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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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Haque MA, Nasrin S, Palit P, Das R, Wahid BZ, Gazi MA, Mahfuz M, Golam Faruque AS, Ahmed T. Site-Specific Analysis of the Incidence Rate of Enterotoxigenic Escherichia coli Infection Elucidates an Association with Childhood Stunting, Wasting, and Being Underweight: A Secondary Analysis of the MAL-ED Birth Cohort. Am J Trop Med Hyg 2023; 108:1192-1200. [PMID: 37011892 PMCID: PMC10540109 DOI: 10.4269/ajtmh.22-0659] [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: 10/13/2022] [Accepted: 01/28/2023] [Indexed: 04/05/2023] Open
Abstract
Asymptomatic infection by fecal enteropathogens is a major contributor to childhood malnutrition. Here, we investigated the incidence rate of asymptomatic infection by enterotoxigenic Escherichia coli (ETEC) and assessed its association with childhood stunting, wasting, and being underweight among children under 2 years of age. The Malnutrition and Enteric Disease birth cohort study included 1,715 children who were followed from birth to 24 months of age from eight distinct geographic locations including Bangladesh, Brazil, India, Peru, Tanzania, Pakistan, Nepal, and South Africa. The TaqMan array card assay was used to determine the presence of ETEC in the nondiarrheal stool samples collected from these children. Poisson regression was used to estimate the incidence rate, and multiple generalized estimating equations with binomial family, logit link function, and exchangeable correlation were used to analyze the association between asymptomatic ETEC infection and anthropometric indicators such as stunting, wasting, and being underweight. The site-specific incidence rates of asymptomatic ETEC infections per 100 child-months were also higher at the study locations in Tanzania (54.81 [95% CI: 52.64, 57.07]) and Bangladesh (46.75 [95% CI: 44.75, 48.83]). In the Bangladesh, India, and Tanzania sites, the composite indicator of anthropometric failure was significantly associated with asymptomatic ETEC infection. Furthermore, a significant association between asymptomatic heat-stable toxin ETEC infections and childhood stunting, wasting, and being underweight was found in only the Bangladesh and Tanzania sites.
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Affiliation(s)
- Md Ahshanul Haque
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Sabiha Nasrin
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts
| | - Parag Palit
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rina Das
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Barbie Zaman Wahid
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
- University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Md Amran Gazi
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Abu Syed Golam Faruque
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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3
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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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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: 12] [Impact Index Per Article: 6.0] [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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5
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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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Nyakarahuka L, Mulei S, Whitmer S, Jackson K, Tumusiime A, Schuh A, Baluku J, Joyce A, Ocom F, Tusiime JB, Montgomery JM, Balinandi S, Lutwama JJ, Klena JD, Shoemaker TR. First laboratory confirmation and sequencing of Zaire ebolavirus in Uganda following two independent introductions of cases from the 10th Ebola Outbreak in the Democratic Republic of the Congo, June 2019. PLoS Negl Trop Dis 2022; 16:e0010205. [PMID: 35192613 PMCID: PMC8896669 DOI: 10.1371/journal.pntd.0010205] [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: 07/22/2021] [Revised: 03/04/2022] [Accepted: 01/26/2022] [Indexed: 11/18/2022] Open
Abstract
Uganda established a domestic Viral Hemorrhagic Fever (VHF) testing capacity in 2010 in response to the increasing occurrence of filovirus outbreaks. In July 2018, the neighboring Democratic Republic of Congo (DRC) experienced its 10th Ebola Virus Disease (EVD) outbreak and for the duration of the outbreak, the Ugandan Ministry of Health (MOH) initiated a national EVD preparedness stance. Almost one year later, on 10th June 2019, three family members who had contracted EVD in the DRC crossed into Uganda to seek medical treatment.
