COVID-19 Lockdowns May Reduce Resistance Genes Diversity in the Human Microbiome and the Need for Antibiotics

Abstract

Recently, much attention has been paid to the COVID-19 pandemic. Yet bacterial resistance to antibiotics remains a serious and unresolved public health problem that kills hundreds of thousands of people annually, being an insidious and silent pandemic. To contain the spreading of the SARS-CoV-2 virus, populations confined and tightened hygiene measures. We performed this study with computer simulations and by using mobility data of mobile phones from Google in the region of Lisbon, Portugal, comprising 3.7 million people during two different lockdown periods, scenarios of 40 and 60% mobility reduction. In the simulations, we assumed that the network of physical contact between people is that of a small world and computed the antibiotic resistance in human microbiomes after 180 days in the simulation. Our simulations show that reducing human contacts drives a reduction in the diversity of antibiotic resistance genes in human microbiomes. Kruskal–Wallis and Dunn’s pairwise tests show very strong evidence (p < 0.000, adjusted using the Bonferroni correction) of a difference between the four confinement regimes. The proportion of variability in the ranked dependent variable accounted for by the confinement variable was η2 = 0.148, indicating a large effect of confinement on the diversity of antibiotic resistance. We have shown that confinement and hygienic measures, in addition to reducing the spread of pathogenic bacteria in a human network, also reduce resistance and the need to use antibiotics.

Metformin Therapy Changes Gut Microbiota Alpha-Diversity in COVID-19 Patients with Type 2 Diabetes: The Role of SARS-CoV-2 Variants and Antibiotic Treatment

“…Therefore, the observed differences in alpha-diversity between the two groups of patients may have important clinical implications. Our findings are consistent with those reported by other researchers who have investigated the impact of antibiotics on gut microbiota diversity in various patient populations, including COVID-19 patients [ 24 , 25 , 26 , 27 , 28 ].…”

Metformin Therapy Changes Gut Microbiota Alpha-Diversity in COVID-19 Patients with Type 2 Diabetes: The Role of SARS-CoV-2 Variants and Antibiotic Treatment

“…Therefore, the observed differences in alpha-diversity between the two groups of patients may have important clinical implications. Our findings are consistent with those reported by other researchers who have investigated the impact of antibiotics on gut microbiota diversity in various patient populations, including COVID-19 patients [14][15][16][17][18].…”

Revealing the drivers of antibiotic resistance trends inStreptococcus pneumoniaeamidst the 2020 COVID-19 pandemic: Insights from mathematical modeling

“…Conversely, using shotgun metagenomics on fecal samples, Peng et al showed a decrease in Actinobacteria richness in the microbiota of healthy adults from Hong-Kong and an increase in resistance genes against β -lactam antibiotics during the first wave of the pandemic compared to a pre-pandemic period [40]. Regarding pandemic impacts on microbiome composition, one simulation study suggests that lockdowns and associated reductions in mobility and human contact (informed by Portuguese mobility data) may have led to reductions in the diversity of antibiotic resistance genes found in the human microbiome [41]. Such disruptions to human microbiota may have further downstream impacts on colonization resistance and the propensity for antibiotic-resistant bacterial symbionts to transmit [13,42].…”