Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 62
Filter
Add filters

Document Type
Year range
1.
Gut Microbes ; 14(1): 2018900, 2022.
Article in English | MEDLINE | ID: covidwho-1585291

ABSTRACT

Mounting evidence suggests that the gut-to-lung axis is critical during respiratory viral infections. We herein hypothesized that disruption of gut homeostasis during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may associate with early disease outcomes. To address this question, we took advantage of the Syrian hamster model. Our data confirmed that this model recapitulates some hallmark features of the human disease in the lungs. We further showed that SARS-CoV-2 infection associated with mild intestinal inflammation, relative alteration in intestinal barrier property and liver inflammation and altered lipid metabolism. These changes occurred concomitantly with an alteration of the gut microbiota composition over the course of infection, notably characterized by a higher relative abundance of deleterious bacterial taxa such as Enterobacteriaceae and Desulfovibrionaceae. Conversely, several members of the Ruminococcaceae and Lachnospiraceae families, including bacteria known to produce the fermentative products short-chain fatty acids (SCFAs), had a reduced relative proportion compared to non-infected controls. Accordingly, infection led to a transient decrease in systemic SCFA amounts. SCFA supplementation during infection had no effect on clinical and inflammatory parameters. Lastly, a strong correlation between some gut microbiota taxa and clinical and inflammation indices of SARS-CoV-2 infection severity was evidenced. Collectively, alteration of the gut microbiota correlates with disease severity in hamsters making this experimental model valuable for the design of interventional, gut microbiota-targeted, approaches for the control of COVID-19.Abbreviations: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; COVID-19, coronavirus disease 2019; SCFAs, short-chain fatty acids; dpi, day post-infection; RT-PCR, reverse transcription polymerase chain reaction; IL, interleukin. ACE2, angiotensin converting enzyme 2; TMPRSS2, transmembrane serine protease 2.


Subject(s)
COVID-19/microbiology , COVID-19/physiopathology , Disease Models, Animal , Gastrointestinal Microbiome , Mesocricetus , Animals , Bacteria/classification , Bacteria/isolation & purification , Bacteria/metabolism , COVID-19/drug therapy , COVID-19/pathology , Cricetinae , Fatty Acids, Volatile/administration & dosage , Fatty Acids, Volatile/metabolism , Humans , Male , SARS-CoV-2/physiology , Severity of Illness Index
2.
Rev Med Virol ; 31(5): 1-13, 2021 09.
Article in English | MEDLINE | ID: covidwho-1574011

ABSTRACT

Coronavirus disease 2019 (Covid-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, is now pandemic. While most Covid-19 patients will experience mild symptoms, a small proportion will develop severe disease, which could be fatal. Clinically, Covid-19 patients manifest fever with dry cough, fatigue and dyspnoea, and in severe cases develop into acute respiratory distress syndrome (ARDS), sepsis and multi-organ failure. These severe patients are characterized by hyperinflammation with highly increased pro-inflammatory cytokines including IL-6, IL-17 and TNF-alpha as well as C-reactive protein, which are accompanied by decreased lymphocyte counts. Clinical evidence supports that gut microbiota dysregulation is common in Covid-19 and plays a key role in the pathogenesis of Covid-19. In this narrative review, we summarize the roles of intestinal dysbiosis in Covid-19 pathogenesis and posit that the associated mechanisms are being mediated by gut bacterial metabolites. Based on this premise, we propose possible clinical implications. Various risk factors could be causal for severe Covid-19, and these include advanced age, concomitant chronic disease, SARS-CoV-2 infection of enterocytes, use of antibiotics and psychological distress. Gut dysbiosis is associated with risk factors and severe Covid-19 due to decreased commensal microbial metabolites, which cause reduced anti-inflammatory mechanisms and chronic low-grade inflammation. The preconditioned immune dysregulation enables SARS-CoV-2 infection to progress to an uncontrolled hyperinflammatory response. Thus, a pre-existing gut microbiota that is diverse and abundant could be beneficial for the prevention of severe Covid-19, and supplementation with commensal microbial metabolites may facilitate and augment the treatment of severe Covid-19.


