Bacterial Coinfections in Coronavirus Disease 2019

Trends in Microbiology, Journal Year: 2021, Volume and Issue: 29(10), P. 930 - 941

Published: April 8, 2021

Bacterial coinfections occur in <4% of patients who are hospitalized with COVID-19 and usually caused by S. aureus, pneumoniae, H. influenzae.Empirical antibacterial therapy diagnostic testing for bacterial pathogens indicated only those critical illness, severe immunosuppression, radiographic findings suggestive a pneumonia, or multiple laboratory parameters compatible infection.Hospital-acquired infections common among prolonged hospitalization COVID-19, hospital-acquired pneumonia is most commonly P. aeruginosa, Klebsiella spp., aureus.Carbapenem-resistant Gram-negative being increasingly reported requiring intensive care. increase the severity respiratory viral were frequent causes mortality influenza pandemics but have not been well characterized coronavirus disease 2019 (COVID-19). The aim this review was to identify frequency microbial etiologies that present upon admission hospital during COVID-19. We found yield routine tests low. When did occur, Staphylococcus Streptococcus Haemophilus influenzae atypical bacteria rare. Although uncommon admission, frequently occurred hospitalization, Pseudomonas aureus pathogens. Antibacterial unnecessary clinicians should be vigilant nosocomial infections. Severe acute syndrome 2 (SARS-CoV-2) cause devastating pandemic has led more than 100 million cases deaths globally span 12 monthsi. Pandemics plagued humans throughout history now becoming common. Influenza responsible 1918 resulted ~50 worldwide, recently 1957, 1968, 2009 [1.Morens D.M. et al.Pandemic Joins History's Pandemic Legion.mBio. 2020; 11e00812-20Crossref PubMed Scopus (106) Google Scholar]. In 2003, near-pandemic (SARS-CoV) occurred, closely followed emergence another lethal coronavirus, Middle East (MERS-CoV), 2012 [2.Memish Z.A. al.Middle syndrome.Lancet. 395: 1063-1077Abstract Full Text PDF (306) coinfection complication many tract leads significantly increased morbidity [3.Gupta R.K. al.Bacterial planning.Emerg. Infect. Dis. 2008; 14: 1187-1192Crossref During pandemic, significant contributor nearly all deaths, upper such as β-hemolytic streptococci, influenzae, [4.Morens al.Predominant role death influenza: implications preparedness.J. 198: 962-970Crossref (1245) also occurring 18–30% admitted care unit (ICU) up 55% published autopsy series [5.Martín-Loeches I. al.Community-acquired critically ill A (H1N1) virus.Chest. 2011; 139: 555-562Abstract (146) Scholar, 6.Rice T.W. al.Critical illness from virus United States.Crit. Care Med. 2012; 40: 1487-1498Crossref (282) 7.Gill J.R. al.Pulmonary pathologic fatal A/H1N1 infections.Arch. Pathol. Lab. 2010; 134: 235-243Crossref associated risk shock failure, ICU length stay, Scholar,6.Rice coronaviruses SARS-CoV MERS-CoV clearly defined because relatively small numbers cases, multicenter study ICUs Saudi Arabia identified 19% MERS had [8.Arabi Y.M. al.Critically Respiratory Syndrome: retrospective cohort study.Crit. 2017; 45: 1683-1695Crossref (133) high clinical significance other novel raises concern could an important SARS-CoV-2 infection. initial reports described presentations outcomes [9.Guan W.J. al.Clinical characteristics China.N. Engl. J. 382: 1708-1720Crossref (20519) Scholar,10.Goyal Covid-19 New York City.N. 2372-2374Crossref (1602) Scholar], few focused on microbiological coinfections. Furthermore, these distinguish secondary acquired hospital. Thus, reviews complicating relied limited data [11.Rawson T.M. fungal co-infection individuals coronavirus: rapid support antimicrobial prescribing.Clin. 71: 2459-2468PubMed Scholar,12.Lansbury L. al.Co-infections people COVID-19: systematic meta-analysis.J. 81: 266-275Abstract (1028) However, since reports, numerous studies patients, thus our understanding evolved. Therefore, focus highlight frequency, factors, etiologies, separating hospital, evaluate diagnostics, assess multidrug-resistant (MDR) infections, provide practical guidance clinicians. reviewed publications which primary objective ten evaluated minimum (Table 1), fewer 4% documented [13.Vaughn V.M. al.Empiric community-onset multi-hospital study.Clin. (Published online August 21, 2020. https://doi.org/10.1093/cid/ciaa1239)Google 14.Wang al.An observational empirical antibiotic presenting hospitals North West London.J. Antimicrob. Chemother. 2021; 76: 796-803Crossref (65) 15.Garcia-Vidal C. al.Incidence co-infections superinfections Microbiol. 27: 83-88Abstract (585) 16.Karami Z. al.Few empiric use early phase results multicentre Netherlands.Infect. (Lond). 