The Rapidly Changing Patterns in Bacterial Co-Infections Reveal Peaks in Limited Gram Negatives during COVID-19 and Their Sharp Drop Post-Vaccination, Implying Potential Evolution of Co-Protection during Vaccine–Virus–Bacterial Interplay

Abstract

SARS-CoV-2 has caused the most devastating pandemic of all time in recent human history. However, there is a serious paucity of high-quality data on aggravating factors and mechanisms of co-infection. This study aimed to identify the trending patterns of bacterial co-infections and types and associated outcomes in three phases of the pandemic. Using quality hospital data, we have investigated the SARS-CoV-2 fatality rates, profiles, and types of bacterial co-infections before, during, and after COVID-19 vaccination. Out of 389 isolates used in different aspects, 298 were examined before and during the pandemic (<i>n</i> = 149 before, <i>n</i> = 149 during). In this group, death rates were 32% during compared to only 7.4% before the pandemic with significant association (<i>p</i>-value = 0.000000075). However, the death rate was 34% in co-infected (<i>n</i> = 170) compared to non-co-infected patients (<i>n</i> = 128), indicating a highly significant value (<i>p</i>-value = 0.00000000000088). However, analysis of patients without other serious respiratory problems (<i>n</i> = 28) indicated that among the remaining 270 patients, death occurred in 30% of co-infected patients (<i>n</i> = 150) and only 0.8% of non-co-infected (<i>n</i> = 120) with a high significant <i>p</i>-value = 0.00000000076. The trending patterns of co-infections before, during, and after vaccination showed a significant decline in <i>Staphylococcus aureus</i> with concomitant peaks in Gram negatives <i>n</i> = 149 before/<i>n</i> = 149 during, including <i>Klebsiella pneumonian</i> = 11/49 before/during, <i>E. coli n</i> = 10/24, <i>A. baumannii n</i> = 8/25, <i>Ps. aeruginosa n</i> = 5/16, and <i>S. aureus</i> 13/1. Nevertheless, in the post-vaccination phase (<i>n</i> = 91), gender-specific co-infections were examined for potential differences in susceptibility. Methicillin-resistant <i>S. aureus</i> dominated both genders followed by <i>E. coli</i> in males and females, with the latter gender showing higher rates of isolations in both species. <i>Klebsiella pneumoniae</i> declined to third place in male patients. The drastic decline in <i>K. pneumoniae</i> and Gram negatives post-vaccination strongly implied a potential co-protection in vaccines. Future analysis would gain more insights into molecular mimicry.