Spatio-temporal responses of urban pathogenic microorganisms and antibiotic resistance genes under extreme rainfall events: a case study of the severe rainstorm in Zhengzhou in 2021

<sec><p indent="0mm">With the intensification of extreme rainfall events under global warming, flood induced public health risks, such as the spread of pathogenic microorganisms and antibiotic resistance genes (ARG) are becoming increasingly prominent. However, previous studies have mostly focused on the short-term outbreaks of pathogenic microorganisms and ARGs after floods, with limited attention to their long-term persistence, spatiotemporal distribution, and associations with urban functional zones. Additionally, the mechanism by which environmental factors indirectly influence ARGs dissemination through modulation of microbial community structure remain poorly understood. This study, centered on the Extreme Storm Event on 20 July of 2021 in Zhengzhou, employed qPCR, metagenomic sequencing, and correlation analysis to construct an integrated framework linking environmental perturbation, microbial response, and ARG transmission. The results provide a systematic depiction of the spatiotemporal dynamics of pathogens and ARGs in urban environments following the extreme rainfall. </sec><sec> qPCR results revealed a 168-fold increase (<italic>P</italic>​&lt;0.05) in the <italic>oprI</italic> gene of <italic>Pseudomonas</italic> <italic>aeruginosa</italic> in hospital-adjacent areas, where ARG abundance was one to two orders of magnitude higher than in other zones (<italic>P</italic>​&lt;0.05). A notable “time–lag effect” was also observed, with <italic>sul1</italic> and <italic>intl-1</italic> gene abundances in water samples one year later exceeding their immediate post-rainstorm levels by 47–116 times (<italic>P</italic>​&lt;0.05). Correlation analysis identified strong positive correlations between the integron gene <italic>intl-1</italic> and <italic>sul1</italic>, <italic>ermB</italic>, and <italic>tetM</italic> gene abundance (<italic>r</italic>​&gt;0.71, <italic>P</italic>​&lt;0.01), suggesting its critical role in ARG propagation. Furthermore, ammonium nitrogen (NH₄⁺-N) and dissolved organic carbon (DOC) were found to co-regulate microbial metabolic activity, facilitating cross-niche ARG migration (<italic>r</italic>=0.62–0.78). </sec><sec> Metagenomic sequencing identified 30 pathogenic microorganisms (25 bacteria and 5 fungi) with high relative abundance across three typical habitats (green spaces, farmlands, and water bodies). In aquatic environments, the total abundance of pathogenic bacteria increased by 19.12%, with opportunistic pathogens such as <italic>Pseudomonas</italic> <italic>cichorii</italic> increasing by over 30%. A total of 25 ARG types were detected, and the extreme rainfall event significantly elevated the total ARG abundance across all three habitats (<italic>P</italic>​&lt;0.01), with the most pronounced increase (22.79%) observed in water bodies. Specifically, the abundances of 9 ARG categories (e.g., aminoglycoside and β-lactam resistance genes) increased by more than 30% (<italic>P</italic>=0.001) in aquatic environments. Farmland ecosystems exhibited similar trends, particularly in macrolide and bicyclomycin-like ARGs. These results indicate that extreme rainfall events may accelerate the spread and diffusion of pathogenic microorganisms and ARGs in the environment, posing a potential threat to public health security. </sec><sec> Despite these microbial shifts, reported incidences of urban cholera and dysentery remained stable (<italic>P</italic>​&gt;0.05), suggesting the effectiveness of multi-level public health interventions. Overall, this study elucidates the spatiotemporal dynamics and environmental drivers of potential pathogens and ARGs after extreme rainfall events. The findings offer critical insights for “One Health” based risk management, support functional urban zoning and targeted management of antibiotic resistance pollution, and contribute to the development of climate-resilient and health-conscious cities. </sec>