Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis

1The coronavirus disease 2019 (COVID-19) pandemic is associated with high morbidity and mortality. Current evidence shows that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is primarily transmitted through respiratory droplets from symptomatic, asymptomatic, or pre-symptomatic individuals. Similar to other respiratory pathogens, such as influenza, where approximately 25% of older patients get secondary bacterial infections, both superinfections and co-infections with SARS-CoV-2 have been reported. However, there is scarce data on the frequency of co-infection and superinfections by viral, bacterial, or fungal infections and associated clinical outcomes among patients infected with SARS-CoV-2.

2We define co-infection as the recovery of other respiratory pathogens in patients with SARS-CoV-2 infection at the time of a SARS-CoV-2 infection diagnosis and superinfection as the subsequent recovery of other respiratory pathogens during care for SARS-CoV-2 infection. Two previous reviews have examined the prevalence of bacterial and fungal co-infection or superinfection in SARS-CoV-2 infected patients. In addition, prior work suggests outcome differences in patients with co-infections vs. superinfections. For example, Garcia-Vidal et al., showed that SARS-CoV-2 infected patients with superinfection s had a longer length of hospital stay (LOS) and higher mortality, while those with co-infections had a higher frequency of admission to the ICU.

3Diagnostic testing and therapeutic decision-making may be affected by the presence of co-infection or superinfection with SARS-CoV-2 and other respiratory pathogens.

4Therefore, we conducted a systematic review and meta-analysis to examine the occurrence and outcomes (e.g., LOS) of respiratory co-infections and superinfections among patients infected with SARS-CoV-2.

5We conducted this systematic review in accordance with the Preferred Reporting in Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We registered this review with PROSPERO: CRD42020189763. The protocol is available as a S1 File.

6With the help of a health sciences librarian (LC), we searched PubMed, Scopus, Wiley, Cochrane Central Register of Controlled Trials, Web of Science Core Collection, and CINAHL Plus databases to identify English-language studies published from October 1, 2019, through February 8, 2021. We executed the search in PubMed and translated the keywords and controlled vocabulary for the other databases, and additional articles were added from reference lists of pertinent articles. The following keywords were used for the search: “coronavirus”,”coronavirus infections”, “HCoV”, “nCoV”, “Covid”, “SARS”, "COVID-19", “2019 nCoV”, “nCoV 19”, “SARS-CoV-2”, “SARS coronavirus2”, “2019 novel corona virus”, “Human”, “pneumonia”, “influenza”, “severe acute respiratory syndrome”, “co-infection”, “Superinfection”, “bacteria”, “fungus”, “concomitant”, “pneumovirinae”, “pneumovirus infections”, "respiratory syncytial viruses", “metapneumovirus”, “influenza”, “human”, “respiratory virus”, “bacterial Infections”, “viral infection”, “fungal infection”, “upper respiratory”, “oxygen inhalation therapy”, “intensive care units”, “nursing homes”, “subacute care”, “skilled nursing”, “intermediate care”, “patient discharge”, “mortality”, “morbidity” and English filter. A complete description of our search strategy is available as a S2 File.

7Citations were uploaded into Covidence®, an online systematic review software for the study selection process. Two authors (JSM and LW) independently screened titles and abstracts and read the full texts to assess if they met the inclusion criteria. The authors met and discussed any articles where there was conflict and decided to either include or exclude such articles. Inclusion criteria were randomized clinical trials (RCTs), quasi-experimental and observational human studies that reported clinical features and outcomes of co-infection or superinfection of SARS-CoV-2 (laboratory-confirmed) and other pathogens–fungal, bacterial, or other viruses–in hospitalized and non-hospitalized patients. We excluded studies that did not report co-infection or superinfection, editorials, reviews, qualitative studies, those published in a non-English language, articles where full texts were not available, and non-peer-reviewed preprints.

