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1.
Rev Med Virol ; 31(5): 1-13, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34546607

RESUMO

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.


Assuntos
Bactérias/metabolismo , COVID-19/microbiologia , Microbioma Gastrointestinal , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , COVID-19/genética , COVID-19/imunologia , COVID-19/virologia , Citocinas/genética , Citocinas/imunologia , Disbiose/genética , Disbiose/imunologia , Disbiose/microbiologia , Disbiose/virologia , Humanos , SARS-CoV-2/genética , SARS-CoV-2/fisiologia
2.
Ann Clin Microbiol Antimicrob ; 20(1): 64, 2021 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-34493302

RESUMO

BACKGROUND: Bacterial superinfections associated with COVID-19 are common in ventilated ICU patients and impact morbidity and lethality. However, the contribution of antimicrobial resistance to the manifestation of bacterial infections in these patients has yet to be elucidated. METHODS: We collected 70 Gram-negative bacterial strains, isolated from the lower respiratory tract of ventilated COVID-19 patients in Zurich, Switzerland between March and May 2020. Species identification was performed using MALDI-TOF; antibiotic susceptibility profiles were determined by EUCAST disk diffusion and CLSI broth microdilution assays. Selected Pseudomonas aeruginosa isolates were analyzed by whole-genome sequencing. RESULTS: Pseudomonas aeruginosa (46%) and Enterobacterales (36%) comprised the two largest etiologic groups. Drug resistance in P. aeruginosa isolates was high for piperacillin/tazobactam (65.6%), cefepime (56.3%), ceftazidime (46.9%) and meropenem (50.0%). Enterobacterales isolates showed slightly lower levels of resistance to piperacillin/tazobactam (32%), ceftriaxone (32%), and ceftazidime (36%). All P. aeruginosa isolates and 96% of Enterobacterales isolates were susceptible to aminoglycosides, with apramycin found to provide best-in-class coverage. Genotypic analysis of consecutive P. aeruginosa isolates in one patient revealed a frameshift mutation in the transcriptional regulator nalC that coincided with a phenotypic shift in susceptibility to ß-lactams and quinolones. CONCLUSIONS: Considerable levels of antimicrobial resistance may have contributed to the manifestation of bacterial superinfections in ventilated COVID-19 patients, and may in some cases mandate consecutive adaptation of antibiotic therapy. High susceptibility to amikacin and apramycin suggests that aminoglycosides may remain an effective second-line treatment of ventilator-associated bacterial pneumonia, provided efficacious drug exposure in lungs can be achieved.


Assuntos
Antibacterianos/farmacologia , COVID-19/microbiologia , Bactérias Gram-Negativas/efeitos dos fármacos , Sistema Respiratório/microbiologia , COVID-19/complicações , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Bactérias Gram-Negativas/isolamento & purificação , Humanos , Testes de Sensibilidade Microbiana , Pneumonia Associada à Ventilação Mecânica/microbiologia , Estudos Prospectivos , Infecções por Pseudomonas/microbiologia , Pseudomonas aeruginosa/efeitos dos fármacos , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/isolamento & purificação , SARS-CoV-2/isolamento & purificação , Suíça
3.
Int J Mol Sci ; 22(18)2021 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-34575864

RESUMO

The importance of a healthy microbiome cannot be overemphasized. Disturbances in its composition can lead to a variety of symptoms that can extend to other organs. Likewise, acute or chronic conditions in other organs can affect the composition and physiology of the gut microbiome. Here, we discuss interorgan communication along the gut-lung axis, as well as interactions between lung and coronary heart diseases and between cardiovascular disease and the gut microbiome. This triangle of organs, which also affects the clinical outcome of COVID-19 infections, is connected by means of numerous receptors and effectors, including immune cells and immune-modulating factors such as short chain fatty acids (SCFA) and trimethlamine-N-oxide (TMAO). The gut microbiome plays an important role in each of these, thus affecting the health of the lungs and the heart, and this interplay occurs in both directions. The gut microbiome can be influenced by the oral uptake of probiotics. With an improved understanding of the mechanisms responsible for interorgan communication, we can start to define what requirements an 'ideal' probiotic should have and its role in this triangle.


