt
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Flock
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kim Remans
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - D. Rebecca Prevots
- Epidemiology and Population Studies Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, San José, Costa Rica
| | - Allan Hildesheim
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, San José, Costa Rica
| | - Viviana Loria
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, San José, Costa Rica
| | - Mitchell H. Gail
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, San José, Costa Rica
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Lipner EM, French JP, Mercaldo RA, Nelson S, Zelazny AM, Marshall JE, Strong M, Falkinham JO, Prevots DR. The risk of pulmonary NTM infections and water-quality constituents among persons with cystic fibrosis in the United States, 2010-2019. Environ Epidemiol 2023; 7:e266. [PMID: 37840858 PMCID: PMC10569765 DOI: 10.1097/ee9.0000000000000266] [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] [Revised: 03/06/2023] [Accepted: 07/17/2023] [Indexed: 10/17/2023] Open
Abstract
Rationale The prevalence of nontuberculous mycobacterial (NTM) pulmonary disease varies geographically in the United States. Previous studies indicate that the presence of certain water-quality constituents in source water increases NTM infection risk. Objective To identify water-quality constituents that influence the risk of NTM pulmonary infection in persons with cystic fibrosis in the United States. Methods We conducted a population-based case-control study using NTM incidence data collected from the Cystic Fibrosis Foundation Patient Registry during 2010-2019. We linked patient zip code to the county and associated patient county of residence with surface water data extracted from the Water Quality Portal. We used logistic regression models to estimate the odds of NTM infection as a function of water-quality constituents. We modeled two outcomes: pulmonary infection due to Mycobacterium avium complex (MAC) and Mycobacterium abscessus species. Results We identified 484 MAC cases, 222 M. abscessus cases and 2816 NTM-negative cystic fibrosis controls resident in 11 states. In multivariable models, we found that for every 1-standardized unit increase in the log concentration of sulfate and vanadium in surface water at the county level, the odds of infection increased by 39% and 21%, respectively, among persons with cystic fibrosis with MAC compared with cystic fibrosis-NTM-negative controls. When modeling M. abscessus as the dependent variable, every 1-standardized unit increase in the log concentration of molybdenum increased the odds of infection by 36%. Conclusions These findings suggest that naturally occurring and anthropogenic water-quality constituents may influence the NTM abundance in water sources that supply municipal water systems, thereby increasing MAC and M. abscessus infection risk.
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Affiliation(s)
- Ettie M. Lipner
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Joshua P. French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado
| | - Rachel A. Mercaldo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Stephen Nelson
- Department of Geological Sciences, Brigham Young University, Provo, Utah
| | - Adrian M. Zelazny
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Julia E. Marshall
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado
| | | | - D. Rebecca Prevots
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Mercaldo RA, Marshall JE, Prevots DR, Lipner EM, French JP. Corrigendum to "Detecting clusters of high nontuberculous mycobacteria infection risk for persons with cystic fibrosis - An analysis of U.S. counties" [Tuberculosis 138 (2023) 102296]. Tuberculosis (Edinb) 2023; 142:102347. [PMID: 37149491 PMCID: PMC10524121 DOI: 10.1016/j.tube.2023.102347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Affiliation(s)
- Rachel A Mercaldo
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Julia E Marshall
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA
| | - D Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA
| | - Ettie M Lipner
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA
| | - Joshua P French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA
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Grigg C, Jackson KA, Barter D, Czaja CA, Johnston H, Lynfield R, Vagnone PS, Tourdot L, Spina N, Dumyati G, Cassidy PM, Pierce R, Henkle E, Prevots DR, Salfinger M, Winthrop KL, Toney NC, Magill SS. Epidemiology of Pulmonary and Extrapulmonary Nontuberculous Mycobacteria Infections at 4 US Emerging Infections Program Sites: A 6-Month Pilot. Clin Infect Dis 2023; 77:629-637. [PMID: 37083882 PMCID: PMC10444004 DOI: 10.1093/cid/ciad214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/28/2023] [Accepted: 04/06/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) cause pulmonary (PNTM) and extrapulmonary (ENTM) disease. Infections are difficult to diagnose and treat, and exposures occur in healthcare and community settings. In the United States, NTM epidemiology has been described largely through analyses of microbiology data from health departments, electronic health records, and administrative data. We describe findings from a multisite pilot of active, laboratory- and population-based NTM surveillance. METHODS The Centers for Disease Control and Prevention's Emerging Infections Program conducted NTM surveillance at 4 sites (Colorado, 5 counties; Minnesota, 2 counties; New York, 2 counties; and Oregon, 3 counties [PNTM] and statewide [ENTM]) from 1 October 2019 through 31 March 2020. PNTM cases were defined using published microbiologic criteria. ENTM cases required NTM isolation from a nonpulmonary specimen, excluding stool and rectal swabs. Patient data were collected via medical record review. RESULTS Overall, 299 NTM cases were reported (PNTM: 231, 77%); Mycobacterium avium complex was the most common species group. Annualized prevalence was 7.5/100 000 population (PNTM: 6.1/100 000; ENTM: 1.4/100 000). Most patients had signs or symptoms in the 14 days before positive specimen collection (ENTM: 62, 91.2%; PNTM: 201, 87.0%). Of PNTM cases, 145 (62.8%) were female and 168 (72.7%) had underlying chronic lung disease. Among ENTM cases, 29 (42.6%) were female, 21 (30.9%) did not have documented underlying conditions, and 26 (38.2%) had infection at the site of a medical device or procedure. CONCLUSIONS Active, population-based NTM surveillance will provide data for monitoring the burden of disease and characterize affected populations to inform interventions.
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Affiliation(s)
- Cheri Grigg
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kelly A Jackson
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Devra Barter
- Division of Disease Control and Public Health Response, Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Christopher A Czaja
- Division of Disease Control and Public Health Response, Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Helen Johnston
- Division of Disease Control and Public Health Response, Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Ruth Lynfield
- Minnesota Department of Health, St. Paul, Minnesota, USA
| | | | - Laura Tourdot
- Minnesota Department of Health, St. Paul, Minnesota, USA
| | - Nancy Spina
- New York State Department of Health, Albany, New York, USA
| | - Ghinwa Dumyati
- University of Rochester Medical Center, Rochester, New York, USA
| | - P Maureen Cassidy
- Public Health Division, Oregon Health Authority, Portland, Oregon, USA
| | - Rebecca Pierce
- Public Health Division, Oregon Health Authority, Portland, Oregon, USA
| | - Emily Henkle
- Oregon Health and Science University, Portland, Oregon, USA
| | - D Rebecca Prevots
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, USA
| | - Max Salfinger
- University of South Florida College of Public Health & Morsani College of Medicine, Tampa, Florida, USA
| | | | - Nadege Charles Toney
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Shelley S Magill
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Marshall JE, Mercaldo RA, Lipner EM, Prevots DR. Incidence of nontuberculous mycobacteria infections among persons with cystic fibrosis in the United States (2010-2019). BMC Infect Dis 2023; 23:489. [PMID: 37488500 PMCID: PMC10364346 DOI: 10.1186/s12879-023-08468-6] [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: 03/22/2023] [Accepted: 07/17/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) are ubiquitous, environmental bacteria that can cause chronic lung disease. Persons with cystic fibrosis (pwCF) are at high risk for NTM. Approximately 1 in 5 pwCF in the United States (U.S.) is affected by pathogenic NTM species, and incidence rates of NTM have been increasing among pwCF as well as in the general population. Prevalence of NTM pulmonary infections (PI) varies widely across the United States because of geographic variation in environmental exposures. This study will present updated region-level incidence of NTM infections in the cystic fibrosis (CF) population in the U.S. METHODS We used the Cystic Fibrosis Foundation Patient Registry (CFFPR) data for the period 2010 through 2019. Our study population comprised persons with CF ≥ 12 years of age who had been tested for NTM PI. We included only registry participants with NTM culture results. We defined incident cases as persons with one positive mycobacterial culture preceded by ≥ two negative mycobacterial cultures. We defined non-cases as persons with ≥ two negative mycobacterial cultures. We estimated average annual NTM PI incidence by region. Using quasi-Poisson models, we calculated annual percent change in incidence by region. RESULTS We identified 3,771 incident NTM infections. Of these cases, 1,816 (48.2%) were Mycobacterium avium complex (MAC) infections and 960 (25.5%) were Mycobacterium abscessus infections. The average annual incidence of NTM PI among pwCF in the U.S. was 58.0 cases per 1,000 persons. The Northeast had the highest incidence of MAC (33.5/1,000 persons tested) and the South had the highest incidence of M. abscessus (20.3/1,000 persons tested). From 2010 to 2019, the annual incidence of total NTM PI increased significantly by 3.5% per year in the U.S. CONCLUSIONS NTM PI incidence is increasing among pwCF. Identifying high risk areas and increasing trends is important for allocating public health and clinical resources as well as evaluating interventions.
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Affiliation(s)
- Julia E Marshall
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA.
| | - Rachel A Mercaldo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - Ettie M Lipner
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
| | - D Rebecca Prevots
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, 5601 Fishers Ln, Bethesda, MD, 20852, USA
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11
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Sun K, Loria V, Aparicio A, Porras C, Vanegas JC, Zúñiga M, Morera M, Avila C, Abdelnour A, Gail MH, Pfeiffer R, Cohen JI, Burbelo PD, Abed MA, Viboud C, Hildesheim A, Herrero R, Prevots DR. Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica. Commun Med (Lond) 2023; 3:102. [PMID: 37481623 PMCID: PMC10363136 DOI: 10.1038/s43856-023-00325-6] [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] [Received: 09/20/2022] [Accepted: 06/21/2023] [Indexed: 07/24/2023] Open
Abstract
INTRODUCTION Variability in household secondary attack rates and transmission risks factors of SARS-CoV-2 remain poorly understood. METHODS We conducted a household transmission study of SARS-CoV-2 in Costa Rica, with SARS-CoV-2 index cases selected from a larger prospective cohort study and their household contacts were enrolled. A total of 719 household contacts of 304 household index cases were enrolled from November 21, 2020, through July 31, 2021. Blood specimens were collected from contacts within 30-60 days of index case diagnosis; and serum was tested for presence of spike and nucleocapsid SARS-CoV-2 IgG antibodies. Evidence of SARS-CoV-2 prior infections among household contacts was defined based on the presence of both spike and nucleocapsid antibodies. We fitted a chain binomial model to the serologic data, to account for exogenous community infection risk and potential multi-generational transmissions within the household. RESULTS Overall seroprevalence was 53% (95% confidence interval (CI) 48-58%) among household contacts. The estimated household secondary attack rate is 34% (95% CI 5-75%). Mask wearing by the index case is associated with the household transmission risk reduction by 67% (adjusted odds ratio = 0.33 with 95% CI: 0.09-0.75) and not sharing bedroom with the index case is associated with the risk reduction of household transmission by 78% (adjusted odds ratio = 0.22 with 95% CI 0.10-0.41). The estimated distribution of household secondary attack rates is highly heterogeneous across index cases, with 30% of index cases being the source for 80% of secondary cases. CONCLUSIONS Modeling analysis suggests that behavioral factors are important drivers of the observed SARS-CoV-2 transmission heterogeneity within the household.
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Affiliation(s)
- Kaiyuan Sun
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Viviana Loria
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Amada Aparicio
- Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Carolina Porras
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Juan Carlos Vanegas
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Michael Zúñiga
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - Melvin Morera
- Caja Costarricense de Seguro Social, San José, Costa Rica
| | - Carlos Avila
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | | | - Mitchell H Gail
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ruth Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Mehdi A Abed
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Cécile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Allan Hildesheim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Rolando Herrero
- Agencia Costarricense de Investigaciones Biomédicas (ACIB) - Fundación INCIENSA (FUNIN), San José, Costa Rica
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, NIAID, NIH, Bethesda, MD, USA.
