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Lappan R, Chown SL, French M, Perlaza-Jiménez L, Macesic N, Davis M, Brown R, Cheng A, Clasen T, Conlan L, Goddard F, Henry R, Knight DR, Li F, Luby S, Lyras D, Ni G, Rice SA, Short F, Song J, Whittaker A, Leder K, Lithgow T, Greening C. Towards integrated cross-sectoral surveillance of pathogens and antimicrobial resistance: Needs, approaches, and considerations for linking surveillance to action. ENVIRONMENT INTERNATIONAL 2024; 192:109046. [PMID: 39378692 DOI: 10.1016/j.envint.2024.109046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/30/2024] [Accepted: 10/01/2024] [Indexed: 10/10/2024]
Abstract
Pathogenic and antimicrobial-resistant (AMR) microorganisms are continually transmitted between human, animal, and environmental reservoirs, contributing to the high burden of infectious disease and driving the growing global AMR crisis. The sheer diversity of pathogens, AMR mechanisms, and transmission pathways connecting these reservoirs create the need for comprehensive cross-sectoral surveillance to effectively monitor risks. Current approaches are often siloed by discipline and sector, focusing independently on parts of the whole. Here we advocate that integrated surveillance approaches, developed through transdisciplinary cross-sector collaboration, are key to addressing the dual crises of infectious diseases and AMR. We first review the areas of need, challenges, and benefits of cross-sectoral surveillance, then summarise and evaluate the major detection methods already available to achieve this (culture, quantitative PCR, and metagenomic sequencing). Finally, we outline how cross-sectoral surveillance initiatives can be fostered at multiple scales of action, and present key considerations for implementation and the development of effective systems to manage and integrate this information for the benefit of multiple sectors. While methods and technologies are increasingly available and affordable for comprehensive pathogen and AMR surveillance across different reservoirs, it is imperative that systems are strengthened to effectively manage and integrate this information.
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Affiliation(s)
- Rachael Lappan
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Securing Antarctica's Environmental Future, Monash University, Melbourne, Australia.
| | - Steven L Chown
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Securing Antarctica's Environmental Future, Monash University, Melbourne, Australia
| | - Matthew French
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Faculty of Art, Design and Architecture (MADA), Monash University, Melbourne, Australia
| | - Laura Perlaza-Jiménez
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Nenad Macesic
- Centre to Impact AMR, Monash University, Melbourne, Australia; Department of Infectious Diseases, Alfred Health, Melbourne, Australia; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Mark Davis
- Centre to Impact AMR, Monash University, Melbourne, Australia; School of Social Sciences, Monash University, Melbourne, Australia
| | - Rebekah Brown
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Monash Sustainable Development Institute, Melbourne, Australia
| | - Allen Cheng
- Centre to Impact AMR, Monash University, Melbourne, Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia; Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, Australia
| | - Thomas Clasen
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lindus Conlan
- Centre to Impact AMR, Monash University, Melbourne, Australia
| | - Frederick Goddard
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Rebekah Henry
- Centre to Impact AMR, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Department of Civil Engineering, Monash University, Melbourne, Australia
| | - Daniel R Knight
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA, Australia; School of Biomedical Sciences, The University of Western Australia, WA, Australia
| | - Fuyi Li
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection and Cancer Programs, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Stephen Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Dena Lyras
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Gaofeng Ni
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Scott A Rice
- Microbiomes for One Systems Health, CSIRO Agriculture and Food, Canberra, Australia
| | - Francesca Short
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jiangning Song
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection and Cancer Programs, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Andrea Whittaker
- Centre to Impact AMR, Monash University, Melbourne, Australia; School of Social Sciences, Monash University, Melbourne, Australia
| | - Karin Leder
- Centre to Impact AMR, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Chris Greening
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Securing Antarctica's Environmental Future, Monash University, Melbourne, Australia.
