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Wang Y, Xia W, Wang Y, Cui Y, Yu L, Liu C, Zhao D, Guan X, Wang Y, Wu S, Li J, Li Y, Hu J, Liu J. Multiplexed bacterial pathogen detection and clinical characteristics of orthopedic infection in hospitalized patients. Front Cell Infect Microbiol 2024; 14:1394352. [PMID: 38938882 PMCID: PMC11210349 DOI: 10.3389/fcimb.2024.1394352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/02/2024] [Indexed: 06/29/2024] Open
Abstract
Introduction Accurate identification of the etiology of orthopedic infection is very important for correct and timely clinical management, but it has been poorly studied. In the current study we explored the association of multiple bacterial pathogens with orthopedic infection. Methods Hospitalized orthopedic patients were enrolled in a rural hospital in Qingdao, China. Wound or exudate swab samples were collected and tested for twelve bacterial pathogens with both culture and multiplex real time PCR. Results and discussion A total of 349 hospitalized orthopedic patients were enrolled including 193 cases presenting infection manifestations upon admission and 156 with no sign of infection. Orthopedic infection patients were mainly male (72.5%) with more lengthy hospital stay (median 15 days). At least one pathogen was detected in 42.5% (82/193) of patients with infection while 7.1% (11/156) in the patients without infection (P < 0.001). S. aureus was the most prevalent causative pathogen (15.5%). Quantity dependent pathogen association with infection was observed, particularly for P. aeruginosa and K. pneumoniae, possibly indicating subclinical infection. Most of the patients with detected pathogens had a previous history of orthopedic surgery (odds ratio 2.8, P = 0.038). Pathogen specific clinical manifestations were characterized. Multiplex qPCR, because of its high sensitivity, superior specificity, and powerful quantification could be utilized in combination with culture to guide antimicrobial therapy and track the progression of orthopedic infection during treatment.
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Affiliation(s)
- Yani Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Wenbo Xia
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Ying Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanxiang Cui
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Linhong Yu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Chao Liu
- School of Public Health, Qingdao University, Qingdao, China
| | - Dan Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Xiaoxuan Guan
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Yingdi Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Shanrui Wu
- School of Public Health, Qingdao University, Qingdao, China
| | - Jie Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Yisong Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Jianqiang Hu
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
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Estep AS, Sanscrainte ND, Okech BA. Aedes aegypti Knockdown Resistance Mutations and Dengue Virus Infection in Haiti. JOURNAL OF THE AMERICAN MOSQUITO CONTROL ASSOCIATION 2024; 40:102-108. [PMID: 38547924 DOI: 10.2987/23-7160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Haiti is home to approximately 11 million people and has a high incidence of vector-borne disease, including more than 70,000 cases of dengue per year. Vector control is difficult in Haiti and adulticide spray of malathion is the main method of control employed during the outbreak of disease although pyrethroids are used in both bed net campaigns and in widely available aerosol cans for personal use. However, limited pathogen or insecticide resistance surveillance data are available for making operational decisions. In this study, we assessed Aedes aegypti from serial surveillance collections from 3 locations for the presence of dengue virus serotypes 1-3 (DENV1-3) by polymerase chain reaction and assessed, by melt curve analysis, samples from 10 locations in 2 departments for the presence of two mutations (V1016I and F1534C), that in combination, are linked to strong pyrethroid insecticide resistance. Only one of the 32 tested pools was positive for the presence of dengue virus. The two knockdown resistance (kdr) mutations were present in all locations. The 1016I mutation frequency varied from 0.29 to 0.91 and was in all sites lower than the 0.58-1.00 frequency of the 1534C mutation. We also observed that the genotype homozygous for both mutations (IICC), which has been linked to strong pyrethroid resistance, varied from 13 to 86% in each population. Notably, 3 locations - Ti Cousin and Christianville in Ouest department and Camp Coq in Nord department had more than 30% of the tested population without the presence of kdr mutations. These results indicate that the kdr markers of pyrethroid resistance are present in Haiti, at high frequency in several locations and, based on previous studies linking kdr genotypes and phenotypic resistance, that operational interventions with pyrethroids are not likely to be as effective as expected.
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Kazazian L, Silver R, Rao CY, Park M, Ciuba C, Farron M, Henao OL. A toolkit for planning and implementing acute febrile illness (AFI) surveillance. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0003115. [PMID: 38635502 PMCID: PMC11025857 DOI: 10.1371/journal.pgph.0003115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/06/2024] [Indexed: 04/20/2024]
Abstract
Acute febrile illness (AFI) is a broad clinical syndrome with a wide range of potential infectious etiologies. The lack of accessible, standardized approaches to conducting AFI etiologic investigations has contributed to significant global gaps in data on the epidemiology of AFI. Based on lessons learned from years of supporting AFI sentinel surveillance worldwide, the U.S. Centers for Disease Control and Prevention developed the toolkit for planning and implementing AFI surveillance, described here. This toolkit provides a comprehensive yet flexible framework to guide researchers, public health officials, and other implementers in developing a strategy to identify and/or monitor the potential causes of AFI. The toolkit comprises a cohesive set of planning aids and supporting materials, including an implementation framework, generic protocol, several generic forms (including screening, case report, specimen collection and testing, and informed consent and assent), and a generic data dictionary. These materials incorporate key elements intended to harmonize approaches for AFI surveillance, as well as setting-specific components and considerations for adaptation based on local surveillance objectives and limitations. Appropriate adaptation and implementation of this toolkit may generate data that expand the global AFI knowledge base, strengthen countries' surveillance and laboratory capacity, and enhance outbreak detection and response efforts.
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Affiliation(s)
- Lilit Kazazian
- Global Epidemiology, Laboratory, and Surveillance Branch, Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rachel Silver
- Global Epidemiology, Laboratory, and Surveillance Branch, Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Carol Y. Rao
- Global Epidemiology, Laboratory, and Surveillance Branch, Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Michael Park
- Global Epidemiology, Laboratory, and Surveillance Branch, Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Chandler Ciuba
- Global Epidemiology, Laboratory, and Surveillance Branch, Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Madeline Farron
- Global Epidemiology, Laboratory, and Surveillance Branch, Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Olga L. Henao
- Global Epidemiology, Laboratory, and Surveillance Branch, Division of Global Health Protection, Global Health Center, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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Colston JM, Fang B, Houpt E, Chernyavskiy P, Swarup S, Gardner LM, Nong MK, Badr HS, Zaitchik BF, Lakshmi V, Kosek MN. The Planetary Child Health & Enterics Observatory (Plan-EO): A protocol for an interdisciplinary research initiative and web-based dashboard for mapping enteric infectious diseases and their risk factors and interventions in LMICs. PLoS One 2024; 19:e0297775. [PMID: 38412156 PMCID: PMC10898779 DOI: 10.1371/journal.pone.0297775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Diarrhea remains a leading cause of childhood illness throughout the world that is increasing due to climate change and is caused by various species of ecologically sensitive pathogens. The emerging Planetary Health movement emphasizes the interdependence of human health with natural systems, and much of its focus has been on infectious diseases and their interactions with environmental and human processes. Meanwhile, the era of big data has engendered a public appetite for interactive web-based dashboards for infectious diseases. However, enteric infectious diseases have been largely overlooked by these developments. METHODS The Planetary Child Health & Enterics Observatory (Plan-EO) is a new initiative that builds on existing partnerships between epidemiologists, climatologists, bioinformaticians, and hydrologists as well as investigators in numerous low- and middle-income countries. Its objective is to provide the research and stakeholder community with an evidence base for the geographical targeting of enteropathogen-specific child health interventions such as novel vaccines. The initiative will produce, curate, and disseminate spatial data products relating to the distribution of enteric pathogens and their environmental and sociodemographic determinants. DISCUSSION As climate change accelerates there is an urgent need for etiology-specific estimates of diarrheal disease burden at high spatiotemporal resolution. Plan-EO aims to address key challenges and knowledge gaps by making and disseminating rigorously obtained, generalizable disease burden estimates. Pre-processed environmental and EO-derived spatial data products will be housed, continually updated, and made publicly available for download to the research and stakeholder communities. These can then be used as inputs to identify and target priority populations living in transmission hotspots and for decision-making, scenario-planning, and disease burden projection. STUDY REGISTRATION PROSPERO protocol #CRD42023384709.
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Affiliation(s)
- Josh M. Colston
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Bin Fang
- Department of Civil and Environmental Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Pavel Chernyavskiy
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Samarth Swarup
- Biocomplexity Institute, University of Virginia, Charlottesville, Virginia, United States of America
| | - Lauren M. Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Malena K. Nong
- University of Virginia College of Arts & Sciences, Charlottesville, Virginia, United States of America
| | - Hamada S. Badr
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Benjamin F. Zaitchik
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Venkataraman Lakshmi
- Department of Civil and Environmental Engineering, University of Virginia, Charlottesville, Virginia, United States of America
| | - Margaret N. Kosek
- Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
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Colston JM, Chernyavskiy P, Gardner L, Nong M, Fang B, Houpt E, Swarup S, Badr H, Zaitchik B, Lakshmi V, Kosek M. The Planetary Child Health & Enterics Observatory (Plan-EO): a protocol for an interdisciplinary research initiative and web-based dashboard for mapping enteric infectious diseases and their risk factors and interventions in LMICs. RESEARCH SQUARE 2024:rs.3.rs-2640564. [PMID: 36993232 PMCID: PMC10055683 DOI: 10.21203/rs.3.rs-2640564/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Background Diarrhea remains a leading cause of childhood illness throughout the world that is increasing due to climate change and is caused by various species of ecologically sensitive pathogens. The emerging Planetary Health movement emphasizes the interdependence of human health with natural systems, and much of its focus has been on infectious diseases and their interactions with environmental and human processes. Meanwhile, the era of big data has engendered a public appetite for interactive web-based dashboards for infectious diseases. However, enteric infectious diseases have been largely overlooked by these developments. Methods The Planetary Child Health and Enterics Observatory (Plan-EO) is a new initiative that builds on existing partnerships between epidemiologists, climatologists, bioinformaticians, and hydrologists as well as investigators in numerous low- and middle-income countries. Its objective is to provide the research and stakeholder community with an evidence base for the geographical targeting of enteropathogen-specific child health interventions such as novel vaccines. The initiative will produce, curate, and disseminate spatial data products relating to the distribution of enteric pathogens and their environmental and sociodemographic determinants. Discussion As climate change accelerates there is an urgent need for etiology-specific estimates of diarrheal disease burden at high spatiotemporal resolution. Plan-EO aims to address key challenges and knowledge gaps by making rigorously obtained, generalizable disease burden estimates freely available and accessible to the research and stakeholder communities. Pre-processed environmental and EO-derived spatial data products will be housed, continually updated, and made publicly available to the research and stakeholder communities both within the webpage itself and for download. These inputs can then be used to identify and target priority populations living in transmission hotspots and for decision-making, scenario-planning, and disease burden projection. Study registration PROSPERO protocol #CRD42023384709.
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Affiliation(s)
| | | | | | - Malena Nong
- University of Virginia College of Arts & Sciences
| | | | - Eric Houpt
- University of Virginia School of Medicine
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Colston JM, Chernyavskiy P, Gardner L, Nong M, Fang B, Houpt E, Swarup S, Badr H, Zaitchik B, Lakshmi V, Kosek M. The Planetary Child Health & Enterics Observatory (Plan-EO): a protocol for an interdisciplinary research initiative and web-based dashboard for mapping enteric infectious diseases and their risk factors and interventions in LMICs. RESEARCH SQUARE 2024:rs.3.rs-2640564. [PMID: 36993232 PMCID: PMC10055683 DOI: 10.21203/rs.3.rs-2640564/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Background Diarrhea remains a leading cause of childhood illness throughout the world that is increasing due to climate change and is caused by various species of ecologically sensitive pathogens. The emerging Planetary Health movement emphasizes the interdependence of human health with natural systems, and much of its focus has been on infectious diseases and their interactions with environmental and human processes. Meanwhile, the era of big data has engendered a public appetite for interactive web-based dashboards for infectious diseases. However, enteric infectious diseases have been largely overlooked by these developments. Methods The Planetary Child Health and Enterics Observatory (Plan-EO) is a new initiative that builds on existing partnerships between epidemiologists, climatologists, bioinformaticians, and hydrologists as well as investigators in numerous low- and middle-income countries. Its objective is to provide the research and stakeholder community with an evidence base for the geographical targeting of enteropathogen-specific child health interventions such as novel vaccines. The initiative will produce, curate, and disseminate spatial data products relating to the distribution of enteric pathogens and their environmental and sociodemographic determinants. Discussion As climate change accelerates there is an urgent need for etiology-specific estimates of diarrheal disease burden at high spatiotemporal resolution. Plan-EO aims to address key challenges and knowledge gaps by making rigorously obtained, generalizable disease burden estimates freely available and accessible to the research and stakeholder communities. Pre-processed environmental and EO-derived spatial data products will be housed, continually updated, and made publicly available to the research and stakeholder communities both within the webpage itself and for download. These inputs can then be used to identify and target priority populations living in transmission hotspots and for decision-making, scenario-planning, and disease burden projection. Study registration PROSPERO protocol #CRD42023384709.
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Affiliation(s)
| | | | | | - Malena Nong
- University of Virginia College of Arts & Sciences
| | | | - Eric Houpt
- University of Virginia School of Medicine
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Rao G, Capone D, Zhu K, Knoble A, Linden Y, Clark R, Lai A, Kim J, Huang CH, Bivins A, Brown J. Simultaneous detection and quantification of multiple pathogen targets in wastewater. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.23.23291792. [PMID: 37425908 PMCID: PMC10327253 DOI: 10.1101/2023.06.23.23291792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Wastewater-based epidemiology has emerged as a critical tool for public health surveillance, building on decades of environmental surveillance work for pathogens such as poliovirus. Work to date has been limited to monitoring a single pathogen or small numbers of pathogens in targeted studies; however, few studies consider simultaneous quantitative analysis of a wide variety of pathogens, which could greatly increase the utility of wastewater surveillance. We developed a novel quantitative multi-pathogen surveillance approach (35 pathogen targets including bacteria, viruses, protozoa, and helminths) using TaqMan Array Cards (TAC) and applied the method on concentrated wastewater samples collected at four wastewater treatment plants in Atlanta, GA from February to October of 2020. From sewersheds serving approximately 2 million people, we detected a wide range of targets including many we expected to find in wastewater (e.g., enterotoxigenic E. coli and Giardia in 97% of 29 samples at stable concentrations) as well as unexpected targets including Strongyloides stercoralis (a human threadworm rarely observed in the USA). Other notable detections included SARS-CoV-2, but also several pathogen targets that are not commonly included in wastewater surveillance like Acanthamoeba spp., Balantidium coli, Entamoeba histolytica, astrovirus, norovirus, and sapovirus. Our data suggest broad utility in expanding the scope of enteric pathogen surveillance in wastewaters, with potential for application in a variety of settings where pathogen quantification in fecal waste streams can inform public health surveillance and selection of control measures to limit infections.
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Affiliation(s)
- Gouthami Rao
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Drew Capone
- Department of Environmental and Occupational Health, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Kevin Zhu
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Abigail Knoble
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yarrow Linden
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ryan Clark
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amanda Lai
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juhee Kim
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ching-Hua Huang
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, Baton Rouge, LA, USA
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Wang HB, Du T, Lin JH, Chen XB, Tu CN. Development and evaluation of an external quality control and internal quality control containing real-time RT-PCR assay for the detection of o'nyong-nyong virus. Biologicals 2023; 84:101717. [PMID: 37801802 DOI: 10.1016/j.biologicals.2023.101717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 06/20/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023] Open
Abstract
O'nyong-nyong fever is a mosquito-borne tropical viral disease while few molecular diagnostic tools have been established for its surveillance until now. In the current study, a single-step, dual-color real-time reverse transcription polymerase chain reaction (RT-PCR) assay which contained both external quality control (EQC) and internal quality control (IQC) prepared by armored RNA technique was developed and evaluated for the detection of o'nyong-nyong virus (ONNV). Results showed that the assay was established successfully without cross-reaction with genetically related or symptom-alike diseases, which showed high specificity of the assay. The coefficient of variation of the assay was 0.97%, far less than 5%, indicating good repeatability of the assay. The lower limit of detection of the assay could reach as low as 100 copies of genome equivalent. During evaluation, the assay could correctly detect ONNV from spiked human serum samples and Anopheles species mosquito samples, while no ONNV positive was observed either from serum samples of patients with acute febrile illness or from local Anopheles species mosquitoes, suggesting no ONNV had been transmitted locally. In conclusion, the assay could potentially provide a valuable platform for ONNV molecular detection, which may improve the preparedness for future o'nyong-nyong fever outbreaks.