53: 102-110Crossref (108) 17.Hughes UK secondary-care setting.Clin. 26: 1395-1399Abstract (431) 18.Lehmann C.J. al.Community experience.Clin. July 1, https://doi.org/10.1093/cid/ciaa902)Google 19.Adler al.Low rate COVID-19.Lancet Microbe. 1e62Abstract (48) 20.Cheng L.S.-K. prescribing practice adults experience single cluster.Ther. Adv. 72049936120978095Google 21.Fu Y. al.Secondary 2019.Open Forum 5ofaa220Crossref Scholar].Table 1Bacterial Coinfections Patients Admitted Hospital COVID-19RefsLocationNo. patientsPrevalence coinfectionProportion received therapy[13.Vaughn Scholar]Michigan, USA (38 hospitals)17053.5%57% (median: 3 days)[14.Wang Scholar]London, England (2 hospitals)13962.7%98%aThe denominator proportion includes 37 randomly selected without coinfection.[15.Garcia-Vidal Scholar]Barcelona, Spain (1 hospital)9892.5%NR[16.Karami Scholar]The Netherlands (4 hospitals)9250.8%60% days)[17.Hughes hospitals)8363.2%NR[18.Lehmann Scholar]Chicago, hospital)3211.2%69%[19.Adler Scholar]Liverpool, hospital)1952.6%NR[20.Cheng Scholar]Hong Kong hospital)1472.7%35%bOf 35% antibiotics, 37% them 1 week.[21.Fu Scholar]Hangzhou, China hospital)1010%NR[22.Elabbadi A. pneumonia.Infection. https://doi.org/10.1007/s15010-020-01553-xCrossref (60) Scholar]Paris, France hospital)101 (ICU only)19.8%58%Abbreviations: ICU, unit; No., number; NR, reported.a coinfection.b Of week. Open table new tab Abbreviations: reported. Despite low prevalence coinfection, majority therapy. For example, 1705 38 Michigan hospitals, 57% median days (interquartile range: 2–6 days); however, 3.5% infection 15% agents targeting methicillin-resistant (MRSA) aeruginosa. wide disparities between treated actually highlights substantial patients. Antibiotic overuse driven uncertainty around course infectious disease, extrapolation experiences [23.Chertow D.S. Memoli M.J. grand rounds review.JAMA. 2013; 309: 275-282Crossref (315) surge lack effective therapies SARS-CoV-2. As knowledge grows, factors essential so can target high-risk Advanced age comorbidities, chronic kidney diabetes, heart some Leukocytosis two largest studies, white blood cell (WBC) counts higher compared (median approximately 10.0×109 11.3×109 cells/μl versus 7×109 cells/μl, respectively) Scholar,14.Wang Wang colleagues absolute neutrophil count 9.2×109 5.5×109 (P <0.0001) [14.Wang Vaughn procalcitonin levels leukocytosis, neutrophilia, elevated do sufficient sensitivity, specificity, positive predictive value accurately diagnose stand-alone al. level >0.5 ng/ml 9.3% Conversely, negative values WBC <8.8×109 <6.8×109 ≤0.5 ≥98%. While overall rare they 6–29% Scholar,22.Elabbadi Scholar,24.Kolenda al.Assessment 2-positive units using conventional culture BioFire, FilmArray Pneumonia Panel Plus Assay.Open 7ofaa484Crossref (42) 25.Soriano M.C. incidence co-infection, ICU-acquired COVID-19.J. 82: e20-e21Abstract (36) 26.Stevenson D.R. al.Improving stewardship critically-ill COVID-19.Clin. October 11, https://doi.org/10.1093/cid/ciaa1559)Crossref (5) 27.Contou D. French ICU.Ann. Intensive Care. 10: 119Crossref (199) 28.Dudoignon E. patients: case series.Clin. 72: 905-906Crossref (64) may related increasing cultures [17.Hughes likely Scholar,29.Caméléna F. al.Performance multiplex polymerase chain reaction panel identifying causing COVID-19.Diagn. 99115183Crossref Scholar,30.Rothe K. al.Rates light stewardship.Eur. Clin. 859-869Crossref (83) Clinicians face difficult challenge deciding treat Figure illustrates recommended approach diagnosing management recommend pursing microbiologic initiating ill, severely immunocompromised, coinfection. warranted, we β-lactam when coverage bacteria, and/or MRSA warranted. Studies demonstrated 1.2–4.2% 2) Scholar,17.Hughes Scholar,19.Adler at least half represent skin contaminants 31.Sepulveda al.Bacteremia utilization City.J. 58e00875-20Crossref (128) 32.Yu bloodstream contamination rates COVID-19.PLoS One. 15e0242533Crossref (37) perhaps part due technical challenges healthcare personnel collecting while wearing personal protective equipment (PPE) required Hospitals City (NYC) noted peak analyzed same time previous year, times overwhelmed capacity instruments [31.Sepulveda Moreover, shown lower [32.Yu initiation therapy, routinely ordered Instead, selectively suspicion would include whom initiated.Table 2Yield Diagnostic Tests Coinfection Presenting COVID-19Blood cultures: contaminants.RefsYield pathogenYield contaminant[13.Vaughn Scholar]31/1063 (2.9%)Not reported[14.Wang Scholar]12/969 (1.2%)65/969 (6.7%)[17.Hughes Scholar]21/643 (