Samples were collected from all the suspected cases using internationally established biosafety protocols and submitted for VHF diagnostic testing at Uganda Virus Research Institute. All samples were initially tested by RT-PCR for ebolaviruses, marburgviruses, Rift Valley fever (RVF) virus and Crimean-Congo hemorrhagic fever (CCHF) virus. Four people were identified as being positive for Zaire ebolavirus, marking the first report of Zaire ebolavirus in Uganda. In-country Next Generation Sequencing (NGS) and phylogenetic analysis was performed for the first time in Uganda, confirming the outbreak as imported from DRC at two different time point from different clades. This rapid response by the MoH, UVRI and partners led to the control of the outbreak and prevention of secondary virus transmission.
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Affiliation(s)
- Luke Nyakarahuka
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
- Department of Biosecurity, Ecosystems and Veterinary Public Health, Makerere University, Kampala, Uganda
- * E-mail:
| | - Sophia Mulei
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kyondo Jackson
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Alex Tumusiime
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Amy Schuh
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jimmy Baluku
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Allison Joyce
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Felix Ocom
- Uganda Public Health Emergency Operations Center, Kampala, Uganda
| | | | - Joel M. Montgomery
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stephen Balinandi
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - Julius J. Lutwama
- Department of Arbovirology, Emerging and Re-emerging Infectious Diseases, Uganda Virus Research Institute, Entebbe, Uganda
| | - John D. Klena
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, United States Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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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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8
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Palit P, Nuzhat S, Khan SS, Gazi MA, Islam MR, Islam MO, Mahfuz M, Liu J, Houpt ER, Haque R, Ahmed T. Use of TaqMan Array Cards to investigate the aetiological agents of diarrhoea among young infants with severe acute malnutrition. Trop Med Int Health 2021; 26:1659-1667. [PMID: 34498343 DOI: 10.1111/tmi.13677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Studies involving less sensitive conventional microscopy and culture-based approaches have identified distinct differences in diarrhoeal aetiology in childhood malnutrition. Our study involved the use of an advanced molecular biology technique, the TaqMan Array Cards (TAC), to elucidate the diarrhoeal aetiology among young infants with severe acute malnutrition (SAM). METHOD A total of 113 faecal samples was collected from SAM infants, aged 2-6 months, upon admission to the Dhaka Hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) with complications of diarrhoea and related comorbidities. We used TAC for the detection of 29 different diarrhoeal enteropathogens from a single faecal sample. For comparison, we also analysed 25 diarrhoeal samples from well-nourished infants of similar age. RESULTS Higher odds of detection of all bacterial enteropathogens were associated with diarrhoea among SAM infants. In particular, the detection of Aeromonas sp (aOR: 25.7, p = 0.011), Campylobacter sp (aOR: 9.6, p < 0.01) and ETEC (aOR: 5.2, p = 0.022) was significantly associated with diarrhoea among SAM infants in comparison to well-nourished infants. 80% higher odds of detection of rotavirus and norovirus GII were associated with diarrhoea among well-nourished infants in comparison to SAM infants (aOR: 0.2, p < 0.05). CONCLUSION Our study findings demonstrate a difference in diarrhoeal aetiology among SAM and well-nourished young infants, which may be useful in providing an evidence-based logic for possible revision of treatment guidelines for treatment of young diarrhoeal infants with SAM in the early management of the menace of antimicrobial resistance.
