Burden of antibiotic resistance in urinary isolates: a retrospective cross-sectional study from a tertiary center in Far-Western Nepal

Abstract

Background

Antibiotic resistance poses a severe public health challenge, particularly in resource-limited settings where data scarcity undermines local infection prevention strategies. This study provides the first comprehensive surveillance of urinary antibiotic resistance from the Far-Western region of Nepal in over a decade, highlighting patterns relevant to antimicrobial stewardship and infection control.

Methods

A retrospective cross-sectional study was conducted using urine culture records collected between April 2024–March 2025. Laboratory data on bacterial isolates and antibiotic susceptibility were extracted from microbiology database, exported to Microsoft^® Excel 2021, entries with missing data removed, cleaned for duplicates, verified for completeness, and de-identified. Organism identification and susceptibility testing were done following CLSI guidelines and Multidrug-resistant (MDR) and extensively drug-resistant (XDR) were identified as per the international standard definition. Data were stratified by age, organism, and antibiotic class (WHO AWaRe classification) to assess trends and inform empirical treatment strategies.

Results

Total 3,155 cultures were processed, among which 754 (23.9%) were positive. Escherichia coli (41.6%) and Klebsiella spp. (22.1%) were the most common uropathogens. MDR and XDR rates were 27.9% and 67.5%, respectively, with XDR prevalence increasing with patient age—peaking at 81.4% in those over 65. Alarmingly high resistance was observed against commonly used oral antibiotics (> 80% for ampicillin, cefixime, and ciprofloxacin), limiting outpatient treatment options. WHO Watch and Reserve group antibiotics such as meropenem and colistin remained comparatively effective. High XDR rates in nosocomial organisms like Pseudomonas aeruginosa and Proteus spp. were noticed.

Conclusion

This study highlights the burden and evolving pattern of antibiotic resistance with high XDR rates in an area with limited resources and a lack of prior surveillance data. These findings reinforce the need for escalating antimicrobial stewardship, strengthening surveillance systems in the region, while also contributing to national infection control strategies.

Clinical trial number

Not applicable.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-025-12074-z.

Introduction

Urinary tract infection (UTI) is a broad clinical term encompassing a spectrum of localized or systemic conditions of the urinary tract, namely urethritis, cystitis, prostatitis, pyelonephritis, and urosepsis [1]. The urine culture antibiogram of uropathogens is pivotal in combating such conditions. The majority of symptomatic UTIs lead to significant morbidity and can progress to life-threatening emergencies if undiagnosed or untreated [2]. This is one of the most frequent reasons for prescribing antibiotics, the inappropriate overuse of which has resulted in an ever-growing problem of resistance [3]. According to the World Health Organization (WHO), antibiotic resistance is a threat to global public health, with an estimated five million deaths each year [4].

Nepal has seven administrative provinces, among which the Sudurpaschim province has a population of 2.69 million, which is 9.2% of Nepal’s total population, as per the National Population and Housing Census 2021 [5]. The data on the prevalence of antibiotic resistance in Nepal are patchy, with a majority of studies originating from the central [6–10] and eastern region [11, 12] of Nepal at different time frames. To date, only a single study on antibiotic resistance, which dates back to 2013, has been conducted in this region [13]. The lack of recent, region-specific data has likely impeded the development of localized antibiotic guidelines, highlighting the relevance of the present study. We hypothesize that XDR organisms are highly prevalent in this under-reported region due to uncontrolled antibiotic use and lack of prior surveillance. This study aims to determine the prevalence and pattern of MDR and XDR among uropathogens at Maya Metro Hospital and by doing so, shed new light on the prevalence and pattern of antibiotic resistance in resource-limited settings in Far-western province of Nepal. By quantifying local resistance trends, this study aims to inform evidence-based prescribing practices, guide empirical therapy, and support regional public health planning and policy formulation.

