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Ahuja S, Tallur S, Kondabagil K. Simultaneous microbial capture and nucleic acid extraction from wastewater with minimal pre-processing and high recovery efficiency. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170347. [PMID: 38336063 DOI: 10.1016/j.scitotenv.2024.170347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/22/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The COVID-19 pandemic accelerated research towards developing low-cost assays for automated urban wastewater monitoring assay that can be integrated into an environmental surveillance system for early warning of frequent disease outbreaks and future pandemics. Microbial concentration is one of the most challenging steps in wastewater surveillance, due to the sample heterogeneity and low pathogen load. Keeping in mind the requirements of large-scale testing in densely populated low- or middle-income countries (LMICs), such assays would need to be low-cost and have rapid turnaround time with high recovery efficiency. In this study, two such methods are presented and evaluated against commercially available kits for pathogen detection in wastewater. The first method utilizes paper dipsticks while the second method comprises of a PTFE membrane filter (PMF) integrated with a peristaltic pump. Both methods were used to concentrate and isolate nucleic acids from different microbes such as SARS-CoV-2, pepper mild mottle virus (PMMoV), bacteriophage Phi6, and E. coli from wastewater samples with minimal or no sample pre-processing. While the paper dipstick method is suitable for sub-milliliter sample volume, the PMF method can be used with larger volumes of wastewater sample (40 mL) and can detect multiple microbes with recovery efficiency comparable to commercially available kits.
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Affiliation(s)
- Shruti Ahuja
- Centre for Research in Nanotechnology & Science (CRNTS), IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Siddharth Tallur
- Department of Electrical Engineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai 400076, Maharashtra, India.
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Kwambana-Adams BA, Clark SA, Tay N, Agbla S, Chaguza C, Kagucia EW, Borrow R, Heyderman RS. Evaluation of Dried Blood and Cerebrospinal Fluid Filter Paper Spots for Storing and Transporting Clinical Material for the Molecular Diagnosis of Invasive Meningococcal Disease. Int J Mol Sci 2022; 23:ijms231911879. [PMID: 36233182 PMCID: PMC9569512 DOI: 10.3390/ijms231911879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
To improve the storage and transport of clinical specimens for the diagnosis of Neisseria meningitidis (Nm) infections in resource-limited settings, we have evaluated the performance of dried blood spot (DBS) and dried cerebrospinal fluid spot (DCS) assays. DBS and DCS were prepared on filter paper from liquid specimens previously tested for Nm in the United Kingdom. Nm was detected and genogrouped by real-time PCR performed on crude genomic DNA extracted from the DBS (n = 226) and DCS (n = 226) specimens. Targeted whole-genome sequencing was performed on a subset of specimens, DBS (n = 4) and DCS (n = 6). The overall agreement between the analysis of liquid and dried specimens was (94.2%; 95% CI 90.8−96.7) for blood and (96.4%; 95% CI 93.5−98.0) for cerebrospinal fluid. Relative to liquid specimens as the reference, the DBS and DCS assays had sensitivities of (89.1%; 95% CI 82.7−93.8) and (94.2%; 95% CI 88.9−97.5), respectively, and both assays had specificities above 98%. A genogroup was identified by dried specimen analysis for 81.9% of the confirmed meningococcal infections. Near full-length Nm genome sequences (>86%) were obtained for all ten specimens tested which allowed determination of the sequence type, clonal complex, presence of antimicrobial resistance and other meningococcal genotyping. Dried blood and CSF filter spot assays offer a practical alternative to liquid specimens for the molecular and genomic characterisation of invasive meningococcal diseases in low-resource settings.
