The research team, led by Shahida Kashif of Liaquat College of Medicine and Dentistry together with Muhammad Sohail of the University of Karachi and collaborators at several Karachi institutions and Taif University in Saudi Arabia, analyzed 308 Gram-negative bacterial isolates recovered from urine samples of patients with catheter-associated urinary tract infections. The samples were collected between June and December 2024, and the work received ethical approval from the Institutional Review Board of Darul Sehat Hospital in Karachi, with written informed consent obtained from all participants or their legal representatives. The study was designed to answer three linked questions: how common carbapenem resistance is in this setting, which carbapenemase-encoding genes are responsible, and what patient characteristics are associated with carrying those genes.

Species identification revealed a familiar hierarchy of uropathogens. Escherichia coli was the dominant organism, accounting for 134 of the 308 isolates, or 43.5 percent, followed by Klebsiella pneumoniae with 96 isolates, or 31.2 percent. The remaining isolates included other Gram-negative species, among them Pseudomonas aeruginosa. This distribution mirrors global patterns of catheter-associated infection, in which Enterobacterales, the family of gut-dwelling bacteria that includes both E. coli and K. pneumoniae, colonize the urinary tract and catheter surfaces with ease. The ubiquity of these organisms in hospital plumbing, on catheter biofilms, and in patients’ own gut flora makes them persistent adversaries in intensive care units and general wards alike.

Antimicrobial susceptibility testing exposed a stark pattern of resistance to the older, cheaper, and more widely used drugs. Resistance to ceftriaxone, a third-generation cephalosporin, was found in 244 of 308 isolates, a rate of 79.2 percent, while resistance to ciprofloxacin, a fluoroquinolone, appeared in 238 isolates, or 77.3 percent. By contrast, resistance to the carbapenems remained lower but far from negligible: 104 isolates, or 33.8 percent, were resistant to meropenem, and 96 isolates, or 31.2 percent, were resistant to imipenem. That roughly one in three Gram-negative uropathogens from catheter-associated infections could shrug off carbapenems underscores how far these last-line drugs have been eroded in this clinical setting, leaving clinicians with progressively fewer options for seriously ill patients.

The molecular core of the study focused on five carbapenemase-encoding genes detected by polymerase chain reaction: bla_NDM, bla_OXA-48, bla_KPC, bla_IMP, and bla_VIM. These genes encode enzymes that hydrolyze carbapenems and most other beta-lactam antibiotics, rendering them ineffective. Among the 104 carbapenem-resistant isolates, bla_NDM, which encodes the New Delhi metallo-beta-lactamase, was by far the most prevalent, detected in 66 isolates, or 63.5 percent. bla_OXA-48, encoding the oxacillinase-48 beta-lactamase, came second at 40 isolates, or 38.5 percent. Notably, bla_KPC, bla_IMP, and bla_VIM were not reported as significant contributors in this collection, marking NDM and OXA-48 as the dominant resistance determinants in these Karachi hospitals.

The distribution of genes across species was not uniform, and this species-specific pattern carries practical implications for diagnostics and treatment. bla_NDM was particularly concentrated in K. pneumoniae, appearing in 31 of 48 carbapenem-resistant K. pneumoniae isolates, or 64.6 percent. bla_OXA-48, by contrast, was more predominant in carbapenem-resistant P. aeruginosa, detected in 4 of 10 such isolates, or 40 percent. The study also documented co-carriage of both bla_NDM and bla_OXA-48 in 12 of the 104 carbapenem-resistant isolates, or 11.5 percent. Dual carriage is especially concerning because enzymes from these two classes, a metallo-beta-lactamase and a class D carbapenemase, together dismantle a broader spectrum of beta-lactam drugs and can complicate the interpretation of phenotypic susceptibility tests, which may fail to flag resistance when multiple mechanisms interact.

