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Bulterys PL, Leung NY, Saleem A, Budvytiene I, Pinsky BA, Banaei N. Postpandemic Effects of COVID-19 Shelter-in-Place Orders on the Gastrointestinal Pathogen Landscape. J Clin Microbiol 2023; 61:e0038523. [PMID: 37466426 PMCID: PMC10446857 DOI: 10.1128/jcm.00385-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023] Open
Affiliation(s)
- Philip L. Bulterys
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Nicole Y. Leung
- Stanford University School of Medicine, Stanford, California, USA
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Indre Budvytiene
- Clinical Virology Laboratory, Stanford University Medical Center, Stanford, California, USA
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Clinical Virology Laboratory, Stanford University Medical Center, Stanford, California, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford University Medical Center, Stanford, California, USA
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Wang H, Williams KM, Elde S, Bulterys PL, Thakore AD, Lucian HJ, Farry JM, Mullis DM, Zhu Y, Paulsen MJ, Woo YJ. Trimmed central venous catheters do not increase endothelial injury in an ovine model. J Vasc Access 2023:11297298231153716. [PMID: 36765464 DOI: 10.1177/11297298231153716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
INTRODUCTION Central venous catheters (CVCs) are often trimmed during heart transplantation and pediatric cardiac surgery. However, the risk of endothelial injury caused by the cut tip of the CVC has not been evaluated. We hypothesized that there is no difference in the degree of endothelial injury associated with trimmed CVCs versus standard untrimmed CVCs. METHODS In four adult male sheep, the left external jugular vein was exposed in three segments, one designated for an untouched control group, one for the trimmed CVC group, and one for the untrimmed CVC group. Trimmed and untrimmed CVC tips were rotated circumferentially within their respective segments to abrade the lumen of the vein. The vein samples were explanted, and two representative sections from each sample were analyzed using hematoxylin and eosin (H&E) staining, as well as with immunohistochemistry against CD31, von Willebrand factor (vWF), endothelial nitric oxide synthase (eNOS), and caveolin. Higher immunohistochemical stain distributions and intensities are associated with normal health and function of the venous endothelium. Data are presented as counts with percentages or as means with standard error. RESULTS H&E staining revealed no evidence of endothelial injury in 6/8 (75%) samples from the untouched control group, and no injury in 4/8 (50%) samples from both the trimmed and untrimmed CVC groups (p = 0.504). In all remaining samples from each group, only mild endothelial injury was observed. Immunohistochemical analysis comparing trimmed CVCs versus untrimmed CVCs revealed no difference in the percentage of endothelial cells staining positive for CD31 (57.5% ± 7.2% vs 55.0% ± 9.2%, p = 0.982), vWF (73.8% ± 8.0% vs 62.5% ± 9.6%, p = 0.579), eNOS (66.3% ± 4.2% vs 63.8% ± 7.5%, p = 0.962), and caveolin (53.8% ± 5.0% vs 51.3% ± 4.4%, p = 0.922). There were no significant differences between the groups in the distributions of stain intensity for CD31, vWF, eNOS, and caveolin. CONCLUSION Trimmed CVCs do not increase endothelial injury compared to standard untrimmed CVCs.
