Antibiotic resistance and β-lactam resistant genes among bacterial isolates from clinical, river water and poultry samples from Kathmandu, Nepal

  

 JAC Antimicrob Resist https://doi.org/10.1093/jacamr/dlaf186 JAC-Antimicrobial Resistance

 

Antibiotic resistance and β-lactam resistant genes among bacterial isolates from clinical, river water and poultry samples from Kathmandu, Nepal

 

Upendra Thapa Shrestha¹, Manash Shrestha², Nabaraj Shrestha³, Komal Raj Rijal¹ and Megha Raj Banjara^1*

 

¹Central Department of Microbiology, Institute of Science and Technology, Tribhuvan University, Kirtipur, Kathmandu, Nepal;

²Asia Pacific Malaria Elimination Network (APMEN), Singapore;

³Central Veterinary Laboratory (CVL), Tripureshwor, Kathmandu, Nepal

 

*Corresponding author. E-mail: megha.banjara@cdmi.tu.edu.np

 

Received 17 August 2025; accepted 25 September 2025

 

Objective: To assess the antibiotic resistance and beta-lactam resistance genes among bacterial isolates from clinical, river water and poultry samples.

Methods: Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa were isolated from clinical, poultry and river water samples collected during 2020–22. They were subjected to antimicrobial susceptibility tests following the CLSI guidelines. The bacteria were screened for β-lactam resistance genes blaTEM, mcr-1, mecA and blaNDM-1.

Results: Among 2835 clinical samples, E. coli was the most frequently isolated bacterium (10.3%, 292), followed by S. aureus (6.0%, 169) and P. aeruginosa (4.0%, 143). Of the E. coli isolates, 64.4% exhibited multidrug resistance (MDR) and 43.8% were extended-spectrum β-lactamase (ESBL) producers, with 44.5% and 16.4% harbouring the blaTEM and mcr-1 genes, respectively. Among S. aureus isolates, 80.9% of methicillin-resistant strains (MRSA) carried the mecA gene, while 30.1% of metallo-β-lactamase (MBL)-producing P. aeruginosa were positive for the blaNDM-1 gene. In poultry samples, 30.4% of E. coli isolates harboured the blaTEM gene among 128 ESBL producers, and the prevalence of colistin-resistant isolates carrying mcr-1 was higher than in clinical samples. In contrast, the occurrence of ESBL-producing E. coli and MRSA, along with their associated resistance genes, was lower in water samples.

Conclusions: This study demonstrated widespread multidrug resistance (MDR) and ESBL production among clinical, poultry and river water bacterial isolates in the Kathmandu valley. Colistin-resistant E. coli carrying the mcr-1 gene, methicillin-resistant S. aureus (MRSA) with mecA and metallo-β-lactamase (MBL)-producing P. aeruginosa harboring blaNDM-1 were detected across sources. These findings emphasize an urgent One Health approach to curb the growing threat of antimicrobial resistance in the region.

Citation: Thapa Shrestha U, Shrestha M, Shrestha N, Rijal KR, Banjara MR. Antibiotic resistance and β-lactam resistant genes among bacterial isolates from clinical, river water and poultry samples from Kathmandu, Nepal. JAC Antimicrob Resist. 2025 Oct 17;7(5):dlaf186. doi: 10.1093/jacamr/dlaf186. PMID: 41113068; PMCID: PMC12531798.

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Antibiogram Profile of Respiratory Pathogens and Identifying Predisposing Factors of Respiratory Tract Infections among Patients Visiting Bhaktapur Hospital

Antibiogram Profile of Respiratory Pathogens and Identifying Predisposing Factors of Respiratory Tract Infections among Patients Visiting Bhaktapur Hospital

Shreemila Bajracharya1†, Jharana Thapa1†, Pushpa Thapa Magar1†, Ananda Kumar Mandal2, Niraj Manandhar2, Avinash Chaudhary1, Dinesh Dhakal1, Upendra Thapa Shrestha3*

 

¹Department of Microbiology, Sainik Awasiya Mahavidhyalaya, Bhaktpur, Nepal

²Bhaktapur Hospital, Bhaktapur, Nepal

³Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal

 

†These authors contributed equally.

 

*Corresponding author: Upendra Thapa Shrestha, Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal, E-mail: upendrats@gmail.com

 

ABSTRACT

 

Objectives: To address the current problem of MDR infections and respiratory bacterial pathogens and identify the risk factors associated with respiratory tract infections (RTIs).

Methods: A total of 327 RTI specimens were cultured using a conventional microbiological method to identify potential bacterial pathogens. The isolates were then subjected to antibiotic susceptibility testing using modified Kirby Bauer’s disc diffusion method. In addition, the risk factors associated with RTIs were obtained by direct interviews with patients using a structured questionnaire.