Subject(s)
Bacteria/metabolism , COVID-19/microbiology , Gastrointestinal Microbiome , Animals , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , COVID-19/genetics , COVID-19/immunology , COVID-19/virology , Cytokines/genetics , Cytokines/immunology , Dysbiosis/genetics , Dysbiosis/immunology , Dysbiosis/microbiology , Dysbiosis/virology , Humans , SARS-CoV-2/genetics , SARS-CoV-2/physiology
3.
Sci Rep ; 11(1): 24042, 2021 12 15.
Article in English | MEDLINE | ID: covidwho-1574556

ABSTRACT

The microbiota of the nasopharyngeal tract (NT) play a role in host immunity against respiratory infectious diseases. However, scant information is available on interactions of SARS-CoV-2 with the nasopharyngeal microbiome. This study characterizes the effects of SARS-CoV-2 infection on human nasopharyngeal microbiomes and their relevant metabolic functions. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 patients = 8, recovered humans = 7, and healthy people = 7) were collected, and underwent to RNAseq-based metagenomic investigation. Our RNAseq data mapped to 2281 bacterial species (including 1477, 919 and 676 in healthy, COVID-19 and recovered metagenomes, respectively) indicating a distinct microbiome dysbiosis. The COVID-19 and recovered samples included 67% and 77% opportunistic bacterial species, respectively compared to healthy controls. Notably, 79% commensal bacterial species found in healthy controls were not detected in COVID-19 and recovered people. Similar dysbiosis was also found in viral and archaeal fraction of the nasopharyngeal microbiomes. We also detected several altered metabolic pathways and functional genes in the progression and pathophysiology of COVID-19. The nasopharyngeal microbiome dysbiosis and their genomic features determined by our RNAseq analyses shed light on early interactions of SARS-CoV-2 with the nasopharyngeal resident microbiota that might be helpful for developing microbiome-based diagnostics and therapeutics for this novel pandemic disease.


Subject(s)
Bacteria/classification , COVID-19/microbiology , Nasopharynx/microbiology , SARS-CoV-2/genetics , Sequence Analysis, RNA/methods , Adult , Aged , Bacteria/genetics , Bacteria/isolation & purification , Bacteria/pathogenicity , Case-Control Studies , Female , High-Throughput Nucleotide Sequencing , Humans , Male , Metagenomics , Middle Aged , Phylogeny , Symbiosis , Young Adult
4.
Retina ; 41(11): 2215-2220, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1483570

ABSTRACT

PURPOSE: To investigate the bacterial growth in the surgical face masks used by patients who received intravitreal injections and study the effect of povidone-iodine on the periocular area (PA) of masks. METHODS: Forty patients who attended for intravitreal injections were divided in those with less (<4 hours) and more (>4 hours) than 4 hours of mask use. Each group was divided depending on the application or not of povidone-iodine in the PA of the mask. Bacterial load was studied on PA and mouth area samples. RESULTS: The bacterial load in the PA was higher in the >4 hours group compared with the <4 hours group (13.2 vs. 48.75 colony-forming units/µL; P = 0.03). The contamination in the PA significantly decreased after applying povidone-iodine in the >4 hours group (P = 0.01). The use or not of povidone-iodine was strongly correlated to a positive culture (OR = 9.0, P = 0.00. CI 1.63-49.44). CONCLUSION: Surgical face masks worn for more than 4 hours present higher contamination in the PA than those with less use. Bacterial load in the PA is reduced with povidone-iodine on masks used for more than 4 hours. This contamination should be considered in the asepsis protocol of intravitreal injections.


Subject(s)
Angiogenesis Inhibitors/administration & dosage , Bacteria/isolation & purification , COVID-19/epidemiology , Equipment Contamination , Masks/microbiology , SARS-CoV-2 , Aged , Aged, 80 and over , Anti-Infective Agents, Local/administration & dosage , Bacterial Load , Bacteriological Techniques , Female , Humans , Intravitreal Injections , Male , Middle Aged , Povidone-Iodine/administration & dosage , Prospective Studies , Retinal Diseases/drug therapy , Vascular Endothelial Growth Factor A/antagonists & inhibitors
5.
Int J Mol Sci ; 22(19)2021 Oct 05.
Article in English | MEDLINE | ID: covidwho-1463710

ABSTRACT

The present Special Issue focuses on the latest approaches to health and public health microbiology using multiomics [...].