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Affiliation(s)
- Hanjay Wang
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Kiah M Williams
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Stefan Elde
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | | | - Akshara D Thakore
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Haley J Lucian
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Justin M Farry
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Danielle M Mullis
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Yuanjia Zhu
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael J Paulsen
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Y Joseph Woo
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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Yang LM, Costales C, Ramanathan M, Bulterys PL, Murugesan K, Schroers-Martin J, Alizadeh AA, Boyd SD, Brown JM, Nadeau KC, Nadimpalli SS, Wang AX, Busque S, Pinsky BA, Banaei N. Cellular and humoral immune response to SARS-CoV-2 vaccination and booster dose in immunosuppressed patients: An observational cohort study. J Clin Virol 2022; 153:105217. [PMID: 35714462 PMCID: PMC9188451 DOI: 10.1016/j.jcv.2022.105217] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 10/29/2022]
Abstract
BACKGROUND Humoral and cellular immune responses to SARS-CoV-2 vaccination among immunosuppressed patients remain poorly defined, as well as variables associated with poor response. METHODS We performed a retrospective observational cohort study at a large Northern California healthcare system of infection-naïve individuals fully vaccinated against SARS-CoV-2 (mRNA-1273, BNT162b2, or Ad26.COV2.S) with clinical SARS-CoV-2 interferon gamma release assay (IGRA) ordered between January through November 2021. Humoral and cellular immune responses were measured by anti-SARS-CoV-2 S1 IgG ELISA (anti-S1 IgG) and IGRA, respectively, following primary and/or booster vaccination. RESULTS 496 immunosuppressed patients (54% female; median age 50 years) were included. 62% (261/419) of patients had positive anti-S1 IgG and 71% (277/389) had positive IGRA after primary vaccination, with 20% of patients having a positive IGRA only. Following booster, 69% (81/118) had positive anti-S1 IgG and 73% (91/124) had positive IGRA. Factors associated with low humoral response rates after primary vaccination included anti-CD20 monoclonal antibodies (P < 0.001), sphingosine 1-phsophate (S1P) receptor modulators (P < 0.001), mycophenolate (P = 0.002), and B cell lymphoma (P = 0.004); those associated with low cellular response rates included S1P receptor modulators (P < 0.001) and mycophenolate (P < 0.001). Of patients who had poor humoral response to primary vaccination, 35% (18/52) developed a significantly higher response after the booster. Only 5% (2/42) of patients developed a significantly higher cellular response to the booster dose compared to primary vaccination. CONCLUSIONS Humoral and cellular response rates to primary and booster SARS-CoV-2 vaccination differ among immunosuppressed patient groups. Clinical testing of cellular immunity is important in monitoring vaccine response in vulnerable populations.
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Affiliation(s)
- Lu M Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Cristina Costales
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Muthukumar Ramanathan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Philip L Bulterys
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Kanagavel Murugesan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Joseph Schroers-Martin
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Ash A Alizadeh
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America; Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA 94305 United States of America
| | - Janice M Brown
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy & Asthma Research, Stanford, CA 94305 United States of America; Department of Medicine, Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Sruti S Nadimpalli
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Stanford University School of Medicine, Stanford CA 94305 United States of America
| | - Aileen X Wang
- Department of Medicine, Division of Nephrology, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Stephan Busque
- Department of Surgery, Division of Abdominal Transplantation, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 United States of America
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 United States of America; Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA 94305 United States of America; Clinical Microbiology Laboratory, Stanford Health Care, Palo Alto, CA 94304 United States of America.
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Bulterys PL, Solis D, Verghese M, Huang C, Sibai M, Costales C, Sahoo MK, Pinsky BA. Diagnosis of Dengue in a returning traveler from Pakistan suspected of COVID-19, California, USA. Diagn Microbiol Infect Dis 2021; 101:115517. [PMID: 34537475 PMCID: PMC8342863 DOI: 10.1016/j.diagmicrobio.2021.115517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/10/2021] [Accepted: 05/15/2021] [Indexed: 11/06/2022]
Abstract
Dengue and COVID-19 cocirculation presents a diagnostic conundrum for physicians evaluating patients with acute febrile illnesses, both in endemic regions and among returning travelers. We present a case of a returning traveler from Pakistan who, following repeated negative SARS-CoV-2 tests, was found to have a Dengue virus serotype 2 infection.