Assuntos
COVID-19 , Doença das Coronárias , Microbioma Gastrointestinal/efeitos dos fármacos , Pneumopatias , Probióticos/administração & dosagem , Animais , COVID-19/microbiologia , COVID-19/patologia , Doença das Coronárias/microbiologia , Doença das Coronárias/patologia , Humanos , Pneumopatias/microbiologia , Pneumopatias/patologia
4.
Molecules ; 26(18)2021 Sep 11.
Artigo em Inglês | MEDLINE | ID: mdl-34576987

RESUMO

Current studies suggest that cariogenic bacteria in dental plaque influence the severity of COVID-19 complications since the oral cavity is a reservoir for respiratory pathogens potentially responsible for the development of hospital-acquired pneumonia. This article focuses on the association between dental plaque and COVID-19 concerning the influence of altered oral biofilm on the risk of increased severity of SARS-CoV-2 infection. Moreover, it concentrates on the usefulness of propolis, with its apitherapeutic antibacterial properties, for treating oral bacterial infections co-occurring with SARS-CoV-2 infection. A review of the literature on PubMed, Cochrane Library and Medline between 2000 and 2021 revealed 56 published articles indicating that a link between dental plaque and COVID-19 complications was probable. Furthermore, they indicated that propolis may minimize COVID-19 severity by reducing dental plaque accumulation. The possibility that improved oral health could reduce the risk of COVID-19 complications should be of interest to scientists.


Assuntos
Biofilmes , COVID-19 , Cárie Dentária , Placa Dentária , Doenças da Boca , Própole/uso terapêutico , Animais , Anti-Infecciosos/uso terapêutico , Biofilmes/efeitos dos fármacos , COVID-19/tratamento farmacológico , COVID-19/microbiologia , Cárie Dentária/tratamento farmacológico , Cárie Dentária/microbiologia , Placa Dentária/tratamento farmacológico , Placa Dentária/microbiologia , Humanos , Doenças da Boca/tratamento farmacológico , Doenças da Boca/microbiologia , Saúde Bucal
5.
Pol J Microbiol ; 70(3): 395-400, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34584533

RESUMO

Opportunistic fungal infections increase morbidity and mortality in COVID-19 patients monitored in intensive care units (ICU). As patients' hospitalization days in the ICU and intubation period increase, opportunistic infections also increase, which prolongs hospital stay days and elevates costs. The study aimed to describe the profile of fungal infections and identify the risk factors associated with mortality in COVID-19 intensive care patients. The records of 627 patients hospitalized in ICU with the diagnosis of COVID-19 were investigated from electronic health records and hospitalization files. The demographic characteristics (age, gender), the number of ICU hospitalization days and mortality rates, APACHE II scores, accompanying diseases, antibiotic-steroid treatments taken during hospitalization, and microbiological results (blood, urine, tracheal aspirate samples) of the patients were recorded. Opportunistic fungal infection was detected in 32 patients (5.10%) of 627 patients monitored in ICU with a COVID-19 diagnosis. The average APACHE II score of the patients was 28 ± 6. While 25 of the patients (78.12%) died, seven (21.87%) were discharged from the ICU. Candida parapsilosis (43.7%) was the opportunistic fungal agent isolated from most blood samples taken from COVID-19 positive patients. The mortality rate of COVID-19 positive patients with candidemia was 80%. While two out of the three patients (66.6%) for whom fungi were grown from their tracheal aspirate died, one patient (33.3%) was transferred to the ward. Opportunistic fungal infections increase the mortality rate of COVID-19-positive patients. In addition to the risk factors that we cannot change, invasive procedures should be avoided, constant blood sugar regulation should be applied, and unnecessary antibiotics use should be avoided.


Assuntos
COVID-19/complicações , COVID-19/microbiologia , Fungos/patogenicidade , Unidades de Terapia Intensiva/estatística & dados numéricos , Micoses/etiologia , Micoses/mortalidade , Infecções Oportunistas/etiologia , Idoso , Idoso de 80 Anos ou mais , Infecção Hospitalar , Feminino , Fungos/classificação , Fungos/isolamento & purificação , Humanos , Tempo de Internação , Masculino , Pessoa de Meia-Idade , Micoses/sangue , Micoses/virologia , Infecções Oportunistas/sangue , Infecções Oportunistas/virologia , Fatores de Risco
7.
BMC Infect Dis ; 21(1): 927, 2021 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-34496774

