Childhood UTIs After COVID-19: Bacteria Testing the Limits of Antibiotic Treatment

Researchers in Chongqing, China, found changes in both the bacteria identified in children’s urine cultures and their response to antibiotics across the years before, during and after the COVID-19 pandemic.

A child's urinary infection can involve bacteria that respond very differently to the same medicine, making local resistance data an important part of choosing treatment. Researchers in Chongqing, China, found changes in both the bacteria identified in children's urine cultures and their response to antibiotics across the years before, during and after the COVID-19 pandemic.

Their paper, "Changes in epidemiology and antibiotic resistance patterns isolated from paediatric urinary tract infections: a multicenter study in China pre-, during and post-COVID-19," published in Frontiers in Cellular and Infection Microbiology, examined 5,618 bacterial isolates collected at four hospitals between 2019 and 2024. E. coli remained the leading pathogen, but resistance to individual antibiotics moved in different directions.

Urinary tract infections, or UTIs, are common bacterial infections in children, and delayed or ineffective treatment can contribute to kidney damage or more serious illness. The findings show why treatment decisions need current evidence about the bacteria circulating locally, with attention to a child's age and the location of the infection.

What six years of urine cultures revealed

The researchers reviewed records for children younger than 18 with community-acquired UTIs, including one infection episode per patient. Children with recurrent infections or congenital kidney and urinary tract abnormalities were excluded. The analysis compared 2019 with the pandemic years of 2020–2022 and the post-pandemic period of 2023–2024, using standardised laboratory criteria to interpret antibiotic susceptibility.

Laboratories identified 100 bacterial species, with Gram-negative bacteria accounting for 71% of isolates and Gram-positive bacteria for 29%. E. coli represented 37.3%, followed by Enterococcus faecium at 12.9%, Enterococcus faecalis and Klebsiella pneumoniae at about 9% each, Proteus mirabilis at 5.1% and Pseudomonas aeruginosa at 3.5%. These proportions describe the bacteria recovered from positive cultures, rather than infection rates across the wider child population.

Boys accounted for 53.9% of samples and girls for 46.1%. Boys predominated among infants and children aged two to three; girls formed the larger share from age four. E. coli led across every age group, reaching 45.7% of isolates among four- to six-year-olds. Resistance to several antibiotics also differed by age, supporting the authors' call for guidance that accounts for children's developmental stages.

Resistance rose for some drugs and fell for others

E. coli resistance to ampicillin/sulbactam fell from 57.9% in 2019 to 36.5% in 2024, with downward trends also recorded for amikacin, gentamicin and nitrofurantoin. Average resistance to amikacin and nitrofurantoin was approximately 2%. Ciprofloxacin resistance climbed from 36.5% to 50.2%, and resistance to ceftriaxone averaged around 59%, illustrating how strongly laboratory results depended on the antibiotic tested.

The team tracked bacteria producing extended-spectrum beta-lactamases, or ESBLs, enzymes that disable several commonly used antibiotics. The proportion of ESBL-producing E. coli rose overall from 54% to 62.2%; the corresponding proportion for K. pneumoniae fell from 66.2% to 52.7%. ESBL-producing strains generally showed greater resistance to multiple antibiotics than strains without these enzymes.

Carbapenems, an important group of antibiotics reserved for difficult infections, retained activity against most E. coli isolates, although carbapenem resistance rose from 2.7% to 4.9%. Resistance in K. pneumoniae fell overall from 23.1% to 18.9%, with considerable fluctuations between years. Carbapenem-resistant strains of both species also resisted numerous other drugs, narrowing the available options. K. pneumoniae resistance to amikacin, ciprofloxacin, levofloxacin and nitrofurantoin increased over the six years.

The post-pandemic years brought a different bacterial mix

E. coli's share of isolates declined from 45.3% before the pandemic to 35% in the post-pandemic period, and E. faecium and K. pneumoniae also accounted for smaller shares. Both E. coli and K. pneumoniae showed increased post-pandemic resistance to piperacillin/tazobactam, cefepime, ciprofloxacin and levofloxacin. K. pneumoniae resistance to ceftriaxone decreased from 66.2% to 49.8%, reinforcing the uneven nature of the changes.

The two Enterococcus species showed increased penicillin resistance after the pandemic, and E. faecium generally had higher resistance to several tested drugs than E. faecalis. No E. faecalis isolates resistant to vancomycin or linezolid were detected. These findings concern laboratory susceptibility and do not establish that a particular medicine will suit every child or every type of urinary infection.

The researchers also examined minimum inhibitory concentrations, the smallest antibiotic concentrations needed to stop visible bacterial growth. Vancomycin measurements showed no clear drift over time. Linezolid measurements shifted downward in both Enterococcus species, indicating greater laboratory susceptibility, with the change more pronounced in E. faecalis from 2022. Tracking these measurements can reveal changes that broad susceptible-or-resistant labels may miss.

Local evidence matters more than a single treatment rule

The Researchers emphasise urine cultures, susceptibility testing and continued resistance monitoring to guide treatment. Nitrofurantoin showed strong laboratory activity against E. coli, but the paper distinguishes uncomplicated bladder infections from kidney infections: the drug reaches high concentrations in urine and poor concentrations in kidney tissue. The Researchers also stress restrictions on fluoroquinolone use in children and the need to preserve carbapenems for selected resistant infections.

Changes in hygiene, antibiotic prescribing and access to healthcare could help explain the patterns surrounding the pandemic, but this retrospective analysis cannot establish that COVID-19 or pandemic policies caused them. Its four hospitals were all in the Chongqing region, limiting how confidently the results can be applied elsewhere, and molecular testing was unavailable to confirm resistance mechanisms. Continued local surveillance is needed to keep treatment guidance aligned with the bacteria clinicians actually encounter.