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Affiliation(s)
| | - Daniel Solis
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Michelle Verghese
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Chunhong Huang
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Mamdouh Sibai
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | | | - Malaya K Sahoo
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Stanford, CA, USA; Clinical Virology Laboratory, Stanford University Medical Center, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Nguyen A, Negrete LM, Bulterys PL, Shen L. Inflammatory pseudotumor-like follicular dendritic cell tumor of the spleen: a case report and approach to differential diagnosis. Radiol Case Rep 2021; 16:3213-3216. [PMID: 34484521 PMCID: PMC8405940 DOI: 10.1016/j.radcr.2021.07.078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/19/2021] [Accepted: 07/24/2021] [Indexed: 11/17/2022] Open
Abstract
We present a case of an inflammatory pseudotumor-like follicular dendritic cell tumor of the spleen. The patient is a 44-year-old woman, without significant underlying history, who presented with nonspecific abdominal pain for a few months. Both a contrast enhanced computed tomography and magnetic resonance imaging revealed a new 2.5 cm enhancing splenic lesion, which demonstrated hypermetabolic activity on subsequent positron emission tomography and computed tomography scan. Since the lesion was new compared to more remote imaging and hypermetabolic, a splenectomy was performed. Pathology confirmed the diagnosis and demonstrated positivity for Epstein-Barr Virus .
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Affiliation(s)
- Andrew Nguyen
- Lake Erie College of Osteopathic Medicine, Erie, PA, USA
| | - Lindsey M Negrete
- Body Imaging Division, Department of Radiology, Stanford University, 300 Pasteur Drive, H1307, Stanford, CA 94305, USA
| | | | - Luyao Shen
- Body Imaging Division, Department of Radiology, Stanford University, 300 Pasteur Drive, H1307, Stanford, CA 94305, USA
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Roberts T, Parker DM, Bulterys PL, Rattanavong S, Elliott I, Phommasone K, Mayxay M, Chansamouth V, Robinson MT, Blacksell SD, Newton PN. A spatio-temporal analysis of scrub typhus and murine typhus in Laos; implications from changing landscapes and climate. PLoS Negl Trop Dis 2021; 15:e0009685. [PMID: 34432800 PMCID: PMC8386877 DOI: 10.1371/journal.pntd.0009685] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Scrub typhus (ST) and murine typhus (MT) are common but poorly understood causes of fever in Laos. We examined the spatial and temporal distribution of ST and MT, with the intent of informing interventions to prevent and control both diseases. METHODOLOGY AND PRINCIPLE FINDINGS This study included samples submitted from 2003 to 2017 to Mahosot Hospital, Vientiane, for ST and MT investigation. Serum samples were tested using IgM rapid diagnostic tests. Patient demographic data along with meteorological and environmental data from Laos were analysed. Approximately 17% of patients were positive for either ST (1,337/8,150 patients tested) or MT (1,283/7,552 patients tested). While both diseases occurred in inhabitants from Vientiane Capital, from the univariable analysis MT was positively and ST negatively associated with residence in Vientiane Capital. ST was highly seasonal, with cases two times more likely to occur during the wet season months of July-September compared to the dry season whilst MT peaked in the dry season. Multivariable regression analysis linked ST incidence to fluctuations in relative humidity whereas MT was linked to variation in temperature. Patients with ST infection were more likely to come from villages with higher levels of surface flooding and vegetation in the 16 days leading up to diagnosis. CONCLUSIONS The data suggest that as cities expand, high risk areas for MT will also expand. With global heating and risks of attendant higher precipitation, these data suggest that the incidence and spatial distribution of both MT and ST will increase.