Methods

Study design and data acquisition

This study was done at Maya Metro Hospital, a tertiary care center in Dhangadhi, which receives referrals from all nine districts within the Sudurpaschim Province, far-western region of Nepal. A retrospective cross-sectional observational study was conducted on urine samples submitted to the hospital laboratory for bacterial culture and antibiotic susceptibility testing (AST). Laboratory records of all urine culture reports from April 2024 to March 2025 were retrieved from electronic database and exported to Microsoft^® Excel 2021. The dataset was cleaned and standardized for uniformity in bacteria and antibiotic nomenclature; incomplete and duplicate entries were removed, data were de-identified, and cross-checked with hospital records. The original identifying dataset was permanently deleted, and the finalized, de-identified dataset was used for analysis. Variables used were age, gender, growth of the organism, and AST result.

Laboratory methods and quality control

Specimens processed included mid-stream clean catch and catheter-collected urine samples, which were stored at 2–8 degrees Celsius for up to 12 h until the start of processing. The samples were cultured on Cystine Lactose Electrolyte Deficient (CLED) agar media and incubated under aerobic condition at 37° C for 24 h. Growth of bacteria was defined as having more than 10⁵ colony-forming units (CFU)/mL, according to the standard microbiological criteria. Bacteria were identified using conventional biochemical tests, including the citrate test and triple sugar iron (TSI) test. Interpretation was done following guidelines adapted from Clinical and Laboratory Standards Institute (CLSI) 2023 edition and Dhulikhel Hospital laboratory protocol.

Antibiotic susceptibility testing (AST) was carried out with the antibiotic discs sourced from HiMedia Laboratories (India) via the Kirby-Bauer disc diffusion method on Mueller-Hinton Agar media. The latest available CLSI breakpoint criteria guidelines were followed for interpreting zone diameters. No phenotypic confirmatory tests were performed, and zone diameters were not specifically documented in the records; instead, susceptibility interpretation (sensitive/intermediate/resistant) was recorded based on guideline cutoffs. Control strains were not routinely used, but quality control was done by internal validation, adherence to CLSI guidelines, and consistent supervision from microbiologist.

Operative definitions

An organism is said to have growth with sensitivity or resistance to a particular antibiotic based on the microbiologist’s reported result in the individual urine culture. For practical purposes, all intermediate results were considered resistant. Multidrug resistance (MDR) was defined as resistance to at least one antibiotic each from three or more antibiotic classes [14]. Similarly, extensively drug-resistant (XDR) was defined as resistant to all but two or fewer antibiotic classes, provided that the organism was tested for at least five classes of antibiotics. This study used the 2023 WHO AWaRe (Access, Watch, Reserve) classification of antibiotics, prepared by the WHO Expert Committee on Selection and Use of Essential Medicines. This classification is based on their clinical importance and the risk of resistance to emphasize the importance of their appropriate use and to assist in antibiotic stewardship [4]. The “Access” group of antibiotics is the first line of drugs that can be used when needed. The “Watch” group of antibiotics is used with caution only when the “Access” group are resistant, whereas the “Reserve” group of antibiotics is the last line of defense and used in serious life-threatening infections.

Data processing and analysis

Data was retrieved, cleaned, and analyzed in Microsoft^® Excel 2021 and expressed in terms of frequency and percentages. Age was divided into subgroups according to broad life stages for better comprehension: children and adolescents (0–18 years), young adults (19–39 years), middle-aged adults (40–64 years), and older adults (65+ years). MDR and XDR rates were calculated based on standard criteria mentioned in the operative definitions section of this study. Confidence intervals for the proportions were calculated using the Wald method, assuming binomial distribution. Visualizations were created using R software version 4.5.0 (R Core Team, 2025) within the RStudio IDE version 2024.12.1 + 563 (RStudio Team, 2025).