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12
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Mercaldo RA, Marshall JE, Cangelosi GA, Donohue M, Falkinham JO, Fierer N, French JP, Gebert MJ, Honda JR, Lipner EM, Marras TK, Morimoto K, Salfinger M, Stout J, Thomson R, Prevots DR. Environmental risk of nontuberculous mycobacterial infection: Strategies for advancing methodology. Tuberculosis (Edinb) 2023; 139:102305. [PMID: 36706504 PMCID: PMC10023322 DOI: 10.1016/j.tube.2023.102305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
The National Institute of Allergy and Infectious Diseases organized a symposium in June 2022, to facilitate discussion of the environmental risks for nontuberculous mycobacteria exposure and disease. The expert researchers presented recent studies and identified numerous research gaps. This report summarizes the discussion and identifies six major areas of future research related to culture-based and culture independent laboratory methods, alternate culture media and culturing conditions, frameworks for standardized laboratory methods, improved environmental sampling strategies, validation of exposure measures, and availability of high-quality spatiotemporal data.
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Affiliation(s)
- Rachel A Mercaldo
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Julia E Marshall
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Gerard A Cangelosi
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA.
| | - Maura Donohue
- United States Environmental Protection Agency, Center for Environmental Solutions and Emergency Response, Cincinnati, OH, USA.
| | | | - Noah Fierer
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
| | - Joshua P French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA.
| | - Matthew J Gebert
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
| | - Jennifer R Honda
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
| | - Ettie M Lipner
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Theodore K Marras
- Department of Medicine, University of Toronto and University Health Network, Toronto, Canada.
| | - Kozo Morimoto
- Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo, Japan.
| | - Max Salfinger
- College of Public Health & Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Janet Stout
- Special Pathogens Laboratory, Pittsburgh, PA, USA; Department of Civil and Environmental Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Rachel Thomson
- Gallipoli Medical Research Institute & Greenslopes Clinical School, The University of Queensland, Brisbane, Australia.
| | - D Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
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13
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Marshall JE, Gebert MJ, Lipner EM, Salfinger M, Falkinham Iii JO, Prevots DR, Mercaldo RA. Methods of isolation and identification of nontuberculous mycobacteria from environmental samples: A scoping review. Tuberculosis (Edinb) 2023; 138:102291. [PMID: 36521261 DOI: 10.1016/j.tube.2022.102291] [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: 09/28/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022]
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous in the environment. Some species of NTM are pathogenic and cause lung disease in susceptible persons. Epidemiologic studies of environmental NTM infection risk rely on both culture-dependent and culture-independent techniques for NTM isolation and identification. In this review, we summarized current methods used to isolate and identify NTM from the environment. We searched PubMed, Embase, Scopus, Web of Science: Core Collection, and Global Health (CAB Direct) for peer-reviewed studies from the last 12 years. We identified 1685 unique citations and 110 studies met our inclusion and exclusion criteria. Approximately half (55%) of the studies identified in this review used a combination of culture-independent and culture-dependent methods. The most common environmental substrate analyzed was water (n = 90). Identification of current, common methods for the isolation and identification of NTM from environmental samples may contribute to the development of standard methodological practices in the future. The choice of isolation method is based on the research question, environment, and species. A summary of common methods may contribute to the development of standard practices for isolation and identification of NTM from environmental samples, which may lead to more robust and comparable results.
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Affiliation(s)
- Julia E Marshall
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Matthew J Gebert
- Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.
| | - Ettie M Lipner
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Max Salfinger
- College of Public Health & Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | | | - D Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Rachel A Mercaldo
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
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14
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Mercaldo RA, Marshall JE, Prevots DR, Lipner EM, French JP. Detecting clusters of high nontuberculous mycobacteria infection risk for persons with cystic fibrosis - An analysis of U.S. counties. Tuberculosis (Edinb) 2023; 138:102296. [PMID: 36571892 PMCID: PMC9944666 DOI: 10.1016/j.tube.2022.102296] [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: 09/30/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022]
Abstract
Nontuberculous mycobacteria are ubiquitous environmental bacteria that frequently cause disease in persons with cystic fibrosis (pwCF). The risks for NTM infection vary geographically. Detection of high-risk areas is important for focusing prevention efforts. In this study, we apply five cluster detection methods to identify counties with high NTM infection risk. Four clusters were detected by at least three of the five methods, including twenty-five counties in five states. The geographic area and number of counties in each cluster depended upon the detection method used. Identifying these clusters supports future studies of environmental predictors of infection and will inform control and prevention efforts.
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Affiliation(s)
- Rachel A Mercaldo
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Julia E Marshall
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - D Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Ettie M Lipner
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, USA.
| | - Joshua P French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA.
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15
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Sun K, Loria V, Aparicio A, Porras C, Vanegas JC, Zúñiga M, Morera M, Avila C, Abdelnour A, Gail M, Pfeiffer R, Cohen J, Burbelo P, Abed M, Viboud C, Hildesheim A, Herrero R, Prevots DR. Behavioral factors and SARS-CoV-2 transmission heterogeneity within a household cohort in Costa Rica. Res Sq 2022:rs.3.rs-2065331. [PMID: 36172128 PMCID: PMC9516868 DOI: 10.21203/rs.3.rs-2065331/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Variability in household secondary attack rates (SAR) and transmission risks factors of SARS-CoV-2 remain poorly understood. To characterize SARS-CoV-2 transmission in a household setting, we conducted a household serologic study of SARS-CoV-2 in Costa Rica, with SARS-CoV-2 index cases selected from a larger prospective cohort study and their household contacts were enrolled. A total of 719 household contacts of 304 household index cases were enrolled from November 21, 2020, through July 31, 2021. Demographic, clinical, and behavioral information was collected from the index cases and their household contacts. Blood specimens were collected from contacts within 30-60 days of index case diagnosis; and serum was tested for presence of spike and nucleocapsid SARS-CoV-2 IgG antibodies. Evidence of SARS-CoV-2 prior infections among household contacts was defined based on the presence of both spike and nucleocapsid antibodies. To avoid making strong assumptions that the index case was the sole source of infections among household contacts, we fitted a chain binomial model to the serologic data, which allowed us to account for exogenous community infection risk as well as potential multi-generational transmissions within the household. Overall seroprevalence was 53% (95% confidence interval (CI) 48% - 58%) among household contacts The estimated household secondary attack rate (SAR) was 32% (95% CI 5% - 74%) and the average community infection risk was 19% (95% CI 14% - 26%). Mask wearing by the index case was associated with the household transmission risk reduction by 67% (adjusted odds ratio = 0.33 with 95% CI: 0.09-0.75) and sleeping in a separate bedroom from the index case reduced the risk of household transmission by 78% (adjusted odds ratio = 0.22 with 95% CI 0.10-0.41). The estimated distribution of household secondary attack rates was highly heterogeneous across index cases, with 30% of index cases being the source for 80% of secondary cases. Modeling analysis suggests behavioral factors were important drivers of the observed SARS-CoV-2 transmission heterogeneity within the household.
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16
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Mayer LM, Strich JR, Kadri SS, Lionakis MS, Evans NG, Prevots DR, Ricotta EE. Machine Learning in Infectious Disease for Risk Factor Identification and Hypothesis Generation: Proof of Concept Using Invasive Candidiasis. Open Forum Infect Dis 2022; 9:ofac401. [DOI: 10.1093/ofid/ofac401] [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] [Received: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Machine learning (ML) models can handle large datasets without assuming underlying relationships and can be useful for evaluating disease characteristics; yet, they are more commonly used for predicting individual disease risk rather than identifying factors at the population level. We offer a proof of concept applying random forest (RF) algorithms to Candida-positive hospital encounters in an electronic health record database of patients in the U.S.
Methods
Candida-positive encounters were extracted from the Cerner HealthFacts database; invasive infections were laboratory positive sterile site Candida infections. Features included demographics, admission source, care setting, physician specialty, diagnostic and procedure codes, and medications received prior to the first positive Candida culture. We used RF to assess risk factors for three outcomes: any invasive candidiasis (IC) vs non-IC, within-species IC vs non-IC (e.g. invasive C. glabrata vs non-invasive C. glabrata), and between-species IC (e.g. invasive C. glabrata vs all other IC).
Results
14 of 169 (8%) variables were consistently identified as important features in the ML models. When evaluating within-species IC, for example invasive C. glabrata vs non-invasive C. glabrata, we identified known features like central venous catheters, ICU stay, and gastrointestinal operations. In contrast, important variables for invasive C. glabrata vs all other IC included renal disease and medications like diabetes therapeutics, cholesterol medications, and antiarrhythmics.
Conclusions
Known and novel risk factors for IC were identified using ML, demonstrating the hypotheses generating utility of this approach for infectious disease conditions about which less is known, specifically at the species-level or for rarer diseases.
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Affiliation(s)
- Lisa M Mayer
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH) , Rockville, MD , USA
| | - Jeffrey R Strich
- Critical Care Medicine Department, NIH Clinical Center, NIH , Bethesda, MD , USA
| | - Sameer S Kadri
- Critical Care Medicine Department, NIH Clinical Center, NIH , Bethesda, MD , USA
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology & Microbiology (LCIM), NIAID, NIH , Bethesda, MD , USA
| | - Nicholas G Evans
- Department of Philosophy, University of Massachusetts Lowell , 883 Broadway Street, Lowell, MA , USA
| | - D Rebecca Prevots
- Epidemiology and Population Studies Unit, LCIM, NIAID, NIH , Bethesda, MD , USA
| | - Emily E Ricotta
- Epidemiology and Population Studies Unit, LCIM, NIAID, NIH , Bethesda, MD , USA
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17
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Blakney RA, Ricotta EE, Frankland TB, Honda S, Zelazny A, Mayer-Barber KD, Dean SG, Follmann D, Olivier KN, Daida YG, Prevots DR. Incidence of Nontuberculous Mycobacterial Pulmonary Infection, by Ethnic Group, Hawaii, USA, 2005-2019. Emerg Infect Dis 2022; 28:1543-1550. [PMID: 35876462 PMCID: PMC9328927 DOI: 10.3201/eid2808.212375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To further clarify differences in the risk for nontuberculous mycobacterial pulmonary infection (NTM-PI) among ethnic populations in Hawaii, USA, we conducted a retrospective cohort study among beneficiaries of Kaiser Permanente Hawaii (KPH). We abstracted demographic, socioeconomic, clinical, and microbiological data from KPH electronic health records for 2005-2019. An NTM-PI case-patient was defined as a person from whom >1 NTM pulmonary isolate was obtained. We performed Cox proportional hazards regression to estimate incidence of NTM-PI while controlling for confounders. Across ethnic groups, risk for NTM-PI was higher among persons who were underweight (body mass index [BMI] <18.5 kg/m2). Among beneficiaries who self-identified as any Asian ethnicity, risk for incident NTM-PI was increased by 30%. Low BMI may increase susceptibility to NTM-PI, and risk may be higher for persons who self-identify as Asian, independent of BMI.