RESUMO

BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is among the most concerning cause of healthcare-associated infections (HAI) due to its high level of antibiotic resistance and high mortality. In the era of the COVID-19 pandemic, the key priority of infection control committees is to contain the dissemination of antibiotic resistant Gram-negative bacteria. Here, we aimed to timely recognize the emergence of CRAB in COVID-19 cases admitted to the wards of a tertiary referral hospital and to identify the genetic relatedness of the isolates. METHODS: From 30 March to 30 May 2020, a total of 242 clinical samples from COVID-19 cases were screened for CRAB isolates using standard microbiologic and antibiotic susceptibility tests. The PCRs targeting oxa23, oxa24, oxa58, blaTEM and blaNDM-1 genes were performed. Two multiplex PCRs for identifying the global clones (GC) of A. baumannii were also performed. The sequence type of CRABs was determined using Institut Pasteur (IP) multilocus sequence typing (MLST) scheme. RESULTS: Eighteen CRAB isolates were recovered from COVID-19 patients with the mean age of 63.94 ± 13.8 years. All but 4 COVID-19 patients co-infected with CRAB were suffering from an underlying disease. Death was recorded as the outcome in ICUs for 9 (50%) COVID-19 patients co-infected with CRAB. The CRAB isolates belong to GC2 and ST2IP and carried the oxa23 carbapenem resistance gene. CONCLUSION: This study demonstrated the co-infection of CRAB isolates and SARS-CoV-2 in the patients admitted to different ICUs at a referral hospital in Tehran. The CRAB isolates were found to belong to ST2IP, share the oxa23 gene and to have caused several outbreaks in the wards admitting COVID-19 patients.


Assuntos
Infecções por Acinetobacter , COVID-19 , Coinfecção , Infecções por Acinetobacter/epidemiologia , Acinetobacter baumannii/efeitos dos fármacos , Acinetobacter baumannii/genética , Idoso , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , COVID-19/epidemiologia , COVID-19/microbiologia , Carbapenêmicos/farmacologia , Coinfecção/epidemiologia , Humanos , Irã (Geográfico)/epidemiologia , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Pandemias , Centros de Atenção Terciária , beta-Lactamases/genética
8.
Aging (Albany NY) ; 13(17): 20860-20885, 2021 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-34517343

RESUMO

Cancer patients are particularly susceptible to the development of severe Covid-19, prompting us to investigate the serum metabolome of 204 cancer patients enrolled in the ONCOVID trial. We previously described that the immunosuppressive tryptophan/kynurenine metabolite anthranilic acid correlates with poor prognosis in non-cancer patients. In cancer patients, we observed an elevation of anthranilic acid at baseline (without Covid-19 diagnosis) and no further increase with mild or severe Covid-19. We found that, in cancer patients, Covid-19 severity was associated with the depletion of two bacterial metabolites, indole-3-proprionate and 3-phenylproprionate, that both positively correlated with the levels of several inflammatory cytokines. Most importantly, we observed that the levels of acetylated polyamines (in particular N1-acetylspermidine, N1,N8-diacetylspermidine and N1,N12-diacetylspermine), alone or in aggregate, were elevated in severe Covid-19 cancer patients requiring hospitalization as compared to uninfected cancer patients or cancer patients with mild Covid-19. N1-acetylspermidine and N1,N8-diacetylspermidine were also increased in patients exhibiting prolonged viral shedding (>40 days). An abundant literature indicates that such acetylated polyamines increase in the serum from patients with cancer, cardiovascular disease or neurodegeneration, associated with poor prognosis. Our present work supports the contention that acetylated polyamines are associated with severe Covid-19, both in the general population and in patients with malignant disease. Severe Covid-19 is characterized by a specific metabolomic signature suggestive of the overactivation of spermine/spermidine N1-acetyl transferase-1 (SAT1), which catalyzes the first step of polyamine catabolism.


Assuntos
COVID-19/sangue , COVID-19/patologia , Neoplasias/sangue , Neoplasias/virologia , Poliaminas/sangue , Acetilação , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/microbiologia , COVID-19/virologia , Estudos de Coortes , Citocinas/sangue , Feminino , Humanos , Mediadores da Inflamação/sangue , Masculino , Metaboloma , Pessoa de Meia-Idade , Propionatos/sangue , Índice de Gravidade de Doença , Adulto Jovem , ortoaminobenzoatos/sangue
9.
Nat Microbiol ; 6(10): 1245-1258, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34465900

RESUMO

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.