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Affiliation(s)
- Brenda A. Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Clinical Sciences Department, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
- Malawi-Liverpool-Wellcome Clinical Research Programme (MLW), Blantyre P.O. Box 30096, Malawi
- Correspondence: (B.A.K.-A.); (S.A.C.)
| | - Stephen A. Clark
- Meningococcal Reference Unit, United Kingdom Health Security Agency (UKHSA), Manchester M13 9WL, UK
- Correspondence: (B.A.K.-A.); (S.A.C.)
| | - Nicole Tay
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Schadrac Agbla
- Department of Health Data Science, University of Liverpool, Liverpool L69 3GF, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Chrispin Chaguza
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT 06510, USA
| | - Eunice W. Kagucia
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi P.O. Box 230-8010, Kenya
| | - Ray Borrow
- Meningococcal Reference Unit, United Kingdom Health Security Agency (UKHSA), Manchester M13 9WL, UK
| | - Robert S. Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
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Evaluation of Multiplex Real-time PCR and WHO Criteria for Diagnosing Childhood Bacterial Meningitis in a Tertiary Referral Hospital in Iran. ARCHIVES OF PEDIATRIC INFECTIOUS DISEASES 2022. [DOI: 10.5812/pedinfect.101822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: Childhood bacterial meningitis (BM) requires prompt and precise diagnosis to provide proper treatment and decline mortality and morbidity. Objectives: We aimed to evaluate the World Health Organization (WHO) criteria and polymerase chain reaction (PCR) for diagnosing BM in children admitted to a tertiary referral hospital in Shiraz, southern Iran. Materials: We included all 492 children aged one month to 17 years suspected of meningitis who had cerebrospinal fluid (CSF) leukocytosis admitted to Nemazi Hospital from August 2016 to September 2017. The CSF specimens were examined for routine analysis, Gram staining, and culture. A multiplex real-time PCR was used to identify Streptococcus pneumoniae, Haemophilus influenzae type b (Hib), and Neisseria meningitidis in the CSF samples. Seven viruses were also investigated using real-time PCR. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated using the WHO criteria and the multiplex real-time PCR results. Results: Seventy-four CSF samples had leukocytosis. Nineteen (22.9%) patients had BM caused by S. pneumoniae (n = 14), Hib (n = 2), Salmonella enterica (n = 2), and N. meningitidis (n = 1). The PCR test detected all cases, except for two with Salmonella meningitis (sensitivity 89.4%, specificity 100%, PPV 100%, and NPV 96%). The WHO criteria detected all cases, except three who received antibiotics at least four days before performing lumbar puncture (sensitivity 84.2%, specificity 98.2%, PPV 94.1%, and NPV 94.7%). Enterovirus was the most common viral etiology (6.75%). Conclusions: The WHO criteria and the multiplex real-time PCR had high accuracy in our setting, and their use could decrease the antibiotic over-prescription in febrile children suspected of meningitis.
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du Plessis M, de Gouveia L, Freitas C, Abera NA, Lula BS, Raboba JL, Nhantumbo AA, Jantjies E, Uwimana J, Phungwayo N, Maphalala G, Masona G, Muyombe J, Mugisha D, Nalumansi E, Odongkara M, Lukwesa-Musyani C, Nakazwe R, Dondo V, Macharaga J, Weldegebriel GG, Mwenda JM, Serhan F, Cohen AL, Lessa FC, von Gottberg A. The Role of Molecular Testing in Pediatric Meningitis Surveillance in Southern and East African Countries, 2008-2017. J Infect Dis 2021; 224:S194-S203. [PMID: 34469556 PMCID: PMC8409535 DOI: 10.1093/infdis/jiab092] [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] [Indexed: 11/13/2022] Open
Abstract
Background As part of the global Invasive Bacterial Vaccine-Preventable Diseases Surveillance Network, 12 African countries referred cerebrospinal fluid (CSF) samples to South Africa’s regional reference laboratory. We evaluated the utility of real-time polymerase chain reaction (PCR) in detecting and serotyping/grouping Haemophilus influenzae, Neisseria meningitidis, and Streptococcus pneumoniae (HNS). Methods From 2008 to 2017, CSF samples collected from children <5 years old with suspected meningitis underwent routine microbiology testing in-country, and 11 680 samples were submitted for HNS PCR at the regional reference laboratory. Unconditional logistic regression, with adjustment for geographic location, was performed to identify factors associated with PCR positivity. Results The overall HNS PCR positivity rate for all countries was 10% (1195 of 11 626 samples). In samples with both PCR and culture results, HNS PCR positivity was 11% (744 of 6747 samples), and HNS culture positivity was 3% (207 of 6747). Molecular serotype/serogroup was assigned in 75% of PCR-positive specimens (762 of 1016). Compared with PCR-negative CSF samples, PCR-positive samples were more often turbid (adjusted odds ratio, 6.80; 95% confidence interval, 5.67–8.17) and xanthochromic (1.72; 1.29–2.28), had elevated white blood cell counts (6.13; 4.71–7.99) and high protein concentrations (5.80; 4.34–7.75), and were more often HNS culture positive (32.70; 23.18–46.12). Conclusion PCR increased detection of vaccine-preventable bacterial meningitis in countries where confirmation of suspected meningitis cases is impeded by limited culture capacity.