Subject(s)
Bacteria/growth & development , Holistic Health/standards , Metabolome , Metagenome , Microbiota , Proteome , Public Health/standards , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Humans
6.
Nat Commun ; 12(1): 5026, 2021 08 18.
Article in English | MEDLINE | ID: covidwho-1363491

ABSTRACT

Nationwide prospective surveillance of all-age patients with acute respiratory infections was conducted in China between 2009‒2019. Here we report the etiological and epidemiological features of the 231,107 eligible patients enrolled in this analysis. Children <5 years old and school-age children have the highest viral positivity rate (46.9%) and bacterial positivity rate (30.9%). Influenza virus, respiratory syncytial virus and human rhinovirus are the three leading viral pathogens with proportions of 28.5%, 16.8% and 16.7%, and Streptococcus pneumoniae, Mycoplasma pneumoniae and Klebsiella pneumoniae are the three leading bacterial pathogens (29.9%, 18.6% and 15.8%). Negative interactions between viruses and positive interactions between viral and bacterial pathogens are common. A Join-Point analysis reveals the age-specific positivity rate and how this varied for individual pathogens. These data indicate that differential priorities for diagnosis, prevention and control should be highlighted in terms of acute respiratory tract infection patients' demography, geographic locations and season of illness in China.


Subject(s)
Bacteria/isolation & purification , Bacterial Infections/microbiology , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology , Virus Diseases/virology , Viruses/isolation & purification , Adolescent , Adult , Bacteria/classification , Bacteria/genetics , Bacterial Infections/epidemiology , Child , Child, Preschool , China/epidemiology , Female , Humans , Infant , Male , Prospective Studies , Respiratory Tract Infections/epidemiology , Seasons , Virus Diseases/epidemiology , Viruses/classification , Viruses/genetics , Young Adult
7.
Ann Clin Microbiol Antimicrob ; 20(1): 69, 2021 Sep 25.
Article in English | MEDLINE | ID: covidwho-1438275

ABSTRACT

BACKGROUND: Coronavirus SARS-CoV-2 causes COVID-19 illness which can progress to severe pneumonia. Empiric antibacterials are often employed though frequency of bacterial coinfection superinfection is debated and concerns raised about selection of bacterial antimicrobial resistance. We evaluated sputum bacterial and fungal growth from 165 intubated COVID-19 pneumonia patients. Objectives were to determine frequency of culture positivity, risk factors for and outcomes of positive cultures, and timing of antimicrobial resistance development. METHODS: Retrospective reviews were conducted of COVID-19 pneumonia patients requiring intubation admitted to a 1058-bed four community hospital system on the east coast United States, March 1 to May 1, 2020. Length of stay (LOS) was expressed as mean (standard deviation); 95% confidence interval (95% CI) was computed for overall mortality rate using the exact binomial method, and overall mortality was compared across each level of a potential risk factor using a Chi-Square Test of Independence. All tests were two-sided, and significance level was set to 0.05. RESULTS: Average patient age was 68.7 years and LOS 19.9 days. Eighty-three patients (50.3% of total) originated from home, 10 from group homes (6.1% of total), and 72 from nursing facilities (43.6% of total). Mortality was 62.4%, highest for nursing home residents (80.6%). Findings from 253 sputum cultures overall did not suggest acute bacterial or fungal infection in 73 (45%) of 165 individuals sampled within 24 h of intubation. Cultures ≥ 1 week following intubation did grow potential pathogens in 72 (64.9%) of 111 cases with 70.8% consistent with late pneumonia and 29.2% suggesting colonization. Twelve (10.8% of total) of these late post-intubation cultures revealed worsened antimicrobial resistance predominantly in Pseudomonas, Enterobacter, or Staphylococcus aureus. CONCLUSIONS: In severe COVID-19 pneumonia, a radiographic ground glass interstitial pattern and lack of purulent sputum prior to/around the time of intubation correlated with no culture growth or recovery of normal oral flora ± yeast. Discontinuation of empiric antibacterials should be considered in these patients aided by other clinical findings, history of prior antimicrobials, laboratory testing, and overall clinical course. Continuing longterm hospitalisation and antibiotics are associated with sputum cultures reflective of hospital-acquired microbes and increasing antimicrobial resistance. TRIAL REGISTRATION: Not applicable as this was a retrospective chart review study without interventional arm.