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Affiliation(s)
- Hai-Bo Wang
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China.
| | - Tian Du
- Futian District Center for Disease Control and Prevention, Shenzhen, 518040, Guangdong, China
| | - Ji-Hong Lin
- Zhongshan International Travel Healthcare Center, Zhongshan, 528400, Guangdong, China
| | - Xin-Bin Chen
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China
| | - Cheng-Ning Tu
- Key Laboratory of Emerging Infectious Disease Detection, Zhuhai International Travel Healthcare Center, Zhuhai, 519020, Guangdong, China
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Garbuglia AR, Lapa D, Pauciullo S, Raoul H, Pannetier D. Nipah Virus: An Overview of the Current Status of Diagnostics and Their Role in Preparedness in Endemic Countries. Viruses 2023; 15:2062. [PMID: 37896839 PMCID: PMC10612039 DOI: 10.3390/v15102062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Nipah virus (NiV) is a paramyxovirus responsible for a high mortality rate zoonosis. As a result, it has been included in the list of Blueprint priority pathogens. Bats are the main reservoirs of the virus, and different clinical courses have been described in humans. The Bangladesh strain (NiV-B) is often associated with severe respiratory disease, whereas the Malaysian strain (NiV-M) is often associated with severe encephalitis. An early diagnosis of NiV infection is crucial to limit the outbreak and to provide appropriate care to the patient. Due to high specificity and sensitivity, qRT-PCR is currently considered to be the optimum method in acute NiV infection assessment. Nasal swabs, cerebrospinal fluid, urine, and blood are used for RT-PCR testing. N gene represents the main target used in molecular assays. Different sensitivities have been observed depending on the platform used: real-time PCR showed a sensitivity of about 103 equivalent copies/reaction, SYBRGREEN technology's sensitivity was about 20 equivalent copies/reaction, and in multiple pathogen card arrays, the lowest limit of detection (LOD) was estimated to be 54 equivalent copies/reaction. An international standard for NiV is yet to be established, making it difficult to compare the sensitivity of the different methods. Serological assays are for the most part used in seroprevalence studies owing to their lower sensitivity in acute infection. Due to the high epidemic and pandemic potential of this virus, the diagnosis of NiV should be included in a more global One Health approach to improve surveillance and preparedness for the benefit of public health. Some steps need to be conducted in the diagnostic field in order to become more efficient in epidemic management, such as development of point-of-care (PoC) assays for the rapid diagnosis of NiV.
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Affiliation(s)
- Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Daniele Lapa
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Silvia Pauciullo
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (D.L.); (S.P.)
| | - Hervé Raoul
- French National Agency for Research on AIDS—Emerging Infectious Diseases (ANRS MIE), Maladies Infectieuses Émergentes, 75015 Paris, France;
| | - Delphine Pannetier
- Institut National de la Santé et de la Recherche Médicale, Jean Mérieux BSL4 Laboratory, 69002 Lyon, France;
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Lehman A, Ellis J, Nalintya E, Bahr NC, Loyse A, Rajasingham R. Advanced HIV disease: A review of diagnostic and prophylactic strategies. HIV Med 2023; 24:859-876. [PMID: 37041113 PMCID: PMC10642371 DOI: 10.1111/hiv.13487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Despite expanded access to antiretroviral therapy (ART) and the rollout of the World Health Organization's (WHO) 'test-and-treat' strategy, the proportion of people with HIV (PWH) presenting with advanced HIV disease (AHD) remains unchanged at approximately 30%. Fifty percent of persons with AHD report prior engagement to care. ART failure and insufficient retention in HIV care are major causes of AHD. People living with AHD are at high risk for opportunistic infections and death. In 2017, the WHO published guidelines for the management of AHD that included a comprehensive package of care for screening and prophylaxis of major opportunistic infections (OIs). In the interim, ART regimens have evolved: integrase inhibitors are first-line therapy globally, and the diagnostic landscape is evolving. The objective of this review is to highlight novel point-of-care (POC) diagnostics and treatment strategies that can facilitate OI screening and prophylaxis for persons with AHD. METHODS We reviewed the WHO guidelines for recommendations for persons with AHD. We summarized the scientific literature on current and emerging diagnostics, along with emerging treatment strategies for persons with AHD. We also highlight the key research and implementation gaps together with potential solutions. RESULTS While POC CD4 testing is being rolled out in order to identify persons with AHD, this alone is insufficient; implementation of the Visitect CD4 platform has been challenging given operational and test interpretation issues. Numerous non-sputum POC TB diagnostics are being evaluated, many with limited sensitivity. Though imperfect, these tests are designed to provide rapid results (within hours) and are relatively affordable for resource-poor settings. While novel POC diagnostics are being developed for cryptococcal infection, histoplasmosis and talaromycosis, implementation science studies are urgently needed to understand the clinical benefit of these tests in the routine care. CONCLUSIONS Despite progress with HIV treatment and prevention, a persistent 20%-30% of PWH present to care with AHD. Unfortunately, these persons with AHD continue to carry the burden of HIV-related morbidity and mortality. Investment in the development of additional POC or near-bedside CD4 platforms is urgently needed. Implementation of POC diagnostics theoretically could improve HIV retention in care and thereby reduce mortality by overcoming delays in laboratory testing and providing patients and healthcare workers with timely same-day results. However, in real-world scenarios, people with AHD have multiple comorbidities and imperfect follow-up. Pragmatic clinical trials are needed to understand whether these POC diagnostics can facilitate timely diagnosis and treatment, thereby improving clinical outcomes such as HIV retention in care.
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Affiliation(s)
- Alice Lehman
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jayne Ellis
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Nathan C. Bahr
- Division of Infectious Diseases, University of Kansas, Kansas City, Kansas, USA
| | - Angela Loyse
- Division of Infection and Immunity Research Institute, St George’s University of London, London, UK
| | - Radha Rajasingham
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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Modise BM, Mpoloka SW, Settypalli TBK, Hyera J, Natale A, Ceglie L, Gcebe N, Marobela-Raborokgwe C, Viljoen GJ, Cattoli G, Lamien CE. A novel multiplex qPCR‑HRM assay for the simultaneous detection of four abortive zoonotic agents in cattle, sheep, and goats. Sci Rep 2023; 13:12282. [PMID: 37507444 PMCID: PMC10382562 DOI: 10.1038/s41598-023-39447-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/25/2023] [Indexed: 07/30/2023] Open
Abstract
Abortifacient pathogens induce substantial economic losses in the livestock industry worldwide, and many of these pathogens are zoonotic, impacting human health. As Brucella spp., Coxiella burnetii, Leptospira spp., and Listeria monocytogenes cause abortion, rapid differential molecular diagnostic tests are needed to facilitate early and accurate detection of abortion to establish effective control measures. However, the available molecular methods are laborious, time-consuming, or costly. Therefore, we developed and validated a novel multiplex real-time polymerase chain reaction (qPCR) method based on high-resolution melting (HRM) curve analysis to simultaneously detect and differentiate four zoonotic abortifacient agents in cattle, goats, and sheep. Our HRM assay generated four well-separated melting peaks allowing the differentiation between the four zoonotic abortifacients. Out of 216 DNA samples tested, Brucella spp. was detected in 45 samples, Coxiella burnetii in 57 samples, Leptospira spp. in 12 samples, and Listeria monocytogenes in 19 samples, co-infection with Brucella spp. and Coxiella burnetii in 41 samples, and 42 samples were negative. This assay demonstrated good analytical sensitivity, specificity, and reproducibility. This is a valuable rapid, cost-saving, and reliable diagnostic tool for detecting individual and co-infections for zoonotic abortifacient agents in ruminants.
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Affiliation(s)
- Boitumelo M Modise
- Botswana National Veterinary Laboratory, Private Bag 0035, Gaborone, Botswana.
- Department of Biological Sciences, University of Botswana, Private Bag 00704, Gaborone, Botswana.
| | - Sununguko W Mpoloka
- Department of Biological Sciences, University of Botswana, Private Bag 00704, Gaborone, Botswana
| | - Tirumala B K Settypalli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
| | - Joseph Hyera
- Botswana Vaccine Institute, Private Bag 0031, Gaborone, Botswana
| | - Alda Natale
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università, 10, 35020, Legnaro, Italy
| | - Letizia Ceglie
- Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Viale dell'Università, 10, 35020, Legnaro, Italy
| | - Nomakorinte Gcebe
- Agricultural Research Council-Bacteriology and Zoonotic Diseases Diagnostic Laboratory, Onderstepoort Veterinary Research, Pretoria, South Africa
| | | | - Gerrit J Viljoen
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
| | - Giovanni Cattoli
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
| | - Charles E Lamien
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Wagramer Strasse 5, P.O. Box 100, 1400, Vienna, Austria
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12
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Ferdousi T, Dutta AK, Chowdhury MAH, Islam K, Islam MT, Islam MZ, Bulbul MRH, Khan AI, Qadri F. Role of TaqMan array card in determining causative organisms of acute febrile illness in hospitalized patients. J Clin Lab Anal 2023; 37:e24948. [PMID: 37496432 PMCID: PMC10492456 DOI: 10.1002/jcla.24948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/23/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Acute febrile illness (AFI) is a prevalent disease in developing countries that is difficult to diagnose due to the diversity of infectious organisms and the poor quality of clinical diagnosis. TaqMan array card (TAC) can detect up to 35 AFI-associated organisms in 1.5 h, addressing diagnostic demands. In this study, we aimed to evaluate the role of TAC in determining the causative organisms in hospitalized AFI patients. METHODS The study had a cross-sectional design and enrolled 120 admitted patients with persistent fever for three or more days from the medicine ward of Chittagong Medical College Hospital (CMCH) and Bangladesh Institute of Tropical and Infectious Diseases Hospital (BITID). Blood samples were collected and then subjected to automated BacT/Alert blood culture, microbial culture, TAC assay, and typhoid/paratyphoid test. RESULTS The total number of study participants was 120, among them 48 (40%) samples showed a positive result in TAC card, 29 (24.16%) were TP positive and nine (7.51%) were culture positive. The number of organisms detected by the TAC card was 13 bacteria, three viruses, one protozoan, and one fungus. The sensitivity and specificity of the TAC assay for different bacterial pathogen compared to blood culture was 44.44%, and 90.99%, respectively. In contrast, the TP test had a sensitivity and specificity of 100% and 80%, respectively, compared to the blood culture test. CONCLUSION TAC can be a handful tool for detecting multiple organisms in AFI with high specificity which can facilitate early diagnosis of different pathogens contributing to AFI.
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Affiliation(s)
- Tabassum Ferdousi
- Bangladesh Institute of Tropical and Infectious DiseasesChattogramBangladesh
| | | | | | - Kamrul Islam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
| | - Md. Taufiqul Islam
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
| | - Md. Zahirul Islam
- Institute for Developing Science and Health Initiatives (ideSHi)DhakaBangladesh
| | | | - Ashraful Islam Khan
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
| | - Firdausi Qadri
- International Centre for Diarrheal Disease Research, Bangladesh (icddr,b)DhakaBangladesh
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13
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Peñataro Yori P, Paredes Olórtegui M, Schiaffino F, Colston JM, Pinedo Vasquez T, Garcia Bardales PF, Shapiama Lopez V, Zegarra Paredes LF, Perez K, Curico G, Flynn T, Zhang J, Ramal Asayag C, Meza Sanchez G, Silva Delgado H, Casapia Morales M, Casanova W, Jiu B, Oberhelman R, Munayco Escate C, Silver R, Henao O, Cooper KK, Liu J, Houpt ER, Kosek MN. Etiology of acute febrile illness in the peruvian amazon as determined by modular formatted quantitative PCR: a protocol for RIVERA, a health facility-based case-control study. BMC Public Health 2023; 23:674. [PMID: 37041550 PMCID: PMC10088183 DOI: 10.1186/s12889-023-15619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/06/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The study of the etiology of acute febrile illness (AFI) has historically been designed as a prevalence of pathogens detected from a case series. This strategy has an inherent unrealistic assumption that all pathogen detection allows for causal attribution, despite known asymptomatic carriage of the principal causes of acute febrile illness in most low- and middle-income countries (LMICs). We designed a semi-quantitative PCR in a modular format to detect bloodborne agents of acute febrile illness that encompassed common etiologies of AFI in the region, etiologies of recent epidemics, etiologies that require an immediate public health response and additional pathogens of unknown endemicity. We then designed a study that would delineate background levels of transmission in the community in the absence of symptoms to provide corrected estimates of attribution for the principal determinants of AFI. METHODS A case-control study of acute febrile illness in patients ten years or older seeking health care in Iquitos, Loreto, Peru, was planned. Upon enrollment, we will obtain blood, saliva, and mid-turbinate nasal swabs at enrollment with a follow-up visit on day 21-28 following enrollment to attain vital status and convalescent saliva and blood samples, as well as a questionnaire including clinical, socio-demographic, occupational, travel, and animal contact information for each participant. Whole blood samples are to be simultaneously tested for 32 pathogens using TaqMan array cards. Mid-turbinate samples will be tested for SARS-CoV-2, Influenza A and Influenza B. Conditional logistic regression models will be fitted treating case/control status as the outcome and with pathogen-specific sample positivity as predictors to attain estimates of attributable pathogen fractions for AFI. DISCUSSION The modular PCR platforms will allow for reporting of all primary results of respiratory samples within 72 h and blood samples within one week, allowing for results to influence local medical practice and enable timely public health responses. The inclusion of controls will allow for a more accurate estimate of the importance of specific prevalent pathogens as a cause of acute illness. STUDY REGISTRATION Project 1791, Registro de Proyectos de Investigación en Salud Pública (PRISA), Instituto Nacional de Salud, Perú.
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Affiliation(s)
- Pablo Peñataro Yori
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Asociación Benefica PRISMA, Iquitos, Loreto, Peru
| | | | - Francesca Schiaffino
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Josh M Colston
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | - Karin Perez
- Asociación Benefica PRISMA, Iquitos, Loreto, Peru
| | | | - Thomas Flynn
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jixian Zhang
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Cesar Ramal Asayag
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
- Hospital Regional de Loreto, Iquitos, Loreto, Peru
| | - Graciela Meza Sanchez
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
- Direccion Regional de Salud, Loreto, Peru
| | | | - Martin Casapia Morales
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
- Hospital Regional de Loreto, Iquitos, Loreto, Peru
| | - Wilma Casanova
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
| | - Bruce Jiu
- Laboratorio de Referencia en Salud Publica de la Direccion Regional de Salud- Diresa, Loreto, Peru
| | - Richard Oberhelman
- Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Cesar Munayco Escate
- Centro Nacional de Epidemiologia, Prevencion, y Control de Enfermedades, Ministerio de Salud de Peru, Jesus Maria, Peru
| | - Rachel Silver
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Olga Henao
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | - Eric R Houpt
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Margaret N Kosek
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA.
- Asociación Benefica PRISMA, Iquitos, Loreto, Peru.
- Division of Infectious Diseases and International Health, Public Health Sciences, 345 Crispell Dr, Rm 2525, Charlottesville, USA.