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Affiliation(s)
- Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Cesar Freitas
- Hospital Pediatrico David Bernardino, Luanda, Angola
| | - Negga Asamene Abera
- Bacteriology National Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Budiaki Sylvie Lula
- Department of Microbiology National Reference Laboratory, Ministry of Health, Maseru, Lesotho
| | - Julia Liliane Raboba
- Department of Child Health, Teaching Hospital, Centre Hospitalier Universitaire Mère Enfant Tsaralàlana, Antananarivo, Madagascar
| | | | - Elana Jantjies
- Namibia Institute of Pathology, Microbiology, and Windhoek Central Reference Laboratory, Windhoek, Namibia
| | | | - Nomcebo Phungwayo
- National Surveillance Laboratory, eSwatini Health Laboratory Services, eSwatini
| | - Gugu Maphalala
- National Surveillance Laboratory, eSwatini Health Laboratory Services, eSwatini
| | - Gilbert Masona
- National Surveillance Laboratory, eSwatini Health Laboratory Services, eSwatini
| | - John Muyombe
- Bacteriology Laboratory, Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - David Mugisha
- Ministry of Health, Bacteriology Laboratory, Mulago Teaching Hospital, Uganda
| | - Esther Nalumansi
- Ministry of Health, Bacteriology Laboratory, Mulago Teaching Hospital, Uganda
| | - Moses Odongkara
- Ministry of Health, Bacteriology Laboratory, Mulago Teaching Hospital, Uganda
| | - Chileshe Lukwesa-Musyani
- Ministry of Health, University Teaching Hospital, Pathology and Microbiology Department, Lusaka, Zambia
| | - Ruth Nakazwe
- Ministry of Health, University Teaching Hospital, Pathology and Microbiology Department, Lusaka, Zambia
| | | | | | - Goitom G Weldegebriel
- World Health Organization Regional Office for Africa, Inter-Country Support Team, Harare, Zimbabwe
| | - Jason M Mwenda
- World Health Organization Regional Office for Africa, Brazzaville, Republic of Congo
| | | | | | - Fernanda C Lessa
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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De Vitis E, Ricci S, Nieddu F, Moriondo M, Cortimiglia M, Casini A, Lodi L, Indolfi G, Azzari C. Real-time polymerase chain reaction on filter paper spotted samples: a gateway to molecular diagnosis of invasive bacterial diseases for rural areas in low-income countries. Trans R Soc Trop Med Hyg 2021; 116:233-241. [PMID: 34328186 DOI: 10.1093/trstmh/trab107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/25/2020] [Accepted: 07/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Bacterial culture is the gold standard for the diagnosis of invasive bacterial diseases (IBDs) but molecular methods are more specific and sensitive. Fresh liquid samples (FLSs) show patent limitations for shipping and storage. We aimed to evaluate the sensitivity and specificity of real-time polymerase chain reaction (PCR) performed on dried sample spots (DSSs) obtained from different biological fluids compared with real-time PCR or culture performed on FLSs. METHODS FLSs positive for Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Escherichia coli, Streptococcus pyogenes, Staphylococcus aureus, Bordetella pertussis and/or Pseudomonas aeruginosa were spotted on filter paper. Real-time PCR was performed on both FLSs and DSSs and results were compared. The stability of the DSS results over time was evaluated. RESULTS Real-time PCR performed on 114 DSSs showed a specificity of 99.1% and a sensitivity of 91.2% for IBD diagnosis. A positive correlation was found between FLS cycle threshold (Ct) and DSS Ct (r=0.84; r2=0.71) with the Pearson statistical test and Bland-Altman analysis showing that 95% of the specimens were within agreeable limits. Although we observed a trend towards signal reduction over time in the DSSs, there was no statistical evidence of an increase in Ct values. Real-time PCR on DSSs was 2.2 times more sensitive than culture. CONCLUSIONS Real-time PCR applied to DSSs may be a useful approach in different situations, such as IBD diagnosis, both for rural areas of low-income countries and family practitioners in various settings.