Ethical consideration

This study complied with the standards of the Declaration of Helsinki and adhered to ethical guidelines. Written permission to conduct the study was sought from the institute. Individual consent of participation was not needed and was waived by the Independent Review Board (IRB) of Nepal Health Research Council (NHRC). Ethical review clearance was obtained from Ethical Review Board of Nepal Health Research Council (NHRC), Kathmandu, Nepal, with registration no. 292_2025.

Results

Demographic characteristics of patients

During the study period, a total of 3,155 urine culture records were found after removing all the duplicates and multiple growths. Among them, 754 isolates yielded positive bacterial growth, giving an overall prevalence of 23.9% (95% CI: 22.3–25.5%). The mean age of the patient was 38.0 ± 18.7 years, with predominantly female patients (74.9%). Table 1 outlines the baseline characteristics of the patients and their urinary isolates.

Table 1.

Baseline characteristics of patients and urinary isolates

Characteristic	Value
Age, mean ± SD (years)	38.0 ± 18.7
Female Patients, n/N (%)	565/754 (74.9%)
Male Patients, n/N (%)	189/754 (25.1%)
Cultures Processed, N (%)	3155 (100%)
Positive Urinary Isolates, n/N (%)	754/3155 (23.9%)
Antibiotic Tests Performed, n	5312
Mean Antibiotics Tested per Isolate	7.05
Overall resistance ratio per tested antibiotic (%)	2637/5312 (49.6%)
Multi-Drug-Resistant (MDR) Isolates, n/N (%)	210/754 (27.9%)
Extensively Drug-Resistant (XDR) Isolates, n/N (%)	509/754 (67.5%)

Prevalence of uropathogenic bacteria

The distribution of uropathogens across age groups along with their MDR and XDR rates is depicted in Fig. 1. Escherichia coli was the most prevalent organism in all age categories, accounting for 36.2% to 42.1% of isolates. In 0–18 years age group, Staphylococci spp. (38.3%) and Klebsiella spp. (19.1%) were also notable contributors. The proportion of XDR organisms increased with age, with an alarming rate of 81.4% in the 65 + age group.

Fig. 1.

Proportion of uropathogens according to age groups with total MDR and XDR rates (in percentage of tested isolates) for each age group

Antibiotic resistance rate

A total of 5,312 antibiotic susceptibility tests (ASTs) were performed across all the growing isolates, with an average of 7.05 antibiotics tested per isolate. The overall rate of resistance was 49.6% across all antibiotics tested, i.e., for every 100 ASTs done across all bacteria and antibiotic classes, 49.6 of them showed resistance. Among the reported isolates, 27.9% were multidrug-resistant (MDR) and 67.5% were extensively drug-resistant (XDR) (Table 1).

The highest rate of MDR was detected in Enterococcus spp. (68.8%) followed by coagulase-negative Staphylococci (62%). Similarly, among the isolated organisms, Pseudomonas aeruginosa had the highest rate of XDR (100%), followed by Proteus spp. (96.6%) (Table 2).

Table 2.

Prevalence of individual organisms isolated with their antibiotic resistance rates

Organism Isolated	Isolates (n)	% of N	MDR% [95% CI]	XDR% [95% CI]
Escherichia coli	314	41.6	20.4 [16.3 to 25.2]	70.7 [65.4 to 75.5]
Klebsiella spp.	167	22.1	21.6 [16.0 to 28.4]	76.0 [69.0 to 81.9]
Coagulase-negative Staphylococci	71	9.4	62.0 [50.3 to 72.4]	36.6 [26.4 to 48.2]
Staphylococcus aureus	55	7.2	56.4 [43.3 to 68.6]	43.6 [31.4 to 56.7]
Pseudomonas aeruginosa	41	5.4	0.0 [0.0 to 8.6]	100.0 [91.4 to 100.0]
Enterococcus spp.	32	4.2	68.8 [51.4 to 82.0]	25.0 [13.3 to 42.1]
Proteus spp.	29	3.8	3.4 [0.6 to 17.2]	96.6 [82.8 to 99.4]
Acinetobacter spp.	28	3.7	17.9 [7.9 to 35.6]	82.1 [64.4 to 92.1]
Morganella spp.	17	2.2	41.2 [21.6 to 64.0]	58.8 [36.0 to 78.4]