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Affiliation(s)
- Parag Palit
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Sharika Nuzhat
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Shaila Sharmeen Khan
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Md Amran Gazi
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Md Ridwan Islam
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Md Ohedul Islam
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.,Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Rashidul Haque
- Emerging Infections and Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh.,James P. Grant School of Public Health, BRAC University, Dhaka, Bangladesh
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9
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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: 11] [Impact Index Per Article: 3.7] [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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10
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Kim JH, Im J, Parajulee P, Holm M, Cruz Espinoza LM, Poudyal N, Mogeni OD, Marks F. A Systematic Review of Typhoid Fever Occurrence in Africa. Clin Infect Dis 2020; 69:S492-S498. [PMID: 31665777 PMCID: PMC6821235 DOI: 10.1093/cid/ciz525] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Our current understanding of the burden and distribution of typhoid fever in Africa relies on extrapolation of data from a small number of population-based incidence rate estimates. However, many other records on the occurrence of typhoid fever are available, and those records contain information that may enrich our understanding of the epidemiology of the disease as well as secular trends in reporting by country and over time. METHODS We conducted a systematic review of typhoid fever occurrence in Africa, published in PubMed, Embase, and ProMED (Program for Monitoring Emerging Diseases). RESULTS At least one episode of culture-confirmed typhoid fever was reported in 42 of 57 African countries during 1900-2018. The number of reports on typhoid fever has increased over time in Africa and was highly heterogeneous between countries and over time. Outbreaks of typhoid fever were reported in 15 countries, with their frequency and size increasing over time. CONCLUSIONS Efforts should be made to leverage existing typhoid data, for example, by incorporating them into models for estimating the burden and distribution of typhoid fever.
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Affiliation(s)
- Jong-Hoon Kim
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea
| | - Justin Im
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea
| | - Prerana Parajulee
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea
| | - Marianne Holm
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea
| | - Ligia Maria Cruz Espinoza
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea
| | - Nimesh Poudyal
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea
| | - Ondari D Mogeni
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea
| | - Florian Marks
- Public Health, Access, and Vaccine Epidemiology (PAVE) Unit, International Vaccine Institute, Seoul, Korea.,Department of Medicine, University of Cambridge, United Kingdom
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11
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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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12
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Diaz MH, Waller JL, Theodore MJ, Patel N, Wolff BJ, Benitez AJ, Morris T, Raghunathan PL, Breiman RF, Whitney CG, Blau DM, Winchell JM. Development and Implementation of Multiplex TaqMan Array Cards for Specimen Testing at Child Health and Mortality Prevention Surveillance Site Laboratories. Clin Infect Dis 2019; 69:S311-S321. [PMID: 31598666 PMCID: PMC7108207 DOI: 10.1093/cid/ciz571] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Child Health and Mortality Prevention Surveillance (CHAMPS) laboratories are employing a variety of laboratory methods to identify infectious agents contributing to deaths of children <5 years old and stillbirths in sub-Saharan Africa and South Asia. In support of this long-term objective, our team developed TaqMan Array Cards (TACs) for testing postmortem specimens (blood, cerebrospinal fluid, lung tissue, respiratory tract swabs, and rectal swabs) for >100 real-time polymerase chain reaction (PCR) targets in total (30-45 per card depending on configuration). Multipathogen panels were configured by syndrome and customized to include pathogens of significance in young children within the regions where CHAMPS is conducted, including bacteria (57 targets covering 30 genera), viruses (48 targets covering 40 viruses), parasites (8 targets covering 8 organisms), and fungi (3 targets covering 3 organisms). The development and application of multiplex real-time PCR reactions to the TAC microfluidic platform increased the number of targets in each panel while maintaining assay efficiency and replicates for heightened sensitivity. These advances represent a substantial improvement in the utility of this technology for infectious disease diagnostics and surveillance. We optimized all aspects of the CHAMPS molecular laboratory testing workflow including nucleic acid extraction, quality assurance, and data management to ensure comprehensive molecular testing of specimens and high-quality data. Here we describe the development and implementation of multiplex TACs and associated laboratory protocols for specimen processing, testing, and data management at CHAMPS site laboratories.
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Affiliation(s)
- Maureen H Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica L Waller
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | - Bernard J Wolff
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alvaro J Benitez
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy Morris
- Public Health Informatics Institute, The Task Force for Global Health, Atlanta, Georgia, USA
| | - Pratima L Raghunathan
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, Georgia, USA
| | - Cynthia G Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dianna M Blau
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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