Antibiotic resistance patterns in uropathogens: insights from a Nepalese tertiary care setting

Abstract

Background:

Antimicrobial resistance in uropathogens is increasing globally, particularly in resource-limited settings such as Nepal, limiting treatment options.

Objectives:

This study aimed to evaluate the antimicrobial resistance patterns of uropathogens isolated from patients with urinary tract infections (UTIs) in a tertiary care hospital in central Nepal.

Design:

This study utilized a retrospective study design.

Methods:

We retrospectively observed medical records from August 2023 to February 2024 at Manmohan Memorial Teaching Hospital in Nepal, focusing on patients with significant bacterial growth in urine samples and antibiotic sensitivity analysis for resistance trends.

Results:

Escherichia coli (E. coli) (64.7%) and Klebsiella pneumoniae (K. pneumoniae) (15.0%) were the most common uropathogens. Both showed the highest resistance to amoxicillin (>95%), while E. coli demonstrated the lowest resistance to gentamicin (7.4%) and nitrofurantoin (12.2%). Klebsiella pneumoniae also showed low resistance to gentamicin (12.0%) but higher resistance to nitrofurantoin (64.0%).

Conclusion:

Empirical therapy, including nitrofurantoin and aminoglycosides, is a viable option for combating antimicrobial resistance in Nepal, necessitating region-specific surveillance and multicentre studies.

Plain language summary

Bacterial resistance to antibiotics in urinary infections: findings from a tertiary hospital of central Nepal

Antibiotic resistance is a growing problem worldwide, making it harder to treat infections. In Nepal, where healthcare resources are limited, this issue is even more challenging. This study looked at the resistance rate of bacteria that cause urinary tract infections (UTIs) among different antibiotics in a tertiary care hospital in central Nepal. We analyzed medical records from August 2023 to February 2024, focusing on patients with UTIs. The most common bacteria found was Escherichia coli (E. coli), making up nearly 65% of infections. Many of these bacteria were highly resistant to commonly used antibiotics like amoxicillin, ampicillin, and levofloxacin. However, gentamicin and nitrofurantoin were still effective against most infections. When we compared our findings with data from eastern Nepal, we found differences in the resistance rate of bacteria among various antibiotics, showing that resistance patterns vary by region. Our study suggests that nitrofurantoin and aminoglycosides could be good treatment options in Nepal, but continuous monitoring and more research across different regions and settings of hospitals are needed to guide the appropriate selection and use of the best antibiotics.

Keywords

antibiotic resistance patterns antimicrobial resistance Nepal urinary tract infections

Introduction

Antimicrobial resistance (AMR) is defined as the ability of microorganisms—such as bacteria, viruses, fungi, and parasites—to adapt and survive in the presence of medications that were once effective against them.¹ Over the past decade, there has been a significant rise in both the percentage and total number of bacterial pathogens exhibiting resistance to multiple antimicrobial medications worldwide.² AMR caused approximately 4.71 million deaths globally in 2021, with a projection of 8.22 million annual deaths by 2050.³ AMR in uropathogens, particularly in urinary tract infections (UTIs), is becoming a critical global health issue. Globally, in 2019, UTIs were reported to be linked with approximately 64,890 deaths directly attributed to AMR.⁴ According to a 2019 report, Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) were responsible for over 50% of AMR-related deaths in UTIs globally, with South Asia, including Nepal, reporting the highest death counts.⁴ Resistance was notably high to fluoroquinolones, carbapenems, and third-generation cephalosporins.⁴ Studies have shown that the overuse of broad-spectrum antibiotics during the COVID-19 pandemic has exacerbated AMR, leading to notably higher resistance of uropathogens to fluoroquinolones.⁵

In Nepal antimicrobial resistance is a growing issue, driven by the greater prevalence of infectious disease, widespread irrational antimicrobial use in animal and agricultural products, poor healthcare infrastructure, and lack of proper infection control.^6–8 Studies revealed high resistance levels to both first and second-line antibiotics among bacterial pathogens in Nepal.^6,9,10 This situation is even worse in the case of uropathogens, where the Penicillin group (ampicillin and piperacillin) showed low antimicrobial activity (sensitive rate only < 20%) against both gram-positive and gram-negative bacteria, and other groups of antibiotics also showed high resistance rate.^10,11 A 2021 study on uropathogens in Nepal revealed that 84.3% exhibited resistance to at least one antibiotic, with 53.6% classified as multidrug-resistant (MDR).¹²

In this brief report, we presented the current pattern of AMR in uropathogens from tertiary care hospitals in central Nepal and compared them with recent studies to inform effective practices aligned with the resistance trend. In addition, this report attempted to contribute to a broader discussion and understanding of the ongoing trend of antimicrobial resistance patterns in developing countries.