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18
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Drummond RA, Desai JV, Ricotta EE, Swamydas M, Deming C, Conlan S, Quinones M, Matei-Rascu V, Sherif L, Lecky D, Lee CCR, Green NM, Collins N, Zelazny AM, Prevots DR, Bending D, Withers D, Belkaid Y, Segre JA, Lionakis MS. Long-term antibiotic exposure promotes mortality after systemic fungal infection by driving lymphocyte dysfunction and systemic escape of commensal bacteria. Cell Host Microbe 2022; 30:1020-1033.e6. [PMID: 35568028 PMCID: PMC9283303 DOI: 10.1016/j.chom.2022.04.013] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 03/08/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022]
Abstract
Antibiotics are a modifiable iatrogenic risk factor for the most common human nosocomial fungal infection, invasive candidiasis, yet the underlying mechanisms remain elusive. We found that antibiotics enhanced the susceptibility to murine invasive candidiasis due to impaired lymphocyte-dependent IL-17A- and GM-CSF-mediated antifungal immunity within the gut. This led to non-inflammatory bacterial escape and systemic bacterial co-infection, which could be ameliorated by IL-17A or GM-CSF immunotherapy. Vancomycin alone similarly enhanced the susceptibility to invasive fungal infection and systemic bacterial co-infection. Mechanistically, vancomycin reduced the frequency of gut Th17 cells associated with impaired proliferation and RORγt expression. Vancomycin's effects on Th17 cells were indirect, manifesting only in vivo in the presence of dysbiosis. In humans, antibiotics were associated with an increased risk of invasive candidiasis and death after invasive candidiasis. Our work highlights the importance of antibiotic stewardship in protecting vulnerable patients from life-threatening infections and provides mechanistic insights into a controllable iatrogenic risk factor for invasive candidiasis.
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Affiliation(s)
- Rebecca A Drummond
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Institute of Immunology & Immunotherapy, Institute of Microbiology & Infection, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Jigar V Desai
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Emily E Ricotta
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Muthulekha Swamydas
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Mariam Quinones
- Bioinformatics and Computational Bioscience Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Veronika Matei-Rascu
- Institute of Immunology & Immunotherapy, Institute of Microbiology & Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lozan Sherif
- Institute of Immunology & Immunotherapy, Institute of Microbiology & Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - David Lecky
- Institute of Immunology & Immunotherapy, Institute of Microbiology & Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chyi-Chia R Lee
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nathaniel M Green
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Nicholas Collins
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD 20892, USA
| | - Adrian M Zelazny
- Department of Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, MD 20892, USA
| | - D Rebecca Prevots
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - David Bending
- Institute of Immunology & Immunotherapy, Institute of Microbiology & Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - David Withers
- Institute of Immunology & Immunotherapy, Institute of Microbiology & Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD 20892, USA; NIAID Microbiome Program, NIAID, NIH, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology (LCIM), National Institute of Allergy & Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
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Affiliation(s)
- Kenneth N. Olivier
- Division of Intramural ResearchNational Heart, Lung, and Blood InstituteBethesda, Maryland
| | - D. Rebecca Prevots
- Division of Intramural ResearchNational Institute of Allergy and Infectious DiseasesBethesda, Maryland
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Schildknecht K, Winthrop KL, Prevots DR, Blakney R, Henkle E. Nontuberculous mycobacterial pulmonary disease incidence among elderly patients with bronchiectasis. Eur Respir J 2022; 59:13993003.00018-2022. [PMID: 35361629 DOI: 10.1183/13993003.00018-2022] [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: 01/04/2022] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Kimberly Schildknecht
- Oregon Health & Science University-Portland State University School of Public Health (OHSU-PSU), Portland, OR, USA
| | - Kevin L Winthrop
- Oregon Health & Science University-Portland State University School of Public Health (OHSU-PSU), Portland, OR, USA
| | | | | | - Emily Henkle
- Oregon Health & Science University-Portland State University School of Public Health (OHSU-PSU), Portland, OR, USA
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Proctor C, Garner E, Hamilton KA, Ashbolt NJ, Caverly LJ, Falkinham JO, Haas CN, Prevost M, Prevots DR, Pruden A, Raskin L, Stout J, Haig SJ. Tenets of a holistic approach to drinking water-associated pathogen research, management, and communication. Water Res 2022; 211:117997. [PMID: 34999316 PMCID: PMC8821414 DOI: 10.1016/j.watres.2021.117997] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/13/2021] [Accepted: 12/19/2021] [Indexed: 05/10/2023]
Abstract
In recent years, drinking water-associated pathogens that can cause infections in immunocompromised or otherwise susceptible individuals (henceforth referred to as DWPI), sometimes referred to as opportunistic pathogens or opportunistic premise plumbing pathogens, have received considerable attention. DWPI research has largely been conducted by experts focusing on specific microorganisms or within silos of expertise. The resulting mitigation approaches optimized for a single microorganism may have unintended consequences and trade-offs for other DWPI or other interests (e.g., energy costs and conservation). For example, the ecological and epidemiological issues characteristic of Legionella pneumophila diverge from those relevant for Mycobacterium avium and other nontuberculous mycobacteria. Recent advances in understanding DWPI as part of a complex microbial ecosystem inhabiting drinking water systems continues to reveal additional challenges: namely, how can all microorganisms of concern be managed simultaneously? In order to protect public health, we must take a more holistic approach in all aspects of the field, including basic research, monitoring methods, risk-based mitigation techniques, and policy. A holistic approach will (i) target multiple microorganisms simultaneously, (ii) involve experts across several disciplines, and (iii) communicate results across disciplines and more broadly, proactively addressing source water-to-customer system management.
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Affiliation(s)
- Caitlin Proctor
- Department of Agricultural and Biological Engineering, Division of Environmental and Ecological Engineering, Purdue University, West Lafayette, IN, USA
| | - Emily Garner
- Wadsworth Department of Civil & Environmental Engineering, West Virginia University, Morgantown, WV, USA
| | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Centre for Environmental Health Engineering, Arizona State University, Tempe, AZ, USA
| | - Nicholas J Ashbolt
- Faculty of Science and Engineering, Southern Cross University, Gold Coast. Queensland, Australia
| | - Lindsay J Caverly
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Charles N Haas
- Department of Civil, Architectural & Environmental Engineering, Drexel University, Philadelphia, PA, USA
| | - Michele Prevost
- Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, Canada
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy Pruden
- Department of Civil & Environmental Engineering, Virginia Tech, Blacksburg, VA USA
| | - Lutgarde Raskin
- Department of Civil & Environmental Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Janet Stout
- Department of Civil & Environmental Engineering, University of Pittsburgh, and Special Pathogens Laboratory, Pittsburgh, PA, USA
| | - Sarah-Jane Haig
- Department of Civil & Environmental Engineering, and Department of Environmental & Occupational Health, University of Pittsburgh, Pittsburgh, PA, USA.
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Lipner EM, Crooks JL, French J, Strong M, Nick JA, Prevots DR. Nontuberculous mycobacterial infection and environmental molybdenum in persons with cystic fibrosis: a case-control study in Colorado. J Expo Sci Environ Epidemiol 2022; 32:289-294. [PMID: 34218259 PMCID: PMC8920885 DOI: 10.1038/s41370-021-00360-2] [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] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 06/01/2023]
Abstract
RATIONALE Nontuberculous mycobacteria (NTM) are ubiquitous environmental bacteria that may cause chronic lung disease and are one of the most difficult-to-treat infections among persons with cystic fibrosis (pwCF). Environmental factors likely contribute to increased NTM densities, with higher potential for exposure and infection. OBJECTIVE To identify water-quality constituents that influence odds of NTM infection among pwCF in Colorado. METHODS We conducted a population-based nested case-control study using patient data from the Colorado CF Center NTM database. We associated data from pwCF and water-quality data extracted from the Water Quality Portal to estimate odds of NTM infection. Using Bayesian generalized linear models with binomial-distributed discrete responses, we modeled three separate outcomes; any NTM infection, infections due to Mycobacterium avium complex species, and infections due to M. abscessus group species. RESULTS We observed a consistent association with molybdenum in the source water and M. abscessus group species infection among pwCF in all models. For every 1-unit increase in the log concentration of molybdenum in surface water, the odds of infection for those with M. abscessus group species compared to those who were NTM culture-negative increased by 79%. The odds of M. abscessus group infection varied by county; the counties with the highest probability of infection are located along the major rivers. CONCLUSIONS We have identified molybdenum in the source water as the most predictive factor of M. abscessus group infection among pwCF in Colorado. This finding will help inform patients at risk for NTM of their relative risks in residing within specific regions.
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Affiliation(s)
- Ettie M Lipner
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA.
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA.
| | - James L Crooks
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, CO, USA
| | - Joshua French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA
| | - Michael Strong
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - D Rebecca Prevots
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Ricotta EE, Prevots DR, Olivier KN. CFTR Modulator Use and Risk of Nontuberculous Mycobacteria Positivity in Cystic Fibrosis, 2011–2018. ERJ Open Res 2022; 8:00724-2021. [PMID: 35415188 PMCID: PMC8995538 DOI: 10.1183/23120541.00724-2021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
Background People with cystic fibrosis are at increased risk of pulmonary nontuberculous mycobacteria (NTM) disease. Cystic fibrosis transmembrane conductance regulator (CFTR) modulators are associated with reduced lung infection with pathogens like Pseudomonas aeruginosa and Staphylococcus aureus. This association has not been studied with NTM. Methods Using encounter-level data from the US Cystic Fibrosis Foundation Patient Registry from 2011 to 2018, we identified individuals aged >12 years with one or more NTM-negative sputum culture and information on receipt of ivacaftor therapy. We used a Cox proportional hazards model to assess the relationship between CFTR modulator usage (any and monotherapy versus combination therapy) and NTM sputum culture positivity, controlling for sex, least severe class of CFTR mutation, receipt of chronic macrolides, age, body mass index and percentage predicted forced expiratory volume. Results Out of 25 987 unique individuals, 17 403 individuals met inclusion criteria. During follow-up, 42% of individuals received CFTR modulator therapy, and 23% had incident NTM. The median (interquartile range) time to event was 6.1 (4.0–7.3) years for those ever receiving CFTR modulators compared to 4.0 (1.6–6.5) years in those never receiving CFTR modulators. CFTR modulator use was associated with a significantly reduced hazard of NTM culture positivity (hazard ratio (HR) 0.88, 95% CI 0.79–0.97); there was no significant difference in the hazard between those receiving ivacaftor monotherapy versus combination therapy (combination HR 1.01, 95% CI 0.79–1.23). Conclusions CFTR modulator therapy is associated with a decreased risk of NTM positivity in individuals with cystic fibrosis. Therapeutic use of cystic fibrosis transmembrane conductance regulator (CFTR) modulators is significantly associated with a decreased risk of NTM positivity in individuals with cystic fibrosishttps://bit.ly/3GZC74b
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Campione A, Lanzieri TM, Ricotta E, Grosse SD, Kadri SS, Nussenblatt V, Prevots DR. Missing diagnoses of congenital cytomegalovirus infection in electronic health records for infants with laboratory-confirmed infection. Curr Med Res Opin 2022; 38:273-275. [PMID: 34775876 PMCID: PMC9575942 DOI: 10.1080/03007995.2021.2006536] [Citation(s) in RCA: 4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Congenital cytomegalovirus (CMV) is a leading cause of non-genetic sensorineural hearing loss and neurodevelopmental disabilities among US children. Studies using administrative healthcare databases have identified infants with congenital CMV using diagnostic codes from the International Classification of Diseases, Ninth and Tenth Revision, Clinical Modification. Using Cerner Health Facts deidentified electronic health records, we assessed the sensitivity of CMV diagnostic codes among infants with laboratory confirmed congenital CMV infection (i.e. a positive CMV laboratory test - polymerase chain reaction, direct fluorescent antibody, or culture from urine, saliva, respiratory secretion or blood samples, or IgM serology - within 21 days of life). During 2010-2017, 668 congenital CMV cases were identified among 7,517,207 infants with encounters within 21 days of life, or 0.89 cases per 10,000 infants. The sensitivity of CMV diagnostic codes assigned within 21 and 90 days of life was 10.3% (95% CI: 8.2-12.9) and 11.1% (95% CI: 8.9-13.7), respectively.
