Introduction
In December 2019, the Wuhan Municipal Health Commission in China reported a few cases of pneumonia with an unknown aetiology. In these cases, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was discovered [
1,
2]. On February 27, 2020, the first case of coronavirus disease 2019 (COVID-19) was reported in the Netherlands [
3]. After this first case, the SARS-CoV-2 virus spread rapidly in the south of the Netherlands. The southern region emerged as the Dutch epicentre of the first wave of COVID-19, putting a large strain on the microbiology laboratories in this area. Numerous analyses of SARS-CoV-2 tests, blood cultures and respiratory samples were performed. It was observed that during this period very few blood cultures were positive as a result of relevant bacteraemia, especially in comparison to blood cultures collected during influenza seasons. This raised questions about the occurrence of bacteraemia and bacterial co-infections in COVID-19 patients.
Bacterial co-infections are frequently identified in influenza infections and are an important cause of morbidity and mortality [
4,
5]. It is estimated that 11–35% of all patients with an influenza infection acquire a bacterial co-infection [
6]. The most frequently isolated pathogens are
Streptococcus pneumoniae,
Staphylococcus aureus and
Haemophilus influenzae [
7]. Although the use of empiric antibiotics is only recommended when a bacterial co-infection is suspected, it is difficult for physicians to differentiate between a viral infection and bacterial co-infection [
8,
9]. This contributes to a widely recognized overuse of antibiotics in patients with viral infections [
6,
10,
11]. For COVID-19, little is known about the occurrence of bacterial co-infections and the causative pathogens. One small observational study in the Netherlands showed an overall co-infection rate of 16% in COVID-19 patients [
12]. Gaining more knowledge on this subject is important, particularly when deciding on the appropriate antibiotic regimen. During the first wave of the COVID-19 pandemic, many patients received empiric antibiotics prior to and during their admission to the hospital [
13]. Numbers range from 31% in the Netherlands to 95% in Asia [
3,
14]. Cephalosporins and broad-spectrum penicillins were most frequently prescribed in the Netherlands [
13]. Unnecessary use of antibiotics has many disadvantages, especially in the view of a rising rate of antibiotic resistance [
15].
Studying the occurrence, causative microorganisms and outcome of bacteraemia in COVID-19 patients in comparison to influenza A and B patients will increase the knowledge about bacterial co-infections in COVID-19 and possibly refine the current guidelines on antibiotic management.
Methods
Study design and population
We performed a retrospective cohort study of patients with an influenza A, influenza B or a COVID-19 diagnosis and analysed blood culture outcomes. Patients were enrolled from two different hospitals in the Netherlands, the Jeroen Bosch Hospital in ‘s-Hertogenbosch and Bernhoven Hospital in Uden. Patients were divided into three cohorts according to their infection status: (1) patients with an influenza A diagnosis in the influenza season 2015/2016 or 2016/2017, (2) patients with an influenza B diagnosis in influenza season 2017/2018 and (3) patients with a COVID-19 diagnosis between 28 February 2020 and 2 June 2020.
Patients were included when an influenza or a COVID-19 infection was confirmed by reverse transcription polymerase chain reaction (RT-PCR) on RNA from oropharyngeal swabs (in case of influenza) or oronasopharyngeal swabs (in case of COVID-19). Blood cultures were collected within a time interval of 48 h before and after the RT-PCR test.
Included into our analysis were patients attending the emergency department, patients diagnosed with influenza or COVID-19 at outpatients clinics who were subsequently hospitalized and patients who developed fever or flu-like symptoms during early hospitalization for other medical reasons. Patients who were discharged from the emergency department were analysed as well.
The following information was recorded and collected in an anonymous database: demographic data, viral diagnosis, blood culture results, names of isolated bacteria, likelihood of contamination, the hospital ward where the blood culture was collected, blood culture collection date and time and outcome of hospitalization expressed as 30-day all-cause mortality. Predominantly the data were extracted from the laboratory information system (MOLIS). Only the outcome of hospitalization was manually collected from the patient’s medical record. Bacteria were categorized as likely contaminants if they were affiliated to groups that represent commensal skin microbiota and were defined in the patient’s medical record as a contaminant by the Department of Medical Microbiology [
16].
The percentage of positive blood cultures served as our primary outcome. Secondary outcomes were the percentage of relevant blood cultures, causative microorganisms and 30-day all-cause mortality.
This study was performed in line with the principles of the Declaration of Helsinki. The board of directors of both the Jeroen Bosch Hospital and Bernhoven Hospital approved this study. Additional ethical approval was granted by the Medical Ethical Review Committee Brabant (METC Brabant). Due to the collected data being held anonymously, informed consent was waived by the scientific review boards of both the Jeroen Bosch Hospital and Bernhoven Hospital for this study. Patients who had stated an objection to utilization of their medical data for scientific research in their electronic medical record were excluded from this study.