Subject(s)
Bacteria/drug effects , Bacterial Infections/complications , COVID-19/therapy , Cross Infection/complications , Fungi/drug effects , Mycoses/complications , Pneumonia/therapy , Sputum/microbiology , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents , Anti-Infective Agents/pharmacology , Bacteria/genetics , Bacteria/isolation & purification , Bacterial Infections/drug therapy , Bacterial Infections/microbiology , COVID-19/complications , COVID-19/mortality , COVID-19/virology , Cross Infection/drug therapy , Cross Infection/microbiology , Drug Resistance, Bacterial , Drug Resistance, Multiple, Fungal , Female , Fungi/genetics , Fungi/isolation & purification , Hospitalization , Humans , Intubation , Length of Stay , Male , Middle Aged , Mycoses/microbiology , Pneumonia/complications , Pneumonia/mortality , Pneumonia/virology , Retrospective Studies , SARS-CoV-2/physiology
8.
J Microbiol ; 59(10): 941-948, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1432635

ABSTRACT

Several follow-up studies have found that COVID-19 (coronavirus disease 2019) patients had persistent symptoms after discharge. Gut microbiota play an important role in human health and immune responses. Therefore, this study investigated the gut microbiota of recovered COVID-19 patients and the correlations between gut microbiota and persistent symptoms after discharge. Stool samples were collected from 15 recovered healthcare workers (HCWs) with COVID-19 at three months after discharge, in addition, stool samples were collected from 14 healthy controls (HCs) to perform 16S rRNA gene sequencing between May and July 2020. Compared with HCs, recovered HCWs had reduced bacterial diversity at three months after discharge, with a significantly higher relative abundance of opportunistic pathogens, and a significantly lower relative abundance of beneficial bacteria. In addition, Escherichia unclassified was positively correlated with persistent symptoms at three months after discharge, including fatigue (r = 0.567, p = 0.028), chest tightness after activity (r = 0.687, p = 0.005), and myalgia (r = 0.523, p = 0.045). Intestinibacter bartlettii was positively correlated with anorexia (r = 0.629, p = 0.012) and fatigue (r = 0.545, p = 0.036). However, Faecalibacterium prausnitzii was negatively correlated with chest tightness after activity (r = -0.591, p = 0.02), and Intestinimonas butyriciproducens was negatively correlated with cough (r = -0.635, p = 0.011). In conclusion, the gut microbiota of recovered HCWs with COVID-19 at three months after discharge was different from that of HCs, and altered gut microbiota was correlated with persistent symptoms after discharge, highlighting that gut microbiota may play an important role in the recovery of patients with COVID-19.


Subject(s)
Bacteria/isolation & purification , COVID-19/complications , COVID-19/microbiology , Gastrointestinal Microbiome , Adult , Bacteria/classification , Bacteria/genetics , COVID-19/therapy , COVID-19/virology , Fatigue/etiology , Fatigue/microbiology , Feces/microbiology , Female , Follow-Up Studies , Humans , Male , Middle Aged , Myalgia/etiology , Myalgia/microbiology , Patient Discharge , Phylogeny , Survivors/statistics & numerical data
9.
PLoS One ; 16(4): e0251049, 2021.
Article in English | MEDLINE | ID: covidwho-1388911

ABSTRACT

Respiratory infections, including SARS-CoV-2, are spread via inhalation or ingestion of airborne pathogens. Airborne transmission is difficult to control, particularly indoors. Manufacturers of high efficiency particulate air (HEPA) filters claim they remove almost all small particles including airborne bacteria and viruses. This study investigates whether modern portable, commercially available air filters reduce the incidence of respiratory infections and/or remove bacteria and viruses from indoor air. We systematically searched Medline, Embase and Cochrane for studies published between January 2000 and September 2020. Studies were eligible for inclusion if they included a portable, commercially available air filter in any indoor setting including care homes, schools or healthcare settings, investigating either associations with incidence of respiratory infections or removal and/or capture of aerosolised bacteria and viruses from the air within the filters. Dual data screening and extraction with narrative synthesis. No studies were found investigating the effects of air filters on the incidence of respiratory infections. Two studies investigated bacterial capture within filters and bacterial load in indoor air. One reported higher numbers of viable bacteria in the HEPA filter than in floor dust samples. The other reported HEPA filtration combined with ultraviolet light reduced bacterial load in the air by 41% (sampling time not reported). Neither paper investigated effects on viruses. There is an important absence of evidence regarding the effectiveness of a potentially cost-efficient intervention for indoor transmission of respiratory infections, including SARS-CoV-2. Two studies provide 'proof of principle' that air filters can capture airborne bacteria in an indoor setting. Randomised controlled trials are urgently needed to investigate effects of portable HEPA filters on incidence of respiratory infections.


