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

The research team, led by Nouh Botan and colleagues, conducted a retrospective cross-sectional review of routine microbiology records collected between January 1 and December 31, 2025. From the laboratory registry, they identified 286 positive bacterial culture records with antimicrobial susceptibility results, which together generated 1,787 individual test records because each isolate was challenged against multiple drugs. Applying the M39-A4 deduplication rule, which counts only the first unique isolate per patient per species to avoid statistical distortion from repeated sampling, the team excluded nine repeat isolates and arrived at a final analytic cohort of 277 unique clinical isolates. Intermediate susceptibility results were conservatively categorized as resistant for antibiogram purposes, in line with the guideline’s recommendations, while routine patient care continued to follow the laboratory’s standard reporting procedures.

The identity of the organisms tells its own story. Escherichia coli dominated the dataset, accounting for 50.9 percent of all isolates, followed by Staphylococcus aureus at 33.6 percent. Pseudomonas species made up 6.9 percent, and other enteric organisms, primarily Proteus and Klebsiella species, contributed 8.6 percent. Half of the isolates came from urine specimens and 39 percent from wound or pus samples, with blood cultures representing only 2.2 percent. The cohort was almost perfectly balanced by sex, and a slight majority of isolates originated from outpatient services. Notably, patient age and detailed clinical diagnoses were unavailable, because the retrospective laboratory database captured only microbiological surveillance variables, a limitation that reflects the sparse data infrastructure typical of the setting.

The susceptibility findings are where the study becomes genuinely alarming. Ampicillin, a legacy frontline agent, showed a susceptibility rate of just 7.3 percent among E. coli isolates, meaning it is essentially useless as an empirical option. Ciprofloxacin, a fluoroquinolone once considered a reliable workhorse, maintained susceptibility in only 19.0 percent of E. coli isolates, translating into an overall resistance burden of 81 percent. Among the broader Enterobacteriaceae pool, ciprofloxacin susceptibility fell to 16.3 percent. These figures align with disturbing trends reported from tertiary hospitals in Ethiopia, Kenya, and elsewhere in East Africa, where Gram-negative organisms have steadily accumulated resistance to fluoroquinolones, aminoglycosides, and third-generation cephalosporins.

Not every result was bleak. Nitrofurantoin, an older drug largely reserved for urinary infections, retained a susceptibility footprint of 78.5 percent among E. coli isolates and performed even better against S. aureus at 88.3 percent, supporting its continued role in empirical treatment of uncomplicated urinary tract infections. Gentamicin offered moderate coverage, with E. coli showing 60.4 percent susceptibility, although the Enterobacteriaceae pool fared worse at 51.1 percent. These patterns suggest that carefully chosen older, inexpensive agents can still deliver clinical value in the region, provided that prescribing decisions are anchored to locally generated susceptibility data rather than habit or availability.

Perhaps the most consequential finding concerns meropenem, a carbapenem antibiotic typically held in reserve as a last-line option for serious Gram-negative infections. Only 30.5 percent of tested E. coli isolates and 30.5 percent of the Enterobacteriaceae pool were classified as susceptible, with an overall susceptibility of 40.0 percent across organisms. The authors are careful to caution that reduced phenotypic susceptibility to meropenem should not be interpreted as evidence of specific carbapenemase-producing organisms without species-level identification and molecular confirmation, tools that were not available in this setting. Nevertheless, the signal is worrying enough that the researchers call urgently for confirmatory molecular characterization and continued prospective surveillance before any definitive epidemiological conclusions about carbapenem resistance in Somaliland can be drawn.

