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Muzembo BA, Kitahara K, Ohno A, Khatiwada J, Dutta S, Miyoshi SI. Rapid diagnostic tests and loop-mediated isothermal amplification method for the detection of Shigella species: A systematic review and meta-analysis. J Infect Public Health 2024; 17:1065-1078. [PMID: 38705059 DOI: 10.1016/j.jiph.2024.04.013] [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: 02/22/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
We meta-analyzed the diagnostic accuracy of rapid diagnostic tests (dipsticks) and loop-mediated isothermal amplification (LAMP) method to detect Shigella species. We searched MEDLINE, Embase, Web of Science and Google Scholar from inception to 2023 for studies reporting on the performance of Shigella dipstick and LAMP tests compared with culture or polymerase chain reaction (PCR). Our search identified 2618 studies, of which fourteen met the inclusion criteria for the systematic review. Ten studies covering 4056 tests (from twelve countries) were included in the meta-analysis. The overall pooled sensitivity and specificity were 98% (95% CI: 94-100) and 97% (95% CI: 92-99), respectively. Pooled sensitivity and specificity of dipsticks were 95% and 98%, respectively. In contrast, LAMP showed higher pooled sensitivity (100%) and diagnostic odds ratio (431752), but similar specificity (97%). LAMP and dipstick tests exhibited promising performance, suggesting that they could be useful for assisting in the diagnosis of shigellosis.
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Affiliation(s)
- Basilua Andre Muzembo
- Research Institute of Nursing Care for People and Community, University of Hyogo, Akashi, Japan; Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
| | - Kei Kitahara
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Collaborative Research Centre of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, India
| | - Ayumu Ohno
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan; Collaborative Research Centre of Okayama University for Infectious Diseases in India at ICMR-NICED, Kolkata, India
| | | | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shin-Ichi Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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Chowdhury G, Ghosh D, Zhou Y, Deb AK, Mukhopadhyay AK, Dutta S, Chakraborty S. Field evaluation of a simple and rapid diagnostic test, RLDT to detect Shigella and enterotoxigenic E. coli in Indian children. Sci Rep 2024; 14:8816. [PMID: 38627472 PMCID: PMC11021469 DOI: 10.1038/s41598-024-59181-6] [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: 08/24/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected additional 12% Shigella and 13% ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.
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Affiliation(s)
- Goutam Chowdhury
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Debjani Ghosh
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Yiyi Zhou
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alok K Deb
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Asish Kumar Mukhopadhyay
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India.
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, P33 CIT Road, Scheme XM, Beliaghata, Kolkata, 700010, India
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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Pajuelo MJ, Noazin S, Cabrera L, Toledo A, Velagic M, Arias L, Ochoa M, Moulton LH, Saito M, Gilman RH, Chakraborty S. Epidemiology of enterotoxigenic Escherichia coli and impact on the growth of children in the first two years of life in Lima, Peru. Front Public Health 2024; 12:1332319. [PMID: 38584932 PMCID: PMC10995271 DOI: 10.3389/fpubh.2024.1332319] [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] [Received: 11/02/2023] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Background Enterotoxigenic E. coli (ETEC) is a leading cause of diarrheal morbidity and mortality in children, although the data on disease burden, epidemiology, and impact on health at the community level are limited. Methods In a longitudinal birth cohort study of 345 children followed until 24 months of age in Lima, Peru, we measured ETEC burden in diarrheal and non-diarrheal samples using quantitative PCR (LT, STh, and STp toxin genes), studied epidemiology and measured anthropometry in children. Results About 70% of children suffered from one or more ETEC diarrhea episodes. Overall, the ETEC incidence rate (IR) was 73 per 100 child-years. ETEC infections began early after birth causing 10% (8.9-11.1) ETEC-attributable diarrheal burden at the population level (PAF) in neonates and most of the infections (58%) were attributed to ST-ETEC [PAF 7.9% (1.9-13.5)] and LT + ST-ETEC (29%) of which all the episodes were associated with diarrhea. ETEC infections increased with age, peaking at 17% PAF (4.6-27.7%; p = 0.026) at 21 to 24 months. ST-ETEC was the most prevalent type (IR 32.1) with frequent serial infections in a child. The common colonization factors in ETEC diarrhea cases were CFA/I, CS12, CS21, CS3, and CS6, while in asymptomatic ETEC cases were CS12, CS6 and CS21. Only few (5.7%) children had repeated infections with the same combination of ETEC toxin(s) and CFs, suggested genotype-specific immunity from each infection. For an average ETEC diarrhea episode of 5 days, reductions of 0.060 weight-for-length z-score (0.007 to 0.114; p = 0.027) and 0.061 weight-for-age z-score (0.015 to 0.108; p = 0.009) were noted in the following 30 days. Conclusion This study showed that ETEC is a significant pathogen in Peruvian children who experience serial infections with multiple age-specific pathotypes, resulting in transitory growth impairment.
