How did trends in invasive bacterial diseases change during the first 2 years of the COVID-19 pandemic?

In a recent article published in the Lancet Digital Health, researchers prospectively analyzed the surveillance data submitted by the Invasive Respiratory Infection Surveillance (IRIS) Consortium, microbiology laboratories network spread across 30 countries and territories to a private project within databases in PubMLST suite between January 1, 2018, and January 2, 2022. Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium. Image Credit: FamVeld/


The study used statistical models to evaluate the effect of coronavirus disease 2019 (COVID-19) containment measures on the spread of invasive infections caused by four bacterial species, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae in the first two years of the COVID-19 pandemic, i.e., 2020–21 relative to two years preceding the pandemic, i.e., 2018–19.


Upon its establishment in 2020, the IRIS Consortium had 26 participant countries and territories. During January–May 2020, the IRIS consortium reported substantial reductions in invasive diseases due to respiratory bacterial pathogens.

For instance, S. pneumoniae infections decreased by 68% at four weeks and by 82% at eight weeks after the implementation of COVID-19 containment measures, with an incidence rate ratio of 0·32 vs. 0·18.

In 2021, the IRIS Consortium expanded and encompassed 30 countries and territories, which all now legally notify about invasive infections due to the four bacterial species to public health registries in most IRIS participating countries.

About the study

In the present study, researchers used time-series modeling to analyze surveillance data of the expanded IRIS Consortium and quantify the effect of COVID-19 containment measures on the four bacterial pathogens, S. pneumoniae, H. influenzae, N. meningitidis, and S. agalactiae, during the initial two years of the COVID-19 pandemic, and the count of cases averted. 

Additionally, they assessed the disease prevalence by patient age and bacterial serotype to investigate the changes in the epidemiology of invasive diseases caused by all four bacterial species during the pandemic vs. pre-pandemic years, as it might have implications for disease burden and vaccination programs. 

All IRIS participants provided national reference data except one laboratory in New South Wales, Australia, and one hospital in Beijing, China.

The team ensured running all automated data integrity checks before data upload, and the curators manually checked the IRIS data for consistency, which helped resolve any discrepancies with the submitting laboratory.

The researchers used Google COVID-19 Community Mobility Reports (CCMRs) to estimate the week of implementation of COVID-19 containment measures for each country. Further, they used the Oxford Blavatnik COVID-19 Government Response Tracker (OxCGRT) to quantify the stringency of COVID-19 containment measures in all participating countries.

They computed a composite stringency index variable between zero and 100 that combined nine daily monitored indicators. 

Furthermore, the researchers converted the daily stringency index into an International Organization for Standardization (ISO) weekly index to help plot total weekly case counts for each organism and country vis-a-vis their weekly stringency index measures.

Additionally, they summed monthly case counts to generate country- and organism-specific 2018–21 time series. In a second time-series analysis, they pooled country-wise case counts by hemisphere, Northern or Southern. Note that data for S. agalactiae was available only from the Northern Hemisphere countries.

The team used seasonal autoregressive integrated moving average (ARIMA) models to execute interrupted time-series analysis. They used the Box-Jenkins methodology to select the final ARIMA models. Next, they used the Dickey-Fuller unit root test and found that the all-time series analyzed in this study were stationary. 

It helped them quantify the COVID-19 containment measures' effect on the incidence of invasive bacterial disease, which they presented as counterfactual trends with 95% prediction intervals (PIs) for all four bacterial pathogens of interest.

The team also estimated the relative risk (RR) of invasive disease and the number of cases averted from March 2020 as the number of cases observed divided by the number of counterfactual cases. The counterfactual prediction helped find an average monthly case estimate and 95% PI, assuming the COVID-19 pandemic did not occur.

Finally, the team performed a meta-analysis using the combined RR estimates for the northern and southern hemispheres and generated a pooled RR, which they used in their sensitivity analyses.

Results and conclusion

During the first two years of the COVID-19 pandemic, the worldwide implementation of COVID-19 containment measures, on average, averted more than 36,000 cases of invasive bacterial diseases caused by S. pneumoniae, H. influenzae, and N. meningitidis in all 30 IRIS participants.

The study findings also showed that by late 2021, these diseases were again increasing in some countries and territories; thus, their incidence rates might return to pre-pandemic levels in due course. So, active surveillance of invasive diseases is warranted even in the future, especially in Hib cases.

Intriguingly, the case counts for H influenzae serotype b (Hib) increased among children aged zero to four years in 2021 versus 2020 (n=146 vs. 87).

Another observation was that the pandemic altered the usual patterns of microbial transmission. An unfortunate event of disruption of the upper respiratory tract microbiome might lead to unanticipated developments, such as increased prevalence or the emergence of serotypes resistant to vaccination.

The study findings also raised concerns about decreased population immunity, also known as immunity debt, which could lead to other disease outbreaks in the future.

To conclude, it is essential to quickly resolve any ongoing disruptions to bacterial vaccination programs to prevent the spread of devastating bacterial diseases for which safe and effective vaccines are available.

However, it would require re-establishing pre-pandemic pediatric vaccination programs globally, one of the biggest post-pandemic challenges.

More importantly, the study findings bring to notice that while substantial changes in invasive diseases occurred during the COVID-19 pandemic lasting more than two years, scientists have the means to detect such changes early.

Journal reference:
Neha Mathur

Written by

Neha Mathur

Neha is a digital marketing professional based in Gurugram, India. She has a Master’s degree from the University of Rajasthan with a specialization in Biotechnology in 2008. She has experience in pre-clinical research as part of her research project in The Department of Toxicology at the prestigious Central Drug Research Institute (CDRI), Lucknow, India. She also holds a certification in C++ programming.


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