Exploring factors shaping antibiotic resistance patterns in Streptococcus pneumoniae during the 2020 COVID-19 pandemic.

Publication date: Mar 07, 2024

Non-pharmaceutical interventions implemented to block SARS-CoV-2 transmission in early 2020 led to global reductions in the incidence of invasive pneumococcal disease (IPD). By contrast, most European countries reported an increase in antibiotic resistance among invasive Streptococcus pneumoniae isolates from 2019 to 2020, while an increasing number of studies reported stable pneumococcal carriage prevalence over the same period. To disentangle the impacts of the COVID-19 pandemic on pneumococcal epidemiology in the community setting, we propose a mathematical model formalizing simultaneous transmission of SARS-CoV-2 and antibiotic-sensitive and -resistant strains of S. pneumoniae. To test hypotheses underlying these trends five mechanisms were built into the model and examined: (1) a population-wide reduction of antibiotic prescriptions in the community, (2) lockdown effect on pneumococcal transmission, (3) a reduced risk of developing an IPD due to the absence of common respiratory viruses, (4) community azithromycin use in COVID-19 infected individuals, (5) and a longer carriage duration of antibiotic-resistant pneumococcal strains. Among 31 possible pandemic scenarios involving mechanisms individually or in combination, model simulations surprisingly identified only two scenarios that reproduced the reported trends in the general population. They included factors (1), (3), and (4). These scenarios replicated a nearly 50% reduction in annual IPD, and an increase in antibiotic resistance from 20% to 22%, all while maintaining a relatively stable pneumococcal carriage. Exploring further, higher SARS-CoV-2 R values and synergistic within-host virus-bacteria interaction mechanisms could have additionally contributed to the observed antibiotic resistance increase. Our work demonstrates the utility of the mathematical modeling approach in unraveling the complex effects of the COVID-19 pandemic responses on AMR dynamics.

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Concepts Keywords
Azithromycin Anti-Bacterial Agents
Host Anti-Bacterial Agents
Mathematical antibiotic resistance
Pneumoniae Communicable Disease Control
COVID-19
COVID-19 pandemic
ecology
epidemiology
global health
Humans
invasive pneumococcal disease
Pandemics
SARS-CoV-2
SARS-CoV-2
Streptococcus pneumoniae
Streptococcus pneumoniae
virus-bacteria interactions

Semantics

Type Source Name
disease IDO antibiotic resistance
disease MESH COVID-19 pandemic
disease MESH pneumococcal disease
disease VO population
disease VO Viruses
drug DRUGBANK Azithromycin
disease IDO host
disease VO Bacteria
drug DRUGBANK Ibuprofen
drug DRUGBANK L-Citrulline
drug DRUGBANK Diethylstilbestrol
drug DRUGBANK L-Valine
disease MESH respiratory infections
disease MESH vector borne diseases
disease MESH dengue
disease MESH non communicable diseases
disease VO organization
disease MESH community acquired infections
disease MESH bacterial diseases
disease MESH infection
disease MESH influenza
disease IDO pathogen
disease MESH Coinfection
disease VO effective
drug DRUGBANK Clarithromycin
drug DRUGBANK Erythromycin
drug DRUGBANK Methyl isocyanate
disease IDO commensal
disease VO dose
drug DRUGBANK Roxithromycin
drug DRUGBANK Isoxaflutole
disease MESH Communicable Disease

Original Article

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