Subject(s)
Air Filters , Air Pollution, Indoor/prevention & control , COVID-19/prevention & control , Respiratory Tract Infections/prevention & control , SARS-CoV-2/isolation & purification , Air Filters/microbiology , Air Filters/virology , Bacteria/isolation & purification , Communicable Disease Control/methods , Housing , Humans , Viruses/isolation & purification , Workplace
11.
Photochem Photobiol Sci ; 20(7): 955-965, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1384775

ABSTRACT

The pandemic created by SARS-CoV-2 has caused a shortage in the supplies of N95 filtering facepiece respirators (FFRs), disposable respirators with at least 95% efficiency to remove non-oily airborne particles, due to increasing cases all over the world. The current article reviewed various possible decontamination methods for FFR reuse including ultraviolet germicidal irradiation (UVGI), hydrogen peroxide vapor (HPV), microwave-generated steam (MGS), hydrogen peroxide gas plasma (HPGP), and 70% or higher ethanol solution. HPV decontamination was effective against bacterial spores (6 log10 reduction of Geobacillus stearothermophilus spores) on FFRs and viruses (> 4 log10 reduction of various types of viruses) on inanimate surfaces, and no degradation of respirator materials and fit has been reported. 70% or higher ethanol decontamination showed high efficacy in inactivation of coronaviruses on inanimate surfaces (> 3.9 log10 reduction) but it was lower on FFRs which filtration efficiency was also decreased. UVGI method had good biocidal efficacy on FFRs (> 3 log10 reduction of H1N1 virus) combined with inexpensive, readily available equipment; however, it was more time-consuming to ensure sufficient reduction in SARS-CoV-2. MGS treatment also provided good viral decontamination on FFRs (> 4 log10 reduction of H1N1 virus) along with less time-intensive process and readily available equipment while inconsistent disinfection on the treated surfaces and deterioration of nose cushion of FFRs were observed. HPGP was a good virucidal system (> 6 log10 reduction of Vesicular stomatitis virus) but filtration efficiency after decontamination was inconsistent. Overall, HPV appeared to be one of the most promising methods based on the high biocidal efficacy on FFRs, preservation of respirator performance after multiple cycles, and no residual chemical toxicity. Nonetheless, equipment cost and time of the HPV process and a suitable operating room need to be considered.


Subject(s)
COVID-19 , Decontamination/methods , N95 Respirators/microbiology , N95 Respirators/virology , Bacteria/drug effects , Bacteria/isolation & purification , Bacteria/radiation effects , COVID-19/epidemiology , Disinfection/methods , Ethanol/pharmacology , Humans , Hydrogen Peroxide/pharmacology , Microwaves , Ultraviolet Rays , Viruses/drug effects , Viruses/isolation & purification , Viruses/radiation effects
12.
Infection ; 49(3): 377-385, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1384709

ABSTRACT

PURPOSE: CRISPR gene-editing technology has the potential to transform the diagnosis and treatment of infectious diseases, but most clinicians are unaware of its broad applicability. Derived from an ancient microbial defence system, these so-called "molecular scissors" enable precise gene editing with a low error rate. However, CRISPR systems can also be targeted against pathogenic DNA or RNA sequences. This potential is being combined with innovative delivery systems to develop new therapeutic approaches to infectious diseases. METHODS: We searched Pubmed and Google Scholar for CRISPR-based strategies in the diagnosis and treatment of infectious diseases. Reference lists were reviewed and synthesized for narrative review. RESULTS: CRISPR-based strategies represent a novel approach to many challenging infectious diseases. CRISPR technologies can be harnessed to create rapid, low-cost diagnostic systems, as well as to identify drug-resistance genes. Therapeutic strategies, such as CRISPR systems that cleave integrated viral genomes or that target resistant bacteria, are in development. CRISPR-based therapies for emerging viruses, such as SARS-CoV-2, have also been proposed. Finally, CRISPR systems can be used to reprogram human B cells to produce neutralizing antibodies. The risks of CRISPR-based therapies include off-target and on-target modifications. Strategies to control these risks are being developed and a phase 1 clinical trials of CRISPR-based therapies for cancer and monogenic diseases are already underway. CONCLUSIONS: CRISPR systems have broad applicability in the field of infectious diseases and may offer solutions to many of the most challenging human infections.