Assuntos
Líquido da Lavagem Broncoalveolar/microbiologia , COVID-19/terapia , Respiração Artificial , SARS-CoV-2/patogenicidade , Imunidade Adaptativa , Adulto , Idoso , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Carga Bacteriana , Líquido da Lavagem Broncoalveolar/imunologia , Líquido da Lavagem Broncoalveolar/virologia , COVID-19/imunologia , COVID-19/microbiologia , COVID-19/mortalidade , Estado Terminal , Feminino , Hospitalização , Humanos , Imunidade Inata , Masculino , Microbiota , Pessoa de Meia-Idade , Razão de Chances , Prognóstico , Estudos Prospectivos , Sistema Respiratório/imunologia , Sistema Respiratório/microbiologia , Sistema Respiratório/virologia , SARS-CoV-2/imunologia , Carga Viral
10.
J Microbiol ; 59(10): 941-948, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34382150

RESUMO

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.


Assuntos
Bactérias/isolamento & purificação , COVID-19/complicações , COVID-19/microbiologia , Microbioma Gastrointestinal , Adulto , Bactérias/classificação , Bactérias/genética , COVID-19/terapia , COVID-19/virologia , Fadiga/etiologia , Fadiga/microbiologia , Fezes/microbiologia , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Mialgia/etiologia , Mialgia/microbiologia , Alta do Paciente , Filogenia , Sobreviventes/estatística & dados numéricos
11.
Acta Biochim Pol ; 68(3): 393-398, 2021 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-34432408

RESUMO

The time of COVID-19 pandemic focused the attention of scientist to recognise the complex medical symptoms of the disease, modes of infection and possible therapies. The organisms' response towards SARS-CoV-2 infection depends on many individual factors and the course of disease is described as unprecedented and complex. Numerous symptoms from the respiratory system, abnormalities in the gastrointestinal tract, stroke, liver damage and coagulopathy, among others, are accompanied by negative side effects of the pandemic lifestyle, including immunity depletion, overall fitness impairment, skin condition worsening, psychological and psychiatric consequences. There is an urgent need to seek all possible routes for assuring favouring conditions to build and support the organisms' microbiological barriers and enhance immunity, which will also help during the ongoing vaccination action. Probiotic Lactic Acid Bacteria (LAB) and environmental Bacillus species are microorganisms typically found in food products or dietary supplements, but also applied on body surfaces or technological surfaces at home and in the industry. Since the contemporary definition of probiotics points to positive health effects, it is of highest importance to follow strict regulations and standards of product manufacturing, especially in the times of biohazard risks and rising public distrust of therapies. There is an urgent need to seek all possible routes for assuring the favouring conditions to build and support the organisms' microbiological barriers and enhance the immunity, that will serve also during the ongoing vaccination action. Probiotic LAB and environmental Bacillus species are microorganisms typically found in food products or dietary supplements, but also applied on body surface or technological surfaces in household and industry. Since the contemporary definition of probiotics points out the positive health effects, it is of highest importance to follow strict regulations and standards of product manufacturing, especially in the times of biohazard and rising public distrust of therapies.


Assuntos
COVID-19/imunologia , Probióticos/uso terapêutico , COVID-19/microbiologia , COVID-19/virologia , Suplementos Nutricionais , Trato Gastrointestinal/microbiologia , Humanos , SARS-CoV-2/isolamento & purificação
12.
Microbiol Spectr ; 9(1): e0053621, 2021 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-34378965