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Dung TTN, Phat VV, Vinh C, Lan NPH, Phuong NLN, Ngan LTQ, Thwaites G, Thwaites L, Rabaa M, Nguyen ATK, Duy PT. Development and validation of multiplex real-time PCR for simultaneous detection of six bacterial pathogens causing lower respiratory tract infections and antimicrobial resistance genes. BMC Infect Dis 2024; 24:164. [PMID: 38326753 PMCID: PMC10848345 DOI: 10.1186/s12879-024-09028-2] [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: 06/17/2023] [Accepted: 01/18/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, Streptococcus pneumoniae and Staphylococcus aureus are major bacterial causes of lower respiratory tract infections (LRTIs) globally, leading to substantial morbidity and mortality. The rapid increase of antimicrobial resistance (AMR) in these pathogens poses significant challenges for their effective antibiotic therapy. In low-resourced settings, patients with LRTIs are prescribed antibiotics empirically while awaiting several days for culture results. Rapid pathogen and AMR gene detection could prompt optimal antibiotic use and improve outcomes. METHODS Here, we developed multiplex quantitative real-time PCR using EvaGreen dye and melting curve analysis to rapidly identify six major pathogens and fourteen AMR genes directly from respiratory samples. The reproducibility, linearity, limit of detection (LOD) of real-time PCR assays for pathogen detection were evaluated using DNA control mixes and spiked tracheal aspirate. The performance of RT-PCR assays was subsequently compared with the gold standard, conventional culture on 50 tracheal aspirate and sputum specimens of ICU patients. RESULTS The sensitivity of RT-PCR assays was 100% for K. pneumoniae, A. baumannii, P. aeruginosa, E. coli and 63.6% for S. aureus and the specificity ranged from 87.5% to 97.6%. The kappa correlation values of all pathogens between the two methods varied from 0.63 to 0.95. The limit of detection of target bacteria was 1600 CFU/ml. The quantitative results from the PCR assays demonstrated 100% concordance with quantitative culture of tracheal aspirates. Compared to culture, PCR assays exhibited higher sensitivity in detecting mixed infections and S. pneumoniae. There was a high level of concordance between the detection of AMR gene and AMR phenotype in single infections. CONCLUSIONS Our multiplex quantitative RT-PCR assays are fast and simple, but sensitive and specific in detecting six bacterial pathogens of LRTIs and their antimicrobial resistance genes and should be further evaluated for clinical utility.
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Affiliation(s)
- Tran Thi Ngoc Dung
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | - Voong Vinh Phat
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | - Chau Vinh
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
| | | | | | | | - Guy Thwaites
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Louise Thwaites
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Maia Rabaa
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Anh T K Nguyen
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Pham Thanh Duy
- Molecular Epidemiology Group, Oxford University Clinical Research Unit, 764 Vo Van Kiet Street, Ward 1, District 5, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK.
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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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Luo Z, Cao P, Zhang C, Xu Z, Xu P, Liang T. Recurrent bacterial meningitis caused by incomplete Type I inner ear malformation: A case report. IBRAIN 2023; 10:231-237. [PMID: 38915941 PMCID: PMC11193859 DOI: 10.1002/ibra.12093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 06/26/2024]
Abstract
The incidence of incomplete partition Type I inner ear malformation is very low; therefore, bacterial meningitis caused by this malformation is also rare. Here, we report a case of such a patient. This case is a young female patient, who is 7 years old, began to have recurrent headaches, and after 5 years, also began to have chest and back pain. The doctor diagnosed meningitis, and the anti-infection treatment was effective. She was followed up annually and continued to have outbreaks repeatedly for 17 years, but the cause of repeated infection was not found. After a detailed diagnosis and treatment in our hospital, the patient was finally diagnosed with incomplete partition Type I inner ear malformation, resulting in repeated bacterial meningitis. The patient recovered well after surgical treatment, and the symptoms did not recur after 1-year follow-up.