Subject(s)
CRISPR-Cas Systems , Communicable Diseases/diagnosis , Communicable Diseases/therapy , Animals , Bacteria/genetics , Bacteria/isolation & purification , Bacteria/pathogenicity , Gene Editing , Humans , Molecular Diagnostic Techniques , Molecular Targeted Therapy , Viruses/genetics , Viruses/isolation & purification , Viruses/pathogenicity
13.
Nat Microbiol ; 6(10): 1245-1258, 2021 10.
Article in English | MEDLINE | ID: covidwho-1380902

ABSTRACT

Respiratory failure is associated with increased mortality in COVID-19 patients. There are no validated lower airway biomarkers to predict clinical outcome. We investigated whether bacterial respiratory infections were associated with poor clinical outcome of COVID-19 in a prospective, observational cohort of 589 critically ill adults, all of whom required mechanical ventilation. For a subset of 142 patients who underwent bronchoscopy, we quantified SARS-CoV-2 viral load, analysed the lower respiratory tract microbiome using metagenomics and metatranscriptomics and profiled the host immune response. Acquisition of a hospital-acquired respiratory pathogen was not associated with fatal outcome. Poor clinical outcome was associated with lower airway enrichment with an oral commensal (Mycoplasma salivarium). Increased SARS-CoV-2 abundance, low anti-SARS-CoV-2 antibody response and a distinct host transcriptome profile of the lower airways were most predictive of mortality. Our data provide evidence that secondary respiratory infections do not drive mortality in COVID-19 and clinical management strategies should prioritize reducing viral replication and maximizing host responses to SARS-CoV-2.


Subject(s)
Bronchoalveolar Lavage Fluid/microbiology , COVID-19/therapy , Respiration, Artificial , SARS-CoV-2/pathogenicity , Adaptive Immunity , Adult , Aged , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Bacterial Load , Bronchoalveolar Lavage Fluid/immunology , Bronchoalveolar Lavage Fluid/virology , COVID-19/immunology , COVID-19/microbiology , COVID-19/mortality , Critical Illness , Female , Hospitalization , Humans , Immunity, Innate , Male , Microbiota , Middle Aged , Odds Ratio , Prognosis , Prospective Studies , Respiratory System/immunology , Respiratory System/microbiology , Respiratory System/virology , SARS-CoV-2/immunology , Viral Load
14.
mBio ; 12(4): e0177721, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1360545

ABSTRACT

Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease. Here, we investigated the respiratory tract microbiome in coronavirus disease 2019 (COVID-19) and its relationship to disease severity, systemic immunologic features, and outcomes. We examined 507 oropharyngeal, nasopharyngeal, and endotracheal samples from 83 hospitalized COVID-19 patients as well as non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, and the commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR. We found that COVID-19 patients had upper respiratory microbiome dysbiosis and greater change over time than critically ill patients without COVID-19. Oropharyngeal microbiome diversity at the first time point correlated inversely with disease severity during hospitalization. Microbiome composition was also associated with systemic immune parameters in blood, as measured by lymphocyte/neutrophil ratios and immune profiling of peripheral blood mononuclear cells. Intubated patients showed patient-specific lung microbiome communities that were frequently highly dynamic, with prominence of Staphylococcus. Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity. Thus, the respiratory tract microbiome and commensal viruses are disturbed in COVID-19 and correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, its possible use as biomarkers, and the role of bacterial and viral taxa identified here in COVID-19 pathogenesis. IMPORTANCE COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, results in highly variable outcomes ranging from minimal illness to death, but the reasons for this are not well understood. We investigated the respiratory tract bacterial microbiome and small commensal DNA viruses in hospitalized COVID-19 patients and found that each was markedly abnormal compared to that in healthy people and differed from that in critically ill patients without COVID-19. Early airway samples tracked with the level of COVID-19 illness reached during hospitalization, and the airway microbiome also correlated with immune parameters in blood. These findings raise questions about the mechanisms linking SARS-CoV-2 infection and other microbial inhabitants of the airway, including whether the microbiome might regulate severity of COVID-19 disease and/or whether early microbiome features might serve as biomarkers to discriminate disease severity.


