Childhood UTI Bacteria Show Soaring Ciprofloxacin Resistance in Six-Year Hospital Study

Urinary tract infections are among the most common bacterial infections of childhood, and the antibiotics long used to treat them are steadily losing their power. A new six-year analysis of more than ten thousand bacterial isolates from children’s urine cultures, conducted at a tertiary hospital in Türkiye and published in BMC Infectious Diseases, offers one of the most detailed recent pictures of which pathogens are driving pediatric urinary infections and how quickly they are outmaneuvering the drugs clinicians reach for first. The findings are a sobering reminder that empirical treatment decisions made without local surveillance data risk failing a substantial share of young patients.

The research team, led by Kevser Erdoğan of Antalya Training and Research Hospital together with collaborators from Gaziantep University, İnönü University, Şanlıurfa Provincial Health Directorate and the University of Health Sciences in Ankara, carried out a retrospective cross-sectional study of laboratory records from children younger than eighteen years whose urine cultures tested positive between January 2019 and December 2024. Rather than sampling a subset, the investigators analyzed the full set of 10,348 isolates recovered during the period, making this one of the larger single-center pediatric uropathogen datasets published to date. The analysis was conducted at the specimen, or isolate, level, and the researchers also ran a proxy patient-level sensitivity analysis, in which patients were approximated by date of birth and sex and only the first isolate from each was retained, to check that their conclusions were not distorted by repeated cultures from the same child.

Laboratory identification and susceptibility testing were performed with an automated Vitek 2 Compact system, and results were interpreted according to the Clinical and Laboratory Standards Institute criteria in force in each calendar year, a detail that matters because breakpoints are periodically revised. Isolates showing intermediate susceptibility were conservatively classified as resistant. After a data audit, duplicate antibiogram entries were resolved so that each specimen-antibiotic combination contributed a single interpretation. Extended-spectrum beta-lactamase production, an enzymatic mechanism that destroys many penicillins and cephalosporins, was determined phenotypically and analyzed only among isolates with a valid recorded result. To detect genuine temporal trends rather than statistical noise, the team used the Cochran-Armitage test with false-discovery-rate adjustment and interpreted trends only for antibiotics with consistently high testing coverage across the study window.

The microbial landscape that emerged was dominated by a familiar adversary. Escherichia coli accounted for 58.3 percent of all isolates, followed by Klebsiella species at 18.1 percent and Proteus species at 6.7 percent. This hierarchy mirrors the global pattern of urinary tract infection epidemiology, in which E. coli, a gut-dwelling bacterium equipped with adhesive pili and a battery of virulence factors, ascends the periurethral region and colonizes the urinary tract. The specimen sources were telling as well: 57.5 percent of the isolates came from inpatient wards and 32.9 percent from the emergency department, meaning the dataset predominantly reflects hospitalized and acutely ill children rather than those managed entirely in outpatient clinics.

The resistance profile of E. coli revealed a stark divide between drug classes. Resistance was highest to ampicillin, at 62.5 percent with a 95 percent confidence interval of 61.3 to 63.7, confirming that this older aminopenicillin can no longer be relied upon as empirical therapy for pediatric urinary infections in this setting. Resistance to trimethoprim-sulfamethoxazole was likewise high, further narrowing the list of inexpensive oral options. At the opposite end of the spectrum, resistance to the carbapenem class was remarkably low: just 0.3 percent for imipenem and 0.4 percent for meropenem, with amikacin, an aminoglycoside, at only 1.6 percent. Nitrofurantoin also retained low resistance, preserving its role as an oral agent for lower urinary tract infections.

The most alarming trend, however, concerned ciprofloxacin, a fluoroquinolone often used when first-line agents fail. Among the antibiotics with consistently high testing coverage, resistance in E. coli rose from 14.7 percent in 2019 to 44.5 percent in 2024, a statistically robust increase with an adjusted p value below 0.001. Over the same period, ampicillin resistance climbed from 58.8 percent to 68.9 percent. By contrast, resistance to amikacin and the carbapenems remained low and stable throughout the six years, suggesting that these reserve drugs have so far been spared the selective pressure that has eroded the utility of the fluoroquinolones in this pediatric population.

