Investigation of the blaNDM-1 and armA Genes in Carbapenem-Resistant Klebsiella pneumoniae Isolated from the Clinical Samples in Kathmandu, Nepal

Rohit Ghimire,¹ Subash Kumar Thakur,² Upendra Thapa Shrestha,¹* Komal Raj Rijal,¹ Prakash Ghimire,¹ and Megha Raj Banjara¹*

¹Central Department of Microbiology, Tribhuvan University, Kirtipur, Kathmandu, Nepal; 

²Paropakar Maternity and Women’s Hospital, Thapathali, Kathmandu, Nepal

Abstract

Klebsiella pneumoniae carbapenemase (KPC) and metallo-β-lactamase production are major causes of carbapenem resistance, whereas aminoglycoside resistance is caused by extrinsically acquired 16S-rRNA methyltransferase. K. pneumoniae coharboring resistance genes are serious health care issues that can cause multidrug resistance (MDR). This study aimed to describe the resistance genes (New Delhi metallo-beta-lactamase 1 [blaNDM-1] and armA) in the plasmids of K. pneumoniae from patients visiting the Paropakar Maternity and Women’s Hospital, Kathmandu, Nepal. Altogether, 8,017 clinical specimens were processed following standard microbiological procedures to identify K. pneumoniae. Antibiotic susceptibility testing and detection of phenotypic carbapenemase production in K. pneumoniae isolates were performed using the modified Kirby-Bauer disc diffusion method. The resistance genes were detected by conventional polymerase chain reaction. Of 8,017 clinical specimens, 6.8% (n = 545) had bacterial growth, and 70 were K. pneumoniae. Colistin (100%, n = 70) and imipenem (80%, n = 56) were the most effective antibiotics. Thirty percent (n = 21) of the isolates were MDR, whereas 66.7% (n = 14) were carbapenemase producers, among which 38.1% (n = 8) had a minimum inhibitory concentration of 64 mg/mL to imipenem. Among carbapenemase producers, 23.8% (n = 5) were KPC and 66.7% (n 5 14) were metallo-β-lactamase producers. Out of 21 MDR K. pneumoniae, 19.5% (n = 4) harbored the blaNDM-1 and armA genes, and 14.3% (n = 2) had both genes. Detection of the coexistence of the resistance genes from K. pneumoniae reveals that there might be increased antibiotic resistance, leading to multidrug resistance and an increased resistance to imipenem. In conclusion, advancing antimicrobial-resistance surveillance in maternity wards and minimizing the use of last-line antibiotics are crucial for safeguarding maternal and neonatal health.

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Evaluation of Antibiotic Resistance Patterns and Biofilm Formation among the Clinical Isolates of Pseudomonas aeruginosa

 Asuma Gurung^{1 ߙ}, Samjhana Gurung^{1 ߙ}, Umesh Kaji Manandhar¹, Raina Chaudhary², Anand Kumar Mandal³ Avinash Chaudhary¹, Dinesh Dhakal¹, Anup Muni Bajracharya⁴, Upendra Thapa Shrestha⁵ *

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

² Shree Birendra Hospital Chhauni, Kathmandu, Nepal

³ Department of Pathology, Bhaktapur Hospital, Bhaktapur, Nepal

⁴ Balkumari College, Chitwan, Nepal

⁵ Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal

 

† These authors contributed equally.

 

*Corresponding author: Upendra Thapa Shrestha, Assistant Professor, Central Department of Microbiology, Tribhuvan University, Kathmandu, Nepal, E-mail: upendra.thapashrestha@cdmi.tu.edu.np

ABSTRACT

Objectives: To evaluate the antibiotic resistance pattern of Pseudomonas aeruginosa isolated from clinical specimen and to detect Metallo beta lactamase producers as well as to accesses their biofilm forming capacity by both qualitative and quantitative analysis.  

Methods: The study was conducted in Shree Birendra Hospital, Chhauni, from June to August 2025. The total of 6444 specimens was cultured and isolates of P. aeruginosa were subjected to antibiotic susceptibility tests. Metallo beta lactamase producers were identified by modified Hodge and EDTA synergy tests. Biofilm was detected by the Congo Red Agar and Microtiter Plate Assay method.

Results: Out of 671 positive isolates (15.05%) from pus, urine and wound, 101 isolates of P. aeruginosa were obtained. The highest rate of distribution was observed in in-patients as well as in the age group of 61-70 years. Among the isolates, high resistance was observed against Aztreonam (65.59%) whereas isolates were most sensitive against Tobramycin (76%). 37 were found to produce Metallo beta lactamase enzyme and almost 46% were MDR. The biofilm isolates accounted for 34 by CRA but MPA detected 100 biofilm producers. The biofilm producers showed high resistance against Aztreonam (59.41%) and Levofloxacin (56.44%). Furthermore, the MBLS were the most resistant against Levofloxacin (28.7%) followed by Aztreonam (27.7%), Cefepime (27.7%), Ceftazidime (25.7%), Imipenem (25.7%) and Meropenem (25.7%). Out of all the isolates, 36 biofilm isolates were highlighted to produce MBL enzyme as well.

 Conclusion: Pseudomonas aeruginosa was most frequent in sputum and pus samples from inpatients and older patients, with rising resistance to monobactams, fourth-generation cephalosporins, and fluoroquinolones. High rates of MBL production and biofilm formation contributed to marked β-lactam resistance, emphasizing the need for alternative therapeutic strategies.

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Keywords: Pseudomonas aeruginosa, Metallo beta lactamase, Microtitre plate, Biofilm

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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