The resistance profiles of approximately 35 antibiotics, particularly the WHO Watch and Reserve categories of antibiotics, revealed marked differences in resistance across genders (Fig. 2). Resistance was notably high (> 80%) for amoxicillin, ampicillin, azithromycin, cefalexin, and cefixime in the Access group of antibiotics. The most sensitive antibiotics among Access, Watch and Reserve groups were amikacin, meropenem, and colistin respectively.

Fig. 2.

Difference in specific antibiotic resistance rates (in percentage of tested isolates) among male and female populations. The AWaRe groups are separated by grey dotted lines

The resistance heatmap clearly shows organism-wise resistance percentages across all the tested antibiotics (Fig. 3). Notably, Pseudomonas aeruginosa and Acinetobacter spp. showed high XDR patterns, with near-total resistance to multiple classes. E. coli showed > 70% resistance to cefuroxime and ciprofloxacin, whereas Klebsiella spp. exhibited high resistance to cephalosporins and β-lactam/β-lactamase inhibitors.

Fig. 3.

Heatmap showing antibiotic resistance in percentage of tested isolates

These findings highlight an alarming rate of resistance, particularly among gram-negative organisms, and stress the need for strict antimicrobial stewardship programs to create awareness among prescribers and more robust infection control strategies.

Discussion

This study found a high burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) uropathogens, predominantly Escherichia coli and Klebsiella species. To our knowledge, this is the first study in over a decade to evaluate antibiotic resistance patterns in uropathogens from the Far-Western region of Nepal. Apart from a single study conducted at Seti Zonal Hospital in 2013 [13], no other published data from this region could be identified. Maya Metro Hospital, where the present study was conducted, serves as one of the major referral centers for all nine districts of Sudurpaschim Province, with over 40,000 outpatient visits annually. This wide catchment area and high patient volume make the study sample broadly representative of the uropathogen burden across the province.

To better understand the implications of the results from this study, it was compared with similar studies conducted in Nepal and comparable settings. In this study, the proportion of positive bacterial growth was 23.9%, of which the majority were females (74.9%), as expected. This finding is comparable to that of a study performed at Seti zonal hospital where Awasthi et al. found significant growth in 25.5% of isolates, also with a female predominance [13]. The higher incidence of UTI among females can be attributed to several risk factors, including a shorter urethral length, proximity of the external urethral meatus to the perineal flora, pregnancy, postmenopausal changes, and pelvic organ prolapse—all of which occur exclusively in females [1].

Escherichia coli (41.6%) was the most frequently isolated gram-negative organism across all age groups, followed by Klebsiella spp. (22.1%). Together, these strains accounted for the majority of isolates, which is in line with global trends in community-acquired urinary tract infections [2, 15]. Among the gram-positive organisms, Staphylococcus spp. accounted for 16.5% of the total isolates. This included coagulase-negative Staphylococci (9.4%) and Staphylococcus aureus (7.2%), both of which are often linked to complicated and catheter-associated UTIs, though some isolates may reflect contamination. Opportunistic and nosocomial pathogens such as Pseudomonas aeruginosa, Enterobacter spp., Acinetobacter spp., and Morganella spp. collectively represented 15.5% of isolates. These organisms are notoriously associated with nosocomial infections, anatomical abnormalities, and exhibit high levels of antimicrobial resistance.