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14
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Peñataro Yori P, Paredes Olórtegui M, Schiaffino F, Perez K, Curico Huansi G, Flynn T, Zhang J, Ramal Asayag C, Meza Sanchez G, Silva Delgado H, Casapia Morales M, Casanova W, Jiu B, Munayco Escate C, Silver R, Henao O, Cooper KK, Liu J, Houpt E, Kosek MN, Colston JM, Oberhelman R, Pinedo Vasquez T, Garcia Bardales PF, Shapiama Lopez WV, Zegarra Paredes LF. Etiology of Acute Febrile Illness in the Peruvian Amazon as determined by modular formatted quantitative PCR: A Protocol for RIVERA, a Health Facility-Based Case-Control Study. RESEARCH SQUARE 2023:rs.3.rs-2635774. [PMID: 37034707 PMCID: PMC10081374 DOI: 10.21203/rs.3.rs-2635774/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Background The study of the etiology of acute febrile illness (AFI) has historically been designed as a prevalence of pathogens detected from a case series. This strategy has an inherent unrealistic assumption that all pathogen detection allows for causal attribution, despite known asymptomatic carriage of the principal causes of acute febrile illness in most low- and middle-income countries (LMICs). We designed a semi-quantitative PCR in a modular format to detect bloodborne agents of acute febrile illness that encompassed common etiologies of AFI in the region, etiologies of recent epidemics, etiologies that require an immediate public health response and additional pathogens of unknown endemicity. We then designed a study that would delineate background levels of transmission in the community in the absence of symptoms to provide corrected estimates of attribution for the principal determinants of AFI. Methods A case-control study of acute febrile illness in patients ten years or older seeking health care in Iquitos, Loreto, Peru, was planned. Upon enrollment, we will obtain blood, saliva, and mid-turbinate nasal swabs at enrollment with a follow-up visit on day 21-28 following enrollment to attain vital status and convalescent saliva and blood samples, as well as a questionnaire including clinical, socio-demographic, occupational, travel, and animal contact information for each participant. Whole blood samples are to be simultaneously tested for 32 pathogens using TaqMan array cards. Mid-turbinate samples will be tested for SARS-CoV-2, Influenza A and Influenza B. Conditional logistic regression models will be fitted treating case/control status as the outcome and with pathogen-specific sample positivity as predictors to attain estimates of attributable pathogen fractions for AFI. Discussion The modular PCR platforms will allow for reporting of all primary results of respiratory samples within 72 hours and blood samples within one week, allowing for results to influence local medical practice and enable timely public health responses. The inclusion of controls will allow for a more accurate estimate of the importance of specific, prevalent pathogens as a cause of acute illness. Study Registration Project 1791, Registro de Proyectos de Investigación en Salud Pública (PRISA), Instituto Nacional de Salud, Perú.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Cesar Munayco Escate
- Centro de Epidemiologia, Prevencion, y Control de Enfermedades, Ministerio de Salud
| | | | - Olga Henao
- Centers for Disease Control and Prevention
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15
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Grundy BS, Parikh H, Jacob S, Banura P, Moore CC, Liu J, Houpt ER. Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda. Microbiol Spectr 2023; 11:e0431222. [PMID: 36625651 PMCID: PMC9927450 DOI: 10.1128/spectrum.04312-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Metagenomic sequencing is a promising new method for pathogen detection. We aimed to detect pathogens from archived plasma using metagenomic sequencing in a previously well-characterized cohort of 254 predominantly HIV-infected patients with sepsis in Uganda. We used Illumina sequencing and the Chan Zuckerberg ID metagenomics platform to sequence and identify pathogens. On average, each plasma sample yielded 3,404,737 ± 2,201,997 reads (mean ± standard deviation), of which 220,032 ± 416,691 (6.3% ± 8.6%) were identified as nonhuman reads. Using a background model filter, 414 genus-specific pathogen identifications were found in the 254 samples. Nineteen pathogens were previously detected positive by quantitative PCR (qPCR), compared to sequencing, which demonstrated 30.2% sensitivity and 99.5% specificity. Sensitivity was higher for viral pathogens than nonviral pathogens (37% versus 5%). For example, HIV viremia was detected in 69% of samples using qPCR, and sequencing revealed 70% sensitivity and 92% specificity. There were 75 genus-specific potential pathogens identified by sequencing in this cohort, including hepatitis B and Epstein-Barr virus (EBV), among several others. qPCR showed a prevalence of hepatitis B and EBV viremia of 17% and 45%, respectively. In-hospital mortality was associated with a lower qPCR threshold cycle value for EBV (adjusted odds ratio, 0.85; P < .001) but not for hepatitis B or HIV. In conclusion, a broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda. Unexpectedly high rates of hepatitis B and EBV viremia were found. Whether these viral infections in HIV patients with sepsis are clinically important requires further study. IMPORTANCE The use of next-generation sequencing (NGS) in blood samples is an emerging technology for clinical microbiology labs. In this work, we performed NGS on plasma samples from a well-characterized cohort, where all samples had been previously tested by PCR for 43 pathogens. Therefore, we could compare sequencing performance against that of PCR and identify clinical correlates. A broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda, particularly viruses, which we confirmed by PCR. In addition to HIV viremia, unexpectedly high rates of hepatitis B and EBV viremia were found, which may have important clinical implications.
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Affiliation(s)
- Brian S. Grundy
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Hardik Parikh
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Shevin Jacob
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Patrick Banura
- Ministry of Health, National Disease Control Department, Kampala, Uganda
| | - Chris C. Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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16
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Bettini A, Lapa D, Garbuglia AR. Diagnostics of Ebola virus. Front Public Health 2023; 11:1123024. [PMID: 36908455 PMCID: PMC9995846 DOI: 10.3389/fpubh.2023.1123024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/31/2023] [Indexed: 02/25/2023] Open
Abstract
Ebola is a highly pathogenic virus, which in humans reaches a mortality rate above 50%. Due to a lack of laboratories in territories where Ebola viruses are endemic and the limited number of surveillance programmes, tests for the confirmation of suspected cases of Ebola are often performed in Reference Laboratories. While this provides guarantees regarding the accuracy of results, the shipment of samples to a centralized facility where the diagnostic test can be performed and the time required to achieve the results takes several days, which increases costs and entails delays in the isolation of positive subjects and therapeutic intervention with negative consequences both for patients and the community. Molecular tests have been the most frequently used tool in Ebola diagnosis in recent outbreaks. One of the most commonly used molecular tests is the Real-Star Altona, which targets a conserved area of the L gene. This assay showed different sensitivities depending on the Ebola virus: 471 copies/mL (EBOV) and 2871 copies/ml (SUDAN virus). The Cepheid system also showed good sensitivity (232 copies/mL). The LAMP platform is very promising because, being an isothermal reaction, it does not require high-precision instrumentation and can be considered a Point of Care (PoC) tool. Its analytical sensitivity is 1 copy/reaction. However, since data from real life studies are not yet available, it is premature to give any indications on its feasibility. Moreover, in November 2014, the WHO recommended the development of rapid diagnostic tests (RDT) according to ASSURED criteria. Several RDT assays have since been produced, most of which are rapid tests based on the search for antibody anti-Ebola viral proteins with immunochromatographic methods. Several viral antigens are used for this purpose: VP40, NP and GP. These assays show different sensitivities according to the protein used: VP40 57.4-93.1%, GP 53-88.9% and 85% for NP compared to reference molecular assays. From these results, it can be deduced that no RDT reaches the 99% sensitivity recommended by the WHO and therefore any RDT negative results in suspected cases should be confirmed with a molecular test.
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Affiliation(s)
- Aurora Bettini
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy
| | - Daniele Lapa
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy
| | - Anna Rosa Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy
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17
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Shih DC, Silver R, Henao OL, Alemu A, Audi A, Bigogo G, Colston JM, Edu-Quansah EP, Erickson TA, Gashu A, Gbelee GB, Gunter SM, Kosek MN, Logan GG, Mackey JM, Maliga A, Manzanero R, Morazan G, Morey F, Munoz FM, Murray KO, Nelson TV, Olortegui MP, Yori PP, Ronca SE, Schiaffino F, Tayachew A, Tedasse M, Wossen M, Allen DR, Angra P, Balish A, Farron M, Guerra M, Herman-Roloff A, Hicks VJ, Hunsperger E, Kazazian L, Mikoleit M, Munyua P, Munywoki PK, Namwase AS, Onyango CO, Park M, Peruski LF, Sugerman DE, Gutierrez EZ, Cohen AL. Incorporating COVID-19 into Acute Febrile Illness Surveillance Systems, Belize, Kenya, Ethiopia, Peru, and Liberia, 2020-2021. Emerg Infect Dis 2022; 28:S34-S41. [PMID: 36502419 DOI: 10.3201/eid2813.220898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Existing acute febrile illness (AFI) surveillance systems can be leveraged to identify and characterize emerging pathogens, such as SARS-CoV-2, which causes COVID-19. The US Centers for Disease Control and Prevention collaborated with ministries of health and implementing partners in Belize, Ethiopia, Kenya, Liberia, and Peru to adapt AFI surveillance systems to generate COVID-19 response information. Staff at sentinel sites collected epidemiologic data from persons meeting AFI criteria and specimens for SARS-CoV-2 testing. A total of 5,501 patients with AFI were enrolled during March 2020-October 2021; >69% underwent SARS-CoV-2 testing. Percentage positivity for SARS-CoV-2 ranged from 4% (87/2,151, Kenya) to 19% (22/115, Ethiopia). We show SARS-CoV-2 testing was successfully integrated into AFI surveillance in 5 low- to middle-income countries to detect COVID-19 within AFI care-seeking populations. AFI surveillance systems can be used to build capacity to detect and respond to both emerging and endemic infectious disease threats.
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Gazal S, Sharma N, Gazal S, Tikoo M, Shikha D, Badroo GA, Rashid M, Lee SJ. Nipah and Hendra Viruses: Deadly Zoonotic Paramyxoviruses with the Potential to Cause the Next Pandemic. Pathogens 2022; 11:pathogens11121419. [PMID: 36558753 PMCID: PMC9784551 DOI: 10.3390/pathogens11121419] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Nipah and Hendra viruses are deadly zoonotic paramyxoviruses with a case fatality rate of upto 75%. The viruses belong to the genus henipavirus in the family Paramyxoviridae, a family of negative-sense single-stranded RNA viruses. The natural reservoirs of NiV and HeV are bats (flying foxes) in which the virus infection is asymptomatic. The intermediate hosts for NiV and HeV are swine and equine, respectively. In humans, NiV infections result in severe and often fatal respiratory and neurological manifestations. The Nipah virus was first identified in Malaysia and Singapore following an outbreak of encephalitis in pig farmers and subsequent outbreaks have been reported in Bangladesh and India almost every year. Due to its extreme pathogenicity, pandemic potential, and lack of established antiviral therapeutics and vaccines, research on henipaviruses is highly warranted so as to develop antivirals or vaccines that could aid in the prevention and control of future outbreaks.
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Affiliation(s)
- Sabahat Gazal
- Division of Veterinary Microbiology and Immunology, Faculty of Veterinary Science and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, R.S. Pura, Jammu 181102, Jammu and Kashmir, India
| | - Neelesh Sharma
- Division of Veterinary Medicine, Faculty of Veterinary Science and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, R.S. Pura, Jammu 181102, Jammu and Kashmir, India
- Correspondence: (N.S.); (S.-J.L.)
| | - Sundus Gazal
- Division of Veterinary Microbiology, College of Veterinary Sciences, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141004, Punjab, India
| | - Mehak Tikoo
- Division of Veterinary Microbiology and Immunology, Faculty of Veterinary Science and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, R.S. Pura, Jammu 181102, Jammu and Kashmir, India
| | - Deep Shikha
- Division of Veterinary Microbiology and Immunology, Faculty of Veterinary Science and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, R.S. Pura, Jammu 181102, Jammu and Kashmir, India
| | - Gulzar Ahmed Badroo
- Division of Veterinary Microbiology and Immunology, Faculty of Veterinary Science and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, R.S. Pura, Jammu 181102, Jammu and Kashmir, India
| | - Mohd Rashid
- Division of Veterinary Microbiology and Immunology, Faculty of Veterinary Science and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, R.S. Pura, Jammu 181102, Jammu and Kashmir, India
| | - Sung-Jin Lee
- Department of Applied Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
- Correspondence: (N.S.); (S.-J.L.)
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19
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Obiero CW, Gumbi W, Mwakio S, Mwangudzah H, Seale AC, Taniuchi M, Liu J, Houpt E, Berkley JA. Detection of pathogens associated with early-onset neonatal sepsis in cord blood at birth using quantitative PCR. Wellcome Open Res 2022; 7:3. [PMID: 35600002 PMCID: PMC9114825 DOI: 10.12688/wellcomeopenres.17386.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background: Early onset neonatal sepsis (EONS) typically begins prior to, during or soon after birth and may be rapidly fatal. There is paucity of data on the aetiology of EONS in sub-Saharan Africa due to limited diagnostic capacity in this region, despite the associated significant mortality and long-term neurological impairment. Methods: We compared pathogens detected in cord blood samples between neonates admitted to hospital with possible serious bacterial infection (pSBI) in the first 48 hours of life (cases) and neonates remaining well (controls). Cord blood was systematically collected at Kilifi County Hospital (KCH) from 2011-2016, and later tested for 21 bacterial, viral and protozoal targets using multiplex PCR via TaqMan Array Cards (TAC). Results: Among 603 cases (101 [17%] of whom died), 179 (30%) tested positive for ≥1 target and 37 (6.1%) tested positive for multiple targets. Klebsiella oxytoca, Escherichia coli/Shigella spp., Pseudomonas aeruginosa, and Streptococcus pyogenes were commonest. Among 300 controls, 79 (26%) tested positive for ≥1 target, 11 (3.7%) were positive for multiple targets, and K. oxytoca and P. aeruginosa were most common. Cumulative odds ratios across controls: cases (survived): cases (died) were E. coli/Shigella spp. 2.6 (95%CI 1.6-4.4); E. faecalis 4.0 (95%CI 1.1-15); S. agalactiae 4.5 (95%CI 1.6-13); Ureaplasma spp. 2.9 (95%CI 1.3-6.4); Enterovirus 9.1 (95%CI 2.3-37); and Plasmodium spp. 2.9 (95%CI 1.4-6.2). Excluding K. oxytoca and P. aeruginosa as likely contaminants, aetiology was attributed in 9.4% (95%CI 5.1-13) cases using TAC. Leading pathogen attributions by TAC were E. coli/Shigella spp. (3.5% (95%CI 1.7-5.3)) and Ureaplasma spp. (1.7% (95%CI 0.5-3.0)). Conclusions: Cord blood sample may be useful in describing EONS pathogens at birth, but more specific tests are needed for individual diagnosis. Careful sampling of cord blood using aseptic techniques is crucial to minimize contamination. In addition to culturable bacteria, Ureaplasma and Enterovirus were causes of EONS.
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Affiliation(s)
- Christina W. Obiero
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Global health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wilson Gumbi
- Bioscience department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Stella Mwakio
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Hope Mwangudzah
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna C. Seale
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - James A. Berkley
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
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20
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Sidote MN, Stoler J, Amoako N, Duodu S, Awandare G. Animal contact and paediatric acute febrile illness in Greater Accra Region, Ghana. Ghana Med J 2022; 56:221-230. [PMID: 37448994 PMCID: PMC10336642 DOI: 10.4314/gmj.v56i3.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Objective To examine the association between animal contact (primarily dogs and cats) and non-malarial fever, as well as with secondary symptoms of headache, nausea, vomiting, and cough, in 687 children in Greater Accra Region, Ghana. Design Cross-sectional study of acute febrile illness among children aged 1-15 years old between October 2016 and August 2017. Setting Ledzokuku-Krowor Municipal Assembly (LEKMA) Hospital, Teshie, Greater Accra Region. Participants The study included children with acute fever, defined as a measured temperature of greater than 37.5°C, occurring less than seven days before the hospital visit, and afebrile children as controls. Main outcome measures Measured fever, self-reported fever, and secondary symptoms, each adjusting for patient household characteristics. Results Animal contact was neither associated with measured fever (OR = 1.04, 95% CI 0.73-1.49) nor with self-reported fever (OR = 0.97, 95% CI 0.68-1.39). Animal contact was associated with headache (OR = 3.26, 95% CI 2.23-4.77, P < .01) and nausea (OR = 3.05, 95% CI 1.99-4.68, P < .01), but not with vomiting or cough. Additional models that used alternate inclusion criteria to define non-malarial fever yielded similar results. Several bacterial zoonoses that could plausibly have been transmitted by dogs and cats were diagnosed in the study population. Conclusion These findings suggest the need for future studies to evaluate animal contact as a risk factor for bacterial zoonoses that may serve as an etiological driver of acute febrile illness. Funding no external funding.