RESUMO

Transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of deaths and declining economies around the world. K18-hACE2 mice develop disease resembling severe SARS-CoV-2 infection in a virus dose-dependent manner. The relationship between SARS-CoV-2 and the intestinal or respiratory microbiome is not fully understood. In this context, we characterized the cecal and lung microbiomes of SARS-CoV-2-challenged K18-hACE2 transgenic mice in the presence or absence of treatment with the Mpro inhibitor GC-376. Cecum microbiome showed decreased Shannon and inverse (Inv) Simpson diversity indexes correlating with SARS-CoV-2 infection dosage and a difference of Bray-Curtis dissimilarity distances among control and infected mice. Bacterial phyla such as Firmicutes, particularly, Lachnospiraceae and Oscillospiraceae, were significantly less abundant, while Verrucomicrobia, particularly, the family Akkermansiaceae, were increasingly more prevalent during peak infection in mice challenged with a high virus dose. In contrast to the cecal microbiome, the lung microbiome showed similar microbial diversity among the control, low-, and high-dose challenge virus groups, independent of antiviral treatment. Bacterial phyla in the lungs such as Bacteroidetes decreased, while Firmicutes and Proteobacteria were significantly enriched in mice challenged with a high dose of SARS-CoV-2. In summary, we identified changes in the cecal and lung microbiomes of K18-hACE2 mice with severe clinical signs of SARS-CoV-2 infection. IMPORTANCE The COVID-19 pandemic has resulted in millions of deaths. The host's respiratory and intestinal microbiome can affect directly or indirectly the immune system during viral infections. We characterized the cecal and lung microbiomes in a relevant mouse model challenged with a low or high dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the presence or absence of an antiviral Mpro inhibitor, GC-376. Decreased microbial diversity and taxonomic abundances of the phyla Firmicutes, particularly, Lachnospiraceae, correlating with infection dosage were observed in the cecum. In addition, microbes within the family Akkermansiaceae were increasingly more prevalent during peak infection, which is observed in other viral infections. The lung microbiome showed similar microbial diversity to that of the control, independent of antiviral treatment. Decreased Bacteroidetes and increased Firmicutes and Proteobacteria were observed in the lungs in a virus dose-dependent manner. These studies add to a better understanding of the complexities associated with the intestinal microbiome during respiratory infections.


Assuntos
COVID-19/imunologia , COVID-19/microbiologia , Microbioma Gastrointestinal/fisiologia , SARS-CoV-2 , Enzima de Conversão de Angiotensina 2 , Animais , Antivirais , Biodiversidade , Modelos Animais de Doenças , Feminino , Pulmão/imunologia , Melfalan , Camundongos , Camundongos Transgênicos , Viroses/imunologia , gama-Globulinas
13.
Ann Clin Microbiol Antimicrob ; 20(1): 51, 2021 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-34353332

RESUMO

PURPOSE: In this study, we aimed to evaluate the epidemiology and antimicrobial resistance (AMR) patterns of bacterial pathogens in COVID-19 patients and to compare the results with control groups from the pre-pandemic and pandemic era. METHODS: Microbiological database records of all the COVID-19 diagnosed patients in the Ege University Hospital between March 15, 2020, and June 15, 2020, evaluated retrospectively. Patients who acquired secondary bacterial infections (SBIs) and bacterial co-infections were analyzed. Etiology and AMR data of the bacterial infections were collected. Results were also compared to control groups from pre-pandemic and pandemic era data. RESULTS: In total, 4859 positive culture results from 3532 patients were analyzed. Fifty-two (3.59%) patients had 78 SBIs and 38 (2.62%) patients had 45 bacterial co-infections among 1447 COVID-19 patients. 22/85 (25.88%) patients died who had bacterial infections. The respiratory culture-positive sample rate was 39.02% among all culture-positive samples in the COVID-19 group. There was a significant decrease in extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (8.94%) compared to samples from the pre-pandemic (20.76%) and pandemic era (20.74%) (p = 0.001 for both comparisons). Interestingly, Acinetobacter baumannii was the main pathogen in the respiratory infections of COVID-19 patients (9.76%) and the rate was significantly higher than pre-pandemic (3.49%, p < 0.002) and pandemic era control groups (3.11%, p < 0.001). CONCLUSION: Due to the low frequency of SBIs reported during the ongoing pandemic, a more careful and targeted antimicrobial prescription should be taken. While patients with COVID-19 had lower levels of ESBL-producing Enterobacterales, the frequency of multidrug-resistant (MDR) A. baumannii is higher.