Resistance to first- and second-line oral agents such as ampicillin, cefalexin, cefixime, and ciprofloxacin was notably high (>80%), significantly limiting empirical treatment options for outpatient urinary tract infections (UTIs). This pattern is consistent with previous reports from tertiary centers in Nepal and India, where fluoroquinolone and cephalosporin resistance among E. coli uropathogens exceeded 70–85% [7, 9, 16]. Such widespread resistance may reflect the irrational and unregulated use of broad-spectrum antibiotics in community settings. In contrast, relatively lower resistance rates were observed for amoxicillin-clavulanate, doxycycline, nitrofurantoin, and cotrimoxazole, supporting their continued role as viable oral options for uncomplicated lower UTIs in this region. The higher susceptibility of aminoglycosides and carbapenems observed in this study aligns with global trends, as reported by the WHO GLASS 2025 data for the South-East Asia Region, which show over 60% resistance to third-generation cephalosporins but only 16–31% to imipenem among E. coli and Klebsiella urinary isolates [16]. These findings underscore the urgent need for antibiotic stewardship and routine surveillance to preserve the efficacy of remaining therapeutic options.

Table 3 compares this study with multiple similar representative studies from Nepal. Studies from the central region, which also includes the capital city of Nepal, report higher overall MDR, documenting rates from 41.1% up to 89%; [7, 10] whereas studies from the eastern part of Nepal report MDR rates from 32% to 41.8% [11, 12]. Alarmingly, our study found a substantially higher XDR rate of 67.5%, which by far exceeds the 5% reported by both Parajuli et al. and Shrestha et al. [9, 12] The low MDR (27.9%) with high XDR (67.5%) invariably implies a deeply concerning shift in resistance pattern in this underserved region, with the emergence and possible spread of extensively drug-resistant organisms. The differences in antibiotic usage patterns, local prescribing behavior, or regional variation in referral patterns may also explain this observation.

Table 3.

Comparison between similar representative studies from the region

Study	Region of Nepal	Study Period	Positive growth (% of N)	Percentage of E. coli	Overall MDR %	Overall XDR %
This study	Far-Western Region	2024-25	754 (23.9%)	41.6%	27.9%	67.5%
Awasthi et al. [13]	Far-Western Region	2013	98 (25.5%)	53.1%	42.9%	NA
Shrestha et al. [7]	Central Region	2018-19	73 (24.0%)	58.0%	89.0%	NA
Ganesh et al. [8]	Central Region	2015-16	197 (12.3%)	57.8%	61.9%*	NA
Parajuli et al. [9]	Central Region	2015-16	1079 (19.7%)	68.5%	64.9%	5.0%
Baral et al. [10]	Central Region	2007	219 (30.8%)	81.3%	41.1%	NA
Baral et al. [11]	Eastern Region	2015-18	19,671 (16.9%)	54.3%	41.8%	NA
Shrestha et al. [12]	Eastern Region	2018	314 (16%)	53.0%	32.0%	5.0%

* Uses MDR definition as resistant to 2 or more classes of antibiotics

Another interesting finding as seen in Fig. 1 is that the percentage of XDR organisms increases with increasing age group, from 60% in the 0–18 years age group to 81.4% in the 65+ age group. This may be due to multiple factors, such as cumulative antibiotic exposure, declining immunity, greater contact with healthcare settings, chronic conditions, and more indwelling devices, all of which are seen more in the older age group [17–19]. This also explains the higher proportion of XDR organisms that cause nosocomial infections, such as Pseudomonas aeruginosa and Enterococcus spp., in the above 40 years of age group than in the below 40 years of age group.

According to the WHO GLASS 2025 report, the South-East Asia Region—including Nepal—has some of the world’s highest antimicrobial resistance rates among uropathogens [16]. Urinary E. coli isolates show 60.4% resistance to third-generation cephalosporins and 16.3% to imipenem, while Klebsiella pneumoniae exhibits 60.1% and 31.1% resistance to the same agents, respectively. These values far exceed global averages (39.8% and 2.6% for E. coli; 45.5% and 10.9% for K. pneumoniae), corroborating the high resistance burden observed in our study.