Results: The overall prevalence of RTIs among the study population was found to be 11.9%. The highest rate of infections was observed among patients of age group 61-70 years in both sexes and from ICU wards. Among the bacterial pathogens, Acinetobacter baumannii was isolated in the highest number followed by Pseudomonas aeruginosa. 64.2% A. baumannii isolates were resistant to Azithromycin but 100% sensitive to meropenem. P. aeruginosa resistance rate was 50% to Piperacillin-tazobactam, ciprofloxacin, Polymyxin B and Ceftriaxone, and had the highest MDR. Half of the Staphylococcus aureus isolates were MRSA. Risk factors such as previous infections, family history with RTIs, chronic use of antibiotics, and smoking were found to be significantly associated with RTIs.

Conclusion: We observed high MDR among the respiratory pathogens with growing resistance to β-lactam, macrolides, and Polymyxins whch necessitates alternative drugs in management. There is also need for targeted preventive strategies, prohibition of irrational use of antibiotics, and avoidance of exposure to risk factors such as smoking, outdoor air pollution, and chronic use of antibiotics.

 

Keywords: Respiratory tract infections, MDR, risk factors, Nepal

Citation: Bajracharya S, Thapa J, Thapa Magar P, Mandal AK, Manandhar N, Chaudhary A, Dhakal D, Thapa Shrestha U. Antibiogram profile of respiratory pathogens and identifying the predisposing factors of respiratory tract infections among the patients visiting Bhaktapur Hospital. TUJM, 2024; 11(1): 119-129.

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Biofilm formation capacity and Carbapenem-resistance in Acinetobacter-calcoaceticus-baumannii isolated from inpatients in a Tertiary Care Hospital in Nepal

Biofilm formation capacity and Carbapenem-resistance in Acinetobacter-calcoaceticus-baumannii isolated from inpatients in a Tertiary Care Hospital in Nepal

Shova Bhandari¹, Milan Kumar Upreti^1, Khadga Bikram Angbuhang¹, Basudha Shrestha², Upendra Thapa Shrestha^{3 *}

 ¹GoldenGate International College, Battisputali, Kathmandu Nepal

²Kathmandu Model Hospital, Kathmandu, Nepal

³Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal

 ^*Corresponding author: Upendra Thapa Shrestha, Assistant Professor, Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal, Email: upendrats@gmail.com / upendra.thapashrestha@cdmi.tu.edu.np

 ABSTRACT

Objective: Acinetobacter calcoaceticus-baumannii complex (ACBC), as an emerging global burden to various clinical infections, has a huge problem in empirical therapy due to the increasing resistance to the majority of antibiotics. The ability of biofilm formation added to its antimicrobial resistance and helped its persistence and survival in the environment. To associate biofilm formation with carbapenem resistance, a hospital-based cross-sectional study was carried out from February 2020 to August 2020 at Kathmandu Model Hospital, Kathmandu, Nepal. ACBC was identified from the clinical samples following standard Microbiological procedures. A modified Kirby-Bauer disk diffusion method was performed to assay the antibiotic susceptibility testing of ACBC isolates to various antibiotic classes. A quantitative adherence assay was used to determine the biofilm assay. A conventional Polymerase Chain Reaction (PCR) method was used to find the targeted biofilm-related genes, Bap, csuE, and bla_PER1 using specific primers.

 

Results: Out of 665 different clinical samples, bacterial growth was observed in 281 (42.3%) clinical samples. Of these, 32 (11.4%) isolates were identified as ACBC. Out of 32 ACBC isolates, 29 (90.6%) of which were carbapenem-resistant.  All carbapenem-resistant ACBC isolates were found to be sensitive to Polymixin B and Colistin. Out of 29 CR-ACBC, 17.2% of isolates were resistant to Tigecycline. The majority of ACBC isolates (93.8%) were multidrug-resistant (MDR) while 13 (40.6%) of isolates were extensively drug-resistant (XDR). A total of 31 ACBC isolates were biofilm producers, out of which 2 were strong biofilm producers followed by 8 moderate, and 21 were weak biofilm producers. The occurrence of biofilm-forming genes; Bap, csuE, and bla_PER1 genes were found to be 65.6%, 65.6%, and 56.3% respectively among ACBC clinical isolates. A significant association was observed between carbapenem resistance, biofilm formation, and biofilm-related genes.

Conclusion: The higher rate of MDR and XDR ACBC isolates associated with biofilm formation in the study alarms the ACBC-related infection in clinical settings among inpatients. The hospital environment and clinical equipment are potential sources of biofilm-forming isolates. Hence, the effective sterilization of clinical equipment and hospital environment are utmost and a strong policy should be made to prescribe the proper antibiotic based on antibiogram profile to fight against an emerging threat of ACBC infections.

Keywords: Acinetobacter baumannii, Biofilm, Carbapenem-resistant, Biofilm related genes; Bap, csuE, and bla_PER1

Citation: Bhandari, S., Upreti, M.K., Angbuhang, K.B. et al. Biofilm formation capacity and Carbapenem-resistance in Acinetobacter-calcoaceticus-baumannii isolated from inpatients in a tertiary care hospital in Nepal. BMC Res Notes 18, 225 (2025). 

DOI: https://doi.org/10.1186/s13104-025-07211-5

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