Subject(s)
Bacteria/classification , Dysbiosis/microbiology , Lung/microbiology , Nasopharynx/microbiology , Oropharynx/microbiology , SARS-CoV-2/immunology , Adult , Aged , Aged, 80 and over , Anelloviridae/classification , Anelloviridae/genetics , Anelloviridae/isolation & purification , Bacteria/genetics , Bacteria/isolation & purification , COVID-19/pathology , Female , Humans , Lymphocyte Count , Male , Microbiota , Middle Aged , RNA, Ribosomal, 16S/genetics , Severity of Illness Index
15.
Diagn Microbiol Infect Dis ; 101(3): 115416, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1356194

ABSTRACT

BACKGROUND: COVID19 is the novel respiratory illness caused by SARS-CoV-2. The presence of other potentially pathogenic microorganisms could worsen the prognosis of these patients. AIM: The study aims to describe coinfections in COVID-19 patients and contrast it between standard ward and critical care patients at Hospital Central de la Defensa Gómez Ulla (HCDGU). METHODS: A retrospective study was carried out of patients with COVID-19 confirmed with RTPCR admitted to the HCDGU from March 5, 2020 to May 7 of 2020. FINDINGS: Of a total of 703 patients with COVID-19, 75(10.7%) had other microbiologically confirmed infections: 9% (58/648) in standard ward patients and 31.5%(17/54) in critical care patients. In total 86 samples of the 75 patients presented some microorganism; clinically relevant bacteraemias, 50%, respiratory cultures, 32.6% and pneumococcal positive antigens, 17.4%. CONCLUSIONS: We found a low frequency of microorganism coinfection in COVID-19 patients, however in critical care these coinfections increased considerably.


Subject(s)
Bacterial Infections/complications , COVID-19/complications , Coinfection/diagnosis , Inpatients , SARS-CoV-2 , Aged , Bacteremia/complications , Bacteremia/microbiology , Bacteria/classification , Bacteria/isolation & purification , Female , Humans , Male , Middle Aged , Retrospective Studies
16.
Cell Rep ; 36(9): 109637, 2021 08 31.
Article in English | MEDLINE | ID: covidwho-1356160

ABSTRACT

Research conducted on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogenesis and coronavirus disease 2019 (COVID-19) generally focuses on the systemic host response, especially that generated by severely ill patients, with few studies investigating the impact of acute SARS-CoV-2 at the site of infection. We show that the nasal microbiome of SARS-CoV-2-positive patients (CoV+, n = 68) at the time of diagnosis is unique when compared to CoV- healthcare workers (n = 45) and CoV- outpatients (n = 21). This shift is marked by an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa, which is also positively associated with viral RNA load. Additionally, we observe a robust host transcriptional response in the nasal epithelia of CoV+ patients, indicative of an antiviral innate immune response and neuronal damage. These data suggest that the inflammatory response caused by SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections.


Subject(s)
Bacteria/classification , Bacterial Infections/microbiology , COVID-19 , Microbiota , Adult , Aged , Aged, 80 and over , Bacteria/isolation & purification , COVID-19/complications , COVID-19/immunology , COVID-19/microbiology , Coinfection/microbiology , Coinfection/virology , Cross-Sectional Studies , DNA, Bacterial/genetics , Female , Humans , Immunity, Innate , Inflammation , Male , Middle Aged , Nose/microbiology , Pseudomonas Infections/microbiology , Pseudomonas aeruginosa/isolation & purification , RNA, Ribosomal, 16S/genetics , RNA, Viral/genetics , RNA-Seq , Transcriptome , Viral Load , Young Adult
17.
Emerg Microbes Infect ; 10(1): 1515-1518, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1313723

ABSTRACT

We show a shift in the prevalence of respiratory viral pathogens in community-acquired pneumonia patients during the COVID-19 pandemic. Our data support the efficiency of non-pharmaceutical interventions on virus circulation except for rhinoviruses. The consequences of an altered circulation on subsequent winter seasons remain unclear and support the importance of systematic virological surveillance.


