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Kolosova NP, Boldyrev ND, Svyatchenko SV, Danilenko AV, Goncharova NI, Shadrinova KN, Danilenko EI, Onkhonova GS, Kosenko MN, Antonets ME, Susloparov IM, Ilyicheva TN, Marchenko VY, Ryzhikov AB. An Investigation of Severe Influenza Cases in Russia during the 2022-2023 Epidemic Season and an Analysis of HA-D222G/N Polymorphism in Newly Emerged and Dominant Clade 6B.1A.5a.2a A(H1N1)pdm09 Viruses. Pathogens 2023; 13:1. [PMID: 38276147 PMCID: PMC10819184 DOI: 10.3390/pathogens13010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
In Russia, during the COVID-19 pandemic, a decrease in influenza circulation was initially observed. Influenza circulation re-emerged with the dominance of new clades of A(H3N2) viruses in 2021-2022 and A(H1N1)pdm09 viruses in 2022-2023. In this study, we aimed to characterize influenza viruses during the 2022-2023 season in Russia, as well as investigate A(H1N1)pdm09 HA-D222G/N polymorphism associated with increased disease severity. PCR testing of 780 clinical specimens showed 72.2% of them to be positive for A(H1N1)pdm09, 2.8% for A(H3N2), and 25% for influenza B viruses. The majority of A(H1N1)pdm09 viruses analyzed belonged to the newly emerged 6B.1A.5a.2a clade. The intra-sample predominance of HA-D222G/N virus variants was observed in 29% of the specimens from A(H1N1)pdm09 fatal cases. The D222N polymorphic variant was registered more frequently than D222G. All the B/Victoria viruses analyzed belonged to the V1A.3a.2 clade. Several identified A(H3N2) viruses belonged to one of the four subclades (2a.1b, 2a.3a.1, 2a.3b, 2b) within the 3C.2a1b.2a.2 group. The majority of antigenically characterized viruses bore similarities to the corresponding 2022-2023 NH vaccine strains. Only one influenza A(H1N1)pdm09 virus showed reduced inhibition by neuraminidase inhibitors. None of the influenza viruses analyzed had genetic markers of reduced susceptibility to baloxavir.
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2
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Wang X, Stelzer-Braid S, Scotch M, Rawlinson WD. Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use. Rev Med Virol 2022; 32:e2375. [PMID: 35775736 PMCID: PMC9539958 DOI: 10.1002/rmv.2375] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/01/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022]
Abstract
Acute respiratory infection is the third most frequent cause of mortality worldwide, causing over 4.25 million deaths annually. Although most diagnosed acute respiratory infections are thought to be of viral origin, the aetiology often remains unclear. The advent of next‐generation sequencing (NGS) has revolutionised the field of virus discovery and identification, particularly in the detection of unknown respiratory viruses. We systematically reviewed the application of NGS technologies for detecting respiratory viruses from clinical samples and outline potential barriers to the routine clinical introduction of NGS. The five databases searched for studies published in English from 01 January 2010 to 01 February 2021, which led to the inclusion of 52 studies. A total of 14 different models of NGS platforms were summarised from included studies. Among these models, second‐generation sequencing platforms (e.g., Illumina sequencers) were used in the majority of studies (41/52, 79%). Moreover, NGS platforms have proven successful in detecting a variety of respiratory viruses, including influenza A/B viruses (9/52, 17%), SARS‐CoV‐2 (21/52, 40%), parainfluenza virus (3/52, 6%), respiratory syncytial virus (1/52, 2%), human metapneumovirus (2/52, 4%), or a viral panel including other respiratory viruses (16/52, 31%). The review of NGS technologies used in previous studies indicates the advantages of NGS technologies in novel virus detection, virus typing, mutation identification, and infection cluster assessment. Although there remain some technical and ethical challenges associated with NGS use in clinical laboratories, NGS is a promising future tool to improve understanding of respiratory viruses and provide a more accurate diagnosis with simultaneous virus characterisation.