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Affiliation(s)
- Zhong Luo
- Department of NeurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Piao Cao
- Department of NeurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Chun‐Lin Zhang
- Department of OtorhinolaryngologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Zu‐Cai Xu
- Department of NeurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Ping Xu
- Department of NeurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Tao Liang
- Department of NeurologyAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
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5
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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] [Grants] [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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Clark JA, Kean IRL, Curran MD, Khokhar F, White D, Daubney E, Conway Morris A, Navapurkar V, Bartholdson Scott J, Maes M, Bousfield R, Gouliouris T, Agrawal S, Inwald D, Zhang Z, Török ME, Baker S, Pathan N. Rapid Assay for Sick Children with Acute Lung infection Study (RASCALS): diagnostic cohort study protocol. BMJ Open 2021; 11:e056197. [PMID: 34845080 PMCID: PMC8634010 DOI: 10.1136/bmjopen-2021-056197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Lower respiratory tract infection (LRTI) is the most commonly treated infection in critically ill children. Pathogens are infrequently identified on routine respiratory culture, and this is a time-consuming process. A syndromic approach to rapid molecular testing that includes a wide range of bacterial and fungal targets has the potential to aid clinical decision making and reduce unnecessary broad spectrum antimicrobial prescribing. Here, we describe a single-centre prospective cohort study investigating the use of a 52-pathogen TaqMan array card (TAC) for LRTI in the paediatric intensive care unit (PICU). METHODS AND ANALYSIS Critically ill children with suspected LRTI will be enrolled to this 100 patient single-centre prospective observational study in a PICU in the East of England. Samples will be obtained via routine non-bronchoscopic bronchoalveolar lavage which will be sent for standard microbiology culture in addition to TAC. A blood draw will be obtained via any existing vascular access device. The primary outcomes of the study will be (1) concordance of TAC result with routine culture and 16S rRNA gene sequencing and (2) time of diagnostic result from TAC versus routine culture. Secondary outcomes will include impact of the test on total antimicrobial prescriptions, a description of the inflammatory profile of the lung and blood in response to pneumonia and a description of the clinical experience of medical and nursing staff using TAC. ETHICS AND DISSEMINATION This study has been approved by the Yorkshire and the Humber-Bradford Leeds Research Ethics Committee (REC reference 20/YH/0089). Informed consent will be obtained from all participants. Results will be published in peer-reviewed publications and international conferences. TRIAL REGISTRATION NUMBER NCT04233268.
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Affiliation(s)
- John Alexander Clark
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge, UK
| | - Fahad Khokhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Deborah White
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Esther Daubney
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Shruti Agrawal
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David Inwald
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Zhenguang Zhang
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Nazima Pathan
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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7
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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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8
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Lappan R, Henry R, Chown SL, Luby SP, Higginson EE, Bata L, Jirapanjawat T, Schang C, Openshaw JJ, O'Toole J, Lin A, Tela A, Turagabeci A, Wong THF, French MA, Brown RR, Leder K, Greening C, McCarthy D. Monitoring of diverse enteric pathogens across environmental and host reservoirs with TaqMan array cards and standard qPCR: a methodological comparison study. Lancet Planet Health 2021; 5:e297-e308. [PMID: 33964239 PMCID: PMC8116308 DOI: 10.1016/s2542-5196(21)00051-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Multiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens are transmited via several pathways through human, animal, and environmental reservoirs. Individual qPCR assays have been extensively used to detect enteropathogens within these types of samples, whereas the TaqMan array card (TAC), which allows simultaneous detection of multiple enteropathogens, has only previously been validated in human clinical samples. METHODS In this methodological comparison study, we compared the performance of a custom 48-singleplex TAC relative to standard qPCR. We established the sensitivity and specificity of each method for the detection of eight enteric targets, by using spiked samples with varying levels of PCR inhibition. We then tested the prevalence and abundance of pathogens in wastewater from Melbourne (Australia), and human, animal, and environmental samples from informal settlements in Suva, Fiji using both TAC and qPCR. FINDINGS Both methods exhibited similarly h specificity (TAC 100%, qPCR 94%), sensitivity (TAC 92%, qPCR 100%), and quantitation accuracy (TAC 91%, qPCR 99%) in non-inhibited sample matrices with spiked gene fragments. PCR inhibitors substantially affected