Language: Английский

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Antimicrobial resistance in patients with COVID-19: a systematic review and meta-analysis

The Lancet Microbe, Journal Year: 2023, Volume and Issue: 4(3), P. e179 - e191

Published: Feb. 1, 2023

BackgroundFrequent use of antibiotics in patients with COVID-19 threatens to exacerbate antimicrobial resistance. We aimed establish the prevalence and predictors bacterial infections resistance COVID-19.MethodsWe did a systematic review meta-analysis studies co-infections (identified within ≤48 h presentation) secondary (>48 after outpatients or hospitalised COVID-19. searched WHO Research Database identify cohort studies, case series, case-control trials, randomised controlled trials populations at least 50 published any language between Jan 1, 2019, Dec 2021. Reviews, editorials, letters, pre-prints, conference proceedings were excluded, as which infection was not microbiologically confirmed (or via nasopharyngeal swab only). screened titles abstracts papers identified by our search, then assessed full text potentially relevant articles. reported pooled doing random-effects meta-regression. Our primary outcomes co-infection infection, antibiotic-resistant pathogens among laboratory-confirmed infections. The study protocol registered PROSPERO (CRD42021297344).FindingsWe included 148 362 976 patients, done December, May, 5·3% (95% CI 3·8–7·4), whereas 18·4% (14·0–23·7). 42 (28%) comprehensive data for Among people infections, proportion that resistant antimicrobials 60·8% 38·6–79·3), isolates 37·5% (26·9–49·5). Heterogeneity organisms substantial (I2=95%).InterpretationAlthough infrequently assessed, is highly prevalent Future research surveillance assessing effect on patient population level are urgently needed.FundingWHO.