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Affiliation(s)
- Elisa De Vitis
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Silvia Ricci
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Francesco Nieddu
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Maria Moriondo
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Martina Cortimiglia
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Arianna Casini
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Lorenzo Lodi
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
| | - Giuseppe Indolfi
- Department of Paediatrics, Meyer Children's University Hospital, Florence, Italy
| | - Chiara Azzari
- Department of Health Sciences, University of Florence and Meyer Children's University Hospital, Florence, Italy
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Evaluation of filter paper to transport inactivated bacteria to detect carbapenem resistance genes by multiplex real-time PCR using high-resolution melting. Braz J Microbiol 2021; 52:1353-1356. [PMID: 34213734 DOI: 10.1007/s42770-021-00530-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/12/2021] [Indexed: 12/31/2022] Open
Abstract
Infections caused by resistant microorganisms are a complex global public health challenge, and the way to combat the increase of resistance is the development of more modern and faster techniques for resistance detection. This study aimed to evaluate the transport of inactivated bacteria impregnated in a filter paper disk to detect carbapenem resistance genes by multiplex real-time PCR (qPCR) using high-resolution melting (HRM). A total of 88 isolates of 10 different species of Enterobacterales harboring well-characterized carbapenem resistance genes were evaluated. A full 10-µL loop of fresh growth of bacteria were impregnated in a filter paper disk, which was left at room temperature for 2 days in order to simulate the time spent in transportation. Bacterial inactivation was performed with 70% ethanol at 15 min. Afterwards, the DNA was extracted from the paper disks for further analysis by qPCR HRM. The time of 15 min in 70% ethanol was enough to inactivate all the isolates tested. It was possible to correctly identify the presence of the carbapenem resistance gene by HRM qPCR in 87 isolates (98.87%) that were transported in the filter paper disks. Our results indicated that it is possible to use filter paper to transport inactivated bacteria and to identify carbapenem resistance genes by qPCR HRM. This alternative tends to facilitate the access to this technology by many laboratories which do not have the qPCR equipment.
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Haemophilus influenzae Meningitis Direct Diagnosis by Metagenomic Next-Generation Sequencing: A Case Report. Pathogens 2021; 10:pathogens10040461. [PMID: 33921275 PMCID: PMC8069228 DOI: 10.3390/pathogens10040461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenzae meningitis in a 22-year-old male patient, during his hospitalisation following a more than six-metre fall. Using an Oxford Nanopore Technologies real-time sequencing run in parallel to real-time PCR, we detected the H. influenzae genome directly from the cerebrospinal fluid sample in six hours. Furthermore, BLAST analysis of the sequence encoding for a partial DUF417 domain-containing protein diagnosed a non-b serotype, non-typeable H.influenzae belonging to lineage H. influenzae 22.1-21. The Oxford Nanopore metagenomic next-generation sequencing approach could be considered for the point-of-care diagnosis of infectious meningitis, by direct identification of pathogenic genomes and their genotypes/serotypes.
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