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Downie DL, Rao P, David-Ferdon C, Courtney S, Lee JS, Kugley S, MacDonald PDM, Barnes K, Fisher S, Andreadis JL, Chaitram J, Mauldin MR, Salerno RM, Schiffer J, Gundlapalli AV. Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health. Health Secur 2024; 22:93-107. [PMID: 38608237 PMCID: PMC11044852 DOI: 10.1089/hs.2023.0100] [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: 05/22/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 04/14/2024] Open
Abstract
To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.
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Affiliation(s)
- Diane L. Downie
- Diane L. Downie, PhD, MPH, is Deputy Associate Director for Science, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Preetika Rao
- Preetika Rao, MPH, is a Health Scientist; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Corinne David-Ferdon
- Corinne David-Ferdon, PhD, is Associate Director of Science, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Sean Courtney
- Sean Courtney, PhD, is a Health Scientist, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Justin S. Lee
- Justin Lee, DVM, PhD, is a Health Scientist, Division of Global Health Protection; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Shannon Kugley
- Shannon Kugley, MLIS, is a Research Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Pia D. M. MacDonald
- Pia D. M. MacDonald, PhD, MPH, is a Senior Infectious Disease Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Keegan Barnes
- Keegan Barnes is a Public Health Analyst; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Shelby Fisher
- Shelby Fisher, MPH, is an Epidemiologist; in Social, Statistical, and Environmental Sciences, RTI International, Research Triangle Park, NC
| | - Joanne L. Andreadis
- Joanne L. Andreadis, PhD, is Associate Director for Science, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jasmine Chaitram
- Jasmine Chaitram, MPH, is Branch Chief, at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Matthew R. Mauldin
- Matthew R. Mauldin, PhD, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Reynolds M. Salerno
- Reynolds M. Salerno, PhD, is Director, Division of Laboratory Systems; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Jarad Schiffer
- Jarad Schiffer, MS, is Health Scientists, Office of Readiness and Response; at the US Centers for Disease Control and Prevention, Atlanta, GA
| | - Adi V. Gundlapalli
- Adi V. Gundlapalli, MD, PhD, is a Senior Advisor, Data Readiness and Response, Office of Public Health Data, Surveillance, and Technology; at the US Centers for Disease Control and Prevention, Atlanta, GA
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Gulholm T, Yeang M, Nguyen I, Andrews PI, Balgahom R, Beresford R, Branley J, Briest R, Britton P, Burrell R, Gehrig N, Kesson A, Kok J, Maley M, Newcombe J, Samarasekara H, Van Hal S, Varadhan H, Thapa K, Jones S, Newton P, Naing Z, Stelzer-Braid S, Rawlinson W. Molecular typing of enteroviruses: comparing 5'UTR, VP1 and whole genome sequencing methods. Pathology 2022; 54:779-783. [PMID: 35738943 DOI: 10.1016/j.pathol.2022.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 12/15/2022]
Abstract
Enteroviruses (EV) commonly cause hand, foot and mouth disease (HFMD), and can also cause potentially fatal neurological and systemic complications. In our laboratory, sequencing 5' untranslated region (UTR) of the viral genome has been the routine method of genotyping EVs. During a recent localised outbreak of aseptic meningitis, sequencing the 5'UTR identified the causative virus as EV-A71, which did not fit with the clinical syndrome or illness severity. When genotyped using a different target gene, VP1, the result was different. This led us to evaluate the accuracy of the two different target genome regions and compare them against whole genome sequencing (WGS). We aimed to optimise the algorithm for detection and characterisation of EVs in the diagnostic laboratory. We hypothesised that VP1 and WGS genotyping would provide different results than 5'UTR in a subset of samples. Clinical samples from around New South Wales which were positive for EV by commercial polymerase chain reaction (PCR) assays were genotyped by targeting three different viral genome regions: the 5'UTR, VP1 and WGS. Sequencing was performed by Sanger and next generation sequencing. The subtyping results were compared. Of the 74/118 (63%) samples that were successfully typed using both the 5'UTR and the VP1 method, the EV typing result was identical for 46/74 (62%) samples compared to WGS as the gold standard. The same EV group but different EV types were found in 22/74 (30%) samples, and 6/74 (8%) samples belonged to different EV groups depending on typing method used. Genotyping with WGS and VP1 is more accurate than 5'UTR. Genotyping by the 5'UTR method is very sensitive, but less specific.