detection via TAC, though this issue was alleviated by ten-fold sample dilution. Among samples from informal settlements, the two techniques performed similarly for detection (89% agreement) and quantitation (R2 0·82) for the eight enteropathogen targets. The TAC additionally included 38 other enteric targets, enabling detection of diverse faecal pathogens and extensive environmental contamination that would be prohibitively labour intensive to assay by standard qPCR. INTERPRETATION The two techniques produced similar results across diverse sample types, with qPCR prioritising greater sensitivity and quantitation accuracy, and TAC trading small reductions in these for a cost-effective larger enteropathogen panel enabling a greater number of enteric pathogens to be analysed concurrently, which is beneficial given the abundance and variety of enteric pathogens in environments such as urban informal settlements. The ability to monitor multiple enteric pathogens across diverse reservoirs could allow better resolution of pathogen exposure pathways, and the design and monitoring of interventions to reduce pathogen load. FUNDING Wellcome Trust Our Planet, Our Health programme.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Rebekah Henry
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Ellen E Higginson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Lamiya Bata
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Christelle Schang
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - John J Openshaw
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Joanne O'Toole
- School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Audrie Lin
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, CA, USA
| | - Autiko Tela
- School of Public Health, Fiji National University, Suva, Fiji
| | | | - Tony H F Wong
- Water Sensitive Cities Institute, Monash University, Clayton, VIC, Australia
| | - Matthew A French
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | - Rebekah R Brown
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | - Karin Leder
- School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David McCarthy
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
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Bonny SQ, Hossain MAM, Uddin SMK, Pulingam T, Sagadevan S, Johan MR. Current trends in polymerase chain reaction based detection of three major human pathogenic vibrios. Crit Rev Food Sci Nutr 2020; 62:1317-1335. [DOI: 10.1080/10408398.2020.1841728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sharmin Quazi Bonny
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - M. A. Motalib Hossain
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Syed Muhammad Kamal Uddin
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Thiruchelvi Pulingam
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Suresh Sagadevan
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
| | - Mohd Rafie Johan
- Nanotechnology and Catalysis Research Centre, Institute of Advanced Studies, University of Malaya, Kuala Lumpur, Malaysia
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10
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Li YX, Long DL, Liu J, Qiu D, Wang J, Cheng X, Yang X, Li RM, Wang G. Gestational diabetes mellitus in women increased the risk of neonatal infection via inflammation and autophagy in the placenta. Medicine (Baltimore) 2020; 99:e22152. [PMID: 33019392 PMCID: PMC7535644 DOI: 10.1097/md.0000000000022152] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) produces numerous problems for maternal and fetal outcomes. However, the precise molecular mechanisms of GDM are not clear. METHODS In our study, we randomly assigned 22 pregnant women with fasting glucose concentrations, 1 hour oral glucose tolerance test (1H-OGTT) and 2 hour oral glucose tolerance test (2H-OGTT), different than 28 normal pregnant women from a sample of 107 pregnant women at the First Affiliated Hospital of Jinan University in China. Lipopolysaccharide (LPS), interleukin 1 alpha (IL-1α), interleukin-6 (IL-6), interleukin-8 (IL-8) and tumor necrosis factor alpha (TNF-α) were measured from blood plasma of pregnant women and umbilical arteries using ultraviolet spectrophotometry. Hematoxylin & Eosin (H&E), Periodic acid-Schiff (PAS) or Masson staining were performed to examine whether diabetes mellitus altered the morphology of placenta. Quantitative PCR (Q-PCR), western blotting and immunofluorescent staining were performed to examine whether diabetes mellitus and autophagy altered the gene expressions of the placental tissue. RESULTS We found that women with GDM exhibited increased placental weight and risk of neonatal infection. The concentrations of IL-6 protein and IL-8 protein in GDM were increased in both maternal and umbilical arterial blood. H&E, Masson and PAS staining results showed an increased number of placental villi and glycogen deposition in patients with GDM, but no placental sclerosis was found. Q-PCR results suggested that the expression levels of HIF-1α and the toll like receptor 4 (TLR4)/ myeloid differential protein-88 (MyD88)/ nuclear factor kappa-B (NF-κB) pathway were increased in the GDM placenta. Through Western Blotting, we found that the expression of NF-kappa-B inhibitor alpha (IKBα) and Nuclear factor-κB p65 (NF-κB p65) in GDM placenta was significantly enhanced. We also showed that the key autophagy-related genes, autophagy-related 7 (ATG7) and microtubule-associated protein 1A/1B-light chain 3 (LC3), were increased in GDM compared with normal pregnant women. CONCLUSIONS Our results suggest that women with GDM exhibit an increased risk of neonatal infection via inflammation and autophagy in the placenta.