8Three reviewers (JSM, LW, and VP) independently abstracted data from individual studies using a standardized template. We abstracted data on study design/methodology, location and setting (intensive care unit [ICU], inpatient non-ICU, or outpatient, where applicable), study population, use of antibiotics, proportion of patients with co-infections, implicated pathogens, method of detection of co-infections and superinfections (laboratory-verified or clinical features only), type of infection (bacterial, viral, or fungal), and outcomes of co-infected patients (death, mechanical ventilation, discharge disposition, length of hospital stay, or mild illness). Discrepancies were resolved by discussion between the three abstractors.

9Risk of bias assessment was conducted by three authors (JSM, LW, and VP) independently. We used two study quality assessment tools, one specific to case series, and one for non-case series study designs.

10The tool for case series examines four domains: selection, ascertainment, causality, and reporting. The selection domain helps to assess whether participants included in a study are representative of the entire population from which they arise. Ascertainment assesses whether the exposure and outcome were adequately ascertained. Causality assesses the potential for alternative explanations and specifically for our study whether the follow-up was long enough for outcomes to occur. Reporting evaluates if a study described participants in sufficient detail to allow for replication of the findings. This tool consists of eight items, but only five were applicable to our study. When an item was present in a study, a score of 1 was assigned and 0 if the item was missing. We added the scores (minimum of 0 and a maximum of 5) and assigned the risk of bias as follows: low risk (5), medium risk (3–4), high risk (0–2).

11For non-case series studies, we used the Modified Downs and Black risk assessment scale to assess the quality of cohort studies and RCTs. This scale consists of 27 items that assess study characteristics, such as internal validity (bias and confounding), statistical power, and external validity. We scored studies as low risk (score 20–27, medium risk (score 15–19), or high risk (score ≤14).

12The primary outcome was the prevalence of co-infections or superinfections by viral, bacterial, or fungal respiratory infections and SARS-CoV-2. We examined whether co-infection or superinfection was associated with an increased risk for the following patient outcomes: 1) mechanical ventilation, 2) admission to the ICU, 3) mortality and LOS.

13We estimated the proportion of patients with co-infection or superinfection of viral, bacterial, and fungal respiratory infections and SARS-CoV-2. We anticipated a high level of heterogeneity given the novelty of COVID-19 and potential differences in testing and management of COVID-19 in the healthcare systems of the countries where the studies were conducted. We conducted all statistical analyses using Stata software, version 16.0 (Stata Corp. College Station, Texas). We used the “metan” and “metaprop” commands in Stata to estimate the pooled proportion of co-infection and superinfection and COVID-19 using a random effects model (DerSimonian Laird). We stabilized the variance using the Freeman-Tukey arcsine transformation methodology in order to correctly estimate extreme proportions (i.e., those close to 0% or 100%). We assessed heterogeneity using the I2 statistic. Frequencies of outcome variables and study characteristics were estimated using descriptive statistics. For example, in studies where data on co-infecting or super-infecting pathogens were reported, we extracted and tallied the number of different pathogens reported. We calculated the proportion of pathogens using the number of pathogens as the numerator and the total number of pathogens of each type (bacteria, viruses, and fungi) from all the studies as the denominator.

14We did not assess for publication bias because standard methods, such as funnel plots and associated tests, were developed for comparative studies and therefore do not produce reliable results for meta-analysis of proportions.

15Our search yielded 14457 records; we excluded 7818 duplicates and screened 6639 articles. At the abstract and title review stage, we excluded 6273 articles, leaving 366 articles for full-text review. Of these, 118 articles met the inclusion criteria and were included in this meta-analysis. The most frequent reason for exclusion of studies at the full-text review stage was the absence of superinfection or co-infection data (Fig 1).