Extended-spectrum beta-lactamase production adds another layer of concern. Phenotypic ESBL positivity was detected in 30.7 percent of the 3,879 E. coli isolates, representing 64.3 percent of all E. coli, that had a valid recorded ESBL result. ESBL-producing organisms hydrolyze most beta-lactam antibiotics, leaving carbapenems as the treatment of choice for serious infections, so a rate of this magnitude in children is a significant clinical burden. The researchers caution, however, that the temporal course of ESBL positivity could not be evaluated reliably, because ESBL testing coverage expanded dramatically during the study, from just 4.5 percent of E. coli isolates in 2019 to 98.7 percent by 2024. Apparent changes in ESBL frequency over time therefore partly reflect changes in how often the test was performed rather than true biological trends, a methodological subtlety that less careful surveillance studies often overlook.

Multidrug resistance, defined as non-susceptibility to at least one agent in three or more antimicrobial classes, was found in 42.1 percent of E. coli isolates overall, rising to 52.9 percent in 2024. Using logistic regression adjusted for sex, age, calendar year and care setting, the team identified several factors associated with ESBL positivity and multidrug resistance: male sex, the twelve-to-sixty-month age group, later calendar years and an inpatient care setting all showed adjusted associations. That hospitalized children carry a heavier burden of resistant organisms is consistent with the known epidemiology of healthcare-associated resistance, where prior antibiotic exposure, indwelling devices and repeated hospital contact create strong selection pressure. Importantly, the proxy patient-level sensitivity analysis produced materially unchanged results, strengthening confidence that the findings are not artifacts of repeated sampling.

The authors are explicit about the limits of their data. Because the study draws on a tertiary hospital laboratory serving predominantly hospitalized and referred children, its results are not generalizable to community settings, where resistance patterns are typically lower and the case mix very different. Laboratory surveillance findings of this kind describe the bacterial population that reaches a specialized laboratory, not the population of all children with urinary symptoms, many of whom are treated empirically without culture. The researchers accordingly emphasize that treatment decisions should follow clinical guidelines and local antimicrobial stewardship policies informed by regularly updated, setting-specific antibiograms rather than by single published figures applied universally.

Even with those caveats, the study delivers a clear public health signal. The near-tripling of ciprofloxacin resistance in six years shows how quickly a drug class can deteriorate under pressure, while the stability of carbapenem and amikacin susceptibility demonstrates that resistance trajectories are not inevitable and can be steered by stewardship. For clinicians caring for children with urinary tract infections, the practical message is twofold: ampicillin and trimethoprim-sulfamethoxazole are increasingly unreliable as empirical choices in this setting, and nitrofurantoin remains a valuable oral option for uncomplicated lower infections, with carbapenems reserved for confirmed severe or resistant disease. For policymakers, the study underscores the value of sustained, methodologically rigorous laboratory surveillance as the foundation of rational antibiotic use in pediatrics, and it arrives at a moment when preserving the efficacy of last-line agents for the next generation has become a global imperative.

Subject of Research: Antibiotic resistance trends in uropathogens from culture-positive pediatric urine samples

Article Title: Uropathogens and antibiotic resistance in culture-positive urine samples from children: a six-year retrospective analysis of resistance trends at a tertiary hospital

Article References: Erdoğan, K., Tiryaki, H. D., Kurt, O., Çekin, Y., Şeker, N., & Küçükkelepçe, O. (2026). Uropathogens and antibiotic resistance in culture-positive urine samples from children: a six-year retrospective analysis of resistance trends at a tertiary hospital. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14543-5

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14543-5

Keywords: urinary tract infection, children, Escherichia coli, antibiotic resistance, uropathogens, ESBL, multidrug resistance, ciprofloxacin, carbapenems, antimicrobial stewardship, pediatrics, surveillance