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Affiliation(s)
- Melissa N Sidote
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Justin Stoler
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Geography and Sustainable Development, University of Miami, Coral Gables, FL, USA
| | - Nicholas Amoako
- Kintampo Health Research Centre, Kintampo, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Samuel Duodu
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
| | - Gordon Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Legon, Ghana
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21
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Das P, Rahman MZ, Banu S, Rahman M, Chisti MJ, Chowdhury F, Akhtar Z, Palit A, Martin DW, Anwar MU, Namwase AS, Angra P, Kato CY, Ramos CJ, Singleton J, Stewart-Juba J, Patel N, Condit M, Chung IH, Galloway R, Friedman M, Cohen AL. Acute febrile illness among outpatients seeking health care in Bangladeshi hospitals prior to the COVID-19 pandemic. PLoS One 2022; 17:e0273902. [PMID: 36048788 PMCID: PMC9436081 DOI: 10.1371/journal.pone.0273902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/18/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding the distribution of pathogens causing acute febrile illness (AFI) is important for clinical management of patients in resource-poor settings. We evaluated the proportion of AFI caused by specific pathogens among outpatients in Bangladesh. During May 2019-March 2020, physicians screened patients aged ≥2 years in outpatient departments of four tertiary level public hospitals. We randomly enrolled patients having measured fever (≥100.4°F) during assessment with onset within the past 14 days. Blood and urine samples were tested at icddr,b through rapid diagnostic tests, bacterial culture, and polymerase chain reaction (PCR). Acute and convalescent samples were sent to the Centers for Disease Control and Prevention (USA) for Rickettsia and Orientia (R/O) and Leptospira tests. Among 690 patients, 69 (10%) had enteric fever (Salmonella enterica serotype Typhi orSalmonella enterica serotype Paratyphi), 51 (7.4%) Escherichia coli, and 28 (4.1%) dengue detected. Of the 441 patients tested for R/O, 39 (8.8%) had rickettsioses. We found 7 (2%) Leptospira cases among the 403 AFI patients tested. Nine patients (1%) were hospitalized, and none died. The highest proportion of enteric fever (15%, 36/231) and rickettsioses (14%, 25/182) was in Rajshahi. Dhaka had the most dengue cases (68%, 19/28). R/O affected older children and young adults (IQR 8-23 years) and was detected more frequently in the 21-25 years age-group (17%, 12/70). R/O was more likely to be found in patients in Rajshahi region than in Sylhet (aOR 2.49, 95% CI 0.85-7.32) between July and December (aOR 2.01, 1.01-5.23), and who had a history of recent animal entry inside their house than not (aOR 2.0, 0.93-4.3). Gram-negative Enterobacteriaceae were the most common bacterial infections, and dengue was the most common viral infection among AFI patients in Bangladeshi hospitals, though there was geographic variability. These results can help guide empiric outpatient AFI management.
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Affiliation(s)
- Pritimoy Das
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - M. Ziaur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sayera Banu
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mahmudur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammod Jobayer Chisti
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Fahmida Chowdhury
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zubair Akhtar
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Anik Palit
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Daniel W. Martin
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Mahabub Ul Anwar
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Angella Sandra Namwase
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Pawan Angra
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Cecilia Y. Kato
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Carmen J. Ramos
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Joseph Singleton
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Jeri Stewart-Juba
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Nikita Patel
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Marah Condit
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Ida H. Chung
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Renee Galloway
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Michael Friedman
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
| | - Adam L. Cohen
- Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, United States of America
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22
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Manabe YC, Betz J, Jackson O, Asoala V, Bazan I, Blair PW, Chang A, Chusri S, Crump JA, Edgel KA, Faix DJ, Fernandez S, Fox AT, Garcia JA, Grogl M, Hansen EA, Heang V, House SL, Jongsakul K, Kaburise MB, Klungthong C, Lamorde M, Letizia AG, Lorenzana I, Luy M, Maro VP, Mores CN, Myers CA, Oduro AR, Parham L, Porzucek AJ, Prouty M, Rabiger DS, Rubach MP, Siles C, Silva M, Ukachu C, Waitumbi JN, Phillips CL, Jones BW. Clinical evaluation of the BioFire Global Fever Panel for the identification of malaria, leptospirosis, chikungunya, and dengue from whole blood: a prospective, multicentre, cross-sectional diagnostic accuracy study. THE LANCET. INFECTIOUS DISEASES 2022; 22:1356-1364. [PMID: 35716700 PMCID: PMC9420791 DOI: 10.1016/s1473-3099(22)00290-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/27/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Acute febrile illness is a common presentation for patients at hospitals globally. Assays that can diagnose a variety of common pathogens in blood could help to establish a diagnosis for targeted disease management. We aimed to evaluate the performance of the BioFire Global Fever Panel (GF Panel), a multiplex nucleic acid amplification test performed on whole blood specimens run on the BioFire FilmArray System, in the diagnosis of several pathogens that cause acute febrile illness. METHODS We did a prospective, multicentre, cross-sectional diagnostic accuracy study to evaluate the GF Panel. Consenting adults and children older than 6 months presenting with fever in the previous 2 days were enrolled consecutively in sub-Saharan Africa (Ghana, Kenya, Tanzania, Uganda), southeast Asia (Cambodia, Thailand), central and South America (Honduras, Peru), and the USA (Washington, DC; St Louis, MO). We assessed the performance of six analytes (chikungunya virus, dengue virus [serotypes 1-4], Leptospira spp, Plasmodium spp, Plasmodium falciparum, and Plasmodium vivax or Plasmodium ovale) on the GF Panel. The performance of the GF Panel was assessed using comparator PCR assays with different primers followed by bidirectional sequencing on nucleic acid extracts from the same specimen. We calculated the positive percent agreement and negative percent agreement of the GF Panel with respect to the comparator assays. This study is registered with ClinicalTrials.gov, NCT02968355. FINDINGS From March 26, 2018, to Sept 30, 2019, 1965 participants were enrolled at ten sites worldwide. Of the 1875 participants with analysable results, 980 (52·3%) were female and the median age was 22 years (range 0-100). At least one analyte was detected in 657 (35·0%) of 1875 specimens. The GF Panel had a positive percent agreement for the six analytes evaluated as follows: chikungunya virus 100% (95% CI 86·3-100), dengue virus 94·0% (90·6-96·5), Leptospira spp 93·8% (69·8-99·8), Plasmodium spp 98·3% (96·3-99·4), P falciparum 92·7% (88·8-95·6), and P vivax or P ovale 92·7% (86·7-96·6). The GF Panel had a negative percent agreement equal to or greater than 99·2% (98·6-99·6) for all analytes. INTERPRETATION This 1 h sample-to-answer, molecular device can detect common causative agents of acute febrile illness with excellent positive percent agreement and negative percent agreement directly in whole blood. The targets of the assay are prevalent in tropical and subtropical regions globally, and the assay could help to provide both public health surveillance and individual diagnoses. FUNDING BioFire Defense, Joint Project Manager for Medical Countermeasure Systems and US Army Medical Materiel Development Activity, and National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
- Yukari C Manabe
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda.
| | - Joshua Betz
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Victor Asoala
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Isabel Bazan
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Paul W Blair
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Aileen Chang
- Department of Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Sarunyou Chusri
- Faculty of Medicine, Prince of Songkhla University, Songkhla, Thailand
| | - John A Crump
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC, USA; Centre for International Health, University of Otago, Dunedin, New Zealand
| | | | - Dennis J Faix
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Anne T Fox
- US Naval Medical Research Unit Three, Ghana Detachment, Accra, Ghana
| | - Jose A Garcia
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Max Grogl
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Erin A Hansen
- Operational Infectious Diseases, Naval Health Research Center, San Diego, CA, USA
| | - Vireak Heang
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Stacey L House
- Washington University School of Medicine, Department of Emergency Medicine, St Louis, MO, USA
| | - Krisada Jongsakul
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mohammed Lamorde
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Andrew G Letizia
- US Naval Medical Research Unit Three, Ghana Detachment, Accra, Ghana
| | - Ivette Lorenzana
- Universidad Nacional Autónoma de Honduras, Centro de Investigaciones Geneticas, Instituto de Investigacion en Microdbiologia, Tegucigalpa, Honduras
| | - Malen Luy
- US Naval Medical Research Unit Two, Phnom Penh, Cambodia
| | - Vanance P Maro
- Department of Medicine, Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Christopher N Mores
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru; Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Christopher A Myers
- Operational Infectious Diseases, Naval Health Research Center, San Diego, CA, USA
| | - Abraham R Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Leda Parham
- Universidad Nacional Autónoma de Honduras, Centro de Investigaciones Geneticas, Instituto de Investigacion en Microdbiologia, Tegucigalpa, Honduras
| | - Abigail J Porzucek
- Department of Global Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Michael Prouty
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | | | - Matthew P Rubach
- Division of Infectious Diseases & International Health, Department of Medicine, Duke University, Durham, NC, USA
| | - Crystyan Siles
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Maria Silva
- Virology and Emerging Infections Department, US Naval Medical Research Unit Six, Lima, Peru
| | - Chinaka Ukachu
- Operational Infectious Diseases, Naval Health Research Center, San Diego, CA, USA
| | - John N Waitumbi
- US Army Medical Research Directorate-Africa, Kenya Medical Research Institute, Nairobi, Kenya
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23
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Etiology of acute febrile illnesses in Southern China: Findings from a two-year sentinel surveillance project, 2017–2019. PLoS One 2022; 17:e0270586. [PMID: 35763515 PMCID: PMC9239456 DOI: 10.1371/journal.pone.0270586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/13/2022] [Indexed: 11/19/2022] Open
Abstract
Background Southern China is at risk for arborvirus disease transmission, including Zika virus and dengue. Patients often present to clinical care with non-specific acute febrile illnesses (AFI). To better describe the etiology of AFI, we implemented a two-year AFI surveillance project at five sentinel hospitals in Yunnan and Guangdong Provinces. Methods Between June 2017 and August 2019, we enrolled patients between 2 and 65 years of age presenting at one sentinel hospital in Mengla County, Yunnan, and four in Jiangmen City, Guangdong, with symptoms of AFI (acute onset of fever ≥ 37.5°C within the past 7 days) without respiratory symptoms or diarrhea. Demographic, epidemiologic, and clinical information was obtained and entered into a web-based AFI surveillance database. A custom TaqMan Array card (TAC) was used to test patients’ whole blood specimens for 27 different pathogens using real-time polymerase chain reaction assays. Results During the two-year project period, 836 patients were enrolled; 443 patients from Mengla County and 393 patients from Jiangmen City. The median age was 33 years [range: 2–65], and most were hospitalized [641, 77%]. Of 796 patients with valid TAC results, 341 (43%) were positive for at least one of the 10 unique pathogens detected. This included 205 (26%) patients positive for dengue virus, 60 (8%) for Orientia tsutsugamushi, and 42 (5%) for Coxiella burnetii. Ten patients (1%) in Jiangmen City tested positive for malaria, 8 of whom reported recent travel outside of China. TAC results were negative for 455 (57%) patients. None of the patients had a positive TAC detection for Zika virus. Conclusions The project detected variability in the etiology of AFI in Southern China and highlighted the importance of differential diagnosis. Dengue, O. tsutsugamushi, and C. burnetii were the most frequently identified pathogens among enrolled AFI patients. As a non-notifiable disease, the frequent detection of C. burnetii is noteworthy and warrants additional investigation. The project provided a framework for routine surveillance for persons presenting with AFI.
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24
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Zhang Y, Wang Z, Wang W, Yu H, Jin M. Applications of polymerase chain reaction‑based methods for the diagnosis of plague (Review). Exp Ther Med 2022; 24:511. [DOI: 10.3892/etm.2022.11438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/22/2022] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yanan Zhang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Wenrui Wang
- General Center for Disease Control and Prevention of Inner Mongolia Autonomous Region, Huhehot, Inner Mongolia 010031, P.R. China
| | - Hui Yu
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
| | - Min Jin
- Inner Mongolia Key Laboratory of Disease‑Related Biomarkers, Baotou Medical College, Baotou, Inner Mongolia 014060, P.R. China
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25
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Obiero CW, Gumbi W, Mwakio S, Mwangudzah H, Seale AC, Taniuchi M, Liu J, Houpt E, Berkley JA. Detection of pathogens associated with early-onset neonatal sepsis in cord blood at birth using quantitative PCR. Wellcome Open Res 2022; 7:3. [PMID: 35600002 PMCID: PMC9114825 DOI: 10.12688/wellcomeopenres.17386.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Early onset neonatal sepsis (EONS) typically begins prior to, during or soon after birth and may be rapidly fatal. There is paucity of data on the aetiology of EONS in sub-Saharan Africa due to limited diagnostic capacity in this region, despite the associated significant mortality and long-term neurological impairment. Methods: We compared pathogens detected in cord blood samples between neonates admitted to hospital with possible serious bacterial infection (pSBI) in the first 48 hours of life (cases) and neonates remaining well (controls). Cord blood was systematically collected at Kilifi County Hospital (KCH) from 2011-2016, and later tested for 21 bacterial, viral and protozoal targets using multiplex PCR via TaqMan Array Cards (TAC). Results: Among 603 cases (101 [17%] of whom died), 179 (30%) tested positive for ≥1 target and 37 (6.1%) tested positive for multiple targets. Klebsiella oxytoca, Escherichia coli/Shigella spp., Pseudomonas aeruginosa, and Streptococcus pyogenes were commonest. Among 300 controls, 79 (26%) tested positive for ≥1 target, 11 (3.7%) were positive for multiple targets, and K. oxytoca and P. aeruginosa were most common. Cumulative odds ratios across controls: cases (survived): cases (died) were E. coli/Shigella spp. 2.6 (95%CI 1.6-4.4); E. faecalis 4.0 (95%CI 1.1-15); S. agalactiae 4.5 (95%CI 1.6-13); Ureaplasma spp. 2.9 (95%CI 1.3-6.4); Enterovirus 9.1 (95%CI 2.3-37); and Plasmodium spp. 2.9 (95%CI 1.4-6.2). Excluding K. oxytoca and P. aeruginosa as likely contaminants, aetiology was attributed in 9.4% (95%CI 5.1-13) cases using TAC. Leading pathogen attributions by TAC were E. coli/Shigella spp. (3.5% (95%CI 1.7-5.3)) and Ureaplasma spp. (1.7% (95%CI 0.5-3.0)). Conclusions: Cord blood sample may be useful in describing EONS pathogens at birth, but more specific tests are needed for individual diagnosis. Careful sampling of cord blood using aseptic techniques is crucial to minimize contamination. In addition to culturable bacteria, Ureaplasma and Enterovirus were causes of EONS.
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Affiliation(s)
- Christina W. Obiero
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Global health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wilson Gumbi
- Bioscience department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Stella Mwakio
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Hope Mwangudzah
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna C. Seale
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - James A. Berkley
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
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26
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Lappan R, Jirapanjawat T, Williamson DA, Lange S, Chown SL, Greening C. Simultaneous detection of multiple pathogens with the TaqMan Array Card. MethodsX 2022; 9:101707. [PMID: 35518918 PMCID: PMC9062751 DOI: 10.1016/j.mex.2022.101707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is a gold standard method for the detection and quantification of pathogenic organisms. Standard qPCR is inexpensive, sensitive and highly specific to the pathogen of interest. While qPCR assays can be multiplexed to allow the detection of multiple organisms in one reaction, it is prohibitively labour intensive to screen large numbers of samples for several pathogens at the same time. The TaqMan Array Card (TAC) is a cost-effective and accurate technique that expands the number of assays that can be simultaneously performed on a sample, with no increase in set-up time and only small reductions in sensitivity. This approach is highly beneficial in settings where there is a need to monitor a large panel of pathogens. We illustrate the application of TAC to the monitoring of gastrointestinal pathogens, which span viral, bacterial, protist and helminth taxa. This protocol outlines the laboratory set-up of a TaqMan Array Card, and some recommended data processing steps to aid in accurate interpretation of the results. A video protocol is additionally provided to assist in the use of the technique.•The TAC is designed primarily for gene expression assays, but has recently been utilised in several studies for pathogen detection in human clinical samples.•We expand the use of TAC for pathogen detection across human, animal and environmental sample types, and have developed a protocol and guidelines for the processing and interpretation of results that circumvents issues with the automated outputs.•This technique is applicable to pathogen or organism detection in any context, if quality nucleic acid extracts can be obtained from the sample type of interest.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sigrid Lange
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven L. Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Mduma E, Halidou T, Kaboré B, Walongo T, Lompo P, Museveni J, Gidabayda J, Gratz J, Guga G, Kimathi C, Liu J, Mdoe P, Moshiro R, Petzold M, Singlovic J, Guillerm M, Gomes MF, Houpt ER, Halleux CM. Etiology of severe invasive infections in young infants in rural settings in sub-Saharan Africa. PLoS One 2022; 17:e0264322. [PMID: 35213629 PMCID: PMC8880396 DOI: 10.1371/journal.pone.0264322] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/08/2022] [Indexed: 11/23/2022] Open
Abstract
Background Serious invasive infections in newborns are a major cause of death. Lack of data on etiological causes hampers progress towards reduction of mortality. This study aimed to identify pathogens responsible for such infections in young infants in sub-Saharan Africa and to describe their antibiotics resistance profile. Methods Between September 2016 and April 2018 we implemented an observational study in two rural sites in Burkina Faso and Tanzania enrolling young infants aged 0–59 days old with serious invasive infection. Blood samples underwent blood culture and molecular biology. Results In total 634 infants with clinical diagnosis of serious invasive infection were enrolled and 4.2% of the infants had a positive blood culture. The most frequent pathogens identified by blood culture were Klebsiella pneumonia and Staphylococcus aureus, followed by Escherichia coli. Gram-negative isolates were only partially susceptible to first line WHO recommended treatment for neonatal sepsis at community level. A total of 18.6% of the infants were PCR positive for at least one pathogen and Escherichia coli and Staphylococcus aureus were the most common bacteria detected. Among infants enrolled, 60/634 (9.5%) died. Positive blood culture but not positive PCR was associated with risk of death. For most deaths, no pathogen was identified either by blood culture or molecular testing, and hence a causal agent remained unclear. Mortality was associated with low body temperature, tachycardia, respiratory symptoms, convulsions, history of difficult feeding, movement only when stimulated or reduced level of consciousness, diarrhea and/or vomiting. Conclusion While Klebsiella pneumonia and Staphylococcus aureus, as well as Escherichia coli were pathogens most frequently identified in infants with clinical suspicion of serious invasive infections, most cases remain without definite diagnosis, making more accurate diagnostic tools urgently needed. Antibiotics resistance to first line antibiotics is an increasing challenge even in rural Africa.
