1
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Liao Y, Liu Y, Feng Y, Zhen D, He F. Rapid Detection of Broad-Spectrum Pathogenic Bacteria Based on Highly Sensitive Proton Response of the Nucleic Acid Amplification SPQC Platform. Anal Chem 2024; 96:6756-6763. [PMID: 38625745 DOI: 10.1021/acs.analchem.4c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Pathogenic bacteria significantly contribute to elevated morbidity and mortality rates, highlighting the urgent need for early and precise detection. Currently, there is a paucity of effective broad-spectrum methods for detecting pathogenic bacteria. We have developed an innovative proton-responsive series piezoelectric quartz crystal (PR-SPQC) platform for the broad-spectrum identification of pathogenic bacteria. This was achieved by retrieving and aligning sequences from the NCBI GenBank database to identify and validate 16S rRNA oligonucleotide sequences that are signatures of pathogenic bacteria but absent in humans or fungi. The hyperbranched rolling circle amplification, activated exclusively by the screened target, exponentially generates protons that are detected by SPQC through a 2D polyaniline (PANI) film. The PR-SPQC platform demonstrates broad-spectrum capabilities in detecting pathogenic bacteria, with a detection limit of 2 CFU/mL within 90 min. Clinical testing of blood samples yielded satisfactory results. With its advantages in miniaturization, cost efficiency, and suitability for point-of-care testing, PR-SPQC has the potential to be extensively used for the rapid identification of diverse pathogenic bacteria within clinical practice and public health sectors.
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Affiliation(s)
- Yusheng Liao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Yu Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Ye Feng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
| | - Deshuai Zhen
- Hunan Key Laboratory of Typical Environment Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, PR China
| | - Fengjiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, PR China
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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3
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Eisenhofer R, Wright S, Weyrich L. Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities. PeerJ 2024; 12:e16770. [PMID: 38440408 PMCID: PMC10911074 DOI: 10.7717/peerj.16770] [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: 08/31/2023] [Accepted: 12/16/2023] [Indexed: 03/06/2024] Open
Abstract
The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.
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Affiliation(s)
| | - Sterling Wright
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
| | - Laura Weyrich
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States
- School of Biological Sciences, University of Adelaide, Adelaide, Australia
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4
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Comtet-Marre S, Chakoory O, Peyret P. Targeted 16S rRNA Gene Capture by Hybridization and Bioinformatic Analysis. Methods Mol Biol 2022; 2605:187-208. [PMID: 36520395 DOI: 10.1007/978-1-0716-2871-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Next-generation sequencing technologies have impressively unlocked capacities to depict the complexity of microbial communities. Microbial community structure is for now routinely monitored by sequencing of 16S rRNA gene, a phylogenetic marker almost conserved among bacteria and archaea. Nevertheless, amplicon sequencing, the most popular used approach, suffers from several biases impacting the picture of microbial communities. Here, we describe an innovative method based on gene capture by hybridization for the targeted enrichment of 16S rDNA biomarker from metagenomic samples. Coupled to near full-length 16S rDNA reconstruction, this approach enables an exhaustive and accurate description of microbial communities by enhancing taxonomic and phylogenetic resolutions. Furthermore, access of captured 16S flanking regions opens link between structure and function in microbial communities.
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Affiliation(s)
| | - Oshma Chakoory
- Université Clermont-Auvergne, INRAE, MEDiS, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont-Auvergne, INRAE, MEDiS, Clermont-Ferrand, France.