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Affiliation(s)
- Tamalee Roberts
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Daniel M. Parker
- University of California, Irvine, California, United States of America
| | - Philip L. Bulterys
- Department of Pathology, Stanford University, California, United States of America
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Ivo Elliott
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Koukeo Phommasone
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of Health, Vientiane, Lao PDR
| | - Vilada Chansamouth
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Matthew T. Robinson
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
| | - Stuart D. Blacksell
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
- Mahidol-Oxford-Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Paul N. Newton
- Lao-Oxford-Mahosot-Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
- Mahidol-Oxford-Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Wang H, Wiredja D, Yang L, Bulterys PL, Costales C, Röltgen K, Manalac J, Yee J, Zehnder J, Shi RZ, Boyd SD, Pinsky BA. Case-Control Study of Individuals with Discrepant Nucleocapsid and Spike Protein SARS-CoV-2 IgG Results. Clin Chem 2021; 67:977-986. [PMID: 33720347 PMCID: PMC7989591 DOI: 10.1093/clinchem/hvab045] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/01/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Laboratory-based methods for SARS-CoV-2 antibody detection vary widely in performance. However, there are limited prospectively-collected data on assay performance, and minimal clinical information to guide interpretation of discrepant results. METHODS Over a 2-week period, 1080 consecutive plasma samples submitted for clinical SARS-CoV-2 IgG testing were tested in parallel for anti-nucleocapsid IgG (anti-N, Abbott) and anti-spike IgG (anti-S1, EUROIMMUN). Chart review was conducted for samples testing positive or borderline on either assay, and for an age/sex-matched cohort of samples negative by both assays. CDC surveillance case definitions were used to determine clinical sensitivity/specificity and conduct receiver operating characteristics curve analysis. RESULTS There were 52 samples positive by both methods, 2 positive for anti-N only, 34 positive for anti-S1 only, and 27 borderline for anti-S1. Of the 34 individuals positive for anti-S1 alone, 8 (24%) had confirmed COVID-19. No anti-S1 borderline cases were positive for anti-N or had confirmed/probable COVID-19. The anti-N assay was less sensitive (84.2% [95% CI 72.1-92.5%] vs 94.7% [95% CI 85.4-98.9%]) but more specific (99.2% [95% CI 95.5-100%] vs 86.9% [95% CI 79.6-92.3%]) than anti-S1. Abbott anti-N sensitivity could be improved to 96.5% with minimal effect on specificity if the index threshold was lowered from 1.4 to 0.6. CONCLUSION Real-world concordance between different serologic assays may be lower than previously described in retrospective studies. These findings have implications for the interpretation of SARS-CoV-2 IgG results, especially with the advent of spike antigen-targeted vaccination, as a subset of patients with true infection are anti-N negative and anti-S1 positive.
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Affiliation(s)
- Hannah Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Danica Wiredja
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lu Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Philip L Bulterys
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Cristina Costales
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin Manalac
- Special Chemistry Laboratory, Stanford Healthcare, Palo Alto, CA, USA
| | - Jennifer Yee
- Special Chemistry Laboratory, Stanford Healthcare, Palo Alto, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Run Zhang Shi
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Special Chemistry Laboratory, Stanford Healthcare, Palo Alto, CA, USA
| | - Scott D Boyd
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
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Bulterys PL, Leung NY, Saleem A, Budvytiene I, Banaei N. Impact of COVID-19 Shelter-in-Place Order on Transmission of Gastrointestinal Pathogens in Northern California. J Clin Microbiol 2021; 59:e0044921. [PMID: 33846223 PMCID: PMC8218763 DOI: 10.1128/jcm.00449-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Philip L. Bulterys
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Nicole Y. Leung
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Indre Budvytiene
- Clinical Microbiology Laboratory, Stanford University Medical Center, Stanford, California, USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California, USA
- Clinical Microbiology Laboratory, Stanford University Medical Center, Stanford, California, USA
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Bulterys PL, Garamani N, Stevens B, Sahoo MK, Huang C, Hogan CA, Zehnder J, Pinsky BA. Comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of SARS-CoV-2. J Clin Virol 2020; 129:104427. [PMID: 32535398 PMCID: PMC7207111 DOI: 10.1016/j.jcv.2020.104427] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 11/18/2022]
Abstract
Four nucleic acid amplification tests for SARS-CoV-2 RNA demonstrated comparable performance using clinical specimens. A limited number of discrepancies were observed in specimens with low viral loads. The isothermal amplification assay was slightly less sensitive but was one hour faster than the other methods. Assay selection requires consideration of test performance, instrument/reagent availability, turnaround and throughput.
Background Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another. Objectives The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs. Study Design A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen’s kappa coefficient. Results Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement. Conclusions Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.