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Affiliation(s)
- Monica J. Pajuelo
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Sassan Noazin
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | | | - Angie Toledo
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirza Velagic
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Lucero Arias
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayra Ochoa
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lawrence H. Moulton
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H. Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Subhra Chakraborty
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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Chakraborty S, Johura FT, Sultana M, Zhang X, Sadique A, George CM, Monira S, Sack DA, Sack RB, Alam M. Epidemiology of Enterotoxigenic Escherichia coli among Children and Adults Seeking Care at Hospitals in Two Geographically Distinct Rural Areas in Bangladesh. Microorganisms 2024; 12:359. [PMID: 38399763 PMCID: PMC10891752 DOI: 10.3390/microorganisms12020359] [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] [Received: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) infections undeniably continue to have substantial morbidity and mortality in younger children; however, limited data are available on the disease burden of older children and adults and on ETEC epidemiology by geographical location at the subnational level. Facility-based surveillance over the years was established to identify patients with ETEC diarrhea in two geographically distinct areas in rural Bangladesh, Chhatak in the north and Mathbaria in the southern coastal area. ETEC was highly prevalent in both areas, while the proportions, toxin types and colonization factors varied by location, season and age groups. Children < 5 years old and adults between 20 and 60 years old were at the highest risk of ETEC diarrhea which required urgent care. This study underscores the importance of capturing subnational and seasonal variations in ETEC epidemiology. ETEC vaccine developers and public health stakeholders may need to target adults between 20 and 60 years of age in addition to young children as new vaccines currently under development become licensed and introduction begins.
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Affiliation(s)
- Subhra Chakraborty
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (F.-T.J.); (X.Z.); (C.M.G.); (D.A.S.); (R.B.S.)
| | - Fatema-Tuz Johura
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (F.-T.J.); (X.Z.); (C.M.G.); (D.A.S.); (R.B.S.)
- International Centre for Diarrhoeal Disease Research, Dhaka 1212, Bangladesh; (M.S.); (A.S.); (S.M.); (M.A.)
| | - Marzia Sultana
- International Centre for Diarrhoeal Disease Research, Dhaka 1212, Bangladesh; (M.S.); (A.S.); (S.M.); (M.A.)
| | - Xueyan Zhang
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (F.-T.J.); (X.Z.); (C.M.G.); (D.A.S.); (R.B.S.)
| | - Abdus Sadique
- International Centre for Diarrhoeal Disease Research, Dhaka 1212, Bangladesh; (M.S.); (A.S.); (S.M.); (M.A.)
| | - Christine M. George
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (F.-T.J.); (X.Z.); (C.M.G.); (D.A.S.); (R.B.S.)
| | - Shirajum Monira
- International Centre for Diarrhoeal Disease Research, Dhaka 1212, Bangladesh; (M.S.); (A.S.); (S.M.); (M.A.)
| | - David A. Sack
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (F.-T.J.); (X.Z.); (C.M.G.); (D.A.S.); (R.B.S.)
| | - Richard Bradley Sack
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; (F.-T.J.); (X.Z.); (C.M.G.); (D.A.S.); (R.B.S.)
| | - Munirul Alam
- International Centre for Diarrhoeal Disease Research, Dhaka 1212, Bangladesh; (M.S.); (A.S.); (S.M.); (M.A.)
