Quantifying the impact of the COVID-19 pandemic on invasive bacterial diseases across 27 countries and territories: prospective surveillance by the IRIS Consortium

BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive bacterial disease worldwide. The aims of this study were to measure post-COVID-19 pandemic changes in the incidence of disease caused by these bacterial pathogens and assess the evidence for any age- or serotype/group-specific changes. MethodsProspectively, cases of invasive disease from 2018-2023 were submitted to national and/or regional microbiology reference laboratories in each of 27 countries/territories. An effective pandemic period was estimated, and interrupted time series analyses quantified the effect of the introduction and withdrawal of pandemic containment measures. Disease incidence rates for S pneumoniae, H influenzae and N meningitidis were calculated, stratified by age and serotype/group. Streptococcus agalactiae was investigated as a comparator invasive pathogen not transmitted via the respiratory route. FindingsThe median duration of pandemic containment measures among all 27 countries was 22 months (range, 14-26 months). Withdrawal of containment measures led to significant increases in invasive disease for S. pneumoniae (42%, incidence rate ratio [IRR] 1.42, 1.30-1.55) and H influenzae (68%, IRR 1.68, 1.47-1.91), but not N meningitidis (15%, IRR 1.15, 0.92-1.44). In the post-pandemic period, the risk of H influenzae disease (risk ratio [RR] 1.02, 0.91-1.14) returned to the pre-pandemic risk. Conversely, for S pneumoniae (RR 0.91, 0.85-0.97) and N meningitidis (RR 0.61, 0.54-0.69) the risk of invasive disease was significantly below pre-pandemic risk. There was no evidence for changed rates of S. agalactiae disease. The distribution of invasive disease by age was broadly as expected, and age-stratified disease incidence by serotype/group was similar to pre-pandemic rates, but with some notable changes. InterpretationBy 2023, while the risk of invasive disease caused by H influenzae returned to pre-pandemic levels, the risk of S pneumoniae and N meningitidis disease remained below pre-pandemic levels. Changes were observed in the post-pandemic incidence and age-stratified distributions of some serotypes/groups. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, bioRxiv, and medRxiv for articles published up to 31 Dec 2019 (before the COVID-19 pandemic) that reported on the effects of containment measures implemented in response to a pandemic. We identified 262 papers by searching for pandemic AND microbial transmission OR transmission AND containment but none of these described the effects of implementing large-scale containment measures during a pandemic. The Invasive Respiratory Infection Surveillance (IRIS) Consortium previously reported that the incidence of invasive bacterial disease due to S pneumoniae, H influenzae and N meningitidis was significantly reduced when COVID-19 pandemic containment measures were implemented to control the transmission of SARS-CoV-2. Added value of this studyWe extended the previous analyses to estimate the effective containment measure period within each of 27 countries across six continents, and calculated rates of invasive bacterial disease after the pandemic containment measures were withdrawn. This demonstrated that invasive bacterial disease caused by all three pathogens increased once pandemic containment measures were removed and incidence rates exceeded the rates observed before the pandemic. Subsequently, disease caused by H influenzae generally returned to pre-pandemic rates, whilst disease caused by S pneumoniae and N meningitidis remained below pre-pandemic rates. Some serotype/group and age-specific changes were also observed for each of the pathogens. Implications of all the available evidenceThe COVID-19 pandemic had profound direct and indirect effects on global public health. The IRIS Consortium has shown that invasive bacterial disease caused by S pneumoniae, H influenzae and N meningitidis was also altered, and that changes in the circulating serotypes/groups were observed among countries participating in the IRIS Consortium. Whether or not these epidemiological changes persist, and to what extent they might affect bacterial vaccination coverage and disease rates, will be revealed over time and thus invasive disease due to these pathogens needs to be closely monitored.