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Affiliation(s)
- Philip L Bulterys
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Natasha Garamani
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bryan Stevens
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Catherine A Hogan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA
| | - James Zehnder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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French CT, Bulterys PL, Woodward CL, Tatters AO, Ng KR, Miller JF. Virulence from the rhizosphere: ecology and evolution of Burkholderia pseudomallei-complex species. Curr Opin Microbiol 2020; 54:18-32. [PMID: 32028234 DOI: 10.1016/j.mib.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 11/01/2019] [Accepted: 12/30/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Christopher T French
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Northern Arizona University, Department of Biological Sciences, Pathogen and Microbiome Institute 1395 S Knoles Drive, Flagstaff, AZ 86011, United States.
| | - Philip L Bulterys
- Department of Pathology, Stanford University, Lane Building, L235, 300 Pasteur Drive, Stanford, CA, 94305, United States
| | - Cora L Woodward
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Avery O Tatters
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Ken R Ng
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States
| | - Jeff F Miller
- California NanoSystems Institute, UCLA, 570 Westwood Plaza Bldg. 114, 4538 West, Los Angeles, CA 90095, United States; Molecular Biology Institute, UCLA, 611 Charles E. Young Drive East, Los Angeles, CA 90095, United States; Department of Microbiology, Immunology, and Molecular Genetics, UCLA, 609 Charles E. Young Drive East, Los Angeles, CA 90095, United States
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Sun AW, Bulterys PL, Bartberger MD, Jorth PA, O'Boyle BM, Virgil SC, Miller JF, Stoltz BM. Incorporation of a chiral gem-disubstituted nitrogen heterocycle yields an oxazolidinone antibiotic with reduced mitochondrial toxicity. Bioorg Med Chem Lett 2019; 29:2686-2689. [PMID: 31383589 PMCID: PMC6711789 DOI: 10.1016/j.bmcl.2019.07.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 07/08/2019] [Accepted: 07/13/2019] [Indexed: 11/20/2022]
Abstract
gem-Disubstituted N-heterocycles are rarely found in drugs, despite their potential to improve the drug-like properties of small molecule pharmaceuticals. Linezolid, a morpholine heterocycle-containing oxazolidinone antibiotic, exhibits significant side effects associated with human mitochondrial protein synthesis inhibition. We synthesized a gem-disubstituted linezolid analogue that when compared to linezolid, maintains comparable (albeit slightly diminished) activity against bacteria, comparable in vitro physicochemical properties, and a decrease in undesired mitochondrial protein synthesis (MPS) inhibition. This research contributes to the structure-activity-relationship data surrounding oxazolidinone MPS inhibition, and may inspire investigations into the utility of gem-disubstituted N-heterocycles in medicinal chemistry.
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Affiliation(s)
- Alexander W Sun
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Philip L Bulterys
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Michael D Bartberger
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Peter A Jorth
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Brendan M O'Boyle
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Scott C Virgil
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jeff F Miller
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Brian M Stoltz
- The Warren and Katharine Schlinger Laboratory for Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.
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Bulterys PL, Bulterys MA, Phommasone K, Luangraj M, Mayxay M, Kloprogge S, Miliya T, Vongsouvath M, Newton PN, Phetsouvanh R, French CT, Miller JF, Turner P, Dance DAB. Climatic drivers of melioidosis in Laos and Cambodia: a 16-year case series analysis. Lancet Planet Health 2018; 2:e334-e343. [PMID: 30082048 PMCID: PMC6076299 DOI: 10.1016/s2542-5196(18)30172-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/02/2018] [Accepted: 07/19/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Burkholderia pseudomallei is the cause of melioidosis, a serious and difficult to treat infection that is endemic throughout the tropics. Melioidosis incidence is highly seasonal. We aimed to identify the climatic drivers of infection and to shed light on modes of transmission and potential preventive strategies. METHODS We examined the records of patients diagnosed with melioidosis at the Microbiology Laboratory of Mahosot Hospital in Vientiane, Laos, between October, 1999, and August, 2015, and all patients with culture-confirmed melioidosis presenting to the Angkor Hospital for Children in Siem Reap, Cambodia, between February, 2009, and December, 2013. We also examined local temperature, humidity, precipitation, visibility, and wind data for the corresponding time periods. We estimated the B pseudomallei incubation period by examining profile likelihoods for hypothetical exposure-to-presentation delays. FINDINGS 870 patients were diagnosed with melioidosis in Laos and 173 patients were diagnosed with melioidosis in Cambodia during the study periods. Melioidosis cases were significantly associated with humidity (p<0·0001), low visibility (p<0·0001), and maximum wind speeds (p<0·0001) in Laos, and humidity (p=0·010), rainy days (p=0·015), and maximum wind speed (p=0·0070) in Cambodia. Compared with adults, children were at significantly higher odds of infection during highly humid months (odds ratio 2·79, 95% CI 1·83-4·26). Lung and disseminated infections were more common during windy months. The maximum likelihood estimate of the incubation period was 1 week (95% CI 0-2). INTERPRETATION The results of this study demonstrate a significant seasonal burden of melioidosis among adults and children in Laos and Cambodia. Our findings highlight the risks of infection during highly humid and windy conditions, and suggest a need for increased awareness among at-risk individuals, such as children. FUNDING Wellcome Trust.