Method

We retrospectively reviewed medical record data of both inpatient and outpatient departments of Manmohan Memorial Teaching Hospital (MMTH) in Kathmandu, Nepal, from August 2023 to February 2024. MMTH is a 300-bed tertiary care hospital providing various services in multiple specialties based in the capital city of central Nepal.¹³

Initially, all data obtained from the medical record department of the hospital were screened, and those with provisional and final diagnoses of UTIs were segregated. A total of 2306 patients were diagnosed with UTIs. Out of all those patients whose urine samples were sent for culture and sensitivity analysis based on the clinical decision, only 167 showed significant bacterial growth and were tested for antibiotic sensitivity analysis. In all those samples, single microorganisms were found to be isolated. Culture and sensitivity tests were conducted in the hospital pathology laboratory as per the hospital’s standard operating procedures and guidelines to meet the highest quality standards. So, this study included patients who underwent urine culture and sensitivity testing related to UTIs. Patients with cultures that did not yield bacterial isolation were excluded.

Descriptive statistics were employed to summarize AMR patterns and patients’ sociodemographic variables. Statistical Package for Social Science (SPSS) version 26 was used for data analysis. Resistant percentages of isolated microorganisms with antimicrobials were presented in a table.

The reporting of this study conforms to the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement (Supplemental Material).¹⁴

Result

Out of 2306 patients, only 167 patients’ samples exhibited significant microbial growth. Most 31–60-year-old females had UTIs (Table 1).

Table 1.

Sociodemographic and clinical characteristics (N = 167).

Characteristics	Category	Frequency	%
Gender	Male	51	30.5
	Female	116	69.5
Age group	1–30	62	37.12
	31–60	72	43.11
	61–90	33	19.76
Bacteria type	Gram negative	147	88.02
	Gram positive	20	11.98

Among 167 urine specimens, 12 different uropathogens were identified, where E. coli was the dominant one (64.7%) (Table 2).

Table 2.

Antimicrobial resistance pattern at Manmohan Memorial Teaching Hospital, central Nepal.

