A high prevalence of multi-drug resistant Gram-negative bacilli in a Nepali tertiary care hospital and associated widespread distribution of Extended-Spectrum Beta-Lactamase (ESBL) and carbapenemase-encoding genes

• Main Authors: Sulochana Manandhar, Raphael M. Zellweger, Nhukesh Maharjan, Sabina Dongol, Krishna G. Prajapati, Guy Thwaites, Buddha Basnyat, Sameer Mani Dixit, Stephen Baker, Abhilasha Karkey
• Format: Article
• Language: English
• Published: BMC 2020-10-01
• Series: Annals of Clinical Microbiology and Antimicrobials
• Subjects: Multi-drug resistance; Antimicrobial resistance; Nepal; ESBL; Gram-negative bacilli; Carbapenemase
• Online Access: http://link.springer.com/article/10.1186/s12941-020-00390-y

Abstract Background Multi-drug resistance (MDR) and extensive-drug resistance (XDR) associated with extended-spectrum beta-lactamases (ESBLs) and carbapenemases in Gram-negative bacteria are global public health concerns. Data on circulating antimicrobial resistance (AMR) genes in Gram-negative bacteria and their correlation with MDR and ESBL phenotypes from Nepal is scarce. Methods A retrospective study was performed investigating the distribution of ESBL and carbapenemase genes and their potential association with ESBL and MDR phenotypes in E. coli, Klebsiella spp., Enterobacter spp. and Acinetobacter spp. isolated in a major tertiary hospital in Kathmandu, Nepal, between 2012 and 2018. Results During this period, the hospital isolated 719 E. coli, 532 Klebsiella spp., 520 Enterobacter spp. and 382 Acinetobacter spp.; 1955/2153 (90.1%) of isolates were MDR and half (1080/2153) were ESBL producers. Upon PCR amplification, bla TEM (1281/1771; 72%), bla CTXM-1 (930/1771; 53%) and bla CTXM-8 (419/1771; 24%) were the most prevalent ESBL genes in the enteric bacilli. Bla OXA and bla OXA-51 were the most common bla OXA family genes in the enteric bacilli (918/1771; 25%) and Acinetobacter spp. (218/382; 57%) respectively. Sixteen percent (342/2153) of all isolates and 20% (357/1771) of enteric bacilli harboured bla NDM-1 and bla KPC carbapenemase genes respectively. Of enteric bacilli, Enterobacter spp. was the most frequently positive for bla KPC gene (201/337; 60%). The presence of each bla CTX-M and bla OXA were significantly associated with non-susceptibility to third generation cephalosporins (OR 14.7, p < 0.001 and OR 2.3, p < 0.05, respectively).The presence of each bla TEM, bla CTXM and bla OXA family genes were significantly associated with ESBL positivity (OR 2.96, p < 0.001; OR 14.2, p < 0.001 and OR 1.3, p < 0.05 respectively) and being MDR (OR 1.96, p < 0.001; OR 5.9, p < 0.001 and OR 2.3, p < 0.001 respectively). Conclusions This study documents an alarming level of AMR with high prevalence of MDR ESBL- and carbapenemase-positive ESKAPE microorganisms in our clinical setting. These data suggest a scenario where the clinical management of infected patients is increasingly difficult and requires the use of last-resort antimicrobials, which in turn is likely to intensify the magnitude of global AMR crisis.