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5
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Van Hoang D, Yamamoto S, Fukunaga A, Inoue Y, Mizoue T, Ohmagari N. Metabolic syndrome and the immunogenicity of Pfizer-BioNTech vaccine: a cross-sectional study in Japanese healthcare workers. Diabetol Metab Syndr 2022; 14:149. [PMID: 36229890 PMCID: PMC9556286 DOI: 10.1186/s13098-022-00918-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/25/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The clustering of metabolic abnormalities may weaken vaccine-induced immunity, but epidemiological data regarding SARS-CoV-2 vaccines are scarce. The present study aimed to examine the cross-sectional association between metabolic syndrome (MetS) and humoral immune response to Pfizer-BioNTech vaccine among the staff of a research center for medical care in Japan. METHODS Participants were the staff (aged 21-75 years) of the National Center of Global Health and Medicine who had completed the second dose of Pfizer-BioNTech vaccine 1-3 months before the survey. MetS was defined according to the Joint Interim Statement. SARS-CoV-2 spike immunoglobulin G (IgG) antibody was measured using quantitative assays. Multivariable linear regression was used to estimate the geometric mean titers (GMT) and geometric mean ratio (GMR) of IgG titers, relative to MetS status. RESULTS Of 946 participants who received the second vaccine dose, 51 (5.4%) had MetS. Those with MetS had a significantly lower IgG titer (GMT 4125; 95% confidence interval [CI], 2885-5896) than those without MetS (GMT 5348; 95% CI, 3914-7309); the GMR was 0.77 (95% CI 0.64-0.93). Taking those having no MetS component as reference, fully adjusted GMR (95% CI) for those having 1, 2, 3 or ≥ 4 components was 1.00 (0.90, 1.11), 0.89 (0.77, 1.04), 0.86 (0.68, 1.10) and 0.61 (0.45, 0.82), respectively (P trend = 0.024). CONCLUSION Results suggest that having MetS and a greater number of its components are associated with a weaker humoral immune response to the Pfizer-BioNTech vaccine.
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Affiliation(s)
- Dong Van Hoang
- Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku, Tokyo, Japan.
| | - Shohei Yamamoto
- Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku, Tokyo, Japan
| | - Ami Fukunaga
- Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku, Tokyo, Japan
| | - Yosuke Inoue
- Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku, Tokyo, Japan
| | - Tetsuya Mizoue
- Department of Epidemiology and Prevention, Center for Clinical Sciences, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku, Tokyo, Japan
| | - Norio Ohmagari
- Disease Control and Prevention Center, National Center for Global Health and Medicine, Toyama 1-21-1, Shinjuku, Tokyo, Japan
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6
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Torres Ortiz A, Fenn Torrente F, Twigg A, Hatcher J, Saso A, Lam T, Johnson M, Wagstaffe H, Dhillon R, Mai AL, Goldblatt D, Still R, Buckland M, Gilmour K, Grandjean L. The influence of time on the sensitivity of SARS-CoV-2 serological testing. Sci Rep 2022; 12:10517. [PMID: 35732870 PMCID: PMC9214469 DOI: 10.1038/s41598-022-14351-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/06/2022] [Indexed: 11/11/2022] Open
Abstract
Sensitive serological testing is essential to estimate the proportion of the population exposed or infected with SARS-CoV-2, to guide booster vaccination and to select patients for treatment with anti-SARS-CoV-2 antibodies. The performance of serological tests is usually evaluated at 14–21 days post infection. This approach fails to take account of the important effect of time on test performance after infection or exposure has occurred. We performed parallel serological testing using 4 widely used assays (a multiplexed SARS-CoV-2 Nucleoprotein (N), Spike (S) and Receptor Binding Domain assay from Meso Scale Discovery (MSD), the Roche Elecsys-Nucleoprotein (Roche-N) and Spike (Roche-S) assays and the Abbott Nucleoprotein assay (Abbott-N) on serial positive monthly samples collected as part of the Co-STARs study (www.clinicaltrials.gov, NCT04380896) up to 200 days following infection. Our findings demonstrate the considerable effect of time since symptom onset on the diagnostic sensitivity of different assays. Using a time-to-event analysis, we demonstrated that 50% of the Abbott nucleoprotein assays will give a negative result after 175 days (median survival time 95% CI 168–185 days), compared to the better performance over time of the Roche Elecsys nucleoprotein assay (93% survival probability at 200 days, 95% CI 88–97%). Assays targeting the spike protein showed a lower decline over the follow-up period, both for the MSD spike assay (97% survival probability at 200 days, 95% CI 95–99%) and the Roche Elecsys spike assay (95% survival probability at 200 days, 95% CI 93–97%). The best performing quantitative Roche Elecsys Spike assay showed no evidence of waning Spike antibody titers over the 200-day time course of the study. We have shown that compared to other assays evaluated, the Abbott-N assay fails to detect SARS-CoV-2 antibodies as time passes since infection. In contrast the Roche Elecsys Spike Assay and the MSD assay maintained a high sensitivity for the 200-day duration of the study. These limitations of the Abbott assay should be considered when quantifying the immune correlates of protection or the need for SARS-CoV-2 antibody therapy. The high levels of maintained detectable neutralizing spike antibody titers identified by the quantitative Roche Elecsys assay is encouraging and provides further evidence in support of long-lasting SARS-CoV-2 protection following natural infection.