An exploratory subgroup analysis compared urinary and wound E. coli isolates and revealed intriguing heterogeneity. Wound isolates showed higher ciprofloxacin susceptibility than urinary isolates, 30.8 percent versus 17.2 percent, and higher gentamicin susceptibility at 68.2 percent versus 58.7 percent, but markedly lower meropenem susceptibility at 13.3 percent versus 35.4 percent. Because the subgroup sample sizes were small, the team used Fisher’s exact test and reported p-values of 0.267, 0.479, and 0.128 respectively, none reaching statistical significance. The authors emphasize that these comparisons are hypothesis-generating rather than conclusive, but they illustrate how specimen source can shape resistance profiles even within a single institution, a nuance that cumulative antibiograms stratified by specimen type can capture and communicate to prescribers.

Methodological honesty is a defining feature of the paper. Antibiotic-specific denominators varied throughout the dataset because susceptibility testing reflected routine clinical practice rather than a uniform research protocol: organism-specific panels, selective testing such as nitrofurantoin applied mainly to urinary isolates, individual clinician requests, and intermittent shortages of susceptibility disks and other consumables all meant that not every isolate was tested against every drug. Species-level identification relied on routine phenotypic and basic biochemical methods, since advanced techniques such as MALDI-TOF mass spectrometry and molecular assays were unavailable, and some organisms were therefore reported only at the genus level. Standardized daily internal quality control with ATCC reference strains could not be performed due to resource limitations, and breakpoint interpretation followed the CLSI- or EUCAST-based criteria accompanying whichever products were procurable. The authors explicitly acknowledge these constraints, arguing that transparent documentation of real-world laboratory conditions is itself a contribution toward building sustainable diagnostic capacity.

Beyond the numbers, the study is a proof of concept. The relatively modest culture volume of 286 positive records over a full year likely reflects broader diagnostic barriers: out-of-pocket costs for patients, heavy reliance on empirical therapy, intermittent supply constraints, and limited culture-guided prescribing. In Somaliland and neighboring Somali territories, healthcare is financed largely through direct patient payments, and antimicrobials are frequently obtainable without prescription oversight, while regional literature has documented incomplete counseling on dosing intervals and treatment duration. The authors also point to wider drivers of resistance that hospital data alone cannot capture, including unregulated retail antibiotic sales, veterinary antimicrobial use in pastoral livestock systems, and environmental exposures, arguing that long-term containment will require integrated collaboration across human health, veterinary medicine, and public health surveillance, consistent with a One Health approach.

What emerges from Hargeisa is both a warning and a template. The warning is that resistance to commonly used and even last-resort antibiotics is already substantial in a population previously invisible to global surveillance, and that without intervention, prescribers in the region are effectively practicing blind. The template is the demonstration that WHONET software, CLSI M39-A4 methodology, and disciplined deduplication of routine laboratory records can produce a credible, facility-specific antibiogram without expensive infrastructure. The researchers conclude that strengthening sustainable laboratory capacity, including reliable procurement of culture media, susceptibility testing materials, and equipment, should accompany routine antibiogram surveillance to support antimicrobial stewardship and evidence-based prescribing. For a region where no standardized cumulative antibiogram existed before, this baseline dataset is a small dataset with outsized significance, offering clinicians their first locally grounded map of which drugs still work and which no longer do.

Subject of Research: Antimicrobial resistance surveillance and cumulative antibiogram development at a tertiary referral hospital in Somaliland

Article Title: Standardized antimicrobial resistance surveillance in Somaliland: A hospital-based baseline evaluation using CLSI M39 and WHONET

Article References: Botan, N., Ali, A. S. O., Warsame, H. A., & Ali, Z. (2026). Standardized antimicrobial resistance surveillance in Somaliland: A hospital-based baseline evaluation using CLSI M39 and WHONET. New Microbes and New Infections, 74, Article 101861. https://doi.org/10.1016/j.nmni.2026.101861

Image Credits: AI Generated

DOI: 10.1016/j.nmni.2026.101861

Keywords: antimicrobial resistance, Somaliland, cumulative antibiogram, CLSI M39-A4, WHONET, Escherichia coli, meropenem, ciprofloxacin, nitrofurantoin, surveillance, Hargeisa, East Africa