Abstract

1. Introduction

According to the World Health Organization, COVID-19 has led to nearly 7 million deaths globally as of May 2023. Vaccination is one of the most important measures in preventing severe symptoms and death [1]. There is increasing evidence of the role of the gut microbiome on the impact of COVID-19 disease as well as vaccine immunogenicity [2,3]. Gut microbiota perturbation induced by antibiotics could impair antibody production and affinity among those with low pre-existing antibody titers against influenza virus [4]. Similarly, the early vaccine immunogenicity of BNT162b2 may be impaired by antibiotic usage [5]. The mechanisms underlying these observations include the expression of viral entry receptor angiotensin-converting enzyme 2 (ACE2) [6], the effects of microbiota-derived short chain fatty acids [7], the modulation of B and T cell immune responses [3], and the mediation of the “gut-lung axis”. Gut microbiota alteration by COVID-19 has been associated with inflammatory bowel disease and COVID-19 severity. Intuitively, it has been postulated that gut dysbiosis induced by antibiotics leads to a higher viral load in the gastrointestinal (GI) tract, resulting in a cytokine storm [8] and the impairment of leukocyte function [9]—which is similar to the effects of proton-pump inhibitors (PPIs) in increasing the risk of COVID-19 and severe clinical outcomes in observational studies [10,11].

Worldwide antibiotic use increased by 65% between 2000 and 2015 [12]. Antibiotic misuse was exemplified in a recent study evaluating antibiotic use among 11,047 COVID-19 cases in Hong Kong, carried out between January 2018 to March 2021, that revealed that nearly 30% of cases were given antibiotics—but only less than 2% had confirmed bacterial co-infections [13]. It has been shown that recent usage of antibiotics affects COVID-19 vaccine immunogenicity [5]. However, there is a lack of population-based studies investigating whether antibiotics could increase the risk of COVID-19 and serious clinical outcomes after vaccination. A differential effect may also exist depending on the number of vaccine doses received and the vaccine platform (messenger RNA (mRNA) vs. inactivated virus).

Here, we conducted a territory-wide cohort study on COVID-19 vaccine recipients to determine the effects of antibiotics on the development of COVID-19 and adverse clinical outcomes, with stratification.

2. Methods

2.3. Exposures of Interest

The primary exposure of interest is the pre-vaccination use of antibiotics. Table S2 shows the list of antibiotics included and their classification in terms of their anti-aerobic/anti-anaerobic effects and anti-bacterial spectrum. Pre-vaccination antibiotic users were those who received any prescription of any antibiotics within 180 days before their first-dose vaccination [5]. Antibiotic non-users were those who did not receive any prescription of antibiotics within 180 days from the first dose of vaccination. Figure 1 shows the study timeframe.

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Figure 1

Study timeframe.

3. Results

4. Discussion

This is the first study to demonstrate the potential undesirable effects of pre-vaccination antibiotics on the COVID-19 disease course, with a higher risk of infection, hospitalization, and severe disease outcomes being demonstrated in a territory-wide cohort study involving >300,000 PS-matched three-dose vaccine recipients, with a biological gradient being demonstrated. Notably, severe infection and death associated with pre-vaccination antibiotic use was only observed in CoronaVac recipients, but not in BNT162b2 recipients.

Antibiotics can cause significant changes in gut microbiota that have both short- and long-term health consequences [28]. Antibiotics reduce the overall diversity of gut microbiota species—including the loss of some important taxa—which causes metabolic shifts, increases gut susceptibility to colonization, and stimulates the development of bacterial antibiotic resistance [29]. Given the high efficacy of two doses of BNT162b2 and CoronaVac (protection from symptomatic COVID-19 is 95% [30] and 70% [31], respectively), it is hardly surprising that the effects of antibiotics on increasing infection risk was only slightly elevated (5–7%) in two- or three-dose vaccine recipients in the current study.

Although booster doses can enhance antibody production [32,33] and reduce the severity of infection outcomes [34], we showed that antibiotics were still associated with 1.8-fold and 1.6-fold higher risks of hospitalization and severe clinical outcomes (including ICU admission, ventilatory support, and death), respectively, in the three-dose vaccine recipients. Bacterial co-infection causes life-threatening complications in patients with severe viral infections [35], including COVID-19. Studies show that early antibiotic exposure poses risks for childhood asthma, allergies, and airway illnesses [36]. Indiscriminate administration of broad-spectrum antibiotics may increase nosocomial bloodstream infection rates in immunocompromised cancer patients [37]. While the baseline composition of the gut microbiota is mostly restored within 1.5 months, several common species (e.g., Bifidobacterium adolescentis, Coprococcus eutactus, Coliinsella aerofaciens, Methanobrevibacter smithii, Bididobacterium catenulatum, Bifidobacterium angulatum, and Eubacterium ventriosum) remain undetectable for at least 180 days [38]. With the combination of the immunocompromising effects of the viral infection and the antibiotic-driven depletion of commensal gut microbes, it has been proven that microorganisms from the dysbiotic gut microbiome translocate into the blood of COVID-19 patients, leading to dangerous blood-streamed infection during COVID-19 [39,40].

Subgroup analysis showed that antibiotic use was associated with a higher risk of adverse outcomes for COVID-19 with CoronaVac, but not BNT162b2, among the three-dose recipients. BNT162b2 mounts a higher neutralizing antibody level of nearly 10-fold more than CoronaVac after two doses of vaccine [40]. Owing to the waning effects of serum antibody levels, vaccine effectiveness against infection progressively diminishes [41]. This corroborates the hypothesis that a higher humoral response induced by BNT162b2 may minimize the unfavorable effects of antibiotics on vaccine immunogenicity and adverse clinical outcomes. A similar phenomenon was observed among older individuals and those with comorbidities, but not among younger age groups and those without comorbidities. The presence of comorbidities is linked to decreased immunity, reduced functional status, and increased healthcare utilization [42]. Advanced age and the number of concurrent comorbidities could also have a synergistic adverse effect on the health status of the elderly, explaining the higher COVID-19 mortality observed among elderly comorbid patients [43].