Assuntos
Infecções Bacterianas/microbiologia , COVID-19/microbiologia , Coinfecção/microbiologia , Farmacorresistência Bacteriana/efeitos dos fármacos , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/farmacologia , Infecções Bacterianas/tratamento farmacológico , Infecções Bacterianas/epidemiologia , COVID-19/epidemiologia , Teste de Ácido Nucleico para COVID-19 , Criança , Pré-Escolar , Coinfecção/epidemiologia , Feminino , Humanos , Lactente , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Estudos Retrospectivos , Turquia/epidemiologia , Adulto Jovem
14.
Cell Rep ; 36(9): 109637, 2021 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-34433082

RESUMO

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.


Assuntos
Bactérias/classificação , Infecções Bacterianas/microbiologia , COVID-19 , Microbiota , Adulto , Idoso , Idoso de 80 Anos ou mais , Bactérias/isolamento & purificação , COVID-19/complicações , COVID-19/imunologia , COVID-19/microbiologia , Coinfecção/microbiologia , Coinfecção/virologia , Estudos Transversais , DNA Bacteriano/genética , Feminino , Humanos , Imunidade Inata , Inflamação , Masculino , Pessoa de Meia-Idade , Nariz/microbiologia , Infecções por Pseudomonas/microbiologia , Pseudomonas aeruginosa/isolamento & purificação , RNA Ribossômico 16S/genética , RNA Viral/genética , RNA-Seq , Transcriptoma , Carga Viral , Adulto Jovem
15.
Eur Rev Med Pharmacol Sci ; 25(13): 4579-4596, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-34286500

RESUMO

OBJECTIVE: The human being has evolved in close symbiosis with its own ecological community of commensal, symbiotic and pathogenic bacteria. After the intestinal microbiome, that of the oral cavity is the largest and most diversified. Its importance is reflected not only in local and systemic diseases, but also in pregnancy since it would seem to influence the placental microbiome. MATERIALS AND METHODS: This is a literature review of articles published in PubMed about Fusobacterium Nucleatum and both its implications with systemic and oral health, adverse pregnancy outcomes, flavors perception and its interference in the oral-nasal mucosal immunity. RESULTS: It is in maintaining the microbiome's homeostasis that the Fusobacterium nucleatum, an opportunistic periodontal pathogen of the oral cavity, plays a crucial role both as a bridge microorganism of the tongue biofilm, and in maintaining the balance between the different species in the oral-nasal mucosal immunity also by taste receptors interaction. It is also involved in the flavor perception and its detection in the oral microbiome of children from the first days of life suggests a possible physiological role. However, the dysbiosis can determine its pathogenicity with local and systemic consequences, including the pathogenesis of respiratory infections. CONCLUSIONS: It is interesting to evaluate its possible correlation with Sars-CoV-2 and the consequences on the microflora of the oral cavity, both to promote a possible broad-spectrum preventive action, in favor of all subjects for whom, by promoting the eubiosis of the oral microbiome, a defensive action could be envisaged by the commensals themselves but, above all, for patients with specific comorbidities and therefore already prone to oral dysbiosis.


Assuntos
COVID-19/microbiologia , Fusobacterium nucleatum/isolamento & purificação , Boca/microbiologia , COVID-19/imunologia , Feminino , Fusobacterium nucleatum/imunologia , Fusobacterium nucleatum/patogenicidade , Humanos , Boca/imunologia , Gravidez
16.
NPJ Biofilms Microbiomes ; 7(1): 61, 2021 07 22.
Artigo em Inglês | MEDLINE | ID: mdl-34294722

RESUMO

The human oral and gut commensal microbes play vital roles in the development and maintenance of immune homeostasis, while its association with susceptibility and severity of SARS-CoV-2 infection is barely understood. In this study, we investigated the dynamics of the oral and intestinal flora before and after the clearance of SARS-CoV-2 in 53 COVID-19 patients, and then examined their microbiome alterations in comparison to 76 healthy individuals. A total of 140 throat swab samples and 81 fecal samples from these COVID-19 patients during hospitalization, and 44 throat swab samples and 32 fecal samples from sex and age-matched healthy individuals were collected and then subjected to 16S rRNA sequencing and viral load inspection. We found that SARS-CoV-2 infection was associated with alterations of the microbiome community in patients as indicated by both alpha and beta diversity indexes. Several bacterial taxa were identified related to SARS-CoV-2 infection, wherein elevated Granulicatella and Rothia mucilaginosa were found in both oral and gut microbiome. The SARS-CoV-2 viral load in those samples was also calculated to identify potential dynamics between COVID-19 and the microbiome. These findings provide a meaningful baseline for microbes in the digestive tract of COVID-19 patients and will shed light on new dimensions for disease pathophysiology, potential microbial biomarkers, and treatment strategies for COVID-19.


