SARS-CoV-2 respiratory co-infections: Incidence of viral and bacterial co-pathogens

Singh, Vijay; Upadhyay, Pallavi; Reddy, Jairus; Granger, John

doi:10.1016/j.ijid.2021.02.087

Cited by 79 publications

(94 citation statements)

References 14 publications

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“…While a limitation of our study is that we were not able to pinpoint the exact timing of EBV reactivation in the subjects we studied, given that we found similar reactivation frequencies in both long-term and short-term long COVID subjects, this indicates a likelihood that EBV reactivation occurs early in SARS-CoV-2 infection. Early EBV reactivation has been previously documented in several studies of COVID-19 ICU patients [ 20 , 21 , 22 , 23 ].…”

Section: Discussionmentioning

confidence: 96%

Investigation of Long COVID Prevalence and Its Relationship to Epstein-Barr Virus Reactivation

Gold¹,

et al. 2021

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Coronavirus disease 2019 (COVID-19) patients sometimes experience long-term symptoms following resolution of acute disease, including fatigue, brain fog, and rashes. Collectively these have become known as long COVID. Our aim was to first determine long COVID prevalence in 185 randomly surveyed COVID-19 patients and, subsequently, to determine if there was an association between occurrence of long COVID symptoms and reactivation of Epstein–Barr virus (EBV) in 68 COVID-19 patients recruited from those surveyed. We found the prevalence of long COVID symptoms to be 30.3% (56/185), which included 4 initially asymptomatic COVID-19 patients who later developed long COVID symptoms. Next, we found that 66.7% (20/30) of long COVID subjects versus 10% (2/20) of control subjects in our primary study group were positive for EBV reactivation based on positive titers for EBV early antigen-diffuse (EA-D) IgG or EBV viral capsid antigen (VCA) IgM. The difference was significant (p < 0.001, Fisher’s exact test). A similar ratio was observed in a secondary group of 18 subjects 21–90 days after testing positive for COVID-19, indicating reactivation may occur soon after or concurrently with COVID-19 infection. These findings suggest that many long COVID symptoms may not be a direct result of the SARS-CoV-2 virus but may be the result of COVID-19 inflammation-induced EBV reactivation.

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Section: Discussionmentioning

confidence: 96%

Investigation of Long COVID Prevalence and Its Relationship to Epstein-Barr Virus Reactivation

Gold¹,

et al. 2021

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“…A recent PCR-based analysis of 50,419 respiratory samples from nasopharyngeal, oro-pharyngeal, and sputum swabs in the USA reported that S. aureus infected SARS-CoV-2-positive patients at a significantly higher rate than SARS-CoV-2-negative individuals (13.17% versus 11.64%, p <0.05). ( 13 ).…”

Section: Emergence Of Reports Of Bacterial Infections Related To Covid-19mentioning

confidence: 99%

The interface between COVID-19 and bacterial healthcare-associated infections

O'Toole

2021

Clinical Microbiology and Infection

129

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Background A wide range of bacterial infections occur in COVID-19 patients, particularly, in those with severe coronaviral disease. Some of these are community acquired co-infections. Objective To review recent data which indicate the occurrence of hospital-onset bacterial infections, including with antibiotic-resistant isolates, in COVID-19 patients. Sources Using PubMed, the literature was searched using terms including: “COVID-19”; “SARS-CoV-2”; “bacterial infection”; “healthcare-associated infection”; “antibiotic resistance”; “antimicrobial resistance”; “multi-drug resistance”; “ Streptococcus ”; “ Staphylococcus ”; “ Pseudomonas ”; “ Escherichia ”; “ Klebsiella ”; “ Enterococcus ”; “ Acinetobacter ”; “ Haemophilus ”; “MRSA”; “VRE”; “ESBL”; “NDM-CRE”; “CR-Ab”; “VRSA”; “MDR”. Content There is a growing number of reports of bacterial infections acquired by patients with severe COVID-19 after hospital admission. Antibiotic-resistant pathogens found to cause healthcare-associated infections (HAIs) in COVID-19 patients include Methicillin-Resistant Staphylococcus aureus (MRSA), New Delhi Metallo-β-lactamase-producing Carbapenem-Resistant Enterobacterales (NDM-CRE), Carbapenem-Resistant Acinetobacter baumannii (CR-Ab), Extended-Spectrum β-Lactamase (ESBL) Klebsiella pneumoniae , and Vancomycin-Resistant Enterococci (VRE). COVID-19 has impacted bacterial HAIs in a number of ways with an increase in the incidence of NDM-CRE and CR-Ab reported at some hospital sites compared to before the pandemic. Recommended guidelines for antimicrobial stewardship in COVID-19 patient treatment are discussed regarding minimisation of empiric broad-spectrum antibiotic use. Other studies have reported a decrease in MRSA and VRE cases that has been attributed to enhanced infection prevention and control (IPC) practices introduced to minimise intra-hospital spread of COVID-19. Implications Poorer outcomes have been observed in hospitalised COVID-19 patients with an antibiotic-resistant infection. While heightened IPC measures have been accompanied by a reduction in some HAIs at specific sites, in other situations, COVID-19 has been associated with an increase in bacterial HAI incidence. Further research is needed to define the cost-benefit relationship of maintaining COVID-19-related IPC protocols beyond the pandemic to reduce the burden of HAIs. In addition, the longer-term impact of high usage of certain broad-spectrum antibiotics during the COVID-19 pandemic requires evaluation.

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“…Of the initial 7317 retrieved publications, there were 4609 duplicate articles, and 2080 articles were found to be irrelevant based on their titles and abstracts and were excluded. An additional 1065 articles were excluded after review, meaning that we included 72 articles in the systematic review [80][81][82], while 68 articles were included in the meta-analysis [2][3][4][5][6][7][8][9][10][11][39][40][41][43][44][45][46][47][48][49][50][51][52][53][54][55][56][57][59][60][61][62][63][64][65][66][67][68][69][70][80][81][82] (Figure 1).…”

Section: Characteristics and Quality Of Included Studiesmentioning

confidence: 99%

“…Thus, timely diagnosis is important to initiate appropriate therapy and limit the overuse of antimicrobial agents. Previous studies, including case series [2,5,8,11,[14][15][16]19,20,, cohort studies [3,4,6,7,9,10,12,13,17,18,21,22,[51][52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70], and meta-analyses [71][72][73], have shown variable results. In light of recent studies evaluating coinfections in SARS-CoV-2 patients, we aimed to re-evaluate the prevalence of bacterial, fungal, and respiratory viral coinfections in a comprehensive meta-analysis.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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

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SARS-CoV-2 respiratory co-infections: Incidence of viral and bacterial co-pathogens

Cited by 79 publications

References 14 publications

Investigation of Long COVID Prevalence and Its Relationship to Epstein-Barr Virus Reactivation

Investigation of Long COVID Prevalence and Its Relationship to Epstein-Barr Virus Reactivation

The interface between COVID-19 and bacterial healthcare-associated infections

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

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