Current pattern of antibiotic resistance and molecular characterization of virulence genes in Klebsiella pneumoniae obtained from urinary tract infection (UTIs) patients, Peshawar

Abstract

The current study investigates the prevalence of virulence genes obtained from clinical isolates of multidrug-resistant (MDR) Klebsiella pneumoniae at Khyber Teaching Hospital Peshawar, from October 2021 to January 2023. Upon proper consent, clinical samples of suspected UTIs patients were collected and inoculated on the nutrients agar media, McConkey agar media, and Cysteine Lysine Electrolyte Deficient (CLED) agar media followed by incubation at 37°C for 24 hrs. The phenotypic and genotypic identification were employed for the bacterial isolates. The phenotypic identification includes gram staining followed by the Analytical Profile Index (API 20E). A total of 215 (3.85%) positive isolates were found with the highest prevalence observed among the female patients (4.35%) followed by male (3.26%). The highest prevalence, constituting 52.55% (n = 113), was detected in the age group of 21-40 years, followed by 31.62% (n = 68) in the 41-60 age group. Additionally, 10.23% (n = 22), 3.25% (n = 7), and 2.32% (n = 5) of cases were identified in the age groups of 01-10 years, 11-20 years, and above 60 years, respectively. Among the total positive samples, 44.65% (n = 96) were collected from the Outpatient department (OPD), while inpatient department (IPD) cases contributed 55.35% (n = 119). The antibiotic susceptibility profile of K. pneumoniae showed significant resistance to trimethoprim/Sulfamethoxazole (93%) and Colistin (79.07%). Tigecycline emerged as the most effective antibiotic with a sensitivity rate of 90%, along with Cefepime at the same level. Minimum Inhibitory Concentration (MIC) values indicated higher resistance for CTX, MEM, CN, AK, DO, CIP, and SXT in K. pneumoniae-causing UTIs from KTH, Peshawar. Molecular characterization of virulence genes reveals the highest prevalence of fimH (80%) followed by SAT (65%), papEF (49%), afa (29%), and VAT (16%). The sequencing data of the virulence genes reveals mutations in fimH and papEF, while sat, afa and vat virulence genes showed no mutations. The Chi-square test indicated a significant association between the types of bacteria, supporting our null hypothesis with a significance level of p ≤  0.05. The current study’s finding is to evaluate the rise of antibiotic resistance in hospital settings, which highly demands the focus of health authorities and clinicians to manage the burden of the disease effectively.