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Affiliation(s)
- Arturo Torres Ortiz
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK.,Department of Infectious Diseases, Imperial College London, Paddington, London, W2 1NY, UK
| | - Fernanda Fenn Torrente
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK.,UCL Medical School, University College London, 74 Huntley Street, London, WC1E 6DE, UK
| | - Adam Twigg
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK.,School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Box 111, Cambridge, CB2 0SP, UK
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Anja Saso
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK.,Department of Tropical and Infectious Diseases, LSHTM, Keppel St, Bloomsbury, London, WC1E 7HT, UK.,MRC Gambia at LSHTM, PO Box 273, Fajara, The Gambia
| | - Tanya Lam
- Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Marina Johnson
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Helen Wagstaffe
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Rishi Dhillon
- Public Health Wales Microbiology, University Hospital of Wales, Heath Park Way, Cardiff, CF14 4XW, UK
| | - Anabelle Lea Mai
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - David Goldblatt
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Rachel Still
- Laboratory Medicine Service Swansea, Bay University Health Board Morriston Hospital, Swansea, SA6 6NL, UK
| | - Matthew Buckland
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Kimberly Gilmour
- Clinical Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK
| | - Louis Grandjean
- Department of Infection, Inflammation and Immunity, Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK. .,Department of Infectious Diseases, Great Ormond Street Hospital, Great Ormond Street, London, WC1N 3JH, UK.
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7
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Hausfater P, Boutolleau D, Lacombe K, Beurton A, Dumont M, Constantin JM, Ghosn J, Combes A, Cury N, Guedj R, Djibré M, Bompard R, Mazerand S, Pourcher V, Gimeno L, Marois C, Teyssou E, Marcelin AG, Hajage D, Tubach F. Cumulative incidence of SARS-CoV-2 infection and associated risk factors among frontline health care workers in Paris: the SEROCOV cohort study. Sci Rep 2022; 12:7211. [PMID: 35508515 PMCID: PMC9068621 DOI: 10.1038/s41598-022-10945-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/30/2022] [Indexed: 12/30/2022] Open
Abstract
With the COVID-19 pandemic, documenting whether health care workers (HCWs) are at increased risk of SARS-CoV-2 contamination and identifying risk factors is of major concern. In this multicenter prospective cohort study, HCWs from frontline departments were included in March and April 2020 and followed for 3 months. SARS-CoV-2 serology was performed at month 0 (M0), M1, and M3 and RT-PCR in case of symptoms. The primary outcome was laboratory-confirmed SARS-CoV-2 infection at M3. Risk factors of laboratory-confirmed SARS-CoV-2 infection at M3 were identified by multivariate logistic regression. Among 1062 HCWs (median [interquartile range] age, 33 [28–42] years; 758 [71.4%] women; 321 [30.2%] physicians), the cumulative incidence of SARS-CoV-2 infection at M3 was 14.6% (95% confidence interval [CI] [12.5; 16.9]). Risk factors were the working department specialty, with increased risk for intensive care units (odds ratio 1.80, 95% CI [0.38; 8.58]), emergency departments (3.91 [0.83; 18.43]) and infectious diseases departments (4.22 [0.92; 18.28]); current smoking was associated with reduced risk (0.36 [0.21; 0.63]). Age, sex, professional category, number of years of experience in the job or department, and public transportation use were not significantly associated with laboratory-confirmed SARS-CoV-2 infection at M3. The rate of SARS-CoV-2 infection in frontline HCWs was 14.6% at the end of the first COVID-19 wave in Paris and occurred mainly early. The study argues for an origin of professional in addition to private life contamination and therefore including HCWs in the first-line vaccination target population. It also highlights that smokers were at lower risk. Trial registration The study has been registered on ClinicalTrials.gov: NCT04304690 first registered on 11/03/2020.
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Affiliation(s)
- Pierre Hausfater
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP, Sorbonne Université, 83 Boulevard de l'Hôpital, 75651, Paris Cedex 13, France. .,GRC-14 BIOSFAST, UMR INSERM 1166, IHU ICAN, Sorbonne Université, Paris, France.