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Héma A, Sermé SS, Sawadogo J, Diarra A, Barry A, Ouédraogo AZ, Nébié I, Tiono AB, Houard S, Chakraborty S, Ouédraogo A, Sirima SB. Contribution of the Rapid LAMP-Based Diagnostic Test (RLDT) to the Evaluation of Enterotoxigenic Escherichia coli (ETEC) and Shigella in Childhood Diarrhea in the Peri-Urban Area of Ouagadougou, Burkina Faso. Microorganisms 2023; 11:2809. [PMID: 38004821 PMCID: PMC10673293 DOI: 10.3390/microorganisms11112809] [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] [Received: 09/23/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
The estimates of enterotoxigenic Escherichia coli (ETEC) and Shigella burden in developing countries are limited by the lack of rapid, accessible, and sensitive diagnostics and surveillance tools. We used a "Rapid LAMP based Diagnostic Test (RLDT)" to detect ETEC and Shigella in diarrheal and non-diarrheal stool samples from a 12-month longitudinal cohort of children under five years of age in a peri-urban area of Ouagadougou in Burkina Faso (West Africa). To allow comparison with the RLDT-Shigella results, conventional culture methods were used to identify Shigella strains in the stool samples. As conventional culture alone cannot detect ETEC cases, a subset of E. coli-like colonies was tested using conventional PCR to detect ETEC toxins genes. Of the 165 stool samples analyzed for ETEC, 24.9% were positive when using RLDT against 4.2% when using culture followed by PCR. ETEC toxin distribution when using RLDT was STp 17.6% (29/165), LT 11.5% (19/165), and STh 8.5% (14/165). Of the 263 specimens tested for Shigella, 44.8% were positive when using RLDT against 23.2% when using culture. The sensitivity and specificity of the RLDT compared to culture (followed by PCR for ETEC) were 93.44% and 69.8% for Shigella and 83.7% and 77.9% for ETEC, respectively. This study indicates that both Shigella and ETEC are substantially underdiagnosed when using conventional culture and highlights the potential contribution of the new RLDT method to improve enteric disease burden estimation and to guide future efforts to prevent and control bacterial enteric infection and disease.
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Affiliation(s)
- Alimatou Héma
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Samuel S. Sermé
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Jean Sawadogo
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Amidou Diarra
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Aissata Barry
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Amidou Z. Ouédraogo
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Issa Nébié
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Alfred B. Tiono
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Sophie Houard
- European Vaccine Initiative (EVI), Universitäts Klinikum Heidelberg Vossstrasse 2, Geb. 4040, 69115 Heidelberg, Germany;
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
| | - Alphonse Ouédraogo
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
| | - Sodiomon B. Sirima
- Groupe de Recherche Action en Santé (GRAS), Ouagadougou 06 BP 10248, Burkina Faso; (S.S.S.); (J.S.); (A.D.); (A.B.); (A.Z.O.); (I.N.); (A.B.T.); (A.O.); (S.B.S.)
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Khalil I, Anderson JD, Bagamian KH, Baqar S, Giersing B, Hausdorff WP, Marshall C, Porter CK, Walker RI, Bourgeois AL. Vaccine value profile for enterotoxigenic Escherichia coli (ETEC). Vaccine 2023; 41 Suppl 2:S95-S113. [PMID: 37951695 DOI: 10.1016/j.vaccine.2023.02.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/28/2022] [Accepted: 02/05/2023] [Indexed: 11/14/2023]
Abstract
Enterotoxigenic Escherichia coli (ETEC) is one of the leading bacterial causes of diarrhoea, especially among children in low-resource settings, and travellers and military personnel from high-income countries. WHO's primary strategic goal for ETEC vaccine development is to develop a safe, effective, and affordable ETEC vaccine that reduces mortality and morbidity due to moderate-to-severe diarrhoeal disease in infants and children under 5 years of age in LMICs, as well as the long-term negative health impact on infant physical and cognitive development resulting from infection with this enteric pathogen. An effective ETEC vaccine will also likely reduce the need for antibiotic treatment and help limit the further emergence of antimicrobial resistance bacterial pathogens. The lead ETEC vaccine candidate, ETVAX, has shown field efficacy in travellers and has moved into field efficacy testing in LMIC infants and children. A Phase 3 efficacy study in LMIC infants is projected to start in 2024 and plans for a Phase 3 trial in travellers are under discussion with the U.S. FDA. Licensing for both travel and LMIC indications is projected to be feasible in the next 5-8 years. Given increasing recognition of its negative impact on child health and development in LMICs and predominance as the leading etiology of travellers' diarrhoea (TD), a standalone vaccine for ETEC is more cost-effective than vaccines targeting other TD pathogens, and a viable commercial market also exists. In contrast, combination of an ETEC vaccine with other vaccines for childhood pathogens in LMICs would maximize protection in a more cost-effective manner than a series of stand-alone vaccines. This 'Vaccine Value Profile' (VVP) for ETEC is intended to provide a high-level, holistic assessment of available data to inform the potential public health, economic and societal value of pipeline vaccines and vaccine-like products. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public private partnerships, and multi-lateral organizations. All contributors have extensive expertise on various elements of the ETEC VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.