The inappropriate and rampant use of antibiotics remains a major driver of antimicrobial resistance in Nepal, particularly in settings where over-the-counter dispensing of antibiotics without prescription is common practice. Clinical guidelines, such as those by the National Institute for Health and Care Excellence (NICE), strongly discourage the use of antibiotics without consultation from a qualified healthcare professional [20]. They also advise against the reuse of leftover antibiotics or sharing them with others, practices that are unfortunately widespread in our region. Such behaviors bypass appropriate clinical assessment and contribute to suboptimal dosing, incomplete treatment courses, and the propagation of resistant strains. Strengthening antimicrobial stewardship at the community level and enforcing prescription-only antibiotic policies are essential public health measures to address this challenge.

From a urologist’s perspective, these resistance patterns have direct implications for surgical prophylaxis and perioperative care. In our context, the use of fluoroquinolones and third-generation cephalosporins may be inadequate for perioperative prophylaxis given the observed resistance rates. This data supports the use of amikacin, with or without cefuroxime or metronidazole, for endourological and open/laparoscopic urological procedures. For clean or clean-contaminated surgeries such as circumcision or urethral reconstruction, cefuroxime remains appropriate, with amikacin added in high-risk or catheterized patients.

Limitations in laboratory testing and quality control

Although control strains were not routinely used due to limited resources, consistent in-house quality monitoring was implemented in adherence to standardized CLSI guidelines. Antimicrobial susceptibility testing (AST) was performed based on resistance patterns observed with first-line antibiotics and, therefore, may not have been conducted for every antibiotic. Consequently, the resistance patterns for individual antibiotics may not precisely represent the true prevalence of resistance and should be interpreted with caution.

Limitations of the study

The absence of patients’ prior antibiotic history and linked clinical information in individual urine culture reports limited this study’s ability to assess presenting symptoms, risk factors for urinary tract infection (UTI), and treatment outcomes. In addition, the dataset lacked segregation based on district of origin, catheterized versus non-catheterized samples, and whether the samples were collected by patients themselves or by healthcare personnel using proper technique; therefore, the interpretation of these findings should be approached with caution. Furthermore, as part of the routine preoperative workup in the Department of Urology at our institution, urine cultures are obtained before all major urological procedures, regardless of symptoms. This practice may have affected the accuracy of estimating the proportion of asymptomatic bacteriuria and, consequently, the true burden of symptomatic UTIs.

Conclusion

This study highlights the burden and evolving pattern of antibiotic resistance in the Far-Western Province of Nepal, an area with limited resources and a lack of prior surveillance data. These findings reinforce the need for escalating antimicrobial stewardship and surveillance systems in the region, as well as reviewing national infection control strategies.

Supplementary Information

Below is the link to the electronic supplementary material.

Abbreviations

AST

Antibiotic Sensitivity Testing

AWaRe

Access, Watch and Reserve

CLED

Cystine Lactose Electrolyte Deficient

CLSI

Clinical and Laboratory Standards Institute

MDR

Multi-Drug Resistance

NICE

National Institute for Health and Care Excellence

TSI

Triple Sugar Iron

UTI

Urinary Tract Infection

WHO

World Health Organization

XDR

eXtended Drug Resistance

Author contributions

S.K. was responsible for the conception and design of the study, data collection, analysis, and interpretation. S.K. also prepared the figures, drafted the manuscript, performed critical revisions, and approved the final version of the manuscript for submission.

Funding

None.

Data availability

All data generated or analysed during this study are included in this published article [and its supplementary information files].

Declarations

Ethics approval and consent to participate

This study complied with the standards of the Declaration of Helsinki and adhered to ethical guidelines. Written permission to conduct the study was sought from the institute. Individual consent of participation was not needed and was waived by the Independent Review Board (IRB) of Nepal Health Research Council (NHRC). Ethical review clearance was obtained from Ethical Review Board of Nepal Health Research Council (NHRC), Kathmandu, Nepal, with registration no. 292_2025.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.