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Affiliation(s)
- Estomih Mduma
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Tinto Halidou
- Institut de Recherche en Sciences de la Santé (IRSS), Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Berenger Kaboré
- Institut de Recherche en Sciences de la Santé (IRSS), Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Thomas Walongo
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Palpouguini Lompo
- Institut de Recherche en Sciences de la Santé (IRSS), Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Justine Museveni
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Joshua Gidabayda
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Godfrey Guga
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Caroline Kimathi
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Paschal Mdoe
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Robert Moshiro
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Max Petzold
- School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan Singlovic
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Martine Guillerm
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Melba F. Gomes
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Christine M. Halleux
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
- * E-mail:
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Obiero CW, Gumbi W, Mwakio S, Mwangudzah H, Seale AC, Taniuchi M, Liu J, Houpt E, Berkley JA. Detection of pathogens associated with early-onset neonatal sepsis in cord blood at birth using quantitative PCR. Wellcome Open Res 2022; 7:3. [PMID: 35600002 PMCID: PMC9114825 DOI: 10.12688/wellcomeopenres.17386.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Early onset neonatal sepsis (EONS) typically begins prior to, during or soon after birth and may be rapidly fatal. There is paucity of data on the aetiology of EONS in sub-Saharan Africa due to limited diagnostic capacity in this region, despite the associated significant mortality and long-term neurological impairment. Methods: We compared pathogens detected in cord blood samples between neonates admitted to hospital with possible serious bacterial infection (pSBI) in the first 48 hours of life (cases) and neonates remaining well (controls). Cord blood was systematically collected at Kilifi County Hospital (KCH) from 2011-2016, and later tested for 21 bacterial, viral and protozoal targets using multiplex PCR via TaqMan Array Cards (TAC). Results: Among 603 cases (101 [17%] of whom died), 179 (30%) tested positive for ≥1 target and 37 (6.1%) tested positive for multiple targets. Klebsiella oxytoca, Escherichia coli/Shigella spp., Pseudomonas aeruginosa, and Streptococcus pyogenes were commonest. Among 300 controls, 79 (26%) tested positive for ≥1 target, 11 (3.7%) were positive for multiple targets, and K. oxytoca and P. aeruginosa were most common. Cumulative odds ratios across controls: cases (survived): cases (died) were E. coli/Shigella spp. 2.6 (95%CI 1.6-4.4); E. faecalis 4.0 (95%CI 1.1-15); S. agalactiae 4.5 (95%CI 1.6-13); Ureaplasma spp. 2.9 (95%CI 1.3-6.4); Enterovirus 9.1 (95%CI 2.3-37); and Plasmodium spp. 2.9 (95%CI 1.4-6.2). Excluding K. oxytoca and P. aeruginosa as likely contaminants, aetiology was attributed in 9.4% (95%CI 5.1-13) cases using TAC. Leading pathogen attributions by TAC were E. coli/Shigella spp. (3.5% (95%CI 1.7-5.3)) and Ureaplasma spp. (1.7% (95%CI 0.5-3.0)). Conclusions: Cord blood sample may be useful in describing EONS pathogens at birth, but more specific tests are needed for individual diagnosis. Careful sampling of cord blood using aseptic techniques is crucial to minimize contamination. In addition to culturable bacteria, Ureaplasma and Enterovirus were causes of EONS.
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Affiliation(s)
- Christina W. Obiero
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Global health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wilson Gumbi
- Bioscience department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Stella Mwakio
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Hope Mwangudzah
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna C. Seale
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - James A. Berkley
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
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Colston JM, Zaitchik BF, Badr HS, Burnett E, Ali SA, Rayamajhi A, Satter SM, Eibach D, Krumkamp R, May J, Chilengi R, Howard LM, Sow SO, Jahangir Hossain M, Saha D, Imran Nisar M, Zaidi AKM, Kanungo S, Mandomando I, Faruque ASG, Kotloff KL, Levine MM, Breiman RF, Omore R, Page N, Platts‐Mills JA, Ashorn U, Fan Y, Shrestha PS, Ahmed T, Mduma E, Yori PP, Bhutta Z, Bessong P, Olortegui MP, Lima AAM, Kang G, Humphrey J, Prendergast AJ, Ntozini R, Okada K, Wongboot W, Gaensbauer J, Melgar MT, Pelkonen T, Freitas CM, Kosek MN. Associations Between Eight Earth Observation-Derived Climate Variables and Enteropathogen Infection: An Independent Participant Data Meta-Analysis of Surveillance Studies With Broad Spectrum Nucleic Acid Diagnostics. GEOHEALTH 2022; 6:e2021GH000452. [PMID: 35024531 PMCID: PMC8729196 DOI: 10.1029/2021gh000452] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/12/2021] [Accepted: 11/18/2021] [Indexed: 05/10/2023]
Abstract
Diarrheal disease, still a major cause of childhood illness, is caused by numerous, diverse infectious microorganisms, which are differentially sensitive to environmental conditions. Enteropathogen-specific impacts of climate remain underexplored. Results from 15 studies that diagnosed enteropathogens in 64,788 stool samples from 20,760 children in 19 countries were combined. Infection status for 10 common enteropathogens-adenovirus, astrovirus, norovirus, rotavirus, sapovirus, Campylobacter, ETEC, Shigella, Cryptosporidium and Giardia-was matched by date with hydrometeorological variables from a global Earth observation dataset-precipitation and runoff volume, humidity, soil moisture, solar radiation, air pressure, temperature, and wind speed. Models were fitted for each pathogen, accounting for lags, nonlinearity, confounders, and threshold effects. Different variables showed complex, non-linear associations with infection risk varying in magnitude and direction depending on pathogen species. Rotavirus infection decreased markedly following increasing 7-day average temperatures-a relative risk of 0.76 (95% confidence interval: 0.69-0.85) above 28°C-while ETEC risk increased by almost half, 1.43 (1.36-1.50), in the 20-35°C range. Risk for all pathogens was highest following soil moistures in the upper range. Humidity was associated with increases in bacterial infections and decreases in most viral infections. Several virus species' risk increased following lower-than-average rainfall, while rotavirus and ETEC increased with heavier runoff. Temperature, soil moisture, and humidity are particularly influential parameters across all enteropathogens, likely impacting pathogen survival outside the host. Precipitation and runoff have divergent associations with different enteric viruses. These effects may engender shifts in the relative burden of diarrhea-causing agents as the global climate changes.
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Giri S, Mohan VR, Srinivasan M, Kumar N, Kumar V, Dhanapal P, Venkatesan J, Gunasekaran A, Abraham D, John J, Kang G. Case-Control Study of Household and Environmental Transmission of Typhoid Fever in India. J Infect Dis 2021; 224:S584-S592. [PMID: 35238355 PMCID: PMC8892545 DOI: 10.1093/infdis/jiab378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background Typhoid fever causes substantial morbidity and mortality in low- and middle-income countries. We conducted a case-control study in Vellore, southern India, to understand risk factors for transmission of typhoid. Methods From April 2018 to October 2019, households of blood culture-confirmed typhoid cases that occurred within a fever surveillance cohort aged 6 months–15 years, and controls matched for age, sex, geographic location, and socioeconomic status, were recruited. Information on risk factors was obtained using standard questionnaires. Household and environmental samples were collected for detection of Salmonella Typhi using real-time polymerase chain reaction. Multivariable analysis was used to evaluate associations between risk factors and typhoid. Results One hundred pairs of cases and controls were recruited. On multivariable regression analysis, mothers eating food from street vendors during the previous week (odds ratio [OR] = 2.04; 95% confidence interval [CI], 1.03–4.12; P = .04) was independently associated with typhoid, whereas treatment of household drinking water (OR = 0.45; 95% CI, 0.25–0.80; P = .007) was protective. There was no significant difference in S Typhi detection between the environmental samples from case and control households. Conclusions Street-vended food is a risk factor for typhoid in densely populated urban communities of Vellore. Improved sanitation facilities and awareness about point-of-use water treatment are likely to contribute to typhoid control.
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Affiliation(s)
- Sidhartha Giri
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | | | - Nirmal Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Vinoth Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Pavithra Dhanapal
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Annai Gunasekaran
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Dilip Abraham
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jacob John
- Department of Community Health, Christian Medical College, Vellore, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
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Calvo-Anguiano G, Lugo-Trampe JDJ, Ponce-García G, Lugo-Trampe A, Martinez-Garza LE, Ibarra-Ramirez M, Campos-Acevedo LD, Caballero-Sosa S, Juache-Villagrana AE, Fernández-Salas I, Flores-Suarez AE, Rodriguez-Sanchez IP, Trujillo-Murillo KDC. Molecular Characterization of Associated Pathogens in Febrile Patients during Inter-Epidemic Periods of Urban Arboviral Diseases in Tapachula Southern Mexico. Pathogens 2021; 10:1450. [PMID: 34832606 PMCID: PMC8618676 DOI: 10.3390/pathogens10111450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
Emerging and re-emerging vector-borne infections are a global public health threat. In endemic regions, fever is the main reason for medical attention, and the etiological agent of such fever is not usually identified. In this study, non-specific febrile pathogens were molecularly characterized in serum samples from 253 patients suspected of arbovirus infection. The samples were collected in the southern border region of Mexico from April to June 2015, and February to March 2016. ZIKV, CHIKV, DENV, leptospirosis, and rickettsiosis were detected by qPCR and nested PCR to identify flavivirus and alphavirus genera. The results indicated that 71.93% of the samples were positive for CHIKV, 0.79% for ZIKV, and 0.39% for DENV, with the number positive for CHIKV increasing to 76.67% and those positive for ZIKV increasing to 15.41% under the nested PCR technique. Leptospira Kmetyi was identified for the first time in Mexico, with a prevalence of 3.16%. This is the first report of ZIKV in Mexico, as well the first detection of the virus in early 2015. In conclusion, the etiological agent of fever was determined in 94% of the analyzed samples.
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Affiliation(s)
- Geovana Calvo-Anguiano
- Departamento Genética, Facultad de Medicina, Universidad Autónoma de Nuevo Leon, Av. Francisco I. Madero S/N, Mitras Centro, Monterrey 64460, Nuevo Leon, Mexico; (G.C.-A.); (J.d.J.L.-T.); (L.E.M.-G.); (M.I.-R.); (L.D.C.-A.)
| | - José de Jesús Lugo-Trampe
- Departamento Genética, Facultad de Medicina, Universidad Autónoma de Nuevo Leon, Av. Francisco I. Madero S/N, Mitras Centro, Monterrey 64460, Nuevo Leon, Mexico; (G.C.-A.); (J.d.J.L.-T.); (L.E.M.-G.); (M.I.-R.); (L.D.C.-A.)
| | - Gustavo Ponce-García
- Facultad de Ciencias Biologicas, Universidad Autonoma de Nuevo Leon, Av. Pedro de Alba S/N, Ciudad Universitaria, San Nicolas de los Garza 66455, Nuevo Leon, Mexico; (G.P.-G.); (A.E.J.-V.); (I.F.-S.); (A.E.F.-S.); (I.P.R.-S.)
| | - Angel Lugo-Trampe
- Facultad de Medicina Humana “Dr. Manuel Velasco Suárez”, Campus IV, Universidad Autónoma de Chiapas, Tapachula 30792, Chiapas, Mexico;
| | - Laura Elia Martinez-Garza
- Departamento Genética, Facultad de Medicina, Universidad Autónoma de Nuevo Leon, Av. Francisco I. Madero S/N, Mitras Centro, Monterrey 64460, Nuevo Leon, Mexico; (G.C.-A.); (J.d.J.L.-T.); (L.E.M.-G.); (M.I.-R.); (L.D.C.-A.)
| | - Marisol Ibarra-Ramirez
- Departamento Genética, Facultad de Medicina, Universidad Autónoma de Nuevo Leon, Av. Francisco I. Madero S/N, Mitras Centro, Monterrey 64460, Nuevo Leon, Mexico; (G.C.-A.); (J.d.J.L.-T.); (L.E.M.-G.); (M.I.-R.); (L.D.C.-A.)
| | - Luis Daniel Campos-Acevedo
- Departamento Genética, Facultad de Medicina, Universidad Autónoma de Nuevo Leon, Av. Francisco I. Madero S/N, Mitras Centro, Monterrey 64460, Nuevo Leon, Mexico; (G.C.-A.); (J.d.J.L.-T.); (L.E.M.-G.); (M.I.-R.); (L.D.C.-A.)
| | - Sandra Caballero-Sosa
- Clínica Hospital Dr. Roberto Nettel Flores, Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Av. Tuxtepec y Oaxaca S/N, Francisco Villa, Tapachula 30740, Chiapas, Mexico;
| | - Alan Esteban Juache-Villagrana
- Facultad de Ciencias Biologicas, Universidad Autonoma de Nuevo Leon, Av. Pedro de Alba S/N, Ciudad Universitaria, San Nicolas de los Garza 66455, Nuevo Leon, Mexico; (G.P.-G.); (A.E.J.-V.); (I.F.-S.); (A.E.F.-S.); (I.P.R.-S.)
| | - Ildefonso Fernández-Salas
- Facultad de Ciencias Biologicas, Universidad Autonoma de Nuevo Leon, Av. Pedro de Alba S/N, Ciudad Universitaria, San Nicolas de los Garza 66455, Nuevo Leon, Mexico; (G.P.-G.); (A.E.J.-V.); (I.F.-S.); (A.E.F.-S.); (I.P.R.-S.)
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autónoma de Nuevo León, Av. Mutualismo, Monterrey 64460, Nuevo León, Mexico
| | - Adriana Elizabeth Flores-Suarez
- Facultad de Ciencias Biologicas, Universidad Autonoma de Nuevo Leon, Av. Pedro de Alba S/N, Ciudad Universitaria, San Nicolas de los Garza 66455, Nuevo Leon, Mexico; (G.P.-G.); (A.E.J.-V.); (I.F.-S.); (A.E.F.-S.); (I.P.R.-S.)
| | - Iram Pablo Rodriguez-Sanchez
- Facultad de Ciencias Biologicas, Universidad Autonoma de Nuevo Leon, Av. Pedro de Alba S/N, Ciudad Universitaria, San Nicolas de los Garza 66455, Nuevo Leon, Mexico; (G.P.-G.); (A.E.J.-V.); (I.F.-S.); (A.E.F.-S.); (I.P.R.-S.)