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Affiliation(s)
- Xinye Wang
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Sacha Stelzer-Braid
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew Scotch
- Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia.,Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - William D Rawlinson
- Virology Research Laboratory, Serology and Virology Division (SAViD), NSW Health Pathology, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia.,School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
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3
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Danilenko AV, Kolosova NP, Shvalov AN, Ilyicheva TN, Svyatchenko SV, Durymanov AG, Bulanovich JA, Goncharova NI, Susloparov IM, Marchenko VY, Tregubchak TV, Gavrilova EV, Maksyutov RA, Ryzhikov AB. Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018-2019. PLoS One 2021; 16:e0251019. [PMID: 33914831 PMCID: PMC8084186 DOI: 10.1371/journal.pone.0251019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Outbreaks of influenza, which is a contagious respiratory disease, occur throughout the world annually, affecting millions of people with many fatal cases. The D222G/N mutations in the hemagglutinin (HA) gene of A(H1N1)pdm09 are associated with severe and fatal human influenza cases. These mutations lead to increased virus replication in the lower respiratory tract (LRT) and may result in life-threatening pneumonia. Targeted NGS analysis revealed the presence of mutations in major and minor variants in 57% of fatal cases, with the proportion of viral variants with mutations varying from 1% to 98% in each individual sample in the epidemic season 2018-2019 in Russia. Co-occurrence of the mutations D222G and D222N was detected in a substantial number of the studied fatal cases (41%). The D222G/N mutations were detected at a low frequency (less than 1%) in the rest of the studied samples from fatal and nonfatal cases of influenza. The presence of HA D222Y/V/A mutations was detected in a few fatal cases. The high rate of occurrence of HA D222G/N mutations in A(H1N1)pdm09 viruses, their increased ability to replicate in the LRT and their association with fatal outcomes points to the importance of monitoring the mutations in circulating A(H1N1)pdm09 viruses for the evaluation of their epidemiological significance and for the consideration of disease prevention and treatment options.
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Affiliation(s)
- Alexey V. Danilenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia P. Kolosova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander N. Shvalov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana N. Ilyicheva
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Svetlana V. Svyatchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander G. Durymanov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Julia A. Bulanovich
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Natalia I. Goncharova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Ivan M. Susloparov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Vasiliy Y. Marchenko
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Tatyana V. Tregubchak
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Elena V. Gavrilova
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Rinat A. Maksyutov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
| | - Alexander B. Ryzhikov
- Vector State Research Center of Virology and Biotechnology, Koltsovo, Novosibirsk Region, Russia
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4
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Fragkou PC, Moschopoulos CD, Karofylakis E, Kelesidis T, Tsiodras S. Update in Viral Infections in the Intensive Care Unit. Front Med (Lausanne) 2021; 8:575580. [PMID: 33708775 PMCID: PMC7940368 DOI: 10.3389/fmed.2021.575580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/02/2021] [Indexed: 12/15/2022] Open
Abstract
The advent of highly sensitive molecular diagnostic techniques has improved our ability to detect viral pathogens leading to severe and often fatal infections that require admission to the Intensive Care Unit (ICU). Viral infections in the ICU have pleomorphic clinical presentations including pneumonia, acute respiratory distress syndrome, respiratory failure, central or peripheral nervous system manifestations, and viral-induced shock. Besides de novo infections, certain viruses fall into latency and can be reactivated in both immunosuppressed and immunocompetent critically ill patients. Depending on the viral strain, transmission occurs either directly through contact with infectious materials and large droplets, or indirectly through suspended air particles (airborne transmission of droplet nuclei). Many viruses can efficiently spread within hospital environment leading to in-hospital outbreaks, sometimes with high rates of mortality and morbidity, thus infection control measures are of paramount importance. Despite the advances in detecting viral pathogens, limited progress has been made in antiviral treatments, contributing to unexpectedly high rates of unfavorable outcomes. Herein, we review the most updated data on epidemiology, common clinical features, diagnosis, pathogenesis, treatment and prevention of severe community- and hospital-acquired viral infections in the ICU settings.
