Plasmid mediated colistin resistant mcr-1 and co-existence of OXA-48 among Escherichia coli from clinical and poultry isolates: first report from Nepal

Abstract

Background Plasmid-mediated resistance to the last-resort drugs: carbapenems and colistin is an emerging public health threat. The studies on the prevalence and co-expression of resistant genes among livestock and human pathogens are rare in Nepal. This is the first study in Nepal exploring the prevalence and co-existence of colistin resistance gene, mcr-1 along with carbapenemase resistance gene, OXA-48 in Escherichia coli isolated from poultry and clinical specimens. Methods A total of 240 rectal swabs from chickens of five different poultry farms of Kathmandu valley and 705 mid-stream urine samples from human subjects attending Kantipur Hospital, Kathmandu were collected between August, 2018 and March, 2019. Rectal swabs and urine specimens were cultured. E. coli isolated from the specimens were screened for antimicrobial susceptibility testing (AST) using disk diffusion method’. Minimum inhibitory concentration (MIC) of colistin was determined by agar dilution method using 0.5 µg/ml to 32 µg/ml. The E. coli isolates were first screened for mcr-1 followed by screening for OXA-48 genes using conventional Polymerase chain reaction (PCR). Results Of the total samples analyzed, E. coli was isolated from 31.7% (76/240) of poultry and 7.9% (56/705) of clinical specimens. In AST, 80% (61/76) of E. coli from poultry and 79% (44/56) from clinical specimens were MDR. The phenotypic prevalence of colistin resistance in poultry specimens were 31.6% (24/76) and clinical specimens were 21.4% (12/56). In PCR assay, 27.6% (21/76) of poultry and 19.6% (11/56) of clinical isolates had colistin resistant mcr-1 gene. MICs value of E. coli isolates ranged from 4 to 32 (µg/ml) in both clinical and poultry isolates. Prevalence of co-existing carbapenem resistance gene, OXA-48, among colistin resistant mcr-1 positive isolates was 38% (8/21) in poultry specimens and 18.2% (2/11) in clinical specimens. Conclusions The high prevalence of colistin and carbapenem resistant genes, and their co-existence in plasmid DNA of E. coli isolates in this study suggests the possible spread to other animal, human and environmental pathogens. Molecular methods in addition to the conventional diagnostics in laboratories can help in early diagnosis, effective management and control of their potential transmission.

Extended-Spectrum β-Lactamase and Carbapenemase Producing Gram-Negative Bacilli Infections Among Patients in Intensive Care Units of Felegehiwot Referral Hospital: A Prospective Cross-Sectional Study

“…The burden of beta-lactamase producing bacterial infections among ICU patients is aggravated by the high percentage (81.5%) of multi-drug resistant strains. The prevailing prevalence of MDR is in accord with studies done in Uganda (58%), 6 India (72.5%), 26 Nepal (62.1% and 79%) 30 , 46 and Mexico (70.96%). 28 The high burden of MDR isolates in the present study could be associated with empirical and non-selective use of antibiotics, irrational dose regimens, and the transfer of MDR determining genes among the isolates.…”

“…28 Another study from Nepal reported 66.1% resistance to ceftazidime. 46 Strong resistance towards third generation cephalosporins occurs among P. aeruginosa, E. cloacae, K. pneumoniae and E. cloacae isolates in the present study as all P. aeruginosa and E. cloacae were resistant against sulfamethoxazole-trimethoprim, cefuroxime, cefotaxime, and ceftazidime. The findings are comparable with a study from Algeria where P. aeruginosa and E. cloacae isolates were 100% resistant to sulfamethoxazoletrimethoprim, cefuroxime, cefotaxime, and ceftazidime.…”

Detection of TEM and CTX-M Genes in Escherichia coli Isolated from Clinical Specimens at Tertiary Care Heart Hospital, Kathmandu, Nepal

“…An axenic culture of ESBL producer E. coli isolates were preserved in 20% glycerol containing tryptic soya broth and kept at −70 °C until further processing for molecular assay [ 28 , 29 ].…”

“…Ten µL of DNA was stained with ethidium bromide (5 µg/mL). Thus, amplified DNA bands were visualized by using a UV transilluminator [ 28 , 29 ]. The amplicon size for bla TEM was 459 bp [ 16 ] and bla CTX-M was 544 bp [ 31 ].…”

Use of antimicrobials and antimicrobial resistance in Nepal: a nationwide survey

“…Common to most LMICs, Nepal experiences an extremely huge burden of infectious diseases such as respiratory tract infections, enteric fever (typhoid, paratyphoid fever), urinary tract infections and other bacterial infections 9 . Researchers have reported high burden of drug resistant/multidrug resistant bacteria in Nepal 18 – 23 . Discrepancy between prescription and OTC use of antibiotic is found to contribute to the rise of AMR in Nepal 10 .…”