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Sahay RR, Shete AM, Yadav PD, Patil S, Majumdar T, Jain R, Nyayanit DA, Kaushal H, Panjwani SJ, Upadhyay KJ, Varevadiya CL, Vora A, Kanani A, Gangakhedkar RR. Sequential determination of viral load, humoral responses and phylogenetic analysis in fatal and non-fatal cases of Crimean-Congo hemorrhagic fever patients from Gujarat, India, 2019. PLoS Negl Trop Dis 2021; 15:e0009718. [PMID: 34460819 PMCID: PMC8432894 DOI: 10.1371/journal.pntd.0009718] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 09/10/2021] [Accepted: 08/08/2021] [Indexed: 11/18/2022] Open
Abstract
Background Thirty-four CCHF cases (17 fatal; 17 survived) were confirmed from Gujarat state, India during the year 2019. We aimed to find out the viral load, antibody kinetics, cytokine profile and phylogenetic analysis between fatal and non- fatal cases. Methods Thirty four cases were included in this study. Blood and urine samples were collected from all the cases on the day of admission to hospital. Non-fatal cases were followed weekly for understanding the profile of viral kinetics, anti-CCHFV IgM and IgG antibodies. We also quantified the cytokines in both fatal and non-fatal cases. For epidemiological correlation, livestock were screened for anti-CCHF IgG antibodies and the tick pool specimens were tested by real time RT-PCR. Virus isolation was attempted on tick pools and human specimens and phylogenetic analysis performed on human and ticks complete genome sequences. Results CCHF cases were detected throughout year in 2019 with the peak in August. Out of 34 cases, eight secondary CCHF cases were reported. Cases were predominantly detected in males and in 19–45 years age group (55.88%). The persistence of viremia was observed till 76th POD (post onset date) in one case whereas anti-CCHFV IgM and IgG was detected amongst these cases from the 2nd and 20th POD respectively. Positivity observed amongst livestock and tick pools were was 21.57% and 7.4% respectively. The cytokine analysis revealed a significant increase in the level of serum IL-6, IL-10 and IFN-γ during the acute phase of the infection, but interestingly IL-10 lowered to normal upon clearance of the virus in the clinically recovered case. Fatal cases had high viral RNA copy numbers. Bleeding from one or two mucosal sites was significantly associated with fatality (OR-16.47;p-0.0034 at 95% CI). We could do CCHF virus isolation from two cases. Phylogenetic analysis revealed circulation of re-assortment of Asian-West African genotypes in humans and ticks. Conclusions The persistence of CCHF viral RNA was detected till 76th POD in one of the survivors. The circulation of a re-assortment Asian-West African genotype in a CCHF case is also reported first time from India. Crimean Congo hemorrhagic fever is a zoonotic tick-borne viral hemorrhagic disease. This disease is reported from Europe, Mediterranean, north-western China, central Asia, Africa, and the Middle East. Several outbreaks of CCHF were reported from Gujarat and Rajasthan states, India from 2011 to 2019. In this study, we discuss the clinical, molecular, serological, and the cytokine data of 34 CCHF cases (17 fatal and 17 survived) which were detected from Gujarat state in the year 2019. A sequential weekly follow up of the CCHF survivors was performed to understand the viral kinetics and the antibody profile. Interestingly, the presence of persistence CCHF viral RNA was observed till 76th POD in one of the survivors. To our knowledge, we are reporting this long term persistence of viremia for the first time. We also observed that the anti-CCHFV IgM detection in the serum samples starts as soon as 2nd POD but anti-CCHFV IgG antibody could be detected in the majority of the cases only after the 28th POD. The cytokine analysis revealed a significant increase in the level of serum IL-6, IL-10 and IFN-γ during the acute phase of the infection, but interestingly IL-10 lowered to normal upon clearance of the virus in the clinically recovered case. We did the phylogenetic analysis and concluded the circulation of the Asian-West African re-assortment genotype in humans, which has not been reported from India prior to this study.
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MESH Headings
- Adolescent
- Adult
- Aged
- Animals
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Cytokines/blood
- Female
- Genotype
- Hemorrhagic Fever Virus, Crimean-Congo/classification
- Hemorrhagic Fever Virus, Crimean-Congo/genetics
- Hemorrhagic Fever Virus, Crimean-Congo/isolation & purification
- Hemorrhagic Fever Virus, Crimean-Congo/physiology
- Hemorrhagic Fever, Crimean/blood
- Hemorrhagic Fever, Crimean/epidemiology
- Hemorrhagic Fever, Crimean/immunology
- Hemorrhagic Fever, Crimean/virology
- Humans
- Immunity, Humoral
- India/epidemiology
- Livestock/blood
- Livestock/virology
- Male
- Middle Aged
- Phylogeny
- RNA, Viral/genetics
- Ticks/virology
- Viral Load
- Young Adult
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Affiliation(s)
- Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
| | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
| | - Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
- * E-mail:
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
| | - Rajlaxmi Jain
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
| | - Dimpal A. Nyayanit
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
| | - Himanshu Kaushal
- Indian Council of Medical Research-National Institute of Virology, Maximum Containment Facility, Pune, Maharashtra, India
| | - Sunil J. Panjwani
- Government Medical College and Sir-T Hospital Bhavnagar, Gujarat, India
| | | | | | - Alpesh Vora
- Government Medical College and Sir-T Hospital Bhavnagar, Gujarat, India
| | - Amit Kanani
- Animal Husbandry Department, Foot and Mouth Disease Scheme, Ahmedabad, Gujarat, India
| | - Raman R. Gangakhedkar
- Epidemiology and Communicable Diseases (ECD) Division, Indian Council of Medical Research, New Delhi, India
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Development of double antibody sandwich ELISA as potential diagnostic tool for rapid detection of Crimean-Congo hemorrhagic fever virus. Sci Rep 2021; 11:14699. [PMID: 34282163 PMCID: PMC8289837 DOI: 10.1038/s41598-021-93319-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/01/2021] [Indexed: 11/30/2022] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF) virus, a highly pathogenic viral agent is responsible for severe fatal hemorrhagic infections in many parts of the world. The early diagnosis of CCHF infection is important for successful clinical management and epidemiological control. The nucleoprotein (NP) of CCHFV being highly conserved and immunogenic is used as early diagnostic marker. In this study, we report a rapid and sensitive double antibody based antigen capture ELISA to detect Crimean-Congo hemorrhagic fever virus (CCHFV). Highly specific polyclonal and monoclonal antibody against NP has been generated and used as capture and detector antibody respectively. The assay was able to detect viral nucleoprotein in different matrices including human serum, ticks and culture supernatant. The detection limit of the developed sandwich ELISA assay was 25 ng of purified antigen. Comparison with a real time RT-PCR revealed its detection limit to be 1000 genome equivalents of CCHFV. Further the assay was comparatively evaluated with a commercial kit employing gamma irradiated CCHFV, revealing a sensitivity and specificity of 100%. This newly developed sandwich ELISA (sELISA) with high sensitivity and specificity could be used as an efficient method for the detection of CCHF virus in humans, ticks and culture supernatant. The assay will be useful as alternate tool for diagnosis of acute infection and is amenable for screening of large scale samples in resource limited settings.
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Petrova V, Kristiansen P, Norheim G, Yimer SA. Rift valley fever: diagnostic challenges and investment needs for vaccine development. BMJ Glob Health 2021; 5:bmjgh-2020-002694. [PMID: 32816810 PMCID: PMC7437696 DOI: 10.1136/bmjgh-2020-002694] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 11/04/2022] Open
Abstract
Rift valley fever virus (RVFV) is a causative agent of a viral zoonosis that constitutes a major clinical burden in wild and domestic ruminants. The virus causes major outbreaks in livestock (sheep, goats, cattle and camels) and can be transmitted to humans by contaminated animal products or via arthropod vectors. Human-to-human transmission has not been reported to date, but spill-over events from animals have led to outbreaks in humans in Africa and the Arabian Peninsula. Currently, there is no licensed human vaccine against RVFV and the virus is listed as a priority pathogen by the World Health Organisation (WHO) due to the high epidemic potential and the lack of effective countermeasures. Multiple large RVFV outbreaks have been reported since the virus was discovered. During the last two decades, over 4000 cases and ~1000 deaths have been reported. The lack of systematic surveillance to estimate the true burden and incidence of human RVF disease is a challenge for planning future vaccine efficacy evaluation. This creates a need for robust diagnostic methodologies that can be deployed in remote regions to aid case confirmation, assessment of seroprevalence as well as pathogen surveillance required for the different stages of vaccine evaluation. Here, we perform comprehensive landscaping of the available diagnostic solutions for detection of RVFV in humans. Based on the identified gaps in the currently available in-house and commercially available methods, we highlight the specific investment needs for diagnostics that are critical for accelerating the development of effective vaccines against RVFV.
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Affiliation(s)
| | - Paul Kristiansen
- Vaccine Research and Development, Coalition for Epidemic Preparedness Innovations, Oslo, Norway
| | | | - Solomon A Yimer
- Vaccine Research and Development, Coalition for Epidemic Preparedness Innovations, Oslo, Norway
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Rao PS, Moore CC, Mbonde AA, Nuwagira E, Orikiriza P, Nyehangane D, Al-Shaer MH, Peloquin CA, Gratz J, Pholwat S, Arinaitwe R, Boum Y, Mwanga-Amumpaire J, Houpt ER, Kagan L, Heysell SK, Muzoora C. Population Pharmacokinetics and Significant Under-Dosing of Anti-Tuberculosis Medications in People with HIV and Critical Illness. Antibiotics (Basel) 2021; 10:antibiotics10060739. [PMID: 34207312 PMCID: PMC8235594 DOI: 10.3390/antibiotics10060739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/18/2022] Open
Abstract
Critical illness from tuberculosis (TB) bloodstream infection results in a high case fatality rate for people living with human immunodeficiency virus (HIV). Critical illness can lead to altered pharmacokinetics and suboptimal drug exposures. We enrolled adults living with HIV and hospitalized with sepsis, with and without meningitis, in Mbarara, Uganda that were starting first-line anti-TB therapy. Serum was collected two weeks after enrollment at 1-, 2-, 4-, and 6-h post-dose and drug concentrations quantified by validated LC-MS/MS methods. Non-compartmental analyses were used to determine total drug exposure, and population pharmacokinetic modeling and simulations were performed to determine optimal dosages. Eighty-one participants were enrolled. Forty-nine completed pharmacokinetic testing: 18 (22%) died prior to testing, 13 (16%) were lost to follow-up and one had incomplete testing. Isoniazid had the lowest serum attainment, with only 4.1% achieving a target exposure over 24 h (AUC0–24) of 52 mg·h/L despite appropriate weight-based dosing. Simulations to reach target AUC0–24 found necessary doses of rifampin of 1800 mg, pyrazinamide of 2500–3000 mg, and for isoniazid 900 mg or higher. Given the high case fatality ratio of TB-related critical illness in this population, an early higher dose anti-TB therapy should be trialed.
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Affiliation(s)
- Prakruti S. Rao
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Christopher C. Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Amir A. Mbonde
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
| | - Edwin Nuwagira
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
| | - Patrick Orikiriza
- Department of Microbiology, University of Global Health Equity, Kigali 6955, Rwanda;
| | - Dan Nyehangane
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Mohammad H. Al-Shaer
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; (M.H.A.-S.); (C.A.P.)
| | - Charles A. Peloquin
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; (M.H.A.-S.); (C.A.P.)
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Rinah Arinaitwe
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Yap Boum
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Juliet Mwanga-Amumpaire
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Leonid Kagan
- Department of Pharmaceutics and Center of Excellence for Pharmaceutical Translational Research and Education, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
- Correspondence:
| | - Conrad Muzoora
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
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Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. Mod Pathol 2021; 34:1093-1103. [PMID: 33536572 PMCID: PMC7856856 DOI: 10.1038/s41379-020-00730-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/25/2020] [Accepted: 11/25/2020] [Indexed: 02/04/2023]
Abstract
There is an urgent and unprecedented need for sensitive and high-throughput molecular diagnostic tests to combat the SARS-CoV-2 pandemic. Here we present a generalized version of the RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) assay, called "capture RASL-seq" (cRASL-seq), which enables highly sensitive (down to ~1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ~10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid purification or reverse transcription, steps that have introduced supply bottlenecks into standard assay workflows. Our simplified protocol additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new technology with the potential to help mitigate the current pandemic and prevent similar public health crises.
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Dhawan S, Althaus T, Lubell Y, Suwancharoen D, Blacksell SD. Evaluation of the Panbio Leptospira IgM ELISA among Outpatients Attending Primary Care in Southeast Asia. Am J Trop Med Hyg 2021; 104:1777-1781. [PMID: 33724923 PMCID: PMC8103482 DOI: 10.4269/ajtmh.20-0818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 01/12/2021] [Indexed: 01/12/2023] Open
Abstract
Despite estimates suggesting Leptospira spp. being endemic in Southeast Asia, evidence remains limited. Diagnostic accuracy evaluations based on Leptospira ELISA mainly rely on hospitalized and severe patients; therefore, studies measuring the pathogen burden may be inaccurate in the community. We evaluated the Panbio Leptospira ELISA IgM among 656 febrile outpatients attending primary care in Chiangrai, Thailand, and Hlaing Tha Yar, Yangon, Myanmar. ELISA demonstrated limited diagnostic accuracy for the detection of acute leptospiral infection using the manufacturer recommended cutoff, with a sensitivity of 71.4% and specificity of 36.4%, and an area under the receiver operator characteristic curve value of 0.65 (95% CI: 0.41-0.89), compared with our reference test, the PCR assay. ELISA also performed poorly as a screening tool for detecting recent exposure to Leptospira spp. compared with the "gold-standard" microscopic agglutination test, with a specificity of 42.7%. We conclude that the utility of the Leptospira IgM ELISA for both serodiagnosis and seroprevalence is limited in our setting.
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Affiliation(s)
- Sandhya Dhawan
- Mahidol-Oxford Tropical Research Medicine Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Thomas Althaus
- Mahidol-Oxford Tropical Research Medicine Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand;,Nuffield Department of Medicine, Nuffield Department of Medicine Research Building, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Yoel Lubell
- Mahidol-Oxford Tropical Research Medicine Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand;,Nuffield Department of Medicine, Nuffield Department of Medicine Research Building, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Duangjai Suwancharoen
- Department of Livestock Development, National Institute of Animal Health, Ministry of Agriculture and Cooperatives, Bangkok, Thailand
| | - Stuart D. Blacksell
- Mahidol-Oxford Tropical Research Medicine Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand;,Nuffield Department of Medicine, Nuffield Department of Medicine Research Building, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom;,Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People’s Democratic Republic,Address correspondence to Stuart D. Blacksell, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand. E-mail:
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Marks F, Liu J, Soura AB, Gasmelseed N, Operario D, Grundy B, Wieser J, Gratz J, Meyer CG, Im J, Lim JK, von Kalckreuth V, Cruz Espinoza LM, Konings F, Jeon HJ, Rakotozandrindrainy R, Zhang J, Panzner U, Houpt E. Pathogens causing acute febrile illness among children and adolescents in Burkina Faso, Madagascar and Sudan. Clin Infect Dis 2021; 73:1338-1345. [PMID: 33822011 PMCID: PMC8528393 DOI: 10.1093/cid/ciab289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
Background The etiology and optimal clinical management of acute febrile illness (AFI) is poorly understood. Methods Blood samples taken from study participants with acute fever (≥37.5°C) or a history of fever and recruited into the previous Typhoid Fever Surveillance in Africa (TSAP) study were evaluated using a polymerase chain reaction (PCR)-based TaqMan-Array Card designed to detect a panel of bacterial, viral, and parasitic pathogens. Clinical metadata were also assessed. Results A total of 615 blood samples available for analysis originated from Burkina Faso (n = 53), Madagascar (n = 364), and Sudan (n = 198) and were taken from participants ranging in age from 0–19 years. Through the TaqMan-Array Card, at least 1 pathogen was detected in 62% (33 of 53), 24% (86 of 364), and 60% (118 of 198) of specimens from Burkina Faso, Madagascar, and Sudan, respectively. The leading identified pathogen overall was Plasmodium spp., accounting for 47% (25 of 53), 2.2% (8 of 364), and 45% (90 of 198) of AFI at the respective sites. In Madagascar, dengue virus was the most prevalent pathogen (10.2%). Overall, 69% (357 of 516) of patients with clinical diagnoses of malaria, respiratory infection, or gastrointestinal infection were prescribed a World Health Organization guideline-recommended empiric antibiotic, whereas only 45% (106 of 237) of patients with pathogens detected were treated with an antibiotic exerting likely activity. Conclusions A PCR approach for identifying multiple bacterial, viral, and parasitic pathogens in whole blood unveiled a diversity of previously undetected pathogens in AFI cases and carries implications for the appropriate management of this common syndrome.