| | - David Boutolleau
- INSERM, Institut Pierre Louis d'Epidémiologie Et de Santé Publique (iPLESP), GH AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Sorbonne Université, Paris, France
| | - Karine Lacombe
- Infectious Disease Department, Sorbonne Université Hôpital Saint-Antoine, Paris, France
| | - Alexandra Beurton
- Service de Pneumologie-Médecine Intensive Réanimation, Hôpital Pitié-Salpêtrière, APHP, Sorbonne Université Inserm UMRS Neurophysiologie Respiratoire Expérimentale et Clinique, Sorbonne Université, Paris, France
| | - Margaux Dumont
- Emergency Department, Hôpital Pitié-Salpêtrière, APHP, Sorbonne Université, 83 Boulevard de l'Hôpital, 75651, Paris Cedex 13, France
| | - Jean-Michel Constantin
- Department of Anaesthesiology and Critical Care, GRC 29, AP-HP, DMU DREAM, Hôpital Pitié-Salpêtrière, GH APHP, Sorbonne Université, Paris, France
| | - Jade Ghosn
- AP-HP, Nord, Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, and Université de Paris, INSERM, UMR 1137 IAME, Paris, France
| | - Alain Combes
- INSERM, UMRS_1166-ICAN, Institute of Cardiometabolism and Nutrition, and Service de Médecine Intensive-Réanimation, Institut de Cardiologie, GH APHP Sorbonne Université Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Nicolas Cury
- Emergency Department, APHP, Sorbonne Université Hôpital Saint-Antoine, Paris, France
| | - Romain Guedj
- Pediatric Emergency Deparment, APHP Hôpital Armand Trousseau-Sorbonne Université, Faculté de Médecine, Paris, France.,Centre of Research in Epidemiology and Statistics-CRESS, INSERM, Université de Paris, 75004, Paris, France
| | - Michel Djibré
- Service de Médecine Intensive Réanimation, APHP, Sorbonne Université Hôpital Tenon, Paris, France
| | - Rudy Bompard
- Emergency Department, Hôpital Tenon, APHP, Sorbonne Université, Paris, France
| | - Sandie Mazerand
- Service de Médecine Intensive-Réanimation, APHP, Sorbonne Université Hôpital Saint-Antoine, Paris, France
| | - Valérie Pourcher
- AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière Charles Foix, Service de Maladies Infectieuses et Tropicales, INSERM 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Sorbonne Université, 75013, Paris, France
| | - Linda Gimeno
- APHP, Unité de Recherche Clinique Pitié Salpêtrière Charles Foix, Sorbonne Université, 75013, Paris, France
| | - Clémence Marois
- Unité de Médecine Intensive Réanimation Neurologique, Département de Neurologie, DMU Neurosciences, APHP, Sorbonne Université Hôpital Pitié-Salpêtrière, Paris, France
| | - Elisa Teyssou
- INSERM, Institut Pierre Louis d'Epidémiologie Et de Santé Publique (iPLESP), GH AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Sorbonne Université, Paris, France
| | - Anne-Geneviève Marcelin
- INSERM, Institut Pierre Louis d'Epidémiologie Et de Santé Publique (iPLESP), GH AP-HP, Hôpital Pitié-Salpêtrière, Service de Virologie, Sorbonne Université, Paris, France
| | - David Hajage
- APHP, Unité de Recherche Clinique Pitié Salpêtrière Charles Foix, Sorbonne Université, 75013, Paris, France.,Département de Santé Publique, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Sorbonne Université, CIC-1422, 75013, Paris, France
| | - Florence Tubach
- APHP, Unité de Recherche Clinique Pitié Salpêtrière Charles Foix, Sorbonne Université, 75013, Paris, France.,Département de Santé Publique, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié Salpêtrière, Sorbonne Université, CIC-1422, 75013, Paris, France
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8
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Lamoureux C, Surgers L, Fihman V, Gricourt G, Demontant V, Trawinski E, N'Debi M, Gomart C, Royer G, Launay N, Le Glaunec JM, Wemmert C, La Martire G, Rossi G, Lepeule R, Pawlotsky JM, Rodriguez C, Woerther PL. Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections. Front Microbiol 2022; 13:761873. [PMID: 35464955 PMCID: PMC9020828 DOI: 10.3389/fmicb.2022.761873] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 03/14/2022] [Indexed: 12/14/2022] Open
Abstract
Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients’ samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.