It was observed that broad-spectrum antibiotics were associated with a higher infection risk in the three-dose vaccine recipients, but not narrow-spectrum antibiotics. Furthermore, the intravenous route of the antibiotics had an overall higher risk of adverse infection outcomes than the oral route. Both gram-positive and gram-negative bacteria are disrupted by broad-spectrum antibiotics, as opposed to narrow spectrum antibiotics [44]. Broad-spectrum antibiotics decrease the Firmicutes to Bacteroidetes (F/B) ratio [45], which is associated with maintaining homeostasis, and changes in this ratio are regarded as dysbiosis. Models have shown that broad-spectrum antimicrobials (specifically vancomycin, metronidazole, and lacticin) cause population shifts from Firmicutes to Proteobacteria in the distal colon. In contrast, the narrow-spectrum bacteriocin (thuricin CD) seems to cause negligible changes in gut flora [46]. One study revealed a significant difference in the antibiotic resistance gene pools in mice treated with tetracycline between intravenous injection and oral administration of the drug, suggesting that drug administration routes influence the level of antibiotic resistance in gut microbiota [47]. The exact mechanism between the type, dosage, duration, administration, and pharmacokinetic and pharmacodynamics properties of antibiotics with vaccine immunogenicity and disease outcomes requires further investigation.

This study had several strengths: First, the population-based study with a large sample size allowed us to detect a statistically significant, albeit small in magnitude, increase in risk of infection—which is important for verifying the hypothesis of antibiotic-induced gut microbiota dysbiosis leading to impaired vaccine immunogenicity. Second, the demonstration of a biological gradient for the majority of outcomes increased the robustness of the study results and strengthened our underlying hypothesis. Third, reverse causality (i.e., symptomatic COVID-19 leading to antibiotic use before infection diagnosis) was minimized, as antibiotic use was defined before the first dose of vaccination while infection outcomes were only counted after the second dose of vaccination. With such a study design, the minimal interval between the commencement of antibiotics was at least three and four weeks for BNT162b2 and CoronaVac recipients, respectively. Fourth, since this was a cohort study, there was less recall and interviewer bias in terms of antibiotics as compared with a case–control study. To minimize the effects of confounding factors on the causality, PS matching ensured the similarity of the baseline characteristics between antibiotic users and non-users in order to reach a quasi-experimental design that may not be otherwise have been achieved by a randomized clinical trial (RCT).

Several limitations of this study should be noted: First, unmeasured confounding may still exist due to the observational study design, although all major confounding factors affecting vaccine immunogenicity and disease outcomes were minimized by the large sample size and PS matching design (Table 1). Second, gut microbiota data was not available; thus, the exact mechanisms of antibiotic-induced gut dysbiosis on vaccine immunogenicity and COVID-19 disease outcomes require further study. Third, asymptomatic infection cannot be ruled out, as this study included only PCR-confirmed positive case, which may overestimate the effects of antibiotics. Fourth, data on further booster doses and bivalent vaccines were not available before the study end date. Fifth, over-the-counter antibiotic usage information was not available, which may bias the study results. For example, self administered antibiotics may be taken incorrectly for too short a time, with wrong doses or timing with food intake. Lastly, COVID-19 vaccination effectiveness may vary in different waves of the epidemic due to the difference in the number of infected cases and prevention protocol/testing criteria from government policies. A prior study showed different frequencies of COVID-19 cases in different waves before the rollout of the vaccination program [48].

5. Conclusions

Antibiotics were associated with a higher COVID-19 risk, hospitalization, and severe infection in three-dose vaccine recipients. Further studies are warranted to investigate the interactions between gut microbiota and antibiotics and their effects on the COVID-19 vaccine’s immunogenicity and clinical outcomes. These results further reinforce the importance of the judicious use of antibiotics to minimize their direct and indirect impact on health.

Abbreviations

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/vaccines11081341/s1, Figure S1: Patient selection flow chart; Table S1: Baseline characteristics of pre-vaccination antibiotic users and non-users before propensity score matching; Table S2: Anti-anaerobic/anti-aerobic activity and anti-bacterial spectrum of various classes of antibiotics; Table S3: Association between pre-vaccination use of different classes of antibiotics and COVID-19 outcomes after vaccination with three doses of BNT162b2/CoronaVac.

Funding Statement

This work was funded by a research grant from the the Food and Health Bureau; HMRF Research on COVID-19, The Government of the Hong Kong Special Administrative Region (Principal Investigator (WP2): EWC; Ref: COVID1903011).

Author Contributions

Conceptualization, K.S.C. and W.K.L.; methodology, K.S.C., V.K.C.Y., E.W.C. and W.K.L.; data collection, V.K.C.Y. and E.W.C.; statistical analysis, V.K.C.Y. and X.Y.; drafting of manuscript, K.S.C., V.K.C.Y. and L.K.L.; supervision and revision of manuscript; I.F.N.H., E.W.C. and W.K.L. All authors have read and agreed to the published version of the manuscript.

Institutional Review Board Statement

This study was approved by the Central Institutional Review Board of the Hospital Authority of Hong Kong (CIRB-2021-005-4) and the DH Ethics Committee (LM171/2021).

Informed Consent Statement

Informed consent was not needed as all subjects were anonymized in the electronic healthcare database system.

Data Availability Statement

Data sharing will be available upon reasonable request.

Conflicts of Interest

The authors declare no conflict of interest.

Footnotes

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