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Affiliation(s)
- Yi-xiao Li
- The First Affiliate Hospital of Jinan University
- International Joint Laboratory for Embryonic Development & Prenatal Medicine, Division of Histology and Embryology, Medical College
| | - Deng-lu Long
- International Joint Laboratory for Embryonic Development & Prenatal Medicine, Division of Histology and Embryology, Medical College
| | - Jia Liu
- The First Affiliate Hospital of Jinan University
| | - Di Qiu
- The First Affiliate Hospital of Jinan University
| | - Jingyun Wang
- The First Affiliate Hospital of Jinan University
| | - Xin Cheng
- International Joint Laboratory for Embryonic Development & Prenatal Medicine, Division of Histology and Embryology, Medical College
- Key Laboratory for Regenerative Medicine of the Ministry of Education, Jinan University, Guangzhou, China
| | - Xuesong Yang
- International Joint Laboratory for Embryonic Development & Prenatal Medicine, Division of Histology and Embryology, Medical College
- Key Laboratory for Regenerative Medicine of the Ministry of Education, Jinan University, Guangzhou, China
| | - Rui-man Li
- The First Affiliate Hospital of Jinan University
| | - Guang Wang
- International Joint Laboratory for Embryonic Development & Prenatal Medicine, Division of Histology and Embryology, Medical College
- Key Laboratory for Regenerative Medicine of the Ministry of Education, Jinan University, Guangzhou, China
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11
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Detection of Eight Respiratory Bacterial Pathogens Based on Multiplex Real-Time PCR with Fluorescence Melting Curve Analysis. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2020; 2020:2697230. [PMID: 32184908 PMCID: PMC7061119 DOI: 10.1155/2020/2697230] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 01/23/2023]
Abstract
Background and Objective. Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Pseudomonas aeruginosa, and Mycobacterium tuberculosis are primary respiratory bacterial pathogens contributing to morbidity and mortality in developing countries. This study evaluated the diagnostic performance of multiplex real-time PCR with fluorescence melting curve analysis (MCA) assay, which was used to detect eight respiratory bacterial pathogens simultaneously. Methods A total of 157 sputum specimens were examined by multiplex real-time with fluorescence MCA, and the results were compared with the conventional culture method. Results Multiplex real-time PCR with fluorescence MCA specifically detected and differentiated eight respiratory bacterial pathogens by different melting curve peaks for each amplification product within 2 hours and exhibited high repeatability. The limit of detection ranged from 64 to 102 CFU/mL in the multiplex PCR system. Multiplex real-time PCR with fluorescence MCA showed a sensitivity greater than 80% and a 100% specificity for each pathogen. The kappa correlation of eight bacteria ranged from 0.89 to 1.00, and the coefficient of variation ranged from 0.05% to 0.80%. Conclusions Multiplex real-time PCR with fluorescence MCA assay is a sensitive, specific, high-throughput, and cost-effective method to detect multiple bacterial pathogens simultaneously.
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