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Affiliation(s)
- Alexandra Campione
- Epidemiology Unit, Division of Intramural Research, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Tatiana M Lanzieri
- National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, Georgia
- Corresponding author: Tatiana M. Lanzieri, MD, MPH, Centers for Disease Control and Prevention, 1600 Clifton Road, Mailstop H24-5; Atlanta, GA 30333 – USA; Phone: 1-404-639-3031;
| | - Emily Ricotta
- Epidemiology Unit, Division of Intramural Research, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - Scott D. Grosse
- National Center on Birth Defects and Developmental Disabilities, US Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sameer S. Kadri
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD
| | - Veronique Nussenblatt
- Infectious Disease National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
| | - D Rebecca Prevots
- Epidemiology Unit, Division of Intramural Research, National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD
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Blakney RA, Ricotta EE, Follmann D, Drew J, Carey KA, Glass LN, Robinson C, MacDonald S, McShane PJ, Olivier KN, Fennelly K, Prevots DR. The 6-minute walk test predicts mortality in a pulmonary nontuberculous mycobacteria-predominant bronchiectasis cohort. BMC Infect Dis 2022; 22:75. [PMID: 35062891 PMCID: PMC8783466 DOI: 10.1186/s12879-022-07054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/12/2022] [Indexed: 12/02/2022] Open
Abstract
Background Bronchiectasis is a chronic lung condition frequently associated with nontuberculous mycobacteria pulmonary (NTM) disease. Persons with these conditions are at increased risk of mortality. Patient reported outcome (PRO) instruments and the 6-minute walk test (6MWT) have been shown to predict mortality for several lung conditions, but these measures have not been fully evaluated for bronchiectasis and NTM. Methods We conducted a retrospective cohort study among adult patients enrolled in a natural history study of bronchiectasis at the National Heart, Lung, and Blood Institute. Electronic medical records were queried for demographic, clinical, microbiologic, radiographic, and PRO instrument data: St. George’s Respiratory Questionnaire (SGRQ), Medical Research Council Dyspnea Scale, and the Pulmonary Symptom Severity Score (PSSS). The study baseline date was defined as the patient’s first visit after January 1st, 2015 with a SGRQ or 6MWT completed. Follow-up was defined as the interval between the study baseline visit and date of death or December 31st, 2019. Sex-stratified Cox proportional-hazards regression was conducted to identify predictors of mortality. Separate models were run for each PRO and 6MWT measure, controlling for age, body mass index (BMI), fibrocavitary disease status, and M. abscessus infection. Results In multivariable Cox proportional-hazards regression models, the PSSS-severity (aHR 1.29, 95% CI 1.04–1.59), the 6MWT total distance walked (aHR 0.938, 95% CI 0.896–0.981) and distance saturation product (aHR 0.930, 95% CI 0.887–0.974) independently predicted mortality. In addition, BMI was significantly predictive of mortality in all models. Conclusions The 6MWT and a PRO instrument capturing symptom severity are independently predictive of mortality in our cohort of bronchiectasis patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07054-6.
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Foote SL, Lipner EM, Prevots DR, Ricotta EE. Environmental predictors of pulmonary nontuberculous mycobacteria (NTM) sputum positivity among persons with cystic fibrosis in the state of Florida. PLoS One 2021; 16:e0259964. [PMID: 34882686 PMCID: PMC8659685 DOI: 10.1371/journal.pone.0259964] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are opportunistic human pathogens that are commonly found in soil and water, and exposure to these organisms may cause pulmonary nontuberculous mycobacterial disease. Persons with cystic fibrosis (CF) are at high risk for developing pulmonary NTM infections, and studies have shown that prolonged exposure to certain environments can increase the risk of pulmonary NTM. It is therefore important to determine the risk associated with different geographic areas. Using annualized registry data obtained from the Cystic Fibrosis Foundation Patient Registry for 2010 through 2017, we conducted a geospatial analysis of NTM infections among persons with CF in Florida. A Bernoulli model in SaTScan was used to identify clustering of ZIP codes with higher than expected numbers of NTM culture positive individuals. Generalized linear mixed models with a binomial distribution were used to test the association of environmental variables and NTM culture positivity. We identified a significant cluster of M. abscessus and predictors of NTM sputum positivity, including annual precipitation and soil mineral levels.
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Affiliation(s)
- Sydney L. Foote
- Office of Data Science and Emerging Technologies, Office of Science Management and Operations, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Rockville, MD, United States of America
| | - Ettie M. Lipner
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States of America
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States of America
| | - D. Rebecca Prevots
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, United States of America
| | - Emily E. Ricotta
- Division of Intramural Research, Epidemiology and Population Studies Unit, NIAID, NIH, Rockville, MD, United States of America
- * E-mail:
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Jackson KA, Barter D, Czaja CA, Johnston H, Lynfield R, Lynfield R, Vagnone PS, Tourdot L, Spina N, Dumyati G, Peters S, Escutia G, Pierce R, Henkle E, Prevots DR, Salfinger M, Winthrop KL, Winthrop KL, Toney NC, Magill S, Grigg C. 1408. Population-based Nontuberculous Mycobacteria Surveillance in Four Emerging Infections Program Sites, October 2019–March 2020. Open Forum Infect Dis 2021. [PMCID: PMC8644464 DOI: 10.1093/ofid/ofab466.1600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) cause pulmonary (PNTM) and extrapulmonary (ENTM) disease. NTM infections are difficult to diagnose and treat; environmental exposures occur in both healthcare and community settings. Few population-based studies describe NTM disease epidemiology. Current data indicate PNTM disease and ENTM skin and soft tissue infections are increasing. We describe findings from a multi-site pilot of population-based NTM surveillance. Methods CDC’s Emerging Infections Program conducted active, laboratory- and population-based surveillance for NTM cases occurring in 4 sites (Colorado [5 counties], Minnesota [2 counties], New York [2 counties], and Oregon [3 counties PNTM; statewide ENTM]) during October 1, 2019–March 31, 2020. PNTM cases were defined according to current published microbiologic criteria, based on isolation of NTM in respiratory cultures or tissue. ENTM cases required NTM isolation from a non-pulmonary specimen, excluding stool or rectal swabs. Demographic, clinical, exposure, and laboratory data were collected via medical record review. We calculated overall incidence per 100,000 population using census data and performed descriptive analyses of medical record data. Results Overall, 299 NTM cases were reported (231 [77%] PNTM); M. avium was the most commonly isolated species (Table). NTM incidence was 3.8 per 100,000 (PNTM 3.1/100,000; ENTM 0.7/100,000). Most patients with available data had ≥1 sign or symptom in the 14 days before culture (63 [97%] ENTM, 203 [92%] PNTM). During the surveillance period, 187 (63%) had their first infection-defining culture collected in an outpatient setting (33 [49%] ENTM, 154 [67%] PNTM). Of PNTM cases, 145 (64%) were female, and 154 (67%) had underlying pulmonary disease. Among ENTM cases, 29 (43%) were female, 9 (13%) had diabetes, 8 (12%) had HIV and 27 (40%) had infection at the site of a medical device or healthcare procedure. Common ENTM infection types were lymphadenitis (16 [24%]) and skin abscess (12 [18%]). Table. Characteristics of persons with NTM infection identified in population-based surveillance, October 1, 2019–March 31, 2020. ![]()
Conclusion Characterizing disease burden and affected populations with population-based NTM surveillance will provide data to inform potential interventions and monitor prevention strategy impact. Disclosures Christopher A. Czaja, MD, DrPH, Centers for Disease Control and Prevention (Grant/Research Support) Ruth Lynfield, MD, Nothing to disclose Ghinwa Dumyati, MD, Pfizer (Grant/Research Support)Roche Diagnostics (Advisor or Review Panel member) Emily Henkle, PhD, MPH, AN2 (Consultant, Advisor or Review Panel member)Zambon (Advisor or Review Panel member) Kevin L. Winthrop, MD, MPH, Insmed (Consultant, Grant/Research Support)Paratek (Consultant)RedHill (Consultant)Spero (Consultant) Kevin L. Winthrop, MD, MPH, Insmed (Consultant, Research Grant or Support)Paratek (Consultant)RedHill Biopharma (Consultant)Spero (Consultant)
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Affiliation(s)
| | - Devra Barter
- Colorado Department of Public Health and Environment, Denver, Colorado
| | | | - Helen Johnston
- Colorado Department of Public Health and Environment, Denver, Colorado
| | | | | | | | | | - Nancy Spina
- New York State Department of Health, Albany, NY
| | - Ghinwa Dumyati
- New York Rochester Emerging Infections Program at the University of Rochester Medical Center, Rochester, NY
| | - Shantel Peters
- University of Rochester Medical Center, Rochester, New York
| | | | | | - Emily Henkle
- Oregon Health & Science University, Portland, OR
| | - D Rebecca Prevots
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Max Salfinger
- University of South Florida College of Public Health, Tampa, Florida
| | | | | | - Nadege Charles Toney
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Cheri Grigg
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
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Prevots DR, Marras TK, Wang P, Mange K, Flume PA. Hospitalization Risk for Medicare Beneficiaries With Nontuberculous Mycobacterial Pulmonary Disease. Chest 2021; 160:2042-2050. [PMID: 34314672 PMCID: PMC8727849 DOI: 10.1016/j.chest.2021.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/16/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022] Open
Abstract
Background Nontuberculous mycobacterial pulmonary disease (NTM-PD) is an uncommon mycobacterial infection characterized by worsening lung function and increased health care resource utilization; however, the overall risk for hospitalization among patients with NTM-PD remains unclear. Research Question What is the hospitalization risk among older adults with NTM-PD? Study Design and Methods A retrospective, nested, case-control study was conducted by using the Medicare claims database. Cases were defined as patients with ≥ 2 NTM-PD claims ≥ 30 days apart between January 1, 2007, and December 31, 2015. The study included individuals aged ≥ 65 years with ≥ 12 months of continuous enrollment in both Parts A and B before the first NTM-PD diagnosis. Cases were matched 1:2 to Medicare beneficiaries without NTM-PD (control subjects) according to age and sex. Hospitalizations following the first NTM-PD claim were compared between case and control subjects by using univariate and multivariate analyses. Results A total of 35,444 case subjects and 65,467 matched control subjects (mean age, 76.6 years; 70% female; ≥ 87% White) were identified. Baseline comorbidities, particularly pulmonary comorbidities, were more common in case subjects than in control subjects (81.1% vs 17.7% for COPD; 44.6% vs 0.6% for bronchiectasis). All-cause hospitalization was observed in 65.7% of case subjects and 44.9% of control subjects. Unadjusted annual hospitalization rates were significantly (P < .05) greater among case subjects than control subjects. Case subjects also had a significantly shorter time to hospitalization than control subjects. The increased burden due to hospitalization was reflected in multivariate analysis adjusting for baseline comorbidities. All-cause hospitalization in patients with NTM-PD relative to control subjects was 1.2 times more likely (relative risk, 1.23; 95% CI, 1.21-1.25; P < .0001) with a 46% greater hazard (hazard ratio, 1.46; 95% CI, 1.43-1.50; P < .0001). Interpretation Patients with NTM-PD were significantly more likely to be hospitalized, had greater annualized hospitalization rates, and had shorter time to hospitalization than age- and sex-matched control subjects without NTM-PD. These findings highlight the significantly increased burden of hospitalizations among patients with NTM-PD.