16Approximately half of the studies (60/118) were retrospective cohort studies, 35% (42/118) were cases series, and 9% (11/118) were prospective cohort studies. There were two case-control studies, two cross-sectional studies, and one clinical trial. The majority of the studies were conducted in China (42% [49/118)]) and the US (15% [18/118]). Most of the studies were conducted in a mixed setting (i.e., ICU and non-ICU setting; 72% [85/118]) and 92% (108/118) were conducted exclusively in hospitalized patients. The majority of studies were conducted among adults (73% [86/118]). Sixty-seven (57%) of the included studies reported that patients included had co-infections, 37% (44/118) reported superinfections, and 6% (7/118) reported both co-infections and superinfections among patients. Viral co-infections in patients were reported in 67% (55/81) of the studies, bacterial infections in 74% (78/105), fungal in 48% (35/73) of studies. Not all of the 118 studies reported data on viral, bacterial or fungal infections (Table 1). Seventy percent (83/118) of the studies reported data on antibiotic use. Of these, antibiotics were administered in 98% (81/83) of the studies.

17The pooled prevalence of co-infection was 19% (95% confidence interval [CI]: 14%-25%; I2 = 98%). The highest prevalence of co-infection was observed among non-ICU patients at 29% (95% CI: 14%-46%), while it was 18% (95% CI: 12%-25%) among combined ICU and non-ICU patients, and 16% (95% CI: 8%-25%) among only ICU co-infected patients (Fig 2). The pooled prevalence of superinfection was 24% (95% CI: 19%-30%), with the highest prevalence among ICU patients (41% [95% CI: 24%-58%]) (Fig 3).

18Pooled prevalence of pathogen type stratified by co- or superinfection was: viral co-infections, 10% (95% CI: 6%-14%) and viral superinfections, 4% (95% CI: 0%-10%); bacterial co-infections, 8% (95% CI: 5%-11%) and bacterial superinfections, 20% (95% CI: 13%-28%); and fungal co-infections, 4% (95% CI: 2%-7%) and fungal superinfections, 8% (95% CI: 4%-13%) (S1–S3 Figs).

19Seventy-eight studies reported data on specific organisms associated with co-infection or superinfection in COVID-19 patients (Table 2). Among patients with co-infections, the three most frequently identified bacteria were Klebsiella pneumoniae (9.9%), Streptococcus pneumoniae (8.2%), and Staphylococcus aureus (7.7%). The three most frequently identified viruses among co-infected patients were influenza type A (22.3%), influenza type B (3.8%), and respiratory syncytial virus (3.8%). For fungi, Aspergillus was the most frequently reported among those co-infected.

20Among those with superinfections, the three most frequently identified bacteria were Acinetobacter spp. (22.0%), Pseudomonas (10.8%), and Escherichia coli (6.9%). For viruses, Rhinovirus was the most frequently identified among those with superinfections, and for fungi, Candida sp. was the most frequent (18.8%).

21The overall prevalence of comorbidities was 42% (95% CI: 35%-49%). Among those with co-infections, the prevalence of comorbidities was 32% (95% CI: 24%-41%), while it was 54% (95% CI: 42%-65%) among those who were super-infected.

22Patients with a co-infection or superinfection had a higher odds of dying than those who only had SARS-CoV-2 infection (odds ratio [OR] = 3.31, 95% CI: 1.82–5.99). Subgroup analysis of mortality showed similar results, where the odds of death was higher among patients who were co-infected (OR = 2.84; 95% CI: 1.42–5.66) and those who were super-infected (OR = 3.54; 95% CI: 1.46–8.58). There was a higher prevalence of mechanical ventilation among patients with superinfections (45% [95% CI: 33%-58%]) compared to those with co-infections (10% [95% CI: 5%-16%]). Fifty studies reported data on average LOS. The average LOS for co-infected patients was 29 days (standard deviation [SD] = 6.7), while the average LOS for super-infected patients was 16 days (SD = 6.2). None of the studies included in this meta-analysis reported data on discharge disposition and readmissions.

23Sixty-two percent (73/118) of studies were rated as having low risk of bias, 34% (40/118) as having medium risk of bias, and 4% (5/118) as having a high risk of bias.