Language: Английский

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Impact of SARS-CoV-2 Epidemic on Antimicrobial Resistance: A Literature Review

Viruses, Journal Year: 2021, Volume and Issue: 13(11), P. 2110 - 2110

Published: Oct. 20, 2021

Antimicrobial resistance is an urgent threat to public health and global development; in this scenario, the SARS-CoV2 pandemic has caused a major disruption of healthcare systems practices. A narrative review was conducted on articles focusing impact COVID-19 multidrug-resistant gram-negative, gram-positive bacteria, fungi. We found that, worldwide, multiple studies reported unexpected high incidence infections due methicillin-resistant

Language: Английский

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Ventilator-Associated Pneumonia in Patients with COVID-19: A Systematic Review and Meta-Analysis

Antibiotics, Journal Year: 2021, Volume and Issue: 10(5), P. 545 - 545

Published: May 7, 2021

The aim of this systematic review and meta-analysis was to estimate the pooled occurrence ventilator-associated pneumonia (VAP) among patients admitted an intensive care unit with COVID-19 mortality those who developed VAP. We performed a search on PubMed, EMBASE Web Science from inception 2nd March 2021 for nonrandomized studies specifically addressing VAP in adult reporting data at least one primary outcome interest. Random effect single-arm (at longest follow up) ICU length stay. Twenty were included meta-analysis, total 2611 episode estimated 45.4% (95% C.I. 37.8–53.2%; 2611/5593 patients; I2 = 96%). 42.7% 34–51.7%; 371/946 82%). summary metric mean LOS 28.58 days 21.4–35.8; 98%). Sensitivity analysis showed that may have higher risk developing than without (OR 3.24; 95% 2.2–4.7; P 0.015; 67.7%; five comparison group).

Language: Английский

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The Gut Microbiota of Critically Ill Patients With COVID-19

Frontiers in Cellular and Infection Microbiology, Journal Year: 2021, Volume and Issue: 11

Published: June 29, 2021

The SARS-CoV-2-associated COVID-19 pandemic has shaken the global healthcare system. Although best-known symptoms are dry cough and pneumonia, viral RNA been detected in stool about half of patients exhibit gastrointestinal upset. In this scenario, special attention is being paid to possible role gut microbiota (GM). Fecal samples from 69 three different hospitals Bologna (Italy) were analyzed by 16S rRNA gene-based sequencing. GM profile was compared with publicly available one healthy age- gender-matched Italians, as well that other critically ill non-COVID-19 patients. appeared severely dysbiotic, reduced diversity, loss health-associated microorganisms enrichment potential pathogens, particularly Enterococcus . This genus far overrepresented developing bloodstream infections (BSI) admitted intensive care unit, while almost absent Interestingly, percentage BSI due spp. significantly higher during than previous 3 years. Monitoring could help clinical management, predicting onset medical complications such difficult-to-treat secondary infections.

Language: Английский

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Overview on the Prevalence of Fungal Infections, Immune Response, and Microbiome Role in COVID-19 Patients

Journal of Fungi, Journal Year: 2021, Volume and Issue: 7(9), P. 720 - 720

Published: Sept. 2, 2021

Patients with severe COVID-19, such as individuals in intensive care units (ICU), are exceptionally susceptible to bacterial and fungal infections. The most prevalent infections aspergillosis candidemia. Nonetheless, other species (for instance,

Language: Английский

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A High Frequency of Candida auris Blood Stream Infections in Coronavirus Disease 2019 Patients Admitted to Intensive Care Units, Northwestern India: A Case Control Study

Open Forum Infectious Diseases, Journal Year: 2021, Volume and Issue: 8(12)

Published: Sept. 7, 2021

The ongoing pandemic of coronavirus disease 2019 (COVID-19) has overwhelmed healthcare facilities and raises an important novel concern nosocomial transmission Candida species in the intensive care units (ICUs).We evaluated incidence risk factors for development candidemia 2384 COVID-19 patients admitted during August 2020-January 2021 ICUs 2 hospitals (Delhi Jaipur) India. A 1:2 case-control matching was used to identify who did not develop as controls.A total 33 developed accounted overall 1.4% over a median ICU stay 24 days. 2-fold increase versus non-COVID-19 observed with rate 14 15/1000 admissions ICUs. auris predominant (42%) followed by tropicalis. Multivariable regression analysis revealed use tocilizumab, duration (24 vs days), raised ferritin level independent predictor candidemia. Azole resistance C tropicalis harboring mutations azole target ERG11 gene. Multilocus sequence typing (MLST) identified identical genotypes patients, raising resistant strains.Secondary bacterial infections have been tocilizumab. In this cohort critically ill tocilizumab associated Surveillance antifungal is warranted prevent multidrug-resistant strains yeasts hospitalized patients.