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Affiliation(s)
| | | | - Ping Wang
- Insmed Incorporated, Bridgewater, NJ
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Ricotta EE, Adjemian J, Blakney RA, Lai YL, Kadri SS, Prevots DR. Extrapulmonary Nontuberculous Mycobacteria Infections in Hospitalized Patients, United States, 2009-2014. Emerg Infect Dis 2021; 27:845-852. [PMID: 33622461 PMCID: PMC7920686 DOI: 10.3201/eid2703.201087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) cause pulmonary and extrapulmonary infections in susceptible persons. To characterize the epidemiology of skin and soft tissue (SST) and disseminated extrapulmonary infections caused by NTM in the United States, we used a large electronic health record database to examine clinical, demographic, and laboratory data for hospitalized patients with NTM isolated from extrapulmonary sources during 2009–2014. Using all unique inpatients as the denominator, we estimated prevalence and summarized cases by key characteristics. Of 9,196,147 inpatients, 831 had confirmed extrapulmonary NTM. The 6-year prevalence was 11 cases/100,000 inpatients; source-specific prevalence was 4.4 SST infections/100,000 inpatients and 3.7 disseminated infections/100,000 inpatients. NTM species varied across geographic region; rapidly growing NTM were most prevalent in southern states. Infection with Mycobacterium avium complex was more common among patients with concurrent HIV and fungal infection, a relevant finding because treatment is more effective for M. avium complex than for other NTM infections.
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Abstract
We studied 31 US healthcare facilities to characterize trends in mycobacterial testing. During 2009-2015, testing for acid-fast bacilli increased 3.2% annually, and prevalence of pathogenic nontuberculous mycobacteria increased 4.5% annually. These increases were highest for subpopulations at high risk of infection, including older women, Asians, and patients with concurrent conditions.
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Ricotta EE, Lai YL, Babiker A, Strich JR, Kadri SS, Lionakis MS, Prevots DR, Adjemian J. Invasive Candidiasis Species Distribution and Trends, United States, 2009-2017. J Infect Dis 2020; 223:1295-1302. [PMID: 32798221 DOI: 10.1093/infdis/jiaa502] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [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: 05/01/2020] [Accepted: 08/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Invasive candidiasis (IC) is a growing concern among US healthcare facilities. A large-scale study evaluating incidence and trends of IC in the United States by species and body site is needed to understand the distribution of infection. METHODS An electronic medical record database was used to calculate incidence and trends of IC in the United States by species and infection site from 2009 through 2017. Hospital incidence was calculated using total unique inpatient hospitalizations in hospitals reporting at least 1 Candida case as the denominator. IC incidence trends were assessed using generalized estimating equations with exchangeable correlation structure to fit Poisson regression models, controlling for changes in hospital characteristics and case mix over time. RESULTS Candida albicans remains the leading cause of IC in the United States, followed by Candida glabrata. The overall incidence of IC was 90/100 000 patients, which did not change significantly over time. There were no changes in incidence among C. albicans, C. glabrata, C. parapsilosis, or C. tropicalis; the incidence of other Candida spp. as a whole increased 7.2% annually. While there was no change in candidemia 2009-2017, abdominal and nonabdominal sterile site IC increased significantly. CONCLUSIONS Nonbloodstream IC is increasing in the United States. Understanding the epidemiology of IC should facilitate improved management of infected patients.
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Affiliation(s)
- Emily E Ricotta
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yi Ling Lai
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ahmed Babiker
- Department of Pathology and Laboratory Medicine, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Jeffrey R Strich
- Critical Care Medicine Department, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, Maryland, USA.,United States Public Health Service, Commissioned Corps, Rockville, Maryland, USA
| | - Sameer S Kadri
- Critical Care Medicine Department, National Institutes of Health Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer Adjemian
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.,United States Public Health Service, Commissioned Corps, Rockville, Maryland, USA
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Lipner EM, French J, Bern CR, Walton-Day K, Knox D, Strong M, Prevots DR, Crooks JL. Nontuberculous Mycobacterial Disease and Molybdenum in Colorado Watersheds. Int J Environ Res Public Health 2020; 17:ijerph17113854. [PMID: 32485845 PMCID: PMC7312647 DOI: 10.3390/ijerph17113854] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/16/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023]
Abstract
Nontuberculous mycobacteria (NTM) are environmental bacteria that may cause chronic lung disease. Environmental factors that favor NTM growth likely increase the risk of NTM exposure within specific environments. We aimed to identify water-quality constituents (Al, As, Cd, Ca, Cu, Fe, Pb, Mg, Mn, Mo, Ni, K, Se, Na, Zn, and pH) associated with NTM disease across Colorado watersheds. We conducted a geospatial, ecological study, associating data from patients with NTM disease treated at National Jewish Health and water-quality data from the Water Quality Portal. Water-quality constituents associated with disease risk were identified using generalized linear models with Poisson-distributed discrete responses. We observed a highly robust association between molybdenum (Mo) in the source water and disease risk. For every 1- unit increase in the log concentration of molybdenum in the source water, disease risk increased by 17.0%. We also observed a statistically significant association between calcium (Ca) in the source water and disease risk. The risk of NTM varied by watershed and was associated with watershed-specific water-quality constituents. These findings may inform mitigation strategies to decrease the overall risk of exposure.
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Affiliation(s)
- Ettie M. Lipner
- National Jewish Health, Denver, CO 80206, USA; (M.S.); (J.L.C.)
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
- Correspondence:
| | - Joshua French
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO 80204, USA;
| | - Carleton R. Bern
- U.S. Geological Survey, Colorado Water Science Center, Denver, CO 80225, USA; (C.R.B.); (K.W.-D.)
| | - Katherine Walton-Day
- U.S. Geological Survey, Colorado Water Science Center, Denver, CO 80225, USA; (C.R.B.); (K.W.-D.)
| | - David Knox
- Department of Computer Science, University of Colorado-Boulder, Boulder, CO 80309, USA;
| | - Michael Strong
- National Jewish Health, Denver, CO 80206, USA; (M.S.); (J.L.C.)
| | - D. Rebecca Prevots
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA;
| | - James L. Crooks
- National Jewish Health, Denver, CO 80206, USA; (M.S.); (J.L.C.)
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
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Daniel-Wayman S, Abate G, Barber DL, Bermudez LE, Coler RN, Cynamon MH, Daley CL, Davidson RM, Dick T, Floto RA, Henkle E, Holland SM, Jackson M, Lee RE, Nuermberger EL, Olivier KN, Ordway DJ, Prevots DR, Sacchettini JC, Salfinger M, Sassetti CM, Sizemore CF, Winthrop KL, Zelazny AM. Advancing Translational Science for Pulmonary Nontuberculous Mycobacterial Infections. A Road Map for Research. Am J Respir Crit Care Med 2020; 199:947-951. [PMID: 30428263 DOI: 10.1164/rccm.201807-1273pp] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Shelby Daniel-Wayman
- 1 Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
| | - Getahun Abate
- 2 Division of Infectious Diseases, Allergy, and Immunology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri
| | - Daniel L Barber
- 3 T Lymphocyte Biology Unit, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases
| | - Luiz E Bermudez
- 4 Department of Biomedical Sciences and.,5 Department of Microbiology, Oregon State University, Corvallis, Oregon
| | - Rhea N Coler
- 6 Infectious Disease Research Institute, Seattle, Washington.,7 Department of Global Health, University of Washington, Seattle, Washington
| | - Michael H Cynamon
- 8 Veterans Administration Medical Center, Syracuse, New York.,9 State University of New York Upstate Medical Center, Syracuse, New York
| | - Charles L Daley
- 10 Division of Mycobacterial and Respiratory Infections, Department of Medicine
| | | | - Thomas Dick
- 12 Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,13 Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey
| | - R Andres Floto
- 14 Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Steven M Holland
- 16 Division of Intramural Research, National Institute of Allergy and Infectious Diseases
| | - Mary Jackson
- 17 Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - Richard E Lee
- 18 Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Eric L Nuermberger
- 19 Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,20 Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Kenneth N Olivier
- 21 Laboratory of Chronic Airway Infection, Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, and
| | - Diane J Ordway
- 17 Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado
| | - D Rebecca Prevots
- 1 Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases
| | - James C Sacchettini
- 22 Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Max Salfinger
- 23 Mycobacteriology and Pharmacokinetics Laboratories, National Jewish Health, Denver, Colorado.,24 College of Public Health, University of South Florida, Tampa, Florida
| | - Christopher M Sassetti
- 25 Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts; and
| | - Christine F Sizemore
- 26 Tuberculosis, Leprosy, and other Mycobacterial Diseases Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Kevin L Winthrop
- 15 OHSU-PSU School of Public Health and.,27 Division of Infectious Disease, Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Adrian M Zelazny
- 28 Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland
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Kadri SS, Adjemian J, Lai YL, Spaulding AB, Ricotta E, Prevots DR, Palmore TN, Rhee C, Klompas M, Dekker JP, Powers JH, Suffredini AF, Hooper DC, Fridkin S, Danner RL. Difficult-to-Treat Resistance in Gram-negative Bacteremia at 173 US Hospitals: Retrospective Cohort Analysis of Prevalence, Predictors, and Outcome of Resistance to All First-line Agents. Clin Infect Dis 2019; 67:1803-1814. [PMID: 30052813 DOI: 10.1093/cid/ciy378] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/07/2018] [Indexed: 12/11/2022] Open
Abstract
Background Resistance to all first-line antibiotics necessitates the use of less effective or more toxic "reserve" agents. Gram-negative bloodstream infections (GNBSIs) harboring such difficult-to-treat resistance (DTR) may have higher mortality than phenotypes that allow for ≥1 active first-line antibiotic. Methods The Premier Database was analyzed for inpatients with select GNBSIs. DTR was defined as intermediate/resistant in vitro to all ß-lactam categories, including carbapenems and fluoroquinolones. Prevalence and aminoglycoside resistance of DTR episodes were compared with carbapenem-resistant, extended-spectrum cephalosporin-resistant, and fluoroquinolone-resistant episodes using CDC definitions. Predictors of DTR were identified. The adjusted relative risk (aRR) of mortality was examined for DTR, CDC-defined phenotypes susceptible to ≥1 first-line agent, and graded loss of active categories. Results Between 2009-2013, 471 (1%) of 45011 GNBSI episodes at 92 (53.2%) of 173 hospitals exhibited DTR, ranging from 0.04% for Escherichia coli to 18.4% for Acinetobacter baumannii. Among patients with DTR, 79% received parenteral aminoglycosides, tigecycline, or colistin/polymyxin-B; resistance to all aminoglycosides occurred in 33%. Predictors of DTR included urban healthcare and higher baseline illness. Crude mortality for GNBSIs with DTR was 43%; aRR was higher for DTR than for carbapenem-resistant (1.2; 95% confidence interval, 1.0-1.4; P = .02), extended-spectrum cephalosporin-resistant (1.2; 1.1-1.4; P = .001), or fluoroquinolone-resistant (1.2; 1.0-1.4; P = .008) infections. The mortality aRR increased 20% per graded loss of active first-line categories, from 3-5 to 1-2 to 0. Conclusion Nonsusceptibility to first-line antibiotics is associated with decreased survival in GNBSIs. DTR is a simple bedside prognostic measure of treatment-limiting coresistance.