Data analysis
Categorical variables are displayed as frequencies and percentages. Means and standard deviations were used to report continuous variables. The categorical variables were compared using the chi-square test or the Fisher’s exact test. The continuous variables were compared using a one-way analysis of variance (ANOVA). A p value < 0.05 was considered statistically significant. All analyses were performed with SPSS version 26.0 for Windows.
Discussion
Our study showed that only 1.0% of COVID-19 patients presenting at a general hospital experienced a clinically relevant bacteraemia, compared to 4.0% in influenza A patients and 3.0% in influenza B patients. E. coli and S. pneumoniae were most frequently isolated from positive blood cultures in COVID-19 patients. The same pathogens were also common in influenza A and B patients. We reported a 30-day all-cause mortality of 28.3% in COVID-19 patients, which was statistically significantly higher than the 30-day all-cause mortality of 7.1 and 6.4% found in respectively influenza A and B patients.
Our results are consistent with findings in a recent study of Sepulveda et al. [
17]. They performed a large multicentre cohort analysis on patients with COVID-19 in New York. The authors reported a true bacteraemia rate of 1.6%. The most common causative microorganisms of bacteraemia in their study population were
E. coli,
S. aureus,
K. pneumoniae and
Enterobacter cloacae complex. A study of Hughes et al. also described similar findings [
18]. The authors reported an occurrence of bacteraemia of 3.2%. This percentage consisted of both hospital- and community-acquired infections. We only reported on community-acquired infections, which may explain the difference. Their most frequently isolated community-acquired pathogens were
Enterobacterales, Streptococcus spp.,
S. aureus and
Enterococcus spp. A recent study of Goyal et al. noted a bacteraemia rate of 5.6% in COVID-19 patients [
19]. This is significantly higher than the 1.0% that our study reported. Like Hughes et al., these authors examined both hospital-acquired and community-acquired infections, which may explain the higher rate of bacteraemia.
We reported a blood culture contamination rate of 89.1% amongst COVID-19 patients. This percentage is fairly consistent with other studies [
17,
18]. This high percentage may be explained by the high workload and the recruitment of more inexperienced health care workers during the pandemic.
We found a 30-day all-cause mortality of 28.3% in our COVID-19 cohort. This number is relatively high compared to recent reports from Europe that describe 30-day all-cause mortality rates ranging from 19.7 to 21.5% [
20,
21]. This disparity may be attributed to the higher risk of severe disease in our study population. During the first wave of COVID-19, family doctors in our region were asked to refer only severe cases to the overloaded hospitals. Furthermore, we only included patients with COVID-19 and analysed blood cultures. The required collection of blood cultures suggests these patients experienced severe febrile illness which indicates more severe disease.
Our findings on bacteraemia in influenza patients are consistent with prior studies [
22,
23]. We reported a slightly lower rate of bacteraemia in influenza B patients in comparison to influenza A patients. This is in agreement with the assertion that influenza B often leads to milder disease and less co-infections when compared to influenza A [
24,
25]. The 30-day all-cause mortality rate amongst influenza patients in our cohort was comparable to mortality rates mentioned in other literature [
20,
26].
Our findings support current guidelines on antibiotic management that do not recommend the use of empiric antibiotics in patients with COVID-19 unless there is a clear suspicion of an accompanying bacterial infection [
8]. However, differentiating between viral disease and a bacterial co-infection can be a challenge for physicians. Procalcitonin levels may be of assistance in determining the likelihood of bacterial co-infection and a potential adverse outcome [
27]. When a bacterial co-infection is suspected and empiric antibiotics are administered, we advise to regularly collect blood cultures and respiratory samples. The antibiotic therapy may then be de-escalated or completely terminated based on the microbiological results. These recommendations will help in preventing overuse and the occurrence of potential side-effects from antibiotics.
A major strength of our study is the inclusion of over 1300 patients from two different hospitals in the Netherlands. This large sample size increases the accuracy and reliability of our results. In addition, we reported on community-acquired infections. Most studies on bacterial co-infections in COVID-19 failed to report on the setting of their study and possibly investigated hospital-acquired infections as well, which negatively affects the interpretability of their results [
17,
28‐
30]. Finally, we did not experience any missing data, which minimizes the potential risk of information bias.
Some limitations should be mentioned. We did not collect data on prior antibiotic use, which may have led to an underestimation of the actual occurrence of bacteraemia in COVID-19 and influenza patients. Although the sample size of this study was of a reasonably large magnitude, the actual number of patients experiencing relevant bacteraemia was quite low, subgroup analyses of the 30-day all-cause mortality are therefore unreliable. In addition, we only reported on patients with bacteraemia and did not investigate other manifestations of bacterial co-infections. Thus, these results do not represent the entirety of bacterial co-infections in influenza and COVID-19 patients.
In conclusion, the proportion of clinically relevant community-acquired bacteraemia in COVID-19 patients was very low in comparison to influenza patients. These results justify the prudent use of empiric antibiotics in COVID-19 patients, when there is insufficient evidence of a bacterial co-infection.
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