Bacteria type		Gram negative								Gram positive
Isolated bacteria	Notation	Escherichia coli	Klebsiella pneumoniae	Citrobacter koseri	Citrobacter freundii	Proteus mirabilis	Klebsiella oxytoca	Pseudomonas aeruginosa	Providencia stuartii	Staphylococcus aureus	Staphylococcus epidermidis	Enterococcus spp.	Staphylococcus saprophyticus
Ceftriaxone	R/T (R%)	48/104 (46.15)	10/24 (41.67)	3/4 (75.00)	1/4 (25.00)	0/1 (0.00)	0/1 (0.00)	NT	NT	4/6 (66.67)	1/4 (25.00)	NT	1/1 (100.00)
Cefixime	R/T (R%)	64/104 (61.54)	10/25 (40.00)	3/4 (75.00)	2/4 (50.00)	0/1 (0.00)	1/1 (100.00)	NT	NT	1/3 (33.33)	2/3 (66.67)	NT	1/1 (100.00)
Amoxicillin	R/T (R%)	95/99 (95.96)	22/23 (95.65)	4/4 (100.00)	3/3 (100.00)	0/1 (0.00)	1/1 (100.00)	NT	NT	3/3 (100.00)	1/1 (100.00)	NT	NT
Ampicillin	R/T (R%)	6/7 (85.71)	1/1 (100.00)	NT	1/1 (100.00)	NT	NT	NT	NT	5/7 (71.43)	1/3 (33.33)	2/3 (66.67)	0/2 (0.00)
Ciprofloxacin	R/T (R%)	33/101 (32.67)	6/18 (33.33)	4/5 (80.00)	1/4 (25.00)	0/2 (0.00)	0/1 (0.00)	0/1 (0.00)	0/1 (0.00)	5/8 (62.50)	2/4 (50.00)	2/3 (66.67)	0/2 (0.00)
Levofloxacin	R/T (R%)	5/6 (83.33)	3/3 (100.00)	1/0 (100.00)	NT	NT	NT	NT	NT	NT	NT	NT	NT
Ofloxacin	R/T (R%)	4 (57.14)	4 (57.14)	NT	NT	NT	NT	NT	NT	NT	NT	NT	NT
Gentamicin	R/T (R%)	8/108 (7.41)	3/25 (12.00)	1/5 (20.00)	0/4 (0.00)	0/2 (0.00)	0/1 (0.00)	0/1 (0.00)	NT	4/10 (40.00)	2/3 (66.67)	0/1 (0.00	0/2 (0.00)
Amikacin	R/T (R%)	5/10 (50.00)	2/3 (66.67)	1/1 (100.00)	NT	NT	NT	NT	NT	0/3 (0.00)	0/1 (0.00)	NT	NT
Nitrofurantoin	R/T (R%)	13/107 (12.15)	16/25 (64.00)	1/5 (20.00)	1/4 (25.00)	1/2 (50.00)	0/1 (0.00)	NT	NT	3/10 (30.00)	0/4 (0.00)	0/3 (0.00)	0/2 (0.00)
Imipenem	R/T (R%)	2/9 (22.22)	3/3 (100.00)	1/2 (50.00)	NT	NT	NT	NT	NT	1/1 (100.00)	0/1 (0.00)	NT	NT
Meropenem	R/T (R%)	1/9 (11.11)	2/3 (66.67)	0/1 (0.00)	NT	NT	NT	NT	NT	NT	NT	1/2 (50.00)	NT
Total (%)	F (%)	108 (64.7%)	25 (15.0%)	5 (3.0%)	4 (2.4%)	2 (1.2%)	1 (0.6%)	1 (0.6%)	1 (0.6%)	10 (6.0%)	4 (2.4%)	4 (2.4%)	2 (1.2%)

F, frequency; NT, not tested; R, resistant; R%, resistance percentage; T, total.

Antimicrobial resistance pattern of central Nepal

Among the Gram-negative isolates, E. coli and K. pneumoniae were the most frequently encountered pathogens, accounting for 64.7% and 15.0% of total isolates, respectively. Notably, E. coli exhibited the highest resistance to amoxicillin (95.96%) and ampicillin (85.71%), whereas the lowest resistance was observed with gentamicin (7.41%) and nitrofurantoin (12.15%). Similarly, K. pneumoniae showed the highest resistance to amoxicillin (95.65%) and nitrofurantoin (64.00%), with relatively low resistance to gentamicin (12.00%). Resistance to third-generation cephalosporins such as cefixime and ceftriaxone remained moderately high in both species. Citrobacter koseri (C. koseri) and Citrobacter freundii (C. freundii) also demonstrated complete resistance to amoxicillin and ampicillin. Among non-fermenters, Pseudomonas aeruginosa (P. aeruginosa) was isolated in a small proportion and showed no resistance to ciprofloxacin or aminoglycosides, though data were limited. Among Gram-positive organisms, Staphylococcus aureus (S. aureus) (6%) and Enterococcus spp. (2.4%) were frequently isolated. S. aureus exhibited complete resistance to amoxicillin and high resistance to ciprofloxacin (62.5%) while showing full susceptibility to amikacin. Conversely, Enterococcus spp. demonstrated no resistance to nitrofurantoin and gentamicin but showed moderate resistance to ampicillin (66.67%) (Table 2).

Discussion

Consistent with global and regional trends, E. coli was the most prevalent uropathogen, accounting for 64.7% of isolates in Nepal, followed by K. pneumoniae (15.0%) and S. aureus (6.0%).^10,15,16 Similarly, the distribution of gender and age in UTIs observed in this study corresponds with international patterns, highlighting that females (69.5%) and those aged 31–60 years (43.11%) are the most impacted demographics.¹⁷ This demographic pattern can be linked to anatomical and hormonal factors and behavioral differences.