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Affiliation(s)
- Philip L Bulterys
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, Los Angeles, CA, USA; Molecular Biology Institute, Los Angeles, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics, Los Angeles, CA, USA.
| | | | - Koukeo Phommasone
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos
| | - Manophab Luangraj
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Faculty of Postgraduate Studies, University of Health Sciences, Ministry of Health, Vientiane, Laos
| | - Sabine Kloprogge
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Thyl Miliya
- Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | | | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Rattanaphone Phetsouvanh
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christopher T French
- Department of Microbiology, Immunology, and Molecular Genetics, Los Angeles, CA, USA; California NanoSystems Institute UCLA, Los Angeles, CA, USA
| | - Jeff F Miller
- Molecular Biology Institute, Los Angeles, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics, Los Angeles, CA, USA; California NanoSystems Institute UCLA, Los Angeles, CA, USA
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Vientiane, Laos; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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13
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Affiliation(s)
- Philip L Bulterys
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles
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14
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Bulterys PL, Le T, Quang VM, Nelson KE, Lloyd-Smith JO. Environmental predictors and incubation period of AIDS-associated penicillium marneffei infection in Ho Chi Minh City, Vietnam. Clin Infect Dis 2013; 56:1273-9. [PMID: 23386634 DOI: 10.1093/cid/cit058] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Penicillium marneffei is an emerging dimorphic mycosis endemic in Southeast Asia, and a leading cause of mortality among human immunodeficiency virus (HIV)-infected people in the region. Factors governing the seasonal incidence of P. marneffei infection are unknown, and may yield critical insights into possible reservoirs or modes of acquisition. METHODS This study included HIV-infected patients presenting with P. marneffei (n = 719) and Cryptococcus neoformans (n = 1598) infection to the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam, from 2004 to 2010, and temperature, humidity, wind, precipitation, and HIV-related admissions data for the corresponding period. We used multivariate regression modeling to identify factors associated with P. marneffei and C. neoformans admissions. We estimated the P. marneffei incubation period by considering profile likelihoods for different exposure-to-admission delays. RESULTS We found that P. marneffei admissions were strongly associated with humidity (P < .001), and that precipitation, temperature, and wind did not add explanatory power. Cryptococcus neoformans admissions were not seasonal, and P. marneffei admissions were more common relative to C. neoformans admissions during months of high (≥85%) humidity (odds ratio, 1.49; 95% confidence interval [CI], 1.10-2.01). Maximum likelihood estimation suggested a P. marneffei incubation period of 1 week (95% CI, 0-3 weeks). CONCLUSIONS Our findings suggest that humidity is the most important environmental predictor of P. marneffei admissions, and may drive exposure by facilitating fungal growth or spore release in the environment. In addition, it appears that a high proportion of penicilliosis patients present to the hospital with primary disseminated infection within 3 weeks of exposure.
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Affiliation(s)
- Philip L Bulterys
- UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, 10833 Le Conte Ave, Los Angeles, CA 90095, USA.
