COVID-19 Reshaped Antibiotic Resistance in Children’s Urinary Infections, Six-Year Study Finds

Urinary tract infections are among the most common bacterial illnesses of childhood, and they are also among the most stubborn. A sweeping six-year surveillance study from southwest China now shows that the COVID-19 pandemic left a measurable fingerprint on which bacteria infect children’s urinary tracts and how resistant those bacteria have become to the drugs meant to clear them. The findings, drawn from nearly 5,700 urine isolates collected at four hospitals between 2019 and 2024, offer clinicians one of the most detailed pre-, during- and post-pandemic pictures yet of pediatric urinary infections.

The retrospective multicenter study, led by researchers at the Children’s Hospital of Chongqing Medical University and published in Frontiers in Cellular and Infection Microbiology, analyzed 5,618 pathogenic bacteria isolated from positive urine samples of children under 18 with community-acquired urinary tract infections. Children with congenital urinary tract anomalies, repeated infection episodes, or bacterial colonization without true infection were excluded, sharpening the picture of ordinary community-acquired disease. All susceptibility results were interpreted against the Clinical and Laboratory Standards Institute’s 2024 M100-S34 breakpoints, ensuring a uniform yardstick across the entire study window.

Gram-negative bacteria dominated the landscape, accounting for 71.0 percent of isolates, with Gram-positive organisms making up the remaining 29.0 percent. Escherichia coli was the undisputed leader, representing 37.3 percent of all isolates and ranking first in every age group and in both sexes. Its closest companions were Enterococcus faecium at 12.9 percent, Klebsiella pneumoniae and E. faecalis at 9.0 percent each, and Proteus mirabilis at 5.1 percent. In total, the team identified one hundred distinct uropathogenic species, a reminder that the urinary tract is anything but a single-pathogen disease niche.

The demographic patterns traced familiar developmental biology. Boys accounted for 53.9 percent of infections, with male susceptibility concentrated in the first year of life, where 59.8 percent of cases were male, and in the toilet-training years up to age three. The balance flipped with age: girls predominated from age four onward, likely reflecting the shorter female urethra and its proximity to enteric bacteria. Infancy carries particular risk for boys because of delayed ureteral maturation, congenital obstructive malformations, and physiological phimosis, all of which foster urinary stasis and bacterial colonization near the urethral opening.

Age stratification also shifted the microbial cast. E. coli peaked at 45.7 percent of pathogens in the four-to-six-year group, while E. faecium took second place in infants at 22.5 percent, and K. pneumoniae clustered most prominently in the youngest children. Notably, resistance to the fluoroquinolones ciprofloxacin and levofloxacin differed significantly across age groups for both E. coli and K. pneumoniae, reinforcing the authors’ argument that empirical treatment decisions should be calibrated to a child’s developmental stage rather than applied uniformly.

The resistance trends over time painted a mixed and sometimes counterintuitive portrait. E. coli resistance to sulbactam/ampicillin fell significantly from 57.9 percent in 2019 to 36.5 percent in 2024, and resistance to amikacin, gentamicin and nitrofurantoin also declined. Yet ciprofloxacin resistance climbed from 36.5 to 50.2 percent over the same period, and carbapenem-resistant E. coli rose from 2.7 to 4.9 percent. K. pneumoniae moved in the opposite direction on some fronts: its carbapenem resistance fell from a peak of 23.1 percent in 2019 to 18.9 percent in 2024, while its resistance to amikacin, the fluoroquinolones and nitrofurantoin rose significantly.

The enzymes that confer much of this resistance also diverged. The proportion of ESBL-producing E. coli, bacteria carrying extended-spectrum beta-lactamases that destroy penicillin-class drugs, crept upward from 54.0 percent to 62.2 percent, while ESBL-producing K. pneumoniae fell sharply from 66.2 to 52.7 percent. ESBL-producing strains of both species were consistently more resistant than their non-ESBL counterparts to nearly every agent tested, and carbapenem-resistant isolates showed broad resistance across the panel. For the enterococci, penicillin resistance averaged a striking 91.5 percent in E. faecium and 63.7 percent in E. faecalis, but no vancomycin- or linezolid-resistant E. faecalis was found anywhere in the cohort.

The pandemic’s influence emerged most clearly when the years were split into pre-COVID (2019), pandemic (2020 to 2022) and post-COVID (2023 to 2024) periods. Detection of E. coli, E. faecium and K. pneumoniae all declined after the pandemic, with E. coli dropping from 45.3 percent of isolates before COVID to 35.0 percent afterward, possibly reflecting more enduring hygiene habits. At the same time, resistance of E. coli and K. pneumoniae to piperacillin/tazobactam, cefepime, ciprofloxacin and levofloxacin rose post-pandemic, while penicillin resistance increased significantly in both enterococcal species. The authors suggest that reduced antibiotic consumption and altered healthcare-seeking behavior during the pandemic years plausibly drove these shifting dynamics.

A particularly subtle finding concerned the minimum inhibitory concentrations, the drug doses needed to halt bacterial growth. Vancomycin MIC values for the enterococci did not drift over the six years, but linezolid MICs did, with the proportion of isolates requiring concentrations of at least 2 micrograms per milliliter falling significantly in both species. The downward drift was more pronounced in E. faecalis, beginning around 2022, and by 2024 only 44.5 percent of E. faecalis isolates sat at or above that threshold, down from 93.3 percent in 2019. That vancomycin and linezolid remained fully effective against E. faecalis offers a rare reassuring note in the resistance literature.

The study’s practical message is sharpened by its limits: it covers only the Chongqing region, and its retrospective design could not confirm resistance mechanisms through molecular analysis. Even so, the surveillance data carry clear clinical guidance. Nitrofurantoin, with just 2.0 percent E. coli resistance, stands out as the only oral option below the 5 percent threshold recommended for empiric use, though it is suitable only for simple bladder infections since it penetrates kidney tissue poorly. Fluoroquinolone resistance rates well above 10 percent rule them out as first-line agents, and the authors argue that carbapenems, vancomycin and linezolid should be preserved as effective last-line options. Above all, they conclude, continued monitoring and age-stratified treatment strategies are essential, because the pandemic has shown that pediatric urinary infections are a moving target.

Subject of Research: Epidemiology and antibiotic resistance of pediatric urinary tract infections before, during and after the COVID-19 pandemic in China

Article Title: Changes in epidemiology and antibiotic resistance patterns isolated from paediatric urinary tract infections: a multicenter study in China pre-, during and post-COVID-19

Article References: Tang, L., Tian, R., Wei, X., Yu, X., Xiong, Z., Xiang, Y., Liu, F., & Jing, C. (2026). Changes in epidemiology and antibiotic resistance patterns isolated from paediatric urinary tract infections: a multicenter study in China pre-, during and post-COVID-19. Frontiers in Cellular and Infection Microbiology, 16, Article 1923862. https://doi.org/10.3389/fcimb.2026.1923862

Image Credits: AI Generated

DOI: 10.3389/fcimb.2026.1923862

Keywords: urinary tract infections, antibiotic resistance, pediatrics, COVID-19, Escherichia coli, Klebsiella pneumoniae, enterococci, ESBL, carbapenem resistance, surveillance, Chongqing, nitrofurantoin