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Affiliation(s)
- Paraskevi C. Fragkou
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “Attikon” University Hospital, Athens, Greece
| | - Charalampos D. Moschopoulos
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “Attikon” University Hospital, Athens, Greece
| | - Emmanouil Karofylakis
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “Attikon” University Hospital, Athens, Greece
| | - Theodoros Kelesidis
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “Attikon” University Hospital, Athens, Greece
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5
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Next-Generation Sequencing Analysis of the Within-Host Genetic Diversity of Influenza A(H1N1)pdm09 Viruses in the Upper and Lower Respiratory Tracts of Patients with Severe Influenza. mSphere 2021; 6:6/1/e01043-20. [PMID: 33408229 PMCID: PMC7845592 DOI: 10.1128/msphere.01043-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The D222G/N substitution in the hemagglutinin (HA) protein of influenza A(H1N1)pdm09 virus has been reported to be associated with disease severity and mortality in numerous previous studies. In the present study, 75% of lower respiratory samples contained heterogeneous influenza populations that carried different amino acids at position 222 of the HA protein, whereas all upper respiratory samples only contained the wild-type 222D. The influenza A(H1N1)pdm09 virus emerged in April 2009 with an unusual incidence of severe disease and mortality, and currently circulates as a seasonal influenza virus. Previous studies using consensus viral genome sequencing data have overlooked the viral genomic and phenotypic diversity. Next-generation sequencing (NGS) may instead be used to characterize viral populations in an unbiased manner and to measure within-host genetic diversity. In this study, we used NGS analysis to investigate the within-host genetic diversity of influenza A(H1N1)pdm09 virus in the upper and lower respiratory samples from nine patients who were admitted to the intensive care unit (ICU). A total of 47 amino acid substitution positions were found to differ between the upper and lower respiratory tract samples from all patients. However, the D222G/N substitution in hemagglutinin (HA) protein was the only amino acid substitution common to multiple patients. Furthermore, the substitution was detected only in the six samples from the lower respiratory tract. Therefore, it is important to investigate influenza A(H1N1)pdm09 virus populations using multiple paired samples from the upper and lower respiratory tract to avoid overlooking potentially important substitutions, especially in patients with severe disease. IMPORTANCE The D222G/N substitution in the hemagglutinin (HA) protein of influenza A(H1N1)pdm09 virus has been reported to be associated with disease severity and mortality in numerous previous studies. In the present study, 75% of lower respiratory samples contained heterogeneous influenza populations that carried different amino acids at position 222 of the HA protein, whereas all upper respiratory samples only contained the wild-type 222D. These results suggest the influenza A(H1N1)pdm09 virus has diversified inside the host owing to differences in tissue specificity. In this study, the within-host genetic diversity of influenza A(H1N1)pdm09 virus was investigated for the first time using next-generation sequencing analysis of the viral whole-genome in samples extracted from the upper and lower respiratory tracts of patients with severe disease.
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6
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Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
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7
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Torres A, Loeches IM, Sligl W, Lee N. Severe flu management: a point of view. Intensive Care Med 2020; 46:153-162. [PMID: 31912206 PMCID: PMC7095473 DOI: 10.1007/s00134-019-05868-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022]
Abstract
Annual flu seasons are typically characterized by changes in types and subtypes of influenza, with variations in terms of severity. Despite remarkable improvements in the prevention and management of patients with suspected or laboratory-confirmed diagnosis of influenza, annual seasonal influenza continues to be associated with a high morbidity and mortality. Admission to the intensive care unit is required for patients with severe forms of seasonal influenza infection, with primary pneumonia being present in most of the cases. This review summarizes the most recent knowledge on the diagnosis and treatment strategies in critically ill patients with influenza, focused on diagnostic testing methods, antiviral therapy, use of corticosteroids, antibacterial and antifungal therapy, and supportive measures. The review focuses on diagnostic testing methods, antiviral therapy, use of corticosteroids, antibacterial and antifungal therapy, supportive measures and relevant existing evidence, in order to provide the non-expert clinician a useful overview. An enhanced understanding of current diagnostic and treatment aspects of influenza infection can contribute to improve outcomes and reduce mortality among ICU patients with influenza.
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Affiliation(s)
- Antoni Torres
- Service of Pneumology, Hospital Clinic of Barcelona, University of Barcelona, Institut d'Investigació August Pi i Sunyer (IDIBAPS) and Centro de Investigación Biomédica en Red, Enfermedades Respiratorias (CIBERES), C/Villarroel 170, 08036, Barcelona, Spain.
| | - Ignacio-Martin- Loeches
- Service of Pneumology, Hospital Clinic of Barcelona, University of Barcelona, Institut d'Investigació August Pi i Sunyer (IDIBAPS) and Centro de Investigación Biomédica en Red, Enfermedades Respiratorias (CIBERES), C/Villarroel 170, 08036, Barcelona, Spain.,Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization (MICRO), St. James's Hospital, Dublin, Ireland
| | - Wendy Sligl
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada.,Department of Critical Care Medicine, University of Alberta, Edmonton, Canada
| | - Nelson Lee
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
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8
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Piralla A, Pariani E, Giardina F, Galli C, Sapia D, Pellegrinelli L, Novazzi F, Anselmi G, Rovida F, Mojoli F, Cereda D, Senatore S, Baldanti F. Molecular Characterization of Influenza Strains in Patients Admitted to Intensive Care Units during the 2017-2018 Season. Int J Mol Sci 2019; 20:ijms20112664. [PMID: 31151205 PMCID: PMC6600310 DOI: 10.3390/ijms20112664] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 01/05/2023] Open
Abstract
This study aimed at assessing the frequency and the distribution of influenza virus types/subtypes in 172 laboratory-confirmed influenza-positive patients admitted to intensive care units (ICUs) during the 2017–2018 season in the Lombardy region (Northern Italy), and to investigate the presence of molecular pathogenicity markers. A total of 102/172 (59.3%) patients had influenza A infections (83 A/H1N1pdm09, 2 H3N2 and 17 were untyped), while the remaining 70/172 (40.7%) patients had influenza B infections. The 222G/N mutation in the hemagglutinin gene was identified in 33.3% (3/9) of A/H1N1pdm09 strains detected in the lower respiratory tract (LRT) samples and was also associated with more severe infections, whereas no peculiar mutations were observed for influenza B strains. A single-point evolution was observed in site 222 of A/H1N1pdm09 viruses, which might advantage viral evolution by favouring virus binding and replication in the lungs. Data from 17 paired upper respiratory tract (URT) and LRT samples showed that viral load in LRT samples was mostly higher than that detected in URT samples. Of note, influenza viruses were undetectable in 35% of paired URT samples. In conclusion, LRT samples appear to provide more accurate clinical information than URT samples, thus ensuring correct diagnosis and appropriate treatment of patients with severe respiratory infections requiring ICU admission.