Beyond cataloguing genes, the investigators used chi-square tests and binary logistic regression to identify independent predictors of carbapenemase gene carriage, with a p-value of 0.05 or less considered statistically significant. Three clinical factors emerged as independent predictors of gene positivity: admission to the intensive care unit, previous exposure to antibiotics, and catheterization lasting longer than seven days. Each of these factors fits a coherent biological and epidemiological narrative. ICU patients are exposed to the highest densities of resistant organisms and the most intensive antimicrobial use. Prior antibiotic exposure selectively eliminates susceptible strains, clearing the way for resistant ones to colonize. And prolonged catheterization gives bacteria time to form biofilms on the device surface, where they are shielded from both immune defenses and antibiotics and can freely exchange resistance genes on plasmids and other mobile elements.

The public health significance of these findings extends well beyond a single city. Carbapenemase genes, particularly bla_NDM, are notorious for their mobility, hitchhiking on plasmids that move readily between bacterial species and genera. A patient colonized with an NDM-producing E. coli strain can serve as a silent reservoir, disseminating the gene into hospital environments, water systems, and community settings. Because catheter-associated infections are so common, the urinary tract represents one of the largest and most underappreciated reservoirs for these genes in healthcare facilities. The identification of modifiable risk factors, especially catheter duration, provides concrete targets for intervention: strict catheter stewardship, daily assessment of the ongoing need for a catheter, and early removal are inexpensive measures that directly shorten the window in which resistance can emerge and spread.

The study also highlights the importance of molecular surveillance in an era where phenotypic testing alone may not capture the full resistance picture. Rapid PCR-based detection of bla_NDM and bla_OXA-48 in carbapenem-resistant isolates allows infection control teams to isolate carriers promptly, adjust antibiotic therapy, and interrupt transmission chains before outbreaks take hold. The authors note that the co-existence of multiple carbapenemase genes in a meaningful fraction of isolates further argues for comprehensive molecular panels rather than single-gene assays, since treatment decisions and infection control responses may differ depending on which enzymes are present. For laboratories in resource-limited settings, the study’s straightforward PCR approach offers a practical template for building such surveillance capacity.

Published open access in BMC Infectious Diseases with a permanent DOI, the study arrives as the global health community intensifies efforts against antimicrobial resistance, a threat the WHO has identified as one of the top challenges facing public health. The Karachi data, showing E. coli as the predominant uropathogen, bla_NDM as the leading carbapenemase in resistant Enterobacterales, and bla_OXA-48 as the more prevalent mechanism in resistant P. aeruginosa, add a valuable regional data point to the global map of resistance. More importantly, the clear linkage of gene carriage to ICU admission, prior antibiotic exposure, and extended catheterization converts an abstract molecular threat into a set of actionable clinical priorities. If hospitals act on these predictors, limiting unnecessary catheter days and curbing indiscriminate antibiotic use, the study suggests that the spread of carbapenemase genes in catheter-associated infections can be slowed, preserving the effectiveness of last-line antibiotics for the patients who need them most.

Subject of Research: Carbapenemase gene prevalence and risk factors in Gram-negative uropathogens causing catheter-associated urinary tract infections

Article Title: Molecular detection and risk factors of carbapenemase -encoding gene among the Gram-negative uropathogens associated with catheter-associated urinary tract infection

Article References: Kashif, S., Sohail, M., Uddin, F., Ansari, A., Alorabi, M., Khan, R. N., & Husain, S. (2026). Molecular detection and risk factors of carbapenemase -encoding gene among the Gram-negative uropathogens associated with catheter-associated urinary tract infection. BMC Infectious Diseases. https://doi.org/10.1186/s12879-026-14568-w

Image Credits: AI Generated

DOI: 10.1186/s12879-026-14568-w

Keywords: carbapenemase, bla_NDM, bla_OXA-48, catheter-associated urinary tract infection, antimicrobial resistance, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, carbapenem-resistant Enterobacterales, risk factors, PCR detection, hospital infection control