Language: Английский

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Predictors and microbiology of respiratory and bloodstream bacterial infection in patients with COVID-19: living rapid review update and meta-regression

Clinical Microbiology and Infection, Journal Year: 2021, Volume and Issue: 28(4), P. 491 - 501

Published: Nov. 26, 2021

Language: Английский

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Coinfections with Bacteria, Fungi, and Respiratory Viruses in Patients with SARS-CoV-2: A Systematic Review and Meta-Analysis

Pathogens, Journal Year: 2021, Volume and Issue: 10(7), P. 809 - 809

Published: June 25, 2021

Background: Coinfection with bacteria, fungi, and respiratory viruses in SARS-CoV-2 is of particular importance due to the possibility increased morbidity mortality. In this meta-analysis, we calculated prevalence such coinfections. Methods: Electronic databases were searched from 1 December 2019 31 March 2021. Effect sizes pooled 95% confidence intervals (CIs). To minimize heterogeneity, performed sub-group analyses. Results: Of 6189 papers that identified, 72 articles included systematic review (40 case series 32 cohort studies) 68 (38 30 meta-analysis. 31,953 patients overall proportion who had a laboratory-confirmed bacterial infection was 15.9% (95% CI 13.6–18.2, n = 1940, 49 studies, I2 99%, p < 0.00001), while 3.7% 2.6–4.8, 177, 16 93%, 0.00001) fungal infections 6.6% 5.5–7.6, 737, 44 96%, other viruses. ICU higher co-infections compared non-ICU as follows: (22.2%, 16.1–28.4, 88% versus 14.8%, 12.4–17.3, 99%), (9.6%, 6.8–12.4, 74% 2.7%, 0.0–3.8, 95%); however, there an identical viral co-infection between all [(ICU non-ICU) only] (6.6%, 0.0–11.3, 58% 6.6%, 5.5–7.7, 96%). Funnel plots for possible publication bias effect coinfections asymmetrical on visual inspection, Egger’s tests confirmed asymmetry (p values 0.05). Conclusion: Bacterial relatively high hospitalized SARS-CoV-2, little evidence S. aureus playing major role. Knowledge type may have diagnostic management implications.

Language: Английский

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Ventilator-associated pneumonia among SARS-CoV-2 acute respiratory distress syndrome patients

Current Opinion in Critical Care, Journal Year: 2021, Volume and Issue: 28(1), P. 74 - 82

Published: Nov. 24, 2021

We conducted a systematic literature review to summarize the available evidence regarding incidence, risk factors, and clinical characteristics of ventilator-associated pneumonia (VAP) in patients undergoing mechanical ventilation because acute respiratory distress syndrome secondary SARS-CoV-2 infection (C-ARDS).Sixteen studies (6484 patients) were identified. Bacterial coinfection was uncommon at baseline (<15%) but high proportion developed positive bacterial cultures thereafter leading VAP diagnosis (range 21-64%, weighted average 50%). Diagnostic criteria varied between most signs have substantial overlap with C-ARDS making it difficult differentiate colonization versus superinfection. Most episodes associated Gram-negative bacteria. Occasional cases also attributed herpes virus reactivations pulmonary aspergillosis. Potential factors driving incidence rates include immunoparalysis, prolonged ventilation, exposure immunosuppressants, understaffing, lapses prevention processes, overdiagnosis.Covid-19 who require for ARDS (>50%) developing VAP, commonly Further work is needed elucidate disease-specific strategies prevention, how best

Language: Английский

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