Subject(s)
COVID-19/epidemiology , Community-Acquired Infections/epidemiology , Pneumonia/epidemiology , Respiratory Tract Infections/epidemiology , Adult , Aged , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , COVID-19/virology , Community-Acquired Infections/microbiology , Community-Acquired Infections/virology , Female , Germany/epidemiology , Humans , Male , Middle Aged , Pandemics , Pneumonia/microbiology , Pneumonia/virology , Prevalence , Prospective Studies , Respiratory Tract Infections/microbiology , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Viruses/classification , Viruses/genetics , Viruses/isolation & purification , Young Adult
18.
OMICS ; 25(8): 484-494, 2021 08.
Article in English | MEDLINE | ID: covidwho-1307504

ABSTRACT

Pandemics and environmental crises evident from the first two decades of the 21st century call for methods innovation in biosurveillance and early detection of risk signals in planetary ecosystems. In crises conditions, conventional methods in public health, biosecurity, and environmental surveillance do not work well. In addition, the standard laboratory amenities and procedures may become unavailable, irrelevant, or simply not feasible, for example, owing to disruptions in logistics and process supply chains. The COVID-19 pandemic has been a wakeup call in this sense to reintroduce point-of-need diagnostics with an eye to limited resource settings and biosurveillance solutions. We report here a methodology innovation, a fast, scalable, and alkaline DNA extraction pipeline for emergency microbiomics biosurveillance. We believe that the presented methodology is well poised for effective, resilient, and anticipatory responses to future pandemics and ecological crises while contributing to microbiome science and point-of-need diagnostics in nonelective emergency contexts. The alkaline DNA extraction pipeline can usefully expand the throughput in emergencies by deployment or to allow backup in case of instrumentation failure in vital facilities. The need for distributed public health genomics surveillance is increasingly evident in the 21st century. This study makes a contribution to these ends broadly, and for future pandemic preparedness in particular. We call for innovation in biosurveillance methods that remain important existentially on a planet under pressure from unchecked human growth and breach of the boundaries between human and nonhuman animal habitats.


Subject(s)
Biosurveillance/methods , DNA/isolation & purification , Microbiological Techniques , Public Health Surveillance/methods , Animals , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Fungi/classification , Fungi/genetics , Fungi/isolation & purification , Genetic Techniques/economics , Humans , Microbiological Techniques/economics , Plants/microbiology
19.
Ocul Immunol Inflamm ; 29(4): 726-729, 2021 May 19.
Article in English | MEDLINE | ID: covidwho-1307411

ABSTRACT

PURPOSE: To report six patients with endogenous endophthalmitis as a complication of COVID-19 infection. METHODS: A multicentric retrospective database review of patients with a diagnosis of endogenous endophthalmitis and a history of COVID-19 infection. RESULTS: Four of six patients were diabetics. All presented after an average duration of 40 days (Range 17-90 days) of COVID-19 infection. Two of six patients had bilateral involvement. Five of six patients had received intravenous corticosteroid for COVID-19. Two of six vitreous samples showed fungi (Candida and Bipolaris species), two showed bacteria (Staphylococcus species) and two samples were culture negative. Control of infection with good visual outcome in four out of eight eyes. CONCLUSIONS: COVID-19 patients with a history of hospitalization and prolonged use of systemic corticosteroids and comorbidities, for example, diabetes mellitus have a high risk of endogenous endophthalmitis. A high index of clinical suspicion with timely intervention can salvage many eyes.


Subject(s)
COVID-19/complications , Endophthalmitis/etiology , Eye Infections, Bacterial/etiology , Eye Infections, Fungal/etiology , Pandemics , Visual Acuity , Vitreous Body/microbiology , Adult , Bacteria/isolation & purification , COVID-19/epidemiology , Endophthalmitis/diagnosis , Endophthalmitis/microbiology , Eye Infections, Bacterial/diagnosis , Eye Infections, Bacterial/microbiology , Eye Infections, Fungal/diagnosis , Eye Infections, Fungal/microbiology , Follow-Up Studies , Fungi/isolation & purification , Humans , India/epidemiology , Male , Middle Aged , Retrospective Studies
20.
Microb Ecol ; 82(2): 365-376, 2021 Aug.
Article in English | MEDLINE | ID: covidwho-1293356

ABSTRACT

The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.


Subject(s)
Bacteria/isolation & purification , Communicable Disease Control/legislation & jurisprudence , Ecosystem , Rivers/microbiology , Bacteria/classification , COVID-19/epidemiology , COVID-19/prevention & control , Drug Resistance, Bacterial , Environmental Monitoring , Hinduism , Human Activities , India/epidemiology , Principal Component Analysis
SELECTION OF CITATIONS
SEARCH DETAIL
...