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Affiliation(s)
- Sameer S Kadri
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland.,Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Jennifer Adjemian
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda.,United States Public Health Service, Commissioned Corps, Rockville
| | - Yi Ling Lai
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda
| | - Alicen B Spaulding
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda
| | - Emily Ricotta
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda
| | - Tara N Palmore
- National Institutes of Health Clinical Center, Bethesda, Maryland
| | - Chanu Rhee
- Department of Medicine, Brigham and Women's Hospital.,Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Michael Klompas
- Department of Medicine, Brigham and Women's Hospital.,Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - John P Dekker
- Department of Laboratory Medicine, National Institutes of Health Clinical Center, Bethesda
| | - John H Powers
- Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., NCI Campus at Frederick, Maryland
| | - Anthony F Suffredini
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland
| | - David C Hooper
- Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Scott Fridkin
- Division of Healthcare Quality and Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Robert L Danner
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland
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Meister L, Zerbe C, Notarangelo LD, Kadri SS, Rebecca Prevots D, Ricotta E. 414. Developing Digital Phenotypes of Primary Immune Deficiencies Using Machine Learning on a Large Electronic Health Record Database. Open Forum Infect Dis 2019. [PMCID: PMC6809140 DOI: 10.1093/ofid/ofz360.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background More than 350 genetic disorders cause immune deficiencies; given the rarity of these conditions, in-depth study of infections associated with primary immune deficiencies (PID) requires extremely large sample sizes from broad populations. Using a large electronic health record (EHR) dataset, we linked clinical and microbiologic data to develop digital phenotypes for PID. Methods Using the Cerner HealthFacts EHR dataset from 2009 to 2017 we extracted clinical and microbiologic data for hospitalizations from patients <18 years old with ICD9/10 PID diagnoses and ≥1 positive culture for infection. Machine learning models were used to identify key features to predict PID diagnosis. Features included patient and hospitalization characteristics; infectious agent and infection site; and selected comorbidities. Model validation was done using the area under the receiver operating characteristic (AUC) curve. Results Overall 1316 patients with a PID were identified (Table 1). The 10 most common pathogens identified by PID are listed in Table 2. The models classified DiGeorge syndrome (positive predictive value 49%), functional disorders of polymorphonuclear neutrophils (PMN) (PPV 43%), and common variable immunodeficiency (CVID) (PPV 47%) better than combined immunodeficiency (CID) (PPV 20%); the overall true positive rate was 47% with an AUC of 0.73. Predictive features for each PID were as follows: CVID—having enteritis, hypertension, and pneumonia (Figure 1a); PMN—having hypoxia and hypertension (Figure 1b); DiGeorge syndrome—having congenital deformities and not having hypertension (Figure 1c); CID—finding Staphylococcus aureus in a wound or Escherichia coli in the blood were predictive of CID (Figure 1d). Conclusion Early models demonstrate some discrimination, specifically for more common PIDs (CVID) and those with highly identifying factors (DiGeorge syndrome). These models can be improved by including a wider array of clinical data, and they provide a first look at a new methodology to digitally phenotype PIDs for future diagnostic use. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Leo Meister
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Christa Zerbe
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Luigi D Notarangelo
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | | | - D Rebecca Prevots
- National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Emily Ricotta
- National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Kadri SS, Ling Lai Y, Warner S, Strich JR, Ricotta E, Rebecca Prevots D, Demirkale CY, Babiker A, Rhee C, Klompas M, Danner RL. 1333. Utility of Admission Procalcitonin Level in Patients Presenting to the Hospital with Bloodstream Infection: Real-World Evidence from 250 US Hospitals. Open Forum Infect Dis 2019. [PMCID: PMC6808911 DOI: 10.1093/ofid/ofz360.1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Serum procalcitonin (PCT) may aid in early detection and treatment of bacterial bloodstream infections (BSI), yet evidence for this indication is inconclusive. We leveraged real-world data to examine biological variability in PCT across host and pathogen factors and its utility for ruling out BSI on admission. Methods PCT measurements within 24 hours of admission were examined in patients presenting with monomicrobial BSI to 250 hospitals in the Cerner Healthfacts Database. The reliability of admission PCT for ruling out BSI at hospital presentation was assessed using two different thresholds (<0.5 and <0.25ng/mL) and then stratifying results by presence vs. absence of sepsis (using CDC Adult Sepsis Event criteria), fever or hypothermia vs. normothermia, various presumed sources of BSI, and organism taxon. Results Between 2007 and 2017, PCT was measured on admission in 4,358/42,465 (10.3%) adults with BSI present on admission at 60 hospitals. Of these, 870 (20%) met CDC surveillance criteria for sepsis. The median admission PCT was 4.89 [0.93, 23.98] and varied by taxon, BSI source, patient temperature, and the presence and severity of sepsis; acute illness severity was the greatest driver of high PCT levels (Fig 1). Using a threshold of ≥ 0.50 ng/mL, the sensitivity of PCT for detection of BSI was 84% for all patients. Notably, BSI without sepsis was 4-fold more likely to yield a false negative PCT (<0.5ng/mL) than bacteremic sepsis. Sensitivity ranged from 77% with normothermia to 83% with fever/hypothermia (P = 0.06), between 81 and 88% across sources of BSI (P = 0.13) and more widely between 64 and 91% across taxa (P = 0.02). Enterococcal BSI was 2- and 4-fold more likely to have a falsely negative PCT than S. aureus or S. pneumoniae BSIs, whereas non-glucose fermenters other than P. aeruginosa had a 2 and 3-fold higher likelihood of being missed compared with P. aeruginosa and Enterobacteriaceae BSIs respectively (Fig 2). Pathogen-level variation in PCT sensitivity was also observed for BSI without sepsis (62–90%; P = 0.02) and upon using a stricter rule-out threshold of <0.25 ng/mL (P = 0.01). Conclusion PCT levels and the reliability of this test for ruling out bacteremia at hospital presentation varies by pathogen, presenting signs, and presence vs. absence of sepsis. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | - Yi Ling Lai
- National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Sarah Warner
- National Institutes of Health, Bethesda, Maryland
| | | | - Emily Ricotta
- National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - D Rebecca Prevots
- National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | | | | | - Chanu Rhee
- Harvard Medical School / Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Michael Klompas
- Harvard Medical School / Harvard Pilgrim Health Care Institute, Boston, Massachusetts
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Ling Lai Y, Ricotta E, Olivier K, Kadri SS, Prevots DR. 1382. Acid-Fast Bacilli Testing Trends at 43 In- and Outpatient Facilities and Nontuberculous Mycobacterial Pulmonary Isolation Rate, United States, 2009–2015. Open Forum Infect Dis 2019. [PMCID: PMC6809242 DOI: 10.1093/ofid/ofz360.1246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background The prevalence of nontuberculous mycobacterial pulmonary disease (NTM PD) is increasing in the United States and globally. The reasons for this increase are not clear but could be related to both gained awareness leading to increased mycobacterial testing, or to a true NTM PD increase. To further examine the role of testing rates in the observed increase, we studied trends in Acid-Fast Bacteria (AFB) testing and NTM isolation positivity using a large Electronic Health Record (EHR) dataset in the United States. Methods Using the Cerner Health Facts EHR dataset, we extracted microbiologic, demographic, and clinical data for patient encounters (inpatient or outpatient), with ≥1 orders for AFB respiratory cultures. The analysis was limited to the 43 facilities reporting continuously for the period 2009–2015. A patient with at least one AFB test was considered tested (AFB) and a patient with at least one pathogenic NTM respiratory isolate was considered positive. Trends in AFB testing and NTM positivity were estimated using log-linked Poisson regression (P < 0.05). Results From 2009 through 2015, of 14.8 million patients, 65,010 had 142,315 AFB tests, averaging 2.2 AFB tests/patient, for an overall testing prevalence of 0.43%; the annual testing prevalence remained unchanged during the study period (P = 0.44) (Figure 1). Of the 65,010 patients with AFB tests, 3,942 (6.1%) had ≥1 pathogenic NTM species, for an overall pulmonary NTM isolation prevalence of 2.7/10,000 patients represented in Cerner Health Facts dataset. Of the patients that had at least one pathogenic NTM, 3,094 (78%) had M. avium complex, and 265 (7%) had M. abscessus/chelonae, (Figure 2). Among patients with at least 1 NTM-positive culture, 138 patients had concomitant growth of M. tuberculosis. Conclusion Increases in NTM PD are not explained by increases in AFB testing, which remained constant in the population represented here. This study was funded in part by the Division of Intramural Research, NIAID, NIH. ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Yi Ling Lai
- National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Emily Ricotta
- National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Kenneth Olivier
- National Institutes of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Sameer S Kadri
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Daniel-Wayman S, Shallom S, Azeem N, Olivier KN, Zelazny AM, Prevots DR. Amikacin exposure and susceptibility of macrolide-resistant Mycobacterium abscessus. ERJ Open Res 2019; 5:00154-2018. [PMID: 31149626 PMCID: PMC6536947 DOI: 10.1183/23120541.00154-2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/15/2019] [Indexed: 11/27/2022] Open
Abstract
Mycobacterium abscessus is associated with antibiotic resistance and poor treatment outcomes. We described within-patient changes in M. abscessus resistance to clarithromycin and amikacin. Patients with amikacin exposure and a >50-month interval between M. abscessus isolates were identified. Antimicrobial susceptibility testing was performed on the first and last isolates by broth microdilution, and genetic markers of resistance were identified. 16 patients were identified with a median amikacin exposure of 2.3 years (range 0.6–8.6 years). 15 patients also received macrolides (median 7.2 years, range 1.3–10.7 years). All initial isolates were resistant to clarithromycin (minimum inhibitory concentration (MIC) ≥8 µg·mL−1). Two patients had later susceptible isolates, which were of a different subspecies (M. abscessus subsp. massiliense) than the initial isolates (M. abscessus subsp. abscessus). All initial isolates were susceptible or intermediately resistant to amikacin, and only one patient had a resistant final isolate (MIC >64 µg·mL−1), accompanied by an A→G mutation at position 1408 of the 16S ribosomal RNA. Forced expiratory volume in 1 s decreased significantly over the study period, while smear quantity and the proportions of patients with elevated C-reactive protein or cavitary lesions all increased significantly. Despite prolonged, mostly inhaled amikacin exposure, development of amikacin resistance was uncommon in this patient population; however, disease progression continued. Patients with long-term amikacin treatment rarely develop resistance but their disease continues to progresshttp://bit.ly/2V7k0kH
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Affiliation(s)
- Shelby Daniel-Wayman
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shamira Shallom
- Dept of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Nabila Azeem