24We found that 19% of patients with SARS-CoV-2 were co-infected with other pathogens, and the prevalence of co-infection was higher among patients who were not in the ICU (29%). We also found a higher prevalence of superinfection compared to co-infection (24%), particularly among ICU patients (41%). Further, we found that super-infected patients had a higher prevalence of mechanical ventilation and comorbidities, and a higher risk of death.

25Two previous reviews found a prevalence of bacterial co-infection of 7–8% and viral co-infection of 3% in SARS-CoV-2 infected patients, which are lower than our estimates. We extended this work by distinguishing between super- and co-infection because of the different implications of co-infections vs. superinfections. In particular, bacteria and other pathogens have been shown to complicate viral pneumonia and lead to poor outcomes. In addition, our review spanned a longer period of time and included many newer studies, which may further account for differences in prevalence data.

26The three most frequently identified bacteria among co-infected patients in our study were Klebsiella pneumonia, Streptococcus pneumoniae, and Staphylococcus aureus. Streptococcus pneumoniae is a frequent cause of superinfection in other respiratory infections, such as influenza. A study by Zhu et al. showed similar results, and a review by Lansbury et al. showed that Klebsiella pneumoniae and Haemophilus influenza were some of the most frequent bacterial co-infecting pathogens. As expected, Staphylococcus aureus also was present in a sizeable number of cases. The most frequent bacteria identified in super-infected patients was Acinetobacter spp., which is a common infection, especially in ventilated patients.

27In our study, the three most frequently identified viruses among co-infected patients were influenza type A, influenza type B, and respiratory syncytial virus. These findings are important particularly for influenza because testing constraints continue to exist, yet clinical presentation of influenza and SARS-CoV-2 is similar. There are major infection control and clinical implications of missing a SARS-CoV-2 or influenza diagnosis if co-infection is not considered and diagnostic testing for both pathogens is not undertaken.

28Our findings have implications for infection preventionists, clinicians, and laboratory leaders. Respiratory virus diagnostic testing protocols should take into account that co-infection with SARS-CoV-2 is not infrequent, and therefore viral panel testing may be advisable in patients with compatible symptoms. Treatment protocols should also include assessment for co-infections, particularly influenza, so that appropriate treatment for both SARS-CoV-2 and influenza can be administered.

29Another key finding from our study was that co-infection or superinfection was associated with an increased odds of death. This is consistent with other studies that have shown a positive association between co-infection or superinfection and increased risk of death among patients with the SARS-CoV-2 infection.

30Our study showed that antibiotics were administered in 98% of the 83 studies that reported this data. The type of antibiotics (i.e., broad or narrow spectrum) were not widely ascertainable, as these details were not provided in many studies. In the spirit of antibiotic stewardship, antibiotic use even in SARS-CoV-2 infected patients should be judicious and only in cases with an objective diagnosis of bacterial co-infection.

31Our study has limitations. We were not able to assess important outcomes, such as discharge disposition and hospital readmissions, due to a lack of these data in the included studies. We were also not able to document time to superinfection, as the included studies did not report this information. Studies provided the number of patients with superinfections without stating the exact time when this determination was made after SARS-CoV-2 diagnosis. Most of the studies included in the meta-analysis were case series with their inherent limitations. It is possible that some of the pathogens that were reported as superinfections or secondary infections were present but not tested for at admission and hence were co-infections. It was not possible to assess this from the studies. There was significant heterogeneity in the studies, as was anticipated given the variation in settings, patient populations, and diagnostic testing platforms across the studies.

32Our study showed that as many as 19% of patients with COVID-19 have co-infections and 24% have superinfections. The presence of either co-infection or superinfection was associated with poor outcomes, such as increased risk of mortality. Our findings support the need for diagnostic testing to identify and treat co-occurring respiratory infections among patients with SARS-CoV-2 infection.