Did the COVID-19 pandemic impact the incidence of life-threatening invasive bacterial infections?

13 September, 2023

 In the wake of the unprecedented COVID-19 pandemic, the global healthcare sector has witnessed the profound and ongoing impact of the viral infection on various aspects of public health. One crucial area of concern pertains to the potential influence of the pandemic on the incidence and distribution of invasive respiratory infections caused by Streptococcus pneumoniae, Hemophilus influenzae and Neisseria meningitidis – three highly invasive bacterial species that colonise the oropharynx/nasopharynx when transmitted via respiratory droplets.1,2,3 Among these species, S. pneumoniae and H. influenzae have been identified as the most potentially ‘fatal’ bacterial species, given their antibiotic resistance.4

The Invasive Respiratory Infection Surveillance (IRIS) Consortium, encompassing 30 countries and territories across five continents, was established in early 2020; their primary objective was to investigate the incidence and geographical distribution of the invasive bacterial infections caused by S. pneumoniae, H. influenzae and N. meningitidis during the first two years of the COVID-19 pandemic (2020–21), versus the pre-pandemic years (2018–19).1,5 To study the aforementioned bacterial pathogens, Streptococcus agalactiae, an invasive pathogen that spreads via a non-respiratory route, was used as a comparator to evaluate the stability of routine disease surveillance during the pandemic.1 The IRIS Consortium submitted surveillance data gathered from January 1 2018 to January 2 2022 to specialized databases within ‘Public databases for molecular typing and microbial genome diversity’ (PubMLST).1 In order to quantify the effect of COVID-19 restrictions on the four invasive pathogens studied, Shaw and colleagues employed time-series modelling methods to assess changes in bacterial disease epidemiology during the first two years of the pandemic, ultimately estimating the quantity of prevented cases.1 The Consortium utilised data such as patient age and bacterial serotype to evaluate shifts in epidemiological patterns that could impact future disease prevalence and vaccination strategies.1

Key findings of the study included1:

  • Complete data on instances of invasive pneumoniae infections, provided by all 30 countries and presented through bacterial isolates, case reports, or a combination of both.
    • The majority of the nations also contributed invasive disease information on influenzae (n=24), N. meningitidis (n=21) and S. agalactiae (n=9).
  • In total, 116,841 cases were examined, of which 76,481 and 40,360 cases occurred during the pre-pandemic (2018–19) and pandemic (2020–21) years, respectively.
    • The incidence of pneumoniae, H. influenzae and N. meningitidis cases in 2020–21 was roughly half of the anticipated yearly count when compared to the pre-pandemic period. However, the incidence of S. agalactiae cases remained consistent each year.
    • Notably, infections related to pneumoniae, H. influenzae and N. meningitidis exhibited an upward trend by the conclusion of 2021.
  • An association was identified between the stringency of COVID-19 containment measures and the number of reported invasive bacterial infections.
    • A concomitant increase in pneumoniae, H. influenzae and N. meningitidis cases was correlated with the easing of containment measures during 2021 across numerous countries.
    • Sensitivity analyses validated the utilization of the ARIMA (autoregressive integrated moving average) model, which estimated that approximately 36,289 cases of bacterial infection (95% prediction interval: 17,145–55,434) were prevented within the 30 countries during the first two years of the pandemic.
  • A meta-analysis of the data demonstrated a significant decrease in the risk of invasive diseases caused by pneumoniae (relative risk [RR]: 0.47; 95% class interval [CI]: 0.40 – 0.55), H. influenzae (RR: 0.51; 95% CI: 0.40 – 0.66) and N. meningitidis (RR: 0.26; 95% CI: 0.21 – 0.31) owing to containment measures; however, S. agalactiae (RR: 1.02; 95% CI: 0.75 – 1.40) did not exhibit such reduction.
  • Researchers further categorised data based on bacterial serotype or group and patient age.
    • S. pneumoniae: A significant reduction in case numbers was observed for all major serotypes in 2020–21, although cases of disease owing to serotypes 8, 3 and 19A spiked toward the end of 2021. During the pandemic, case numbers reduced across all age groups, and there were no significant alterations in overarching disease patterns in relation to age or serotype.
    • H. influenzae: Case numbers decreased for all serotypes except serotype B (Hib), which exhibited a decline in 2020 that was followed by an increase in prevalence towards the end of 2021 (p<0.0001). Overall, the number of Hib cases remained minimal, with only 276 reported cases among 24 countries in 2021, of which 146 cases occurred in children aged 0–4 years.
    • N. meningitidis: A significant reduction in infections of all serotypes (particularly capsule groups W, C and Y) were noted; no obvious changes in the patterns of disease by age group were observed during the pandemic.

Overall, findings from this comprehensive analysis unveiled critical insights regarding the complex relationship between the COVID-19 pandemic and invasive respiratory infections. The sustained decline in invasive diseases observed may be attributed to the global enforcement of COVID-19 containment strategies designed to curtail the spread of SARS-CoV-2 infections, which simultaneously reduced the transmission of other respiratory infections.1 The substantial number of averted cases (~36,000) is understood to have alleviated the burden on health-care systems amid the pandemic.1

Nevertheless, such altered patterns of microbial transmission and disruptions in routine global immunisation schedules have raised concerns of decreased population immunity, or ‘immunity-debt’ (a higher proportion of susceptible individuals within a population, owing to reduced exposure to commonly circulating microbes) that could potentially lead to future disease outbreaks.1 Thereby, it is essential to proactively monitor disease patterns and rapidly address antimicrobial resistance among invasive pathogens through optimization of clinical practices and judicious use of antibiotics.




  1. Shaw D, et al. Lancet Digit Health 2023;S2589-7500(23):00108-5.
  2. GBD 2019 Antimicrobial Resistance Collaborators. Lancet 2022;400: 2221-48.
  3. Mazamay S, et al. BMC Infect Dis 2021;21:1027.
  4. Antimicrobial Resistance Collaborators. Lancet 2022;399:629-55.
  5. Brueggemann AB, et al. Lancet Digit Health 2021;3: e360-70.