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Affiliation(s)
- Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea.,University of Antananarivo, Antananarivo, Madagascar.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - Nagla Gasmelseed
- Faculty of Medicine at the University of Gezira, Wad Medani, Sudan
| | - Darwin Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Brian Grundy
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - John Wieser
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Christian G Meyer
- Faculty of Medicine, Duy Tan University, Da Nang, Vietnam.,Institute of Tropical Medicine, Eberhard Karls University, Tübingen, Germany
| | - Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
| | | | | | | | - Frank Konings
- International Vaccine Institute, Seoul, Republic of Korea
| | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, Republic of Korea.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Jixian Zhang
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Ursula Panzner
- International Vaccine Institute, Seoul, Republic of Korea.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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High incidence of human brucellosis in a rural Pastoralist community in Kenya, 2015. PLoS Negl Trop Dis 2021; 15:e0009049. [PMID: 33524052 PMCID: PMC7877737 DOI: 10.1371/journal.pntd.0009049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 02/11/2021] [Accepted: 12/07/2020] [Indexed: 11/19/2022] Open
Abstract
Background Brucellosis occurs globally with highly variable incidence in humans from very low in North America and Western Europe to high in the Middle East and Asia. There are few data in Sub-Saharan Africa. This study estimated the incidence of human brucellosis in a pastoralist community in Kenya. Methods Between February 2015 and January 2016, we enrolled persons living in randomly selected households in Kajiado County. Free health care was offered at three facilities in the study area. Those who met the study clinical case definition completed a standardized questionnaire on demographics, clinical history and presentation. A blood sample was collected and tested by Rose Bengal test (RBT), then later tested at the Kenya Medical Research Institute laboratory for Brucella IgG and IgM by ELISA. Those who tested positive by both RBT and ELISA (IgG or IgM antibodies) were classified as confirmed while those that only tested positive for IgG or IgM antibodies were classified as probable. Further, sera were tested by polymerase chain reaction using a TaqMan Array Card (TAC) for a panel of pathogens causing AFI including Brucella spp. Annual incidence of brucellosis was calculated as the number of confirmed cases in one year/total number in the study population. Results We enrolled a cohort of 4746 persons in 804 households. Over half (52.3%) were males and the median age was 18 years (Interquartile range (IQR) 9 months– 32 years). A total of 236 patients were enrolled at three health facilities; 64% were females and the median age was 40.5 years (IQR 28–53 years). Thirty-nine (16.5%) were positive for Brucella antibodies by IgG ELISA, 5/236 (2.1%) by IgM ELISA and 4/236 (1.7%) by RBT. Ten percent (22/217) were positive by TAC. We confirmed four (1.7%) brucellosis cases giving an annual incidence of 84/100,000 persons/year (95% CI 82, 87). The incidence did not significantly vary by gender, age and location of residence. Conclusion We report a high incidence of brucellosis in humans among members of this pastoralist community. Brucellosis was the most common cause of febrile illness in this community. Brucellosis is a bacterial disease that affects both humans and animals. Humans get infected via ingestion of unpasteurized animal products from infected animals and direct contact during animal abortions and deliveries. Infected animals shed bacteria for life through milk and during deliveries posing a risk to those with occupational exposure to infected animals. As such, human disease is disproportionately high in regions with high prevalence of animal brucellosis. While human brucellosis is distributed globally, incidence is low in North America and Western Europe and high in Asia and the Middle East where the disease is endemic. Data from Africa are scarce. We set out to estimate the incidence of brucellosis in a pastoralist community with documented high Brucella sero-prevalence in humans and livestock. We followed up a cohort of 804 households for one year and tested household members who became ill in three designated health facilities. We estimated an incidence of 84 cases per 100,000 persons per year in this community. We also found that Brucella was the most common pathogen among persons who had febrile illness highlighting the importance of this pathogen in this rural pastoralist community. No brucellosis intervention measures were being implemented.
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Koliopoulos P, Kayange NM, Daniel T, Huth F, Gröndahl B, Medina-Montaño GC, Pretsch L, Klüber J, Schmidt C, Züchner A, Ulbert S, Mshana SE, Addo M, Gehring S. Multiplex-RT-PCR-ELISA panel for detecting mosquito-borne pathogens: Plasmodium sp. preserved and eluted from dried blood spots on sample cards. Malar J 2021; 20:66. [PMID: 33526038 PMCID: PMC7851927 DOI: 10.1186/s12936-021-03595-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/15/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Children are the most vulnerable group affected by malaria and other tropical, vector-borne diseases in low-resource countries. Infants presenting with acute onset fever represent a major sector of outpatient care in the Lake Victoria region. Misclassification and overuse of antibiotics and anti-malarial medications are consistent problems. Identifying the prevalent mosquito-borne pathogens in the region will reduce the prescription of non-indicated medicines. METHODS The literature was reviewed focusing on the mosquito-borne pathogens most prevalent in sub-Saharan Africa. Accordingly, an assay comprised of a multiplex-reverse transcriptase-polymerase chain reaction and an enzyme-linked immunosorbent assay (multiplex-RT-PCR-ELISA) was designed and validated in its ability to identify and differentiate nine human mosquito-borne pathogens including eight arboviruses and Plasmodium sp., the aetiologic agents of malaria. Blood samples obtained from 132 children suspected of having malaria were spotted and preserved on Whatman® 903 protein sample cards. Multiplex-RT-PCR-ELISA analysis was assessed and compared to results obtained by blood smear microscopy and the malaria rapid diagnostic test (RDT). RESULTS Nine out of nine pathogens were amplified specifically by the multiplex-RT-PCR-ELISA panel. Twenty-seven out of 132 paediatric patients presenting with acute fever were infected with Plasmodium sp., confirmed by multiplex-RT-PCR. The results of blood smear microscopy were only 40% sensitive and 92.8% specific. The malaria RDT, on the other hand, detected acute Plasmodium infections with 96.3% sensitivity and 98.1% specificity. The preservation of Plasmodium sp. in clinical sera and whole blood samples spotted on sample cards was evaluated. The duration of successful, sample card storage was 186 to 312 days. CONCLUSIONS Reliable, easy-to-use point of care diagnostic tests are a powerful alternative to laboratory-dependent gold standard tests. The multiplex-RT-PCR-ELISA amplified and identified nine vector-borne pathogens including Plasmodium sp. with great accuracy. Translation of improved diagnostic approaches, i.e., multiplex-RT-PCR-ELISA, into effective treatment options promises to reduce childhood mortality and non-indicated prescriptions.
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Affiliation(s)
- Philip Koliopoulos
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Neema Mathias Kayange
- Department of Pediatric and Adolescent Medicine, Bugando Medical Centre, Mwanza, Tanzania
| | - Tim Daniel
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Florian Huth
- Department of Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Eppendorf, Germany
| | - Britta Gröndahl
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany.
| | | | - Leah Pretsch
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
| | - Julia Klüber
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany.,Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Christian Schmidt
- Department of Pediatric and Adolescent Medicine, St. Vinzenz-Hospital, Dinslaken, Germany
| | - Antke Züchner
- Department of Pediatric and Adolescent Medicine, Bugando Medical Centre, Mwanza, Tanzania
| | - Sebastian Ulbert
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Steven E Mshana
- Department of Microbiology and Immunology, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
| | - Marylyn Addo
- Department of Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Eppendorf, Germany
| | - Stephan Gehring
- Center of Pediatric and Adolescent Medicine, University Medical Center, Mainz, Germany
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Abstract
Rift Valley fever (RVF) is a zoonotic, vector-borne infectious disease of ruminants and camels transmitted mainly by the Aedes and Culex mosquito species. Contact with the blood or organs of infected animals may infect humans. Its etiological factor is the Rift Valley fever virus (RVFV) of the Phlebovirus genus and Bunyaviridae family. Sheep and goats are most susceptible to infection and newborns and young individuals endure the most severe disease course. High abortion rates and infant mortality are typical for RVF; its clinical signs are high fever, lymphadenitis, nasal and ocular secretions and vomiting. Conventional diagnosis is done by the detection of specific IgM or IgG antibodies and RVFV nucleic acids and by virus isolation. Inactivated and live-attenuated vaccines obtained from virulent RVFV isolates are available for livestock. RVF is endemic in sub-Saharan Africa and the Arabian Peninsula, but in the last two decades, it was also reported in other African regions. Seropositive animals were detected in Turkey, Tunisia and Libya. The wide distribution of competent vectors in non-endemic areas coupled with global climate change threaten to spread RVF transboundarily. The EFSA considers the movement of infected animals and vectors to be other plausible pathways of RVF introduction into Europe. A very low risk both of introduction of the virus through an infected animal or vector and of establishment of the virus, and a moderate risk of its transmission through these means was estimated for Poland. The risk of these specific modes of disease introduction into Europe is rated as very low, but surveillance and response capabilities and cooperation with the proximal endemic regions are recommended.
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Osborn J, Roberts T, Guillen E, Bernal O, Roddy P, Ongarello S, Sprecher A, Page AL, Ribeiro I, Piriou E, Tamrat A, de la Tour R, Rao VB, Flevaud L, Jensen T, McIver L, Kelly C, Dittrich S. Prioritising pathogens for the management of severe febrile patients to improve clinical care in low- and middle-income countries. BMC Infect Dis 2020; 20:117. [PMID: 32041536 PMCID: PMC7011354 DOI: 10.1186/s12879-020-4834-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 01/28/2020] [Indexed: 11/26/2022] Open
Abstract
Background Severe febrile illness without a known source (SFWS) is a challenge for clinicians when deciding how to manage a patient, particularly given the wide spectrum of potential aetiologies that contribute to fever. These infections are difficult to distinguish clinically, and accurate diagnosis requires a plethora of diagnostics including blood cultures, imaging techniques, molecular or serological tests, and more. When laboratory services are available, a limited test menu hinders clinical decision-making and antimicrobial stewardship, leading to empiric treatment and suboptimal patient outcomes. To specifically address SFWS, this work aimed to identify priority pathogens for a globally applicable panel for fever causing pathogens. Method A pragmatic two-pronged approach combining currently available scientific data in an analytical hierarchy process and systematically gathered expert input, was designed to address the lack of comprehensive global aetiology data. The expert re-ranked list was then further adapted for a specific use case to focus on community acquired infections in whole blood specimens. The resulting list was further analysed to address different geographical regions (Asia, Africa, and Latin America), and Cohen kappa scores of agreement were calculated. Results The expert ranked prioritized pathogen list generated as part of this two-pronged approach included typhoidal Salmonella, Plasmodium species and Mycobacterium tuberculosis as the top 3 pathogens. This pathogen list was then further adapted for the SFWS use case to develop a final pathogen list to inform product development. Subsequent analysis comparing the relevance of the SFWS pathogen list to multiple populations and geographical regions showed that the SFWS prioritized list had considerable utility across Africa and Asia, but less so for Latin America. In addition, the list showed high levels of agreement across different patient sub-populations, but lower relevance for neonates and symptomatic HIV patients. Conclusion This work highlighted once again the challenges of prioritising in global health, but it also shows that taking a two-pronged approach, combining available prevalence data with expert input, can result in a broadly applicable priority list. This comprehensive utility is particularly important in the context of product development, where a sufficient market size is essential to achieve a sustainable commercialized diagnostic product to address SFWS.
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Cleland A, Malloy K, Donnelly MC, Davidson J, Simpson KJ, Petrik J. Design and evaluation of Taqman low density array for monitoring post-transplant viral infections. Transpl Infect Dis 2020; 23:e13499. [PMID: 33118224 DOI: 10.1111/tid.13499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 09/10/2020] [Accepted: 10/18/2020] [Indexed: 11/27/2022]
Abstract
BACKGROUND The majority of transplant recipients undergo immunosuppressive treatment to prevent organ or tissue rejection. Consequently, they are more susceptible to infection agents including a number of viruses causing a significant morbidity and mortality. Only a limited number of viruses are currently tested for in transplant donors and recipients due to the cost and complexity. Taqman low density array (TLDA) may provide a suitable format to address more systematic testing approach. METHODS One hundred and one liver transplant recipient samples were retrospectively tested for 48 viral targets including two controls (bovine viral diarrhea virus and MS2) and two common viruses (TTV and HPgV), using a custom designed TLDA. Eight samples were analysed simultaneously on 384-well TLDA. Samples giving a signal considered positive/indeterminant were re-tested by different individual confirmatory assays. RESULTS Infections with six previously untested for viruses-EBV, HPIV3, HuPuV9, KIV, HMPV and HPV-were detected in fourteen patients. Previously detected HCV infections were also confirmed. These infections did not seem have an effect on 5 year post-transplant outcome. 55 of 79 and 17 of 87 samples available for confirmatory assays were positive for TTV and HPgV, included for the evaluation of the TLDA performance. CONCLUSIONS The custom viral TLDA can be successfully used for simultaneous detection of a range of post-transplant viral infections. To fully exploit its potential for monitoring and intervention, a whole blood testing should be applied in a prospective setting.
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Affiliation(s)
- Alexander Cleland
- Microbiology Research, Development and Innovation, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Kristen Malloy
- Microbiology Research, Development and Innovation, Scottish National Blood Transfusion Service, Edinburgh, UK
| | - Mhairi C Donnelly
- Department of Hepatology, Division of Health Sciences, Edinburgh Medical School, Edinburgh, UK
| | - Janice Davidson
- Scottish Liver Transplantation Unit, Royal Infirmary, Edinburgh, UK
| | - Kenneth J Simpson
- Department of Hepatology, Division of Health Sciences, Edinburgh Medical School, Edinburgh, UK
| | - Juraj Petrik
- Microbiology Research, Development and Innovation, Scottish National Blood Transfusion Service, Edinburgh, UK
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Meng Y, Zhang Y, Wang S, Wu S, Zhou H, Ke C, Qi X, Rainey JJ. Lessons Learned in the Development of a Web-based Surveillance Reporting System and Dashboard to Monitor Acute Febrile Illnesses in Guangdong and Yunnan Provinces, China, 2017-2019. Health Secur 2020; 18:S14-S22. [PMID: 32004129 DOI: 10.1089/hs.2019.0079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Global spread of Zika virus in 2015 and 2016 highlighted the importance of surveillance to rapidly detect, report, and respond to emerging infections. We describe the lessons learned from the development and deployment of a web-based surveillance reporting system for Zika virus and other acute febrile illnesses (AFI) in Guangdong and Yunnan provinces, China. In less than 2 months, we customized the China Epidemiologic Dynamic Data Collection (EDDC) platform to collect, manage, and visualize data in close to real time. According to provincial and sentinel hospital staff requirements, the customized platform provided specific user authorization management, online/offline data collection, data quality control, and secure data transmission and protection and visualization tools. AFI case data and laboratory test results were entered through a web-based interface by hospital and provincial-level staff and saved on a China CDC server in Beijing. The dashboard visualized aggregate data by hospital, age, onset date, and laboratory test results. From June 2017 to December 2018, data from 768 patients with AFI were entered into the web-based surveillance system and visualized by hospital and provincial-level decision makers. Input from provincial and hospital staff was essential for developing the AFI case-reporting and feedback tools appropriate for specific settings and decision-making requirements. Web-based systems (eg, EDDC, data collection, and visualization tools that can be easily adapted to meet local surveillance needs) can help shorten time for system deployment, thereby strengthening global health security to rapidly detect and respond to emerging infections and outbreaks.