Assuntos
COVID-19/microbiologia , Microbioma Gastrointestinal/fisiologia , SARS-CoV-2/isolamento & purificação , Carga Viral , Bactérias/classificação , Bactérias/genética , COVID-19/diagnóstico , COVID-19/virologia , Fezes/microbiologia , Feminino , Hospitalização , Humanos , Masculino , Boca/microbiologia , RNA Ribossômico 16S , SARS-CoV-2/genética
17.
Cells ; 10(6)2021 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-34200572

RESUMO

The implications of the microbiome on Coronavirus disease 2019 (COVID-19) prognosis has not been thoroughly studied. In this study we aimed to characterize the lung and blood microbiome and their implication on COVID-19 prognosis through analysis of peripheral blood mononuclear cell (PBMC) samples, lung biopsy samples, and bronchoalveolar lavage fluid (BALF) samples. In all three tissue types, we found panels of microbes differentially abundant between COVID-19 and normal samples correlated to immune dysregulation and upregulation of inflammatory pathways, including key cytokine pathways such as interleukin (IL)-2, 3, 5-10 and 23 signaling pathways and downregulation of anti-inflammatory pathways including IL-4 signaling. In the PBMC samples, six microbes were correlated with worse COVID-19 severity, and one microbe was correlated with improved COVID-19 severity. Collectively, our findings contribute to the understanding of the human microbiome and suggest interplay between our identified microbes and key inflammatory pathways which may be leveraged in the development of immune therapies for treating COVID-19 patients.


Assuntos
COVID-19/diagnóstico , Leucócitos Mononucleares/microbiologia , Pulmão/microbiologia , Microbiota/fisiologia , Líquido da Lavagem Broncoalveolar/microbiologia , Líquido da Lavagem Broncoalveolar/virologia , COVID-19/imunologia , COVID-19/microbiologia , COVID-19/virologia , Estudos de Casos e Controles , Humanos , Leucócitos Mononucleares/virologia , Biópsia Líquida , Pulmão/patologia , Pulmão/virologia , Microbiota/genética , Microbiota/imunologia , Prognóstico , RNA Bacteriano/análise , RNA Fúngico/análise , RNA-Seq , SARS-CoV-2/fisiologia
18.
Pediatr Infect Dis J ; 40(8): e313-e316, 2021 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-34250979

RESUMO

Masking and social distancing have been adopted to mitigate the severe acute respiratory syndrome coronavirus 2 pandemic. We evaluated the indirect impact of severe acute respiratory syndrome coronavirus 2 prevention strategies on invasive Staphylococcus aureus, Streptococcus pneumoniae (pneumococcus) and Group A Streptococcus in Houston area children. We observed a decline in invasive pneumococcal disease and invasive Group A Streptococcus temporally associated with social distancing/masking/school closures.


Assuntos
COVID-19/epidemiologia , Infecções Pneumocócicas/epidemiologia , Infecções Estafilocócicas/epidemiologia , Infecções Estreptocócicas/epidemiologia , COVID-19/microbiologia , COVID-19/prevenção & controle , Criança , Coinfecção/epidemiologia , Coinfecção/microbiologia , Coinfecção/virologia , Hospitalização , Humanos , Pandemias , Infecções Pneumocócicas/prevenção & controle , Infecções Pneumocócicas/virologia , Estudos Prospectivos , SARS-CoV-2/isolamento & purificação , Infecções Estafilocócicas/prevenção & controle , Infecções Estafilocócicas/virologia , Staphylococcus aureus/isolamento & purificação , Infecções Estreptocócicas/prevenção & controle , Infecções Estreptocócicas/virologia , Streptococcus pneumoniae/isolamento & purificação , Streptococcus pyogenes/isolamento & purificação
19.
PLoS One ; 16(7): e0254671, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34255801