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Affiliation(s)
- Ibrahim Khalil
- Department of Global Health, University of Washington, Seattle, WA 98195, USA.
| | - John D Anderson
- Bagamian Scientific Consulting, LLC, Gainesville, FL 32601, USA; Office of Health Affairs, West Virginia University, Morgantown, WV 26505, USA
| | - Karoun H Bagamian
- Bagamian Scientific Consulting, LLC, Gainesville, FL 32601, USA; Department of Environmental and Global Health, University of Florida, Gainesville, FL 32603, USA
| | - Shahida Baqar
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Birgitte Giersing
- Department of Immunization, Vaccines and Biologicals (IVB), World Health Organization (WHO), Geneva, Switzerland
| | - William P Hausdorff
- PATH, Center for Vaccine Innovation and Access, 455 Massachusetts Ave NW, Washington, DC 20001 USA; Faculty of Medicine, Université Libre de Bruxelles, Brussels 1070, Belgium
| | - Caroline Marshall
- Department of Immunization, Vaccines and Biologicals (IVB), World Health Organization (WHO), Geneva, Switzerland
| | - Chad K Porter
- Directorate for DoD Infectious Diseases Research, Naval Medical Research Command, Silver Spring, MD 20190, USA
| | - Richard I Walker
- PATH, Center for Vaccine Innovation and Access, 455 Massachusetts Ave NW, Washington, DC 20001 USA
| | - A Louis Bourgeois
- PATH, Center for Vaccine Innovation and Access, 455 Massachusetts Ave NW, Washington, DC 20001 USA
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7
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Chowdhury G, Ghosh D, Zhou Y, Deb AK, Mukhopadhyay AK, Dutta S, Chakraborty S. Field evaluation of a simple and rapid diagnostic test, RLDT to detect Shigella and enterotoxigenic E. coli in Indian children. RESEARCH SQUARE 2023:rs.3.rs-3293791. [PMID: 37886599 PMCID: PMC10602125 DOI: 10.21203/rs.3.rs-3293791/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: 10/28/2023]
Abstract
The diagnostic assays currently used to detect Shigella spp. (Shigella) and enterotoxigenic Escherichia coli (ETEC) are complex or elaborate which make them difficult to apply in resource poor settings where these diseases are endemic. The simple and rapid nucleic acid amplification-based assay "Rapid LAMP-based Diagnostic Test (RLDT)" was evaluated to detect Shigella spp (Shigella) and enterotoxigenic Escherichia coli (ETEC) and determine the epidemiology of these pathogens in Kolkata, India. Stool samples (n = 405) from children under five years old with diarrhea seeking care at the hospitals were tested, and 85(21%) and 68(17%) by RLDT, 91(23%) and 58(14%) by quantitative PCR (qPCR) and 35(9%) and 15(4%) by culture, were positive for Shigella and ETEC, respectively. The RLDT showed almost perfect agreement with qPCR, Kappa 0.96 and 0.89; sensitivity 93% and 98%; specificity 100% and 97% for Shigella and ETEC, respectively. While RLDT detected 12% more Shigella and 13% more ETEC than culture, all culture positives for Shigella and ETEC except one each were also positive by the RLDT, sensitivity 97% and 93% respectively. RLDT is a simple, sensitive, and rapid assay that could be implemented with minimum training in the endemic regions to strengthen the disease surveillance system and rapid outbreak detection.
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Affiliation(s)
| | - Debjani Ghosh
- ICMR-National Institute of Cholera and Enteric Diseases
| | - YiYi Zhou
- Johns Hopkins Bloomberg School of Public Health
| | - Alok K Deb
- ICMR-National Institute of Cholera and Enteric Diseases
| | | | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases
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Chakraborty S, Velagic M, Connor S. Development of a simple, rapid, and sensitive molecular diagnostic assay for cholera. PLoS Negl Trop Dis 2023; 17:e0011113. [PMID: 36745674 PMCID: PMC9934353 DOI: 10.1371/journal.pntd.0011113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 02/16/2023] [Accepted: 01/19/2023] [Indexed: 02/07/2023] Open
Abstract
Cholera continues to inflict high rates of morbidity and mortality. Prompt identification of cholera cases facilitates rapid outbreak responses in the short term while providing reliable surveillance data to guide long-term policies and interventions. Microbiological stool culture, the current recognized gold standard for diagnosing cholera, has significant limitations. Rapid diagnostic tests (RDTs) represent promising alternatives for diagnosing cholera in areas with limited laboratory infrastructure. However, studies conducted with the current cholera RDTs demonstrated wide variations in sensitivity and specificity. To address this gap in the diagnosis of cholera, we developed a simple, rapid, and sensitive diagnostic assay, "Rapid LAMP based Diagnostic Test (RLDT)." With a novel, simple sample preparation method directly from the fecal samples along with lyophilized reaction strips and using established Loop-mediated Isothermal Amplification (LAMP) platform, cholera toxin gene (ctxA) and O1 (O1rfb) gene could be detected in less than an hour. Cholera RLDT assay is cold chain and electricity-free. To avoid any end-user bias, a battery-operated, handheld reader was used to read the RLDT results. The performance specifications of the cholera RLDT assay, including analytical sensitivity and specificity, were evaluated using direct fecal samples, dried fecal samples on filter paper, and environmental water samples spiked with cholera strain. The limit of detection (LOD) was ~104 CFU/gm of stool for both ctxA and O1 genes, corresponding to about 1 CFU of Vibrio cholerae per reaction within 40 minutes. The LOD was 10 bacteria per ml of environmental water when tested with RLDT directly, without enrichment. Being simple, RLDT has the potential to be applied in resource-poor endemic settings for rapid, sensitive, and reliable diagnosis of cholera.