High resistance rates to beta-lactams, particularly amoxicillin, were observed in this study, with E. coli and K. pneumoniae showing resistance rates of 95.96% and 95.65%, respectively. A similar resistance rate was reported in a recent eastern Nepal study (82.5%)¹⁰ and previous studies from other regions of Nepal indicating 55.6%–79.7% resistance to amoxicillin.^12,16,18 Resistance to ampicillin was slightly lower in this study (85.71%) compared to eastern Nepal (92.5%).¹⁰ Similarly, K. pneumonia demonstrated a significant resistance rate to amoxicillin (95.65%), aligning with the observations made by past studies of Nepal, Baral et al. (100%),¹⁹ and Raya et al. (93.3%).²⁰ Extended-spectrum beta-lactamase was reported to be produced by 27.2%–38.9% of E. coli and 23.3% of K. pneumonia isolated in the past studies of Nepal.^20,21 Furthermore, we observed significant fluoroquinolone resistance. E. coli demonstrated resistance rates of 32.67% to ciprofloxacin, which is 63.9% in Eastern Nepal¹⁰ and 35.9% in a 2012 study from central Nepal.¹⁹ Conversely, resistance to levofloxacin was higher in this study (83.33%) compared to eastern Nepal (22.1%).¹⁰

The resistance patterns for aminoglycosides were relatively lower, with 7.41% gentamicin resistance to E. coli, which is lower than previous reports (16.4%), suggesting gentamicin can be a more effective option against uropathogens in the Nepalese population.²¹ Alternatively, the resistance to amikacin was notably elevated at 50.00%, which is higher than the previous study (3.9% in Raya et al. 2020),²⁰ potentially restricting its effectiveness as a last-resort antibiotic in certain situations. Similarly, a notable finding is the low resistance to nitrofurantoin among E. coli isolates (12.15%), maintaining one of the highest susceptibility rates among uropathogens. However, it is higher compared to previous studies (6.3% in Shrestha et al. 2019,²¹ 5.7% in Raya et al. 2020)²⁰ and a recent study of eastern Nepal (30.4%), demonstrating significant regional variations.¹⁰ The low resistance to nitrofurantoin in central Nepal makes it a viable empirical option and supports its inclusion in first-line treatment protocols for UTIs, but it is limited in the local context only due to the different resistance patterns in different regions. Nitrofurantoin has consistently demonstrated exceptional durability against resistance,²² with previous studies confirming its low resistance rates in pediatric patients, including those with E. coli-induced UTIs.²³ Notably, this study highlighted its superior efficacy over ampicillin and co-trimoxazole in pediatric UTIs, reinforcing its role in empirical therapy for lower UTIs.²³ Given its affordability, accessibility, and effectiveness, nitrofurantoin remains a valuable treatment option, particularly in resource-limited settings. While its use may be limited in upper UTIs due to low renal parenchymal concentration,²³ incorporating global data—such as its low resistance in uropathogens findings from Europe²⁴ and the USA²⁵—would further contextualize its significance in combating antimicrobial resistance.

A significant distinction between our findings and earlier studies is evident in the resistance rates observed for carbapenems. E. coli exhibited a relatively low resistance to imipenem (22.22%) and meropenem (11.11%). In a 2019 study by Shrestha et al. in Kathmandu, Nepal, 8.8% of E. coli isolates were resistant to meropenem.²¹ Conversely, a recent 2023 study by Sah et al. noted that carbapenems were highly effective against multidrug-resistant (MDR) and extensively drug-resistant (XDR) uropathogens, with nearly no resistance detected.¹⁰ The study also documented high resistance rates in less common pathogens, such as C. koseri, with 75% resistance to ceftriaxone and cefixime. These findings parallel the eastern Nepal study, which noted rising resistance among nondominant uropathogens such as P. mirabilis.¹⁰ These results align with existing literature that has reported a rising occurrence of MDR and XDR uropathogens in Nepal.^10,26