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Affiliation(s)
- Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy.
| | - Federica Giardina
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy.
| | - Davide Sapia
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy.
| | - Federica Novazzi
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Giovanni Anselmi
- Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy.
| | - Francesca Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
| | - Francesco Mojoli
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy.
- Anesthesia and Intensive Care, Emergency Department, Fondazione IRCCS Policlinico S. Matteo, 27100 Pavia, Italy.
| | - Danilo Cereda
- DG Welfare, UO Prevenzione, Lombardy Region, 20124 Milan, Italy.
| | - Sabrina Senatore
- DG Welfare, UO Prevenzione, Lombardy Region, 20124 Milan, Italy.
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy.
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy.
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9
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Torres A, Chalmers JD, Dela Cruz CS, Dominedò C, Kollef M, Martin-Loeches I, Niederman M, Wunderink RG. Challenges in severe community-acquired pneumonia: a point-of-view review. Intensive Care Med 2019; 45:159-171. [PMID: 30706119 PMCID: PMC7094947 DOI: 10.1007/s00134-019-05519-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/04/2019] [Indexed: 12/28/2022]
Abstract
Purpose Severe community-acquired pneumonia (SCAP) is still associated with substantial morbidity and mortality. In this point-of-view review paper, a group of experts discuss the main controversies in SCAP: the role of severity scores to guide patient settings of care and empiric antibiotic therapy; the emergence of pathogens outside the core microorganisms of CAP; viral SCAP; the best empirical treatment; septic shock as the most lethal complication; and the need for new antibiotics. Methods For all topics, the authors describe current controversies and evidence and provide recommendations and suggestions for future research. Evidence was based on meta-analyses, most recent RCTs and recent interventional or observational studies. Recommendations were reached by consensus of all the authors. Results and conclusions The IDSA/ATS criteria remain the most pragmatic tool to predict ICU admission. The authors recommend a combination of a beta-lactam/beta-lactamase inhibitor or a third G cephalosporin plus a macrolide in most SCAP patients, and to empirically cover PES (P. aeruginosa, extended spectrum beta-lactamase producing Enterobacteriaceae, methicillin-resistant S. aureus) pathogens when at least two specific risk factors are present. In patients with influenza CAP, the authors recommend the use of oseltamivir and avoidance of the use of steroids. Corticosteroids can be used in case of refractory shock and high systemic inflammatory response.
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Affiliation(s)
- Antoni Torres
- Department of Pulmonary Medicine, Hospital Clinic of Barcelona, C/Villarroel 170, 08036, Barcelona, Spain.
- August Pi i Sunyer Biomedical Research Institute, IDIBAPS, University of Barcelona, Barcelona, Spain.
- Biomedical Research Networking Centres in Respiratory Diseases (Ciberes), Barcelona, Spain.
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine and Microbial Pathogenesis, Center of Pulmonary Infection Research and Treatment, Yale University School of Medicine, New Haven, CT, USA
| | - Cristina Dominedò
- Department of Anesthesiology and Intensive Care Medicine, Fondazione Policlinico Universitario A. Gemelli, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marin Kollef
- Division of Pulmonary and Critical Care Medicine, Barnes-Jewish Hospital, St. Louis, MO, USA
| | - Ignacio Martin-Loeches
- Biomedical Research Networking Centres in Respiratory Diseases (Ciberes), Barcelona, Spain
- St. James's Hospital, Multidisciplinary Intensive Care Research Organization (MICRO), Dublin, Ireland
| | - Michael Niederman
- Weill Cornell Medical College and New York Presbyterian/Weill Cornell Medical Center, New York City, USA
| | - Richard G Wunderink
- Pulmonary and Critical Care Division, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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