RESUMO

COVID-19 represents high morbidity and mortality, its complications and lethality have increased due to bacterial superinfections. We aimed to determine the prevalence of bacterial superinfection in adults with COVID-19, hospitalized in two clinics in Medellín-Colombia during 2020, and its distribution according to sociodemographic and clinical conditions. A cross sectional study was made with 399 patients diagnosed with COVID-19 by RT-PCR. We determined the prevalence of bacterial superinfection and its factors associated with crude and adjusted prevalence ratios by a generalized linear model. The prevalence of superinfection was 49.6%, with 16 agents identified, the most frequent were Klebsiella (pneumoniae and oxytoca) and Staphylococcus aureus. In the multivariate adjustment, the variables with the strongest association with bacterial superinfection were lung disease, encephalopathy, mechanical ventilation, hospital stay, and steroid treatment. A high prevalence of bacterial superinfections, a high number of agents, and multiple associated factors were found. Among these stood out comorbidities, complications, days of hospitalization, mechanical ventilation, and steroid treatment. These results are vital to identifying priority clinical groups, improving the care of simultaneous infections with COVID-19 in people with the risk factors exposed in the population studied, and identifying bacteria of public health interest.


Assuntos
COVID-19/microbiologia , Infecções por Klebsiella/epidemiologia , Infecções Estafilocócicas/epidemiologia , Superinfecção/epidemiologia , Idoso , COVID-19/complicações , Colômbia , Tratamento Farmacológico/estatística & dados numéricos , Feminino , Humanos , Tempo de Internação/estatística & dados numéricos , Masculino , Pessoa de Meia-Idade , Prevalência , Respiração Artificial/estatística & dados numéricos
20.
J Infect Dev Ctries ; 15(6): 761-765, 2021 06 30.
Artigo em Inglês | MEDLINE | ID: mdl-34242183

RESUMO

INTRODUCTION: The aim of this study is to determine the coinfections with other respiratory pathogens in SARS-CoV-2 infected children patients in a pediatric unit in Istanbul. METHODOLOGY: This retrospective descriptive study was conducted in a 1000-bedded tertiary education and research hospital in Istanbul. All children hospitalized with the diagnosis of SARS-CoV-2 infection had been investigated for respiratory agents in nasopharyngeal secretions. Laboratory confirmation of SARS-CoV-2 and the other respiratory pathogens were performed using reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: A total of 209 hospitalized children with suspected SARS-CoV-2 infection between March 2020-May 2020 were enrolled in this study. Among 209 children, 93 (44.5%) were RT-PCR positive for SARS-CoV-2 infection, and 116 (55.5%) were RT-PCR negative. The most common clinical symptoms in all children with SARS-CoV-2 infection were fever (68.8%) and cough (57.0%). The other clinical symptoms in decreasing rates were headache (10.8%), myalgia (5.4%), sore throat (3.2%), shortness of breath (3.2%), diarrhea (2.2%) and abdominal pain in one child. In 7 (7.5%) patients with SARS-CoV-2 infection, coinfection was detected. Two were with rhinovirus/enterovirus, two were with Coronavirus NL63, one was with adenovirus, and one was with Mycoplasma pneumoniae. In one patient, two additional respiratory agents (rhinovirus/enterovirus and adenovirus) were detected. There was a significantly longer hospital stay in patients with coinfection (p = 0.028). CONCLUSIONS: Although the coinfection rate was low in SARS-CoV-2 infected patients in our study, we found coinfection as a risk factor for length of hospital stay in the coinfected patient group.


Assuntos
COVID-19/microbiologia , COVID-19/virologia , Coinfecção/microbiologia , Coinfecção/virologia , Vírus/genética , Adenoviridae/genética , Adolescente , COVID-19/diagnóstico , Criança , Pré-Escolar , Coinfecção/diagnóstico , Coinfecção/epidemiologia , Hospitalização/estatística & dados numéricos , Humanos , Tempo de Internação/estatística & dados numéricos , Mycoplasma pneumoniae/genética , Mycoplasma pneumoniae/isolamento & purificação , Nasofaringe/microbiologia , Nasofaringe/virologia , Pesquisa Qualitativa , Sistema Respiratório/microbiologia , Sistema Respiratório/virologia , Estudos Retrospectivos , SARS-CoV-2/genética , Centros de Atenção Terciária/estatística & dados numéricos , Turquia/epidemiologia , Vírus/classificação , Vírus/isolamento & purificação
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