- Dept of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth N Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Dept of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Adjemian J, Lai YL, Ricotta E, Prevots DR. 1720. Regional Differences in Trends of Hospitalizations Associated With Tick-Borne Diseases in the United States, 2009–2014. Open Forum Infect Dis 2018. [PMCID: PMC6252667 DOI: 10.1093/ofid/ofy209.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Tick-borne diseases are increasing in incidence in the United States; however, limited data exist on regional trends of associated hospitalizations. Using a nationally distributed dataset of US hospital-based medical records, we aimed to assess trends in incidence of hospitalizations from tick-borne disease by geographic region. Methods Data were examined from 156 US hospitals from 2009 to 2014 to identify hospitalizations with tick-borne disease. Cases were described and Poisson regression used to estimate the annual percent change (APC) and associated 95% confidence intervals (CI) in incidence by region over time. Results Overall, 2,543 hospitalized patients with tick-borne disease were identified (average annual incidence = 28.4 cases/100,000 hospitalized persons), including 1,613 (63%) with Lyme disease, 379 (15%) tick-borne fever, 293 (12%) ehrlichiosis, 93 (4%) babesiosis, 43 (2%) rickettsiosis, and 122 (4%) multiple tick-related diagnoses. Tick-borne diseases varied significantly by region, with Lyme disease more frequent in those residing in the Northeast (68%) than the South (57%) or West (42%) and tick-borne fever more common in the West (28%) vs. the South (18%), Midwest (14%), and Northeast (13%) (P < 0.0001). Significant increases in tick-borne disease hospitalizations were identified across nearly all US regions, ranging from 15% per year in the South (95% CI=8–24%) to 45% per year in the West (34–58%), with the exception of the Northeast, where incidence declined by 6% per year (0.04–11%). Lyme disease hospitalizations showed similar trends, with the greatest increase in the South (APC = 53%, 95% CI = 33–76%) and a decrease in the Northeast (APC = 13%; 3%–23%). Hospitalizations with tick-borne fever increased in the Midwest (APC = 49%; 8–206%) and Northeast (APC = 18%; 4–34%); with ehrlichiosisincreased in the West (APC = 231%; 75–306%); and with babesiosis increased in the South (APC = 50%; 12–201%) and the Midwest (APC = 21%; 5–39%). Conclusion Incidence of hospitalizations from tick-borne disease is increasing throughout much of the nation, except in the Northeast where decreases in Lyme disease were observed. While hospitalizations with tick-borne diseases remain rare, the increases noted are substantial and may reflect rising incidence of these diseases within the represented states. ![]()
Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Jennifer Adjemian
- United States Public Health Service, Commissioned Corps, Rockville, Maryland
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
| | - Yi Ling Lai
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
| | - Emily Ricotta
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
| | - D Rebecca Prevots
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
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40
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Ricotta E, Lai YL, Kadri SS, Lionakis M, Prevots DR, Adjemian J. 362. Species Distribution and Trends of Invasive Candidiasis in the United States, 2009–2015, Using a Large Electronic Medical Record Database. Open Forum Infect Dis 2018. [PMCID: PMC6255070 DOI: 10.1093/ofid/ofy210.373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background While 50% of invasive candidiasis (IC) has historically been caused by C. albicans, the changing epidemiology and rise in drug-resistant Candida necessitates understanding the contribution of specific Candida species to IC. To date, species and site-specific trends in IC have not been reported on a large scale using US clinical data. Methods Using the Cerner Health Facts electronic health record (EHR) dataset, inpatient hospitalizations with any Candida spp. isolated from blood or a sterile site (SS) (abdominal or other) were identified from 2009 to 2015. Patient characteristics were described by species. Significant relationships (P ≤ 0.05) were assessed using chi-squared or exact binomial tests. Annual percent change in IC incidence by site and species were assessed via Poisson regression. Results Overall, 19,310 Candida isolates from 10,313 patients were identified. Of these, 46% of isolates were C. albicans, 22% C. glabrata, 14% C. parapsilosis, 7% C. tropicalis, and 11% other/unspeciated; no C. auris infections were identified. The overall incidence of IC was 99 cases/100,000 patients. Compared with C. albicans, isolation of other species was 35% more frequent from blood, and 43% and 30% less frequent from non-blood abdominal and non-abdominal SSs, respectively (Table 1). Total IC increased by 1% (95% CI = 0.2–2%) annually; while abdominal and SS IC significantly increased by 6% (4–8%) and 11% (9–13%) per year, respectively, candidemia decreased significantly by 4.5% (3–6%) annually. Among C. albicansinfections candidemia decreased by 6.5% (5–8%) annually, while abdominal (5%, 3–8%) and other SS infections (10%, 7–13%) increased (Figure 1). Candidemia incidence remained unchanged for the other species. SS infections increased for every species, and abdominal infections increased for all but C. parapsilosis (Figure 2). Conclusion In this first large-scale study on trends in IC using US hospital EHR data, the species distribution of IC isolates varied between blood and non-blood SSs. The incidence of candidemia is decreasing, but not for potentially drug-resistant species such as C. glabrata, which continue to pose treatment challenges. This work was supported in part by the Division of Intramural Research, NIAID, NIH ![]()
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Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Emily Ricotta
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
| | - Yi Ling Lai
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
| | - Sameer S Kadri
- Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland
| | - Michail Lionakis
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - D Rebecca Prevots
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
| | - Jennifer Adjemian
- Epidemiology Unit, Division of Intramural Research, NIAID, NIH, Bethesda, Maryland
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Ricotta EE, Olivier KN, Lai YL, Prevots DR, Adjemian J. Hospital-based antibiotic use in patients with Mycobacterium avium complex. ERJ Open Res 2018; 4:00109-2018. [PMID: 30402451 PMCID: PMC6213287 DOI: 10.1183/23120541.00109-2018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 07/10/2018] [Accepted: 09/02/2018] [Indexed: 11/17/2022] Open
Abstract
Treatment guidelines exist for pulmonary Mycobacterium avium complex (MAC) infection, although studies suggest poor concordance in clinician practice. Using a national database including hospital encounters of laboratory-confirmed MAC patients, we sought to characterise US treatment practices. We assessed patients in the Premier Healthcare Database from 2009 to 2013 with two or more MAC-positive cultures or one MAC-positive culture and the International Classification of Diseases (9th revision) code for pulmonary nontuberculous mycobacteria (PNTM). Treatment was characterised by patient-, provider- and facility-level factors; significant differences were assessed (p<0.05). Multilevel Poisson regression estimated adjusted relative risks (aRR) of receiving guidelines-based or macrolide resistance-promoting regimens. Of 1326 MAC patients, 645 (49%) received treatment: 10% received guidelines-based treatment and 18% resistance-associated therapy. Patients were more likely to receive guidelines-based therapy if they had multiple hospital encounters (aRR 1.5), codes for PNTM (aRR 5.7) or tuberculosis (aRR 4.5) or radiological procedures (aRR 10.9); multiple hospital encounters (aRR 0.8) or a tuberculosis code (aRR 0.1) were less likely to be associated with receiving resistance-promoting regimens. In hospital-based MAC patients, half received antibiotics active against MAC, a low proportion received therapy based on MAC guidelines and many received antibiotics that promote macrolide resistance. Improved implementation of guidelines-based treatment is needed to decrease use of regimens associated with macrolide resistance. Few MAC patients receive recommended therapy and improved treatment is needed to prevent resistancehttp://ow.ly/4F0S30lIihn
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Affiliation(s)
- Emily E Ricotta
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth N Olivier
- Pulmonary Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yi Ling Lai
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - D Rebecca Prevots
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer Adjemian
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.,United States Public Health Service, Commissioned Corps, Rockville, MD, USA
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Daniel-Wayman S, Fahle G, Palmore T, Green KY, Prevots DR. Norovirus, astrovirus, and sapovirus among immunocompromised patients at a tertiary care research hospital. Diagn Microbiol Infect Dis 2018; 92:143-146. [PMID: 29934072 PMCID: PMC11036324 DOI: 10.1016/j.diagmicrobio.2018.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 04/06/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023]
Abstract
We estimated the prevalence of astrovirus, sapovirus, and norovirus among patients enrolled in research protocols and receiving medical care at the Clinical Center of the National Institutes of Health, Bethesda, MD, a clinical research hospital with a large immunocompromised patient population. We identified patients whose fecal specimens were submitted to the Clinical Center for testing on the Biofire FilmArray Gastrointestinal Panel from September 15, 2015 through November 30, 2016. Among 442 patients with fecal specimens submitted for multiplex testing, 11% had norovirus identified, 2% had astrovirus, and 2% had sapovirus. Like norovirus, astrovirus was detected in multiple sequential samples from a single patient, consistent with chronic infection or the occurrence of multiple reinfections. Coinfection with non-viral gastrointestinal pathogens was detected in 31% of patients with positive results for norovirus, astrovirus, or sapovirus. Norovirus remains common in this immunocompromised patient population, and both sapovirus and astrovirus are present.
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Affiliation(s)
- Shelby Daniel-Wayman
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 8 West Drive, MSC 2665, Bethesda, MD 20892, USA.
| | - Gary Fahle
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
| | - Tara Palmore
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
| | - Kim Y Green
- Calicivirus Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg 50 Rm 6318 MSC 8026, 50 South Dr, Bethesda, MD 20892, USA.
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 8 West Drive, MSC 2665, Bethesda, MD 20892, USA.
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Adjemian J, Olivier KN, Prevots DR. Epidemiology of Pulmonary Nontuberculous Mycobacterial Sputum Positivity in Patients with Cystic Fibrosis in the United States, 2010-2014. Ann Am Thorac Soc 2018; 15:817-826. [PMID: 29897781 PMCID: PMC6137684 DOI: 10.1513/annalsats.201709-727oc] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [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: 11/30/2017] [Accepted: 02/22/2018] [Indexed: 01/13/2023] Open
Abstract
RATIONALE Pulmonary nontuberculous mycobacteria (NTM) disease represents a significant threat to patients with cystic fibrosis (CF), with an estimated annual prevalence of 12%. Prior studies reported an increasing annual NTM prevalence in the general population, though similar trends in persons with CF have not been assessed. OBJECTIVES In this study we aimed to identify the prevalence, geographic patterns, temporal trends, and risk factors for NTM positivity by mycobacterial species among persons with CF throughout the United States. METHODS Using annualized CF Patient Registry (CFFPR) data from 2010 to 2014, we identified patients with mycobacterial culture results to estimate the annual and period prevalence of pathogenic NTM species by demographic and geographic factors. Regression models were used to estimate the annual percent change over time and risk factors for NTM isolation. Geographic patterns were described and mapped. RESULTS Of 16,153 included persons with CF, 3,211 (20%) had a pathogenic NTM species isolated at least once over the 5-year period; 1,949 (61%) had Mycobacterium avium complex (MAC), and 1,249 (39%) had M. abscessus. The period prevalence was 12% for MAC (confidence interval [CI], 12-13%), 8% for M. abscessus (CI, 7-8%), and 4% for other NTM species (CI, 3.8-4.3%). The period prevalence for MAC was nearly three times greater among patients ≥60 years old with a body mass index < 19 (33% [CI, 16-51%]); this trend was not present for patients with M. abscessus (4% [CI, 0-11%]). NTM prevalence showed a significant relative increase of 5% per year, from 11.0% in 2010 to 13.4% in 2014 (P = 0.0008), although this varied by geographic area. For M. abscessus, the states with the highest prevalence were Hawaii (50%), Florida (17%), and Louisiana (16%), and for MAC they were Nevada (24%), Kansas (21%), and Hawaii and Arizona (both 20%). Study participants with either MAC or M. abscessus were significantly more likely to have been diagnosed with CF at an older age (P < 0.0001), have a lower body mass index (P < 0.0001), higher forced expiratory volume in 1 second % predicted (P < 0.01), and fewer years on chronic macrolide therapy (P < 0.0001). CONCLUSIONS NTM remains highly prevalent among adults and children with CF in the United States, with one in five affected, and appears to be increasing over time. Prevalence varies by geographic region and by patient-level factors, including older age and receiving an initial CF diagnosis later in life. Routine screening for NTM, including mycobacterial speciation, especially in high-risk geographic areas, is critical to increase our understanding of its epidemiology and changes in prevalence over time.