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Affiliation(s)
- T Gulholm
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; UNSW Clinical School, Faculty of Medicine UNSW, Kensington, NSW, Australia.
| | - M Yeang
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia
| | - I Nguyen
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - P I Andrews
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - R Balgahom
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - R Beresford
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Branley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia; Nepean Clinical School, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - R Briest
- Department of Neurology, Sydney Children's Hospital, Randwick, NSW, Australia
| | - P Britton
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; University of Sydney Children's Hospital Westmead Clinical School, NSW, Australia
| | - R Burrell
- Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, NSW, Australia
| | - N Gehrig
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - A Kesson
- Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, NSW, Australia; Discipline of Child and Adolescent Health, The University of Sydney, Sydney, NSW, Australia
| | - J Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, NSW, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW, Australia
| | - M Maley
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Liverpool, NSW, Australia
| | - J Newcombe
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, Sydney, NSW, Australia
| | - H Samarasekara
- Department of Microbiology and Infectious Diseases, NSW Health Pathology, Nepean Blue Mountains Pathology Service, Penrith, NSW, Australia
| | - S Van Hal
- Department of Infectious Diseases and Microbiology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - H Varadhan
- NSW Health Pathology, John Hunter Hospital, Newcastle, NSW, Australia
| | - K Thapa
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Jones
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - P Newton
- Department of Microbiology, NSW Health Pathology, The Wollongong Hospital, Wollongong, NSW, Australia
| | - Z Naing
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - S Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - W Rawlinson
- Serology and Virology Division (SAViD), NSW Health Pathology East, Department of Microbiology, Prince of Wales Hospital, Randwick, NSW, Australia; Department of Infectious Diseases, Prince of Wales Hospital, Randwick, NSW, Australia; Virology Research Laboratory, Serology and Virology Division (SAViD), New South Wales Health Pathology East, Prince of Wales Hospital, Randwick, NSW, Australia; School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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Luciani L, Morand A, Zandotti C, Piorkowski G, Boutin A, Mazenq J, Minodier P, Ninove L, Nougairède A. Circulation of enterovirus A71 during 2019-2020, Marseille, France. J Med Virol 2021; 93:5163-5166. [PMID: 33605462 DOI: 10.1002/jmv.26893] [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] [Received: 11/09/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 11/11/2022]
Abstract
Enteroviruses A71 (EVs-A71) are known to cause serious neurological infections, especially in the pediatric population. We report here eight cases of EV-A71 infection diagnosed in Marseille over the past 2 years (seven cases in 2019 and one case in 2020). Only children under 5 years of age were affected, including one case of acute flaccid paralysis. Viral RNA was detected by RT-PCR in peripheral samples for all cases (feces and upper respiratory samples). Phylogenetic analyses based on VP1 and 2C3C coding regions revealed that all these cases of EV-A71 infection were caused by viruses belonging to the subgenogroup C1 that currently circulates in Europe and that these viruses are genetically closed to other EVs-A71 recently detected in European countries. These data therefore reinforce the usefulness of the enterovirus surveillance network and the need for systematic screening for EV-A71 in case of an enteroviral infection. This study therefore suggests that the systematic screening for EV-A71 in case of enteroviral infection could provide additional data for enterovirus surveillance networks.
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Affiliation(s)
- Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
| | - Aurélie Morand
- Service de médecine infantile et pédiatrie spécialisée, CHU Timone, AP-HM, Marseille, France.,Aix Marseille University, IRD, MEPHI, AP-HM, IHU Méditerranée Infection, Marseille, France
| | - Christine Zandotti
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France
| | - Aurélie Boutin
- Service des urgences pédiatriques, CHU Timone AP-HM, Marseille, France
| | - Julie Mazenq
- Service des urgences pédiatriques, CHU Timone AP-HM, Marseille, France
| | - Philippe Minodier
- Service des urgences pédiatriques, CHU Nord AP-HM, Marseille, France
| | - Laetitia Ninove
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille University, IRD 190, Inserm 1207), Marseille, France.,Laboratoire de microbiologie (Assistance Publique - Hôpitaux de Marseille (AP-HM), IHU Méditerranée Infection), Marseille, France
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