The comparison between central and eastern Nepal reveals both similarities and distinctions in AMR patterns. The difference in the resistance pattern might be the influence of antimicrobial usage patterns, healthcare practices, or variations in infection. However, it indicates the possibility of overuse or reduced regulation of antimicrobial utilization. The distinct resistant pattern at different regions directs the need for contextual or region-specific antimicrobial utilization guidelines. Specifically, both regions exhibit high resistance to beta-lactams and fluoroquinolones, underscoring the growing difficulties in managing UTIs. Similar to global trends,²⁷ the prevalent resistance pattern underscores the urgent need for enhanced antimicrobial stewardship initiatives in Nepal. Enhancing surveillance systems and executing national-level interventions is essential in reducing the effects of AMR on public health in Nepal.

Limitations and future research

The limitations of this study stem from its retrospective design and the focus on a single site, which may not adequately reflect the wider trends of AMR in Nepal. However, this study provided collective evidence on the current pattern of antimicrobial resistance, compiling recent study data. Furthermore, the representative data of Kathmandu, central Nepal, encompasses a diverse and wide range of patient groups. Second, the percentage value of resistance needs careful interpretation with viewing the number values; otherwise, it might be interpreted inappropriately because of the lower number of cultures and sensitivity tests of some pathogens. Future studies should focus on incorporating larger and multicentre datasets, including AMR patterns across different age groups and severities of UTIs, antimicrobial prescribing practices, their quality, and patient compliance, to explore the underlying factors influencing AMR.

Conclusion

This study revealed that E. coli and K. pneumoniae are the predominant uropathogens, exhibiting broad resistance, particularly to commonly used antibiotics such as penicillins and cephalosporins. While low resistance to nitrofurantoin and carbapenems presents viable treatment options, their prudent use is essential. Addressing antimicrobial resistance in Nepal requires proactive surveillance, strong stewardship programs, and evidence-based policies guided by current research.

Supplemental Material

sj-docx-1-tai-10.1177_20499361251339383 – Supplemental material for Antibiotic resistance patterns in uropathogens: insights from a Nepalese tertiary care setting

Supplemental material, sj-docx-1-tai-10.1177_20499361251339383 for Antibiotic resistance patterns in uropathogens: insights from a Nepalese tertiary care setting by Rahi Bikram Thapa, Sabin Shrestha, Pharsuram Adhikari and Rajeev Shrestha in Therapeutic Advances in Infectious Disease

Footnotes

Acknowledgements

The authors would like to acknowledge the team of the Department of Pharmacy, Manmohan Memorial Institute of Health Sciences, and Manmohan Memorial Teaching Hospital for providing invaluable support for conducting this study.

Declarations

ORCID iDs

Rahi Bikram Thapa

Sabin Shrestha

Pharsuram Adhikari

Rajeev Shrestha

Supplemental material

Supplemental material for this article is available online.

References

Dadgostar

Antimicrobial resistance: implications and costs. Infect Drug Resist 2019; 12: 3903–3910.

Roca

Akova

Baquero

, et al. The global threat of antimicrobial resistance: science for intervention. New Microbes New Infect 2015; 6: 22–29.

Naghavi

Vollset

Ikuta

, et al. Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050. Lancet 2024; 404: 1199–1226.

Fan

, et al. Global and regional burden of bacterial antimicrobial resistance in urinary tract infections in 2019. J Clin Med 2022; 11: 2817.

Gavi

Fiori

Gandi

, et al. Prevalence and antimicrobial resistance patterns of hospital acquired infections through the COVID-19 pandemic: real-word data from a Tertiary Urological Centre. J Clin Med 2023; 12: 7278.

Acharya

Wilson

RT.

Antimicrobial resistance in Nepal. Front Med 2019; 6: 105.

Thapa

Dahal

Karki

, et al. Exploration of drug therapy related problems in a general medicine ward of a tertiary care hospital of Eastern Nepal. Exploratory Res Clin Social Pharmacy 2024; 16: 100528.

Sapkota

Sah

Thapa

, et al. Morbidity and drug prescribing pattern in pediatric outpatient Department of Kankai Nagar Hospital of Eastern Nepal. Sage Open Pediatrics 2025; 12.