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Affiliation(s)
- Jennifer Adjemian
- Epidemiology Unit, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
- United States Public Health Service, Commissioned Corps, Rockville, Maryland; and
| | - Kenneth N. Olivier
- Cardiovascular and Pulmonary Branch, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - D. Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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Abstract
Annual prevalence estimates for pulmonary nontuberculous mycobacterial (PNTM) disease in the contiguous United States range from 1.4 to 13.9 per 100,000 persons, while one study found an annual prevalence of up to 44 per 100,000 persons in Hawaii. PNTM prevalence varies by region, sex, and race/ethnicity, with higher prevalence among women and persons of Asian ancestry, as well as in the Southern United States and Hawaii. Studies consistently indicate that PNTM prevalence is increasing, with estimates ranging from 2.5 to 8% per year. Most PNTM disease is associated with Mycobacterium avium complex (MAC), although the proportion of disease attributed to MAC varies by region. Host factors identified as influencing disease risk include structural lung disease, immunomodulatory medication, as well as variants in connective tissue, mucociliary clearance, and immune genes. Environmental variables including measures of atmospheric moisture and concentrations of certain soil factors have also been shown to correlate with higher PNTM prevalence. Prevalence of extrapulmonary NTM disease is lower, stable, and associated with different risk factors, including primary immune deficiencies or HIV infection.
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Affiliation(s)
- Jennifer Adjemian
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
- Commissioned Corps, United States Public Health Service, Rockville, Maryland
| | - Shelby Daniel-Wayman
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Emily Ricotta
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - D. Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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45
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Adjemian J, Frankland TB, Daida YG, Honda JR, Olivier KN, Zelazny A, Honda S, Prevots DR. Epidemiology of Nontuberculous Mycobacterial Lung Disease and Tuberculosis, Hawaii, USA. Emerg Infect Dis 2018; 23:439-447. [PMID: 28221128 PMCID: PMC5382761 DOI: 10.3201/eid2303.161827] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Previous studies found Hawaiians and Asian-Americans/Pacific Islanders to be independently at increased risk for nontuberculous mycobacterial pulmonary disease (NTMPD) and tuberculosis (TB). To better understand NTM infection and TB risk patterns in Hawaii, USA, we evaluated data on a cohort of patients in Hawaii for 2005–2013. Period prevalence of NTMPD was highest among Japanese, Chinese, and Vietnamese patients (>300/100,000 persons) and lowest among Native Hawaiians and Other Pacific Islanders (50/100,000). Japanese patients were twice as likely as all other racial/ethnic groups to have Mycobacterium abscessus isolated (adjusted odds ratio 2.0, 95% CI 1.2–3.2) but were not at increased risk for infection with other mycobacteria species. In contrast, incidence of TB was stable and was lowest among Japanese patients (no cases) and highest among Filipino, Korean, and Vietnamese patients (>50/100,000). Substantial differences exist in the epidemiology of NTMPD by race/ethnicity, suggesting behavioral and biologic factors that affect disease susceptibility.
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Strollo S, Lionakis MS, Adjemian J, Steiner CA, Prevots DR. Epidemiology of Hospitalizations Associated with Invasive Candidiasis, United States, 2002-2012 1. Emerg Infect Dis 2017; 23:7-13. [PMID: 27983497 PMCID: PMC5176241 DOI: 10.3201/eid2301.161198] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Highest hospitalization rates were for men ≥65 years of age, and rates
decreased during 2005−2012. Invasive candidiasis is a major nosocomial fungal disease in the United States
associated with high rates of illness and death. We analyzed inpatient
hospitalization records from the Healthcare Cost and Utilization Project to
estimate incidence of invasive candidiasis–associated hospitalizations in
the United States. We extracted data for 33 states for 2002–2012 by using
codes from the International Classification of Diseases, 9th Revision, Clinical
Modification, for invasive candidiasis; we excluded neonatal cases. The overall
age-adjusted average annual rate was 5.3 hospitalizations/100,000 population.
Highest risk was for adults >65 years of age,
particularly men. Median length of hospitalization was 21 days; 22% of patients
died during hospitalization. Median unadjusted associated cost for inpatient
care was $46,684. Age-adjusted annual rates decreased during 2005–2012
for men (annual change –3.9%) and women (annual change –4.5%) and
across nearly all age groups. We report a high mortality rate and decreasing
incidence of hospitalizations for this disease.
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Gonçalves BP, Sagara I, Coulibaly M, Wu Y, Assadou MH, Guindo A, Ellis RD, Diakite M, Gabriel E, Prevots DR, Doumbo OK, Duffy PE. Hemoglobin variants shape the distribution of malaria parasites in human populations and their transmission potential. Sci Rep 2017; 7:14267. [PMID: 29079846 PMCID: PMC5660173 DOI: 10.1038/s41598-017-14627-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Abstract
Hemoglobin variants C and S protect against severe malaria but their influence on parameters not directly linked to disease severity such as gametocyte carriage and infection chronicity is less well understood. To assess whether these infection-related phenotypes depend on the host hemoglobin genotype, we followed 500 Malian individuals over 1–2 years and determined their parasitological status during monthly visits and incidental clinical episodes. While adults heterozygous for hemoglobin S mutation were less often parasitemic compared to AA adults (odds ratio [OR] 0.50 95% confidence interval [CI] 0.31–0.79, P = 0.003), schoolchildren (but not toddlers or adults) with AC genotype carried parasites, including gametocytes, more often than their AA counterparts (OR 3.01 95% CI 1.38–6.57, P = 0.006). AC children were also likelier to be parasite-positive during the dry season, suggesting longer infections, and were more infectious in mosquito skin feeding assays than AA children. Notably, AC school-aged children, who comprise ~5% of the population, harbor a third of infections with patent gametocytes between May and August, when transmission transitions from very low to intense. These findings indicate that schoolchildren with hemoglobin C mutation might contribute disproportionately to the seasonal malaria resurgence in parts of West Africa where the HbC variant is common.
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Affiliation(s)
- Bronner P Gonçalves
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, United States of America.,Laboratory of Clinical Infectious Diseases - Epidemiology Unit, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States of America.,Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Issaka Sagara
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mamadou Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Yimin Wu
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, United States of America.,PATH-Malaria Vaccine Initiative, Washington DC, USA
| | - Mahamadoun H Assadou
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Agnes Guindo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ruth D Ellis
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, United States of America.,Biologics Consulting Group Inc, Alexandria, USA
| | - Mahamadou Diakite
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Erin Gabriel
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, United States of America
| | - D Rebecca Prevots
- Laboratory of Clinical Infectious Diseases - Epidemiology Unit, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, United States of America
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, NIH, Rockville, MD, United States of America.
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Daniel-Wayman S, Fahle G, Palmore T, Green K, Prevots DR. Norovirus, Astrovirus, and Sapovirus in a Tertiary Care Research Hospital. Open Forum Infect Dis 2017. [PMCID: PMC5631400 DOI: 10.1093/ofid/ofx163.742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Norovirus, astrovirus, and sapovirus are known to cause acute gastroenteritis and are associated with chronic viral excretion in stool among immunocompromised patients. Because molecular tools for their detection only recently became widely available, the prevalence and chronic excretion of these viruses has not been well defined. We describe features of these viral infections among patients receiving care at the Clinical Center of the National Institutes of Health. Methods We identified patients with a positive BioFire FilmArray® gastrointestinal panel result for norovirus, astrovirus, or sapovirus from September 15, 2015 through November 30, 2016. We reviewed patient medical records to abstract clinical and microbiologic information. Chronic excretion was defined as more than one positive test for a given virus with more than 30 days between tests. Results Of 932 samples tested, 102 (11%) samples from 48 patients tested positive for norovirus, 15 (2%) samples from 11 patients tested positive for sapovirus, and 16 (2%) samples from 7 patients tested positive for astrovirus. One of these patients had a sample that tested positive for both sapovirus and norovirus, and one tested positive for astrovirus and sapovirus at separate points during the study period. Of the 48 patients with norovirus, 16 (33%) had evidence of chronic excretion, with a median duration of 189 days (range 72–372). Of these 16, 14 were known or suspected to be immunodeficient, and 4 had hematologic malignancies. Of 7 patients with astrovirus, 1 (14%) had evidence of chronic excretion (132 days). This patient had a hematologic malignancy and was taking immunosuppressive medication. No patients with sapovirus had evidence of chronic excretion. Overall, 20 (31%) patients additionally tested positive for another gastrointestinal pathogen, most commonly enteropathogenic E. coli and C. difficile. Conclusion Norovirus remains common in this immunocompromised patient population, and both sapovirus and astrovirus are present. Additional follow-up in this and other cohorts with new molecular tools will enable more complete description of the prevalence, excretion duration, and clinical features of infection with these enteric viruses. This research was supported by the Intramural Research Program of the NIH, NIAID, and the NIH CC. Disclosures All authors: No reported disclosures.
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Affiliation(s)
- Shelby Daniel-Wayman
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gary Fahle
- Department of Laboratory Medecine, Clinical Center, National Institutes of Health, Bethesda, Maryland
| | - Tara Palmore
- Hospital Epidemiology Service, National Institutes of Health Clinical Center, Bethesda, Maryland
| | - Kim Green
- Laboratory of Infectious Disease, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - D Rebecca Prevots
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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49
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Nash SD, Prevots DR, Kabyemela E, Khasa YP, Lee KL, Fried M, Duffy PE. A Malaria-Resistant Phenotype with Immunological Correlates in a Tanzanian Birth Cohort Exposed to Intense Malaria Transmission. Am J Trop Med Hyg 2017; 96:1190-1196. [PMID: 28500801 DOI: 10.4269/ajtmh.16-0554] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractMalaria incidence is highly heterogeneous even in areas of high transmission, although no conclusive evidence exists that innate or naturally acquired resistance can prevent infection over an extended period of time. This longitudinal study examined immunoparasitological evidence for a malaria-resistant phenotype in which children do not develop malaria despite an extended period of exposure to parasites. Within a birth cohort followed from 2002 to 2006 in Muheza, Tanzania, an area of intense transmission, children (N = 687) provided blood smears biweekly during infancy and monthly thereafter. Maternal and childhood characteristics were obtained, cord-blood cytokines were measured, and antibody responses were assayed as measures of stage-specific exposure. Sixty-three (9.2%) children had no blood smear-positive slides over 2 years of follow-up (range: 1-3.5 years) and were identified as malaria resistant. Malaria-resistant children were similar to other children with respect to completeness of follow-up and all maternal and childhood characteristics except residence area. Antibody seroprevalence was similar for two sporozoite antigens, but malaria-resistant children had a lower antibody seroprevalence to merozoite antigens merozoite surface protein 1 (5.4% versus 30.2%; P < 0.0001) and apical membrane antigen 1 (7.2% versus 33.3%; P < 0.0001). Malaria-resistant children had higher cytokine levels in cord blood, particularly interleukin-1β. In summary, a subset of children living in an area of intense transmission was exposed to malaria parasites, but never developed patent parasitemia; this phenotype was associated with a distinct cytokine profile at birth and antibody profile during infancy. Further research with malaria-resistant children may identify mechanisms for naturally acquired immunity.
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Affiliation(s)
- Scott D Nash
- Epidemiology Unit, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Laboratory of Malaria Immunology and Vaccinology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Infectious Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - Yogender P Khasa
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Kun-Lin Lee
- Laboratory of Malaria Immunology and Vaccinology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Michal Fried
- Laboratory of Malaria Immunology and Vaccinology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Patrick E Duffy
- Laboratory of Malaria Immunology and Vaccinology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
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Prevots DR, Loddenkemper R, Sotgiu G, Migliori GB. Nontuberculous mycobacterial pulmonary disease: an increasing burden with substantial costs. Eur Respir J 2017; 49:1700374. [PMID: 28446563 PMCID: PMC11037024 DOI: 10.1183/13993003.00374-2017] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 11/05/2022]
Affiliation(s)
- D Rebecca Prevots
- Epidemiology Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Giovanni Sotgiu
- Clinical Epidemiology and Medical Statistics Unit, Dept of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanni Battista Migliori
- Director, WHO Collaborating Centre for TB and Lung Diseases, Maugeri Care and Research Institute, IRCCS, Tradate, Italy
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