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Bulterys PL, Chao A, Dalai SC, Zink MC, Dushimimana A, Katzenstein D, Saah AJ, Bulterys M. Placental malaria and mother-to-child transmission of human immunodeficiency virus-1 in rural Rwanda. Am J Trop Med Hyg 2011; 85:202-6. [PMID: 21813835 DOI: 10.4269/ajtmh.2011.10-0589] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [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
We conducted a nested case-control study of placental malaria (PM) and mother-to-child transmission (MTCT) of human immunodeficiency virus-1 (HIV-1) within a prospective cohort of 627 mother-infant pairs followed from October 1989 until April 1994 in rural Rwanda. Sixty stored placentas were examined for PM and other placental pathology, comparing 20 HIV-infected mother-infant (perinatal transmitter) pairs, 20 HIV-uninfected pairs, and 20 HIV-infected mothers who did not transmit to their infant perinatally. Of 60 placentas examined, 45% showed evidence of PM. Placental malaria was associated with increased risk of MTCT of HIV-1 (adjusted odds ratio [aOR] = 6.3; 95% confidence interval [CI] = 1.4-29.1), especially among primigravidae (aOR = 12.0; 95% CI = 1.0-150; P < 0.05). Before antiretroviral therapy or prophylaxis, PM was associated with early infant HIV infection among rural Rwandan women living in a hyper-endemic malaria region. Primigravidae, among whom malaria tends to be most severe, may be at higher risk.
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Affiliation(s)
- Philip L Bulterys
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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Bulterys PL, Dalai SC, Katzenstein DA. Viral sequence analysis from HIV-infected mothers and infants: molecular evolution, diversity, and risk factors for mother-to-child transmission. Clin Perinatol 2010; 37:739-50, viii. [PMID: 21078447 PMCID: PMC3175486 DOI: 10.1016/j.clp.2010.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Great progress has been made in understanding the pathogenesis, treatment, and transmission of HIV and the factors influencing the risk of mother-to-child transmission (MTCT). Many questions regarding the molecular evolution and genetic diversity of HIV in the context of MTCT remain unanswered. Further research to identify the selective factors governing which variants are transmitted, how the compartmentalization of HIV in different cells and tissues contributes to transmission, and the influence of host immunity, viral diversity, and recombination on MTCT may provide insight into new prevention strategies and the development of an effective HIV vaccine.
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Affiliation(s)
- Philip L Bulterys
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305-4200, USA
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Bulterys PL, Mharakurwa S, Thuma PE. Cattle, other domestic animal ownership, and distance between dwelling structures are associated with reduced risk of recurrent Plasmodium falciparum infection in southern Zambia. Trop Med Int Health 2009; 14:522-8. [PMID: 19389038 DOI: 10.1111/j.1365-3156.2009.02270.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To examine the associations between household Plasmodium falciparum infection and a number of factors including domestic animal ownership, potential mosquito breeding sites, indoor darkness, density of people, distance between dwelling structures, and insecticide-treated bed net use. METHODS Analyses were based on data collected from a household survey conducted in Macha, Zambia. Thirty-four households with recurrent malaria infection in 2005-2008 were selected as case households and compared with 37 control households with no malaria infection randomly selected from the same geographic area. Logistic regression models were used to identify factors associated with household P. falciparum infection. RESULTS In multivariate analysis, cattle ownership was associated with reduced risk of P. falciparum infection (adjusted odds ratio = 0.19; 95% CI = 0.05-0.69), as was increased distance between dwelling structures (aOR = 0.26; 95% CI = 0.07-0.98). Ownership of the highest category of cattle, goats, dogs, or cats dramatically reduced the risk of P. falciparum infection (aOR = 0.13; 95% CI = 0.03-0.56). CONCLUSION Domestic animal, in particular cattle, ownership and greater distance between dwelling structures were associated with reduced risk of recurrent P. falciparum infection at the household level. These factors should be further investigated as supplemental measures for malaria control in rural African settings.
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Affiliation(s)
- Philip L Bulterys
- Department of Biology, Stanford University, Stanford, CA 94309, USA.
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