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Affiliation(s)
- Yujie Meng
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
| | - Yuzhi Zhang
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
| | - Songwang Wang
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
| | - Shuyu Wu
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
| | - Hongning Zhou
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
| | - Changwen Ke
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
| | - Xiaopeng Qi
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
| | - Jeanette J Rainey
- Yujie Meng, MS, and Songwang Wang, MD, are with the Information Center, and Xiaopeng Qi, PhD, is Deputy Director, Center for Global Public Health; all at the Chinese Center for Disease Control and Prevention, Beijing, China. Yuzhi Zhang, PhD, Shuyu Wu, PhD, and Jeanette J. Rainey, PhD, are with the Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Country Office in China, Beijing, China. Hongning Zhou, MSc, is Director, Yunnan Institute of Parasitic Diseases, Pu'er, China. Changwen Ke, MS, is Director, Institute of Pathogenic Microbiology, Guangdong Provincial Centre for Disease Control and Prevention, Guangzhou, China. The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of any organization
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Bai Y, Motin V, Enscore RE, Osikowicz L, Rosales Rizzo M, Hojgaard A, Kosoy M, Eisen RJ. Pentaplex real-time PCR for differential detection of Yersinia pestis and Y. pseudotuberculosis and application for testing fleas collected during plague epizootics. Microbiologyopen 2020; 9:e1105. [PMID: 32783386 PMCID: PMC7568250 DOI: 10.1002/mbo3.1105] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/04/2020] [Accepted: 07/18/2020] [Indexed: 12/13/2022] Open
Abstract
Upon acquiring two unique plasmids (pMT1 and pPCP1) and genome rearrangement during the evolution from Yersinia pseudotuberculosis, the plague causative agent Y. pestis is closely related to Y. pseudotuberculosis genetically but became highly virulent. We developed a pentaplex real-time PCR assay that not only detects both Yersinia species but also differentiates Y. pestis strains regarding their plasmid profiles. The five targets used were Y. pestis-specific ypo2088, caf1, and pst located on the chromosome, plasmids pMT1 and pPCP1, respectively; Y. pseudotuberculosis-specific chromosomal gene opgG; and 18S ribosomal RNA gene as an internal control for flea DNA. All targets showed 100% specificity and high sensitivity with limits of detection ranging from 1 fg to 100 fg, with Y. pestis-specific pst as the most sensitive target. Using the assay, Y. pestis strains were differentiated 100% by their known plasmid profiles. Testing Y. pestis and Y. pseudotuberculosis-spiked flea DNA showed there is no interference from flea DNA on the amplification of targeted genes. Finally, we applied the assay for testing 102 fleas collected from prairie dog burrows where prairie dog die-off was reported months before flea collection. All flea DNA was amplified by 18S rRNA; no Y. pseudotuberculosis was detected; one flea was positive for all Y. pestis-specific targets, confirming local Y. pestis transmission. Our results indicated the assay is sensitive and specific for the detection and differentiation of Y. pestis and Y. pseudotuberculosis. The assay can be used in field investigations for the rapid identification of the plague causative agent.
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Affiliation(s)
- Ying Bai
- Bacterial Disease BranchDivision of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsColoradoUSA
| | - Vladimir Motin
- Department of PathologyDepartment of Microbiology & ImmunologyThe University of Texas Medical Branch at GalvestonGalvestonTexasUSA
| | - Russell E. Enscore
- Bacterial Disease BranchDivision of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsColoradoUSA
| | - Lynn Osikowicz
- Bacterial Disease BranchDivision of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsColoradoUSA
| | - Maria Rosales Rizzo
- Bacterial Disease BranchDivision of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsColoradoUSA
| | - Andrias Hojgaard
- Bacterial Disease BranchDivision of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsColoradoUSA
| | | | - Rebecca J. Eisen
- Bacterial Disease BranchDivision of Vector‐Borne DiseasesCenters for Disease Control and PreventionFort CollinsColoradoUSA
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Credle JJ, Robinson ML, Gunn J, Monaco D, Sie B, Tchir A, Hardick J, Zheng X, Shaw-Saliba K, Rothman RE, Eshleman SH, Pekosz A, Hansen K, Mostafa H, Steinegger M, Larman HB. Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.03.130591. [PMID: 32577648 PMCID: PMC7302202 DOI: 10.1101/2020.06.03.130591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The emergence of SARS-CoV-2 has caused the current COVID-19 pandemic with catastrophic societal impact. Because many individuals shed virus for days before symptom onset, and many show mild or no symptoms, an emergent and unprecedented need exists for development and deployment of sensitive and high throughput molecular diagnostic tests. RNA-mediated oligonucleotide Annealing Selection and Ligation with next generation DNA sequencing (RASL-seq) is a highly multiplexed technology for targeted analysis of polyadenylated mRNA, which incorporates sample barcoding for massively parallel analyses. Here we present a more generalized method, capture RASL-seq ("cRASL-seq"), which enables analysis of any targeted pathogen- (and/or host-) associated RNA molecules. cRASL-seq enables highly sensitive (down to ~1-100 pfu/ml or cfu/ml) and highly multiplexed (up to ~10,000 target sequences) detection of pathogens. Importantly, cRASL-seq analysis of COVID-19 patient nasopharyngeal (NP) swab specimens does not involve nucleic acid extraction or reverse transcription, steps that have caused testing bottlenecks associated with other assays. Our simplified workflow additionally enables the direct and efficient genotyping of selected, informative SARS-CoV-2 polymorphisms across the entire genome, which can be used for enhanced characterization of transmission chains at population scale and detection of viral clades with higher or lower virulence. Given its extremely low per-sample cost, simple and automatable protocol and analytics, probe panel modularity, and massive scalability, we propose that cRASL-seq testing is a powerful new surveillance technology with the potential to help mitigate the current pandemic and prevent similar public health crises.
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Affiliation(s)
- Joel J. Credle
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew L Robinson
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jonathan Gunn
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Monaco
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Brandon Sie
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Alexandra Tchir
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Justin Hardick
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xuwen Zheng
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Kathryn Shaw-Saliba
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Richard E. Rothman
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Susan H. Eshleman
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kasper Hansen
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Heba Mostafa
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Martin Steinegger
- Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - H. Benjamin Larman
- Institute for Cell Engineering, Immunology Division, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
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Gikunju SW, Agola EL, Ondondo RO, Kinyua J, Kimani F, LaBeaud AD, Malhotra I, King C, Thiong'o K, Mutuku F. Prevalence of pfdhfr and pfdhps mutations in Plasmodium falciparum associated with drug resistance among pregnant women receiving IPTp-SP at Msambweni County Referral Hospital, Kwale County, Kenya. Malar J 2020; 19:190. [PMID: 32448228 PMCID: PMC7247205 DOI: 10.1186/s12936-020-03263-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 05/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prevention and treatment of malaria during pregnancy is crucial in dealing with maternal mortality and adverse fetal outcomes. The World Health Organization recommendation to treat all pregnant women with sulfadoxine-pyrimethamine (SP) through antenatal care structures was implemented in Kenya in the year 1998, but concerns about its effectiveness in preventing malaria in pregnancy has arisen due to the spread of SP resistant parasites. This study aimed to determine the prevalence of SP resistance markers in Plasmodium falciparum parasites isolated from pregnant women seeking antenatal care at Msambweni County Referral Hospital, located in coastal Kenya, between the year 2013 and 2015. METHODS This hospital-based study included 106 malaria positive whole blood samples for analysis of SP resistance markers within the Pfdhfr gene (codons 51, 59 and 108) and Pfdhps gene (codons 437 and 540). The venous blood collected from all pregnant women was tested for malaria via light microscopy, then the malaria positive samples were separated into plasma and red cells and stored in a - 86° freezer for further studies. Archived red blood cells were processed for molecular characterization of SP resistance markers within the Pfdhfr and Pfdhps genes using real time PCR platform and Sanger sequencing. RESULTS All samples had at least one mutation in the genes associated with drug resistance; polymorphism prevalence of Pfdhfr51I, 59R and 108N was at 88.7%, 78.3% and 93.4%, respectively, while Pfdhps polymorphism accounted for 94.3% and 91.5% at 437G and 540E, respectively. Quintuple mutations (at all the five codons) conferring total SP resistance had the highest prevalence of 85.8%. Quadruple mutations were observed at a frequency of 10.4%, and 24.5% had a mixed outcome of both wildtype and mutant genotypes in the genes of interest. CONCLUSION The data suggest a high prevalence of P. falciparum genetic variations conferring resistance to SP among pregnant women, which may explain reduced efficacy of IPTp treatment in Kenya. There is need for extensive SP resistance profiling in Kenya to inform IPTp drug choices for successful malaria prevention during pregnancy.
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Affiliation(s)
- Stella Wanjiku Gikunju
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya. .,Kenya Medical Research Institute (KEMRI), Centre for Biotechnology Research and Development (CBRD), Nairobi, Kenya.
| | - Eric L Agola
- Kenya Medical Research Institute (KEMRI), Centre for Biotechnology Research and Development (CBRD), Nairobi, Kenya.,Technical University of Kenya, Nairobi, Kenya
| | | | - Johnson Kinyua
- Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, Kenya
| | - Francis Kimani
- Kenya Medical Research Institute (KEMRI), Centre for Biotechnology Research and Development (CBRD), Nairobi, Kenya
| | - Angelle Desiree LaBeaud
- Department of Pediatrics, Division of Infectious Disease, Stanford University School of Medicine, Stanford, CA, USA
| | - Indu Malhotra
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Charles King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Kelvin Thiong'o
- Kenya Medical Research Institute (KEMRI), Centre for Biotechnology Research and Development (CBRD), Nairobi, Kenya
| | - Francis Mutuku
- Department of Environment and Health Sciences, Technical University of Mombasa, Mombasa, Kenya
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Kwambana-Adams BA, Liu J, Okoi C, Mwenda JM, Mohammed NI, Tsolenyanu E, Renner LA, Ansong D, Tagbo BN, Bashir MF, Hama MK, Sonko MA, Gratz J, Worwui A, Ndow P, Cohen AL, Serhan F, Mihigo R, Antonio M, Houpt E, On Behalf Of The Paediatric Bacterial Meningitis Surveillance Network In West Africa. Etiology of Pediatric Meningitis in West Africa Using Molecular Methods in the Era of Conjugate Vaccines against Pneumococcus, Meningococcus, and Haemophilus influenzae Type b. Am J Trop Med Hyg 2020; 103:696-703. [PMID: 32458777 PMCID: PMC7410464 DOI: 10.4269/ajtmh.19-0566] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite the implementation of effective conjugate vaccines against the three main bacterial pathogens that cause meningitis, Streptococcus pneumoniae, Haemophilus influenzae type b (Hib), and Neisseria meningitidis serogroup A, the burden of meningitis in West Africa remains high. The relative importance of other bacterial, viral, and parasitic pathogens in central nervous system infections is poorly characterized. Cerebrospinal fluid (CSF) specimens were collected from children younger than 5 years with suspected meningitis, presenting at pediatric teaching hospitals across West Africa in five countries including Senegal, Ghana, Togo, Nigeria, and Niger. Cerebrospinal fluid specimens were initially tested using bacteriologic culture and a triplex real-time polymerase chain reaction (PCR) assay for N. meningitidis, S. pneumoniae, and H. influenzae used in routine meningitis surveillance. A custom TaqMan Array Card (TAC) assay was later used to detect 35 pathogens including 15 bacteria, 17 viruses, one fungus, and two protozoans. Among 711 CSF specimens tested, the pathogen positivity rates were 2% and 20% by the triplex real-time PCR (three pathogens) and TAC (35 pathogens), respectively. TAC detected 10 bacterial pathogens, eight viral pathogens, and Plasmodium. Overall, Escherichia coli was the most prevalent (4.8%), followed by S. pneumoniae (3.5%) and Plasmodium (3.5%). Multiple pathogens were detected in 4.4% of the specimens. Children with human immunodeficiency virus (HIV) and Plasmodium detected in CSF had high mortality. Among 220 neonates, 17% had at least one pathogen detected, dominated by gram-negative bacteria. The meningitis TAC enhanced the detection of pathogens in children with meningitis and may be useful for case-based meningitis surveillance.
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Affiliation(s)
- Brenda A Kwambana-Adams
- Division of Infection and Immunity, NIHR Global Health Research Unit on Mucosal Pathogens, University College London, London, United Kingdom.,WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Catherine Okoi
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Jason M Mwenda
- World Health Organization (WHO), Regional Office for Africa, Brazzaville, Congo
| | - Nuredin I Mohammed
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Enyonam Tsolenyanu
- Department of Paediatrics, Sylvanus Olympio Teaching Hospital, Lomé, Togo
| | - Lorna Awo Renner
- University of Ghana School of Medicine and Dentistry, Accra, Ghana
| | | | - Beckie N Tagbo
- Department of Paediatrics, University of Nigeria Teaching Hospital Ituku-Ozalla, Enug, Nigeria.,Institute of Child Health, University of Nigeria Teaching Hospital, Enug, Nigeria
| | - Muhammad F Bashir
- Department of Paediatrics, Abubakar Tafawa Balewa University Teaching Hospital, Bauchi, Nigeria
| | | | | | - Jean Gratz
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Archibald Worwui
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Peter Ndow
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | | | - Richard Mihigo
- World Health Organization (WHO), Regional Office for Africa, Brazzaville, Congo
| | - Martin Antonio
- Division of Microbiology and Immunity, Warwick Medical School, University of Warwick, Coventry, United Kingdom.,WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eric Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia
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Moore CC, Jacob ST, Banura P, Zhang J, Stroup S, Boulware DR, Scheld WM, Houpt ER, Liu J. Etiology of Sepsis in Uganda Using a Quantitative Polymerase Chain Reaction-based TaqMan Array Card. Clin Infect Dis 2020; 68:266-272. [PMID: 29868873 DOI: 10.1093/cid/ciy472] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/31/2018] [Indexed: 01/08/2023] Open
Abstract
Background Knowledge of causes of sepsis in sub-Saharan Africa is limited. A better understanding of the microbiology of bloodstream infections could improve outcomes. Methods We used a quantitative polymerase chain reaction (qPCR)-based TaqMan Array Card (TAC) to directly test for 43 targets from whole blood. We analyzed 336 cryopreserved specimens from adult Ugandans with sepsis enrolled in a multisite study; 84% were infected with human immunodeficiency virus. We compared qPCR TAC results with blood culture and determined the association of qPCR with study participant outcomes using logistic regression. Results The most frequently detected targets were cytomegalovirus (CMV, n = 139, 41%), Mycobacterium tuberculosis (TB, n = 70, 21%), Plasmodium (n = 35, 10%), and Streptococcus pneumoniae (n = 31, 9%). Diagnostic performance varied by target with qPCR sensitivity averaging 61 ± 28% and specificity 98 ± 3% versus culture. In multivariable analysis, independent factors associated with in-hospital mortality included CMV viremia (adjusted odds ratio [aOR] 3.2, 95% confidence interval [CI], 1.8-5.5; p < .01) and TB qPCR-positivity, whether blood culture-positive (aOR 4.6, 95% CI, 2.1-10.0; p < .01) or blood culture-negative (aOR 2.9, 95% CI, 1.2-6.9; p = .02). Conclusions Using qPCR TAC on direct blood specimens, CMV and TB were the most commonly identified targets and were independently associated with increased in-hospital mortality. qPCR TAC screening of blood for multiple targets may be useful to guide triage and treatment of sepsis in sub-Saharan Africa.
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Affiliation(s)
- Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | | | - Patrick Banura
- Ministry of Health, National Disease Control Department, Kampala, Uganda
| | - Jixian Zhang
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Suzanne Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - David R Boulware
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis
| | - W Michael Scheld
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville
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Kading RC, Abworo EO, Hamer GL. Rift Valley Fever Virus, Japanese Encephalitis Virus, and African Swine Fever Virus: Three Transboundary, Vector-Borne, Veterinary Biothreats With Diverse Surveillance, and Response Capacity Needs. Front Vet Sci 2019; 6:458. [PMID: 31921916 PMCID: PMC6923192 DOI: 10.3389/fvets.2019.00458] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
Early detection of emerging foreign animal diseases is critical to pathogen surveillance and control programs. Rift valley fever virus (RVFV), Japanese encephalitis virus (JEV), and African swine fever virus (ASFV) represent three taxonomically and ecologically diverse vector-borne viruses with the potential to be introduced to the United States. To promote preparedness for such an event, we reviewed the current surveillance strategies and diagnostic tools in practice around the world for these emerging viruses, and summarized key points pertaining to the availability of existing guidelines and strategic approaches for early detection, surveillance, and disease management activities. We compare and contrast the surveillance and management approaches of these three diverse agents of disease as case studies to emphasize the importance of the ecological context and biology of vectors and vertebrate hosts. The information presented in this review will inform stakeholders of the current state of surveillance approaches against these transboundary foreign animal disease which threaten the United States.
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Affiliation(s)
- Rebekah C Kading
- Arthropod-Borne Infectious Disease Laboratory, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | | | - Gabriel L Hamer
- Department of Entomology, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX, United States
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