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Affiliation(s)
- Claudie Lamoureux
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Brest, France.,Univ Brest, INSERM, EFS, UMR 1078, GGB, Brest, France
| | - Laure Surgers
- GHU AP-HP Sorbonne Université, Service des Maladies Infectieuses et Tropicales, Hôpital Saint-Antoine, Paris, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Vincent Fihman
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France
| | - Guillaume Gricourt
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Vanessa Demontant
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Elisabeth Trawinski
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Melissa N'Debi
- NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Camille Gomart
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Guilhem Royer
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Nathalie Launay
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jeanne-Marie Le Glaunec
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Charlotte Wemmert
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Giulia La Martire
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Geoffrey Rossi
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Raphaël Lepeule
- Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
| | - Jean-Michel Pawlotsky
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France
| | - Christophe Rodriguez
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,INSERM U955, IMRB Institute, University of Paris-Est Créteil, Créteil, France.,NGS Platform, Henri Mondor Hospital, AP-HP, and IMRB Institute, University of Paris-Est-Créteil, Créteil, France
| | - Paul-Louis Woerther
- Microbiology Unit, Department of Diagnostic, Prevention and Treatment of Infections, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France.,EA 7380 Dynamyc, EnvA, UPEC, University of Paris-Est Créteil, Créteil, France.,Antimicrobial Stewardship Unit, Diagnostic, Prevention and Treatment of Infections Department, Henri Mondor Hospital, AP-HP, University of Paris-Est-Créteil, Créteil, France
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9
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Marre S, Gasc C, Forest C, Lebbaoui Y, Mosoni P, Peyret P. Revealing microbial species diversity using sequence capture by hybridization. Microb Genom 2021; 7. [PMID: 34882529 PMCID: PMC8767324 DOI: 10.1099/mgen.0.000714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales, 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.
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Affiliation(s)
- Sophie Marre
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Cyrielle Gasc
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France.,Present address: MaaT Pharma, F-69007 LYON, France
| | - Camille Forest
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Yacine Lebbaoui
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Pascale Mosoni
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France
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10
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Beaudry MS, Wang J, Kieran TJ, Thomas J, Bayona-Vásquez NJ, Gao B, Devault A, Brunelle B, Lu K, Wang JS, Rhodes OE, Glenn TC. Improved Microbial Community Characterization of 16S rRNA via Metagenome Hybridization Capture Enrichment. Front Microbiol 2021; 12:644662. [PMID: 33986735 PMCID: PMC8110821 DOI: 10.3389/fmicb.2021.644662] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/22/2021] [Indexed: 01/04/2023] Open
Abstract
Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases, but are much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having <78% sequence identity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average > 400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely due in part to the extent and curation of the reference databases considered. Thus, enriching existing aliquots of shotgun metagenomic libraries and obtaining modest numbers of reads from them offers an efficient orthogonal method for assessment of bacterial community composition.
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Affiliation(s)
- Megan S. Beaudry
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jincheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jesse Thomas
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | | | | | - Kun Lu
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
| | - Jia-Sheng Wang
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, Aiken, SC, United States
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
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11
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Vandenberg O, Martiny D, Rochas O, van Belkum A, Kozlakidis Z. Considerations for diagnostic COVID-19 tests. Nat Rev Microbiol 2021; 19:171-183. [PMID: 33057203 PMCID: PMC7556561 DOI: 10.1038/s41579-020-00461-z] [Citation(s) in RCA: 447] [Impact Index Per Article: 149.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 02/07/2023]
Abstract
During the early phase of the coronavirus disease 2019 (COVID-19) pandemic, design, development, validation, verification and implementation of diagnostic tests were actively addressed by a large number of diagnostic test manufacturers. Hundreds of molecular tests and immunoassays were rapidly developed, albeit many still await clinical validation and formal approval. In this Review, we summarize the crucial role of diagnostic tests during the first global wave of COVID-19. We explore the technical and implementation problems encountered during this early phase in the pandemic, and try to define future directions for the progressive and better use of (syndromic) diagnostics during a possible resurgence of COVID-19 in future global waves or regional outbreaks. Continuous global improvement in diagnostic test preparedness is essential for more rapid detection of patients, possibly at the point of care, and for optimized prevention and treatment, in both industrialized countries and low-resource settings.
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Affiliation(s)
- Olivier Vandenberg
- Innovation and Business Development Unit, Laboratoire Hospitalier Universtaire de Bruxelles - Universitair Laboratorium Brussel, Université Libre de Bruxelles, Brussels, Belgium.
- Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles, Brussels, Belgium.
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK.