Ghimire

Banjara

Marasini

, et al. Antibiotics prescription, dispensing practices and antibiotic resistance pattern in common pathogens in Nepal: a narrative review. Microbiology Insights 2023; 16.

10.

Sah

Dahal

Mallik

, et al. Uropathogens and their antimicrobial-resistant pattern among suspected urinary tract infections patients in eastern Nepal: a hospital inpatients-based study. SAGE Open Med 2023; 11.

11.

Dahal

Shrestha

Karki

, et al. Antimicrobial resistance and biofilm production in uropathogens from renal disease patients admitted to Tribhuvan University Teaching Hospital, Nepal. J Clin Pharm Therapeutics 2023; 2023: 4867817.

12.

Shakya

Edwards

Gupte

, et al. High multidrug resistance in urinary tract infections in a tertiary hospital, Kathmandu, Nepal. Public health action 2021; 11: 24–31.

13.

Manmohan Memorial Medical College and Teaching Hospital, https://mmth.edu.np/ (2024).

14.

Von Elm

Altman

Egger

, et al. The strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies. Lancet 2007; 370: 1453–1457.

15.

Ganesh

Shrestha

Bhattachan

, et al. Epidemiology of urinary tract infection and antimicrobial resistance in a pediatric hospital in Nepal. BMC Infect Dis 2019; 19: 420.

16.

Parajuli

Bharati

Bhandari

, et al. Antibiotic resistance pattern of bacteria isolated from clinical specimens: a hospital-based cross-sectional study in Kathmandu, Nepal. Nepal Medical College J 2024; 26: 132–137.

17.

Yang

Chen

Zheng

, et al. Disease burden and long-term trends of urinary tract infections: a worldwide report. Front Public Health 2022; 10: 888205.

18.

Pandit

Awal

Shrestha

, et al. Extended-spectrum β-lactamase (ESBL) genotypes among multidrug-resistant uropathogenic Escherichia coli clinical isolates from a Teaching Hospital of Nepal. Interdiscip Perspect Infect Dis 2020; 2020: 6525826.

19.

Baral

Neupane

Marasini

, et al. High prevalence of multidrug resistance in bacterial uropathogens from Kathmandu, Nepal. BMC Res Notes 2012; 5: 38.

20.

Raya

Dhoubhadel

Shrestha

, et al. Multidrug-resistant and extended-spectrum beta-lactamase-producing uropathogens in children in Bhaktapur, Nepal. Trop Med Health 2020; 48: 65.

21.

Shrestha

Khanal

Poudel

, et al. Extended spectrum β-lactamase producing uropathogenic Escherichia coli and the correlation of biofilm with antibiotics resistance in Nepal. Ann Clin Microbiol Antimicrob 2019; 18: 42.

22.

Kettlewell

Jones

Felton

, et al. Insights into durability against resistance from the antibiotic nitrofurantoin. npj Antimicrob Resist 2024; 2: 41.

23.

Yüksel

Öztürk

Kavaz

, et al. Antibiotic resistance of urinary tract pathogens and evaluation of empirical treatment in Turkish children with urinary tract infections. Int J Antimicrob Agents 2006; 28: 413–416.

24.

Hrbacek

Cermak

Zachoval

Current antibiotic resistance trends of uropathogens in central europe: survey from a tertiary hospital urology department 2011–2019. Antibiotics 2020; 9: 630.

25.

Sanchez

Baird

AMG

Karlowsky

, et al. Nitrofurantoin retains antimicrobial activity against multidrug-resistant urinary Escherichia coli from US outpatients. J Antimicrob Chemother 2014; 69: 3259–3262.

26.

Pradhan

Rajbhandari

Nagaraja

, et al. Prevalence of methicillin-resistant staphylococcus aureus in a tertiary hospital in Nepal. Public Health Action 2021; 11: 46–51.

27.

Guerriero

Matteini

Gross

, et al. Complicated urinary tract infections: an update of new and developing antibiotics. Expert Opin Pharmacother 2025; 26: 167–177.

Supplementary Material

Please find the following supplemental material available below.

For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.

For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.

0.00 MB

0.03 MB