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Affiliation(s)
- Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Mirza Velagic
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Sean Connor
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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Silwamba S, Chilyabanyama ON, Liswaniso F, Chisenga CC, Chilengi R, Dougan G, Kwenda G, Chakraborty S, Simuyandi M. Field evaluation of a novel, rapid diagnostic assay, and molecular epidemiology of enterotoxigenic E. coli among Zambian children presenting with diarrhea. PLoS Negl Trop Dis 2022; 16:e0010207. [PMID: 35930612 PMCID: PMC9385031 DOI: 10.1371/journal.pntd.0010207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 08/17/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background Enterotoxigenic Escherichia coli (ETEC) is one of the top aetiologic agents of diarrhea in children under the age of 5 in low-middle income countries (LMICs). The lack of point of care diagnostic tools for routine ETEC diagnosis results in limited data regarding the actual burden and epidemiology in the endemic areas. We evaluated performance of the novel Rapid LAMP based Diagnostic Test (RLDT) for detection of ETEC in stool as a point of care diagnostic assay in a resource-limited setting. Methods We conducted a cross-sectional study of 324 randomly selected stool samples from children under 5 presenting with moderate to severe diarrhea (MSD). The samples were collected between November 2012 to September 2013 at selected health facilities in Zambia. The RLDT was evaluated by targeting three ETEC toxin genes [heat labile toxin (LT) and heat stable toxins (STh and STp)]. Quantitative PCR was used as the “gold standard” to evaluate the diagnostic sensitivity and specificity of RLDT for detection of ETEC. We additionally described the prevalence and seasonality of ETEC. Results The study included 324 participants, 50.6% of which were female. The overall prevalence of ETEC was 19.8% by qPCR and 19.4% by RLDT. The children between 12 to 59 months had the highest prevalence of 22%. The study determined ETEC toxin distribution was LT 28/321(9%), ST 18/321(6%) and LT/ST 16/321(5%). The sensitivity and specificity of the RLDT compared to qPCR using a Ct 35 as the cut-off, were 90.7% and 97.5% for LT, 85.2% and 99.3% for STh and 100% and 99.7% for STp, respectively. Conclusion The results of this study suggest that RLDT is sufficiently sensitive and specific and easy to implement in the endemic countries. Being rapid and simple, the RLDT also presents as an attractive tool for point-of-care testing at the health facilities and laboratories in the resource-limited settings. ETEC is one of the top causes of diarrheal diseases in low and middle income countries. The advancement of molecular diagnosis has made it possible to accurately detect ETEC in endemic areas. However, the complexity, infrastructure and cost implication of these tests has made it a challenge to routinely incorporate them in health facilities in endemic settings. The ETEC RLDT is a simple and cost-effective molecular tool that can be used to screen for ETEC in resource limited settings. Here, we described the performance of the RLDT against a qPCR as the gold standard. Our findings showed that the ETEC RLDT performs comparable to the qPCR and would be a suitable screening tool in health facilities in recourse limited settings.
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Affiliation(s)
- Suwilanji Silwamba
- Enteric Diseases and Vaccines Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Obvious N. Chilyabanyama
- Enteric Diseases and Vaccines Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Fraser Liswaniso
- Enteric Diseases and Vaccines Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Caroline C. Chisenga
- Enteric Diseases and Vaccines Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Roma Chilengi
- Enteric Diseases and Vaccines Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Gordon Dougan
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (SC); (MS)
| | - Michelo Simuyandi
- Enteric Diseases and Vaccines Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
- * E-mail: (SC); (MS)
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