Changes in Bacterial Etiology and Antimicrobial Resistance of Lower Respiratory Tract Infections Following the COVID-19 Pandemic: A Five-Year Comparative Study in Central China

Abstract

Objective

To investigate the impact of the coronavirus disease 2019 (COVID-19) pandemic on the bacterial profile of lower respiratory tract infections (LRTIs) and the prevalence of major drug-resistant bacteria in Hubei Province, China, by comparing five-year periods before (2015–2019) and after (2020–2024) the pandemic.

Methods

A retrospective analysis was conducted on microbial culture and antimicrobial susceptibility test results from sputum and bronchoalveolar lavage fluid (BALF) samples obtained from patients with LRTIs. Pathogen distribution and the prevalence of key drug-resistant bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), cefotaxime/ceftriaxone-resistant Enterobacterales, carbapenem-resistant Enterobacterales (CRE), carbapenem-resistant Pseudomonas aeruginosa (CRPAE), carbapenem-resistant Acinetobacter baumannii (CRABA), ampicillin-resistant Haemophilus influenzae (ARHI), and penicillin/erythromycin-resistant Streptococcus pneumoniae (PRSP/ERSP), were compared between the two periods.

Results

The overall number of bacterial isolates significantly increased during the post-pandemic period. Gram-negative bacteria remained dominant, although their relative composition shifted. The detection rates of common community-acquired pathogens (Haemophilus influenzae, Streptococcus pneumoniae) decreased sharply during the strict control phase (2020–2022) but rebounded from 2023 to 2024. The overall prevalence of most key drug-resistant bacteria followed a decreasing trend. Notably, the detection rates of MRSA and cefotaxime/ceftriaxone-resistant Enterobacterales decreased most markedly (> 15%). The prevalence of CRE and CRABA followed a “decrease-then-increase” trend, while carbapenem-resistant Klebsiella pneumoniae detection rates remained higher than the 2015 baseline, and carbapenem-resistant Escherichia coli  prevalence was on par with the 2015 level in 2024. Although the detection rate of CRABA tended to decrease, it remained above 60%. In contrast, the detection rate of the ERSP was consistently high (> 90%), whereas that of the ARHI exhibited a continuous upward trend (increasing by more than 30%).

Conclusion

The COVID-19 pandemic significantly altered the bacterial ecology and resistance patterns of LRTIs. While stringent public health measures initially suppressed the transmission of some resistant pathogens, they may have facilitated the subsequent emergence and spread of more formidable drug-resistant bacteria. Continuous surveillance and reinforced infection control measures are crucial in the post-pandemic era.

Keywords

COVID-19 / Lower respiratory tract infections / Bacterial etiology / Antimicrobial resistance / Methicillin-resistant Staphylococcus aureus (MRSA) / Carbapenem-resistant Enterobacterales (CRE) / Klebsiella pneumoniae / Drug resistance surveillance / Epidemiology / China

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