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universtaire de Bruxelles - Universitair Laboratorium Brussel, Université Libre de Bruxelles, Brussels, Belgium
| | - Olivier Rochas
- Strategic Intelligence, Corporate Business Development, bioMérieux, Chemin de L'Orme, France
| | - Alex van Belkum
- Open Innovation and Partnerships, bioMérieux, La Balme Les Grottes, France.
| | - Zisis Kozlakidis
- Laboratory Services and Biobank Group, International Agency for Research on Cancer, World Health Organization, Lyon, France
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12
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Fong D, San Nicolò KO, Alber M, Mitterer M. Evaluating the longitudinal effectiveness of preventive measures against COVID-19 and seroprevalence of IgG antibodies to SARS-CoV-2 in cancer outpatients and healthcare workers. Wien Klin Wochenschr 2021; 133:359-363. [PMID: 33502609 PMCID: PMC7838655 DOI: 10.1007/s00508-020-01807-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/30/2020] [Indexed: 02/06/2023]
Abstract
Background It has been assumed that cancer patients, especially those undergoing chemotherapy, are at increased risk for infection and severe illness from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compared to the general population. After the first alert message from the local healthcare service, a series of drastic measures were taken at our outpatient clinic to contain the spread of coronavirus disease 2019 (COVID-19). Methods In this retrospective study, all consecutive cancer outpatients completed a baseline SARS-CoV‑2 test via real-time polymerase chain reaction (RT-PCR) from 15 March to 26 May 2020. In the later phase, after the peak of the pandemic, patients as well as healthcare workers were tested for anti-SARS-CoV‑2 IgG antibodies. Results Between 15 March and 26 May 2020, 0.78% (N = 5/640) cancer patients tested positive for SARS-CoV‑2 by RT-PCR. Between 22 June and 17 July 2020, anti-SARS-CoV‑2 IgG antibodies were detected in 2 out of 250 (0.8%) cancer patients and 2 out of 36 (5.5%) healthcare workers. In only 1 out of 4 cancer patients with confirmed COVID-19 infection, could SARS-CoV‑2 antibodies be detected. Conclusion Our findings suggest that the majority of our patients and healthcare workers had not been infected with SARS-CoV‑2 and rapidly implemented measures were effective. Maintenance of preventive measures should be continued until vaccines or specific treatments are available.
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Affiliation(s)
- Dominic Fong
- Department of Oncology and Hematology, Franz Tappeiner Hospital, Rossinistraße 5, 39012, Merano, Italy.
| | - Katja Olga San Nicolò
- Department of Oncology and Hematology, Franz Tappeiner Hospital, Rossinistraße 5, 39012, Merano, Italy
| | - Monika Alber
- Department of Oncology and Hematology, Franz Tappeiner Hospital, Rossinistraße 5, 39012, Merano, Italy
| | - Manfred Mitterer
- Department of Oncology and Hematology, Franz Tappeiner Hospital, Rossinistraße 5, 39012, Merano, Italy
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13
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Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies. Cell Mol Life Sci 2020; 78:1501-1522. [PMID: 32623480 PMCID: PMC7334636 DOI: 10.1007/s00018-020-03580-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/10/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022]
Abstract
The recent severe acute respiratory syndrome, known as Coronavirus Disease 2019 (COVID-19) has spread so much rapidly and severely to induce World Health Organization (WHO) to declare a state of emergency over the new coronavirus SARS-CoV-2 pandemic. While several countries have chosen the almost complete lock-down for slowing down SARS-CoV-2 spread, the scientific community is called to respond to the devastating outbreak by identifying new tools for diagnosis and treatment of the dangerous COVID-19. With this aim, we performed an in silico comparative modeling analysis, which allows gaining new insights into the main conformational changes occurring in the SARS-CoV-2 spike protein, at the level of the receptor-binding domain (RBD), along interactions with human cells angiotensin-converting enzyme 2 (ACE2) receptor, that favor human cell invasion. Furthermore, our analysis provides (1) an ideal pipeline to identify already characterized antibodies that might target SARS-CoV-2 spike RBD, aiming to prevent interactions with the human ACE2, and (2) instructions for building new possible neutralizing antibodies, according to chemical/physical space restraints and complementary determining regions (CDR) mutagenesis of the identified existing antibodies. The proposed antibodies show in silico high affinity for SARS-CoV-2 spike RBD and can be used as reference antibodies also for building new high-affinity antibodies against present and future coronaviruses able to invade human cells through interactions of their spike proteins with the human ACE2. More in general, our analysis provides indications for the set-up of the right biological molecular context for investigating spike RBD–ACE2 interactions for the development of new vaccines, diagnostic kits, and other treatments based on the targeting of SARS-CoV-2 spike protein.
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