Occurrence and genetic characteristics of mcr-1-positive colistin-resistant E. coli from poultry environments in Bangladesh

ObjectivesColistin is one of the last-resort antibiotics for treatment of multi-drug resistant (MDR) Gram negative bacterial infections. We determined occurrence and characteristics of mcr-1-producing E. coli obtained from live bird markets (LBM), rural poultry farms (RPF) and rural household backyard poultry (HBP) in Bangladesh.MethodsWe tested 104 extended-spectrum β-lactamase (ESBL)-producing E. coli isolated during 2017-2018 from poultry sources for colistin resistance. We analyzed the resistant isolates for mcr gene and characterized mcr positive isolates for antibiotic susceptibility, antibiotic resistance genes, transmissible plasmids and clonal diversity.ResultsOf 104 isolates, 98 (94%) had MICcolistin ≥4 μg/mL and 14 (13.5%) were positive for mcr-1 of which 10 were from LBM (n = 10), 3 from RFP and 1 from HBP. All 14 mcr-1 E. coli were resistant to third generation cephalosporin and tetracycline, while 12 were resistant to fluoroquinolone and sulphamethoxazole, 10 were to aminoglycosides and 3 were to nitrofurantoin. Four isolates carried conjugative mcr-1 plasmid of 23 to 55 MDa in size. The 55 MDa plasmid found in 2 isolates carried additional resistant genes including blaCTX-M-group-1 and blaTEM-1 (ESBL), qnrB (fluoroquinolone) and rmtB (aminoglycoside). These plasmids belong to IncF family with additional replicons: HI1 and N. ERIC-PCR revealed a heterogeneous banding pattern of mcr-1 positive isolates.ConclusionWe report a 13.5% prevalence of mcr-1 positive MDR E. coli in poultry fecal samples predominantly from LBMs in Bangladesh accentuating the need for safe disposal of poultry feces and hygiene practices among people exposed to poultry.</div

Prevalence of 3GCr and carbapenem-resistant pathogens among patients with community-acquired UTI.

Prevalence of 3GCr and carbapenem-resistant pathogens among patients with community-acquired UTI.</p

Data file for Figs 1–3 and the frequency of polymicrobial infections.

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Antibiotic resistance profiles of four major pathogens causing community-acquired UTI from 2016 to 2018.

Only those antibiotics were included in the analysis for which the minimum number of isolates tested was 10.</p

Prevalence of major bacterial pathogens causing community-acquired UTI among patients from 2016 to 2018.

Prevalence of major bacterial pathogens causing community-acquired UTI among patients from 2016 to 2018.</p

High prevalence of plasmid-mediated quinolone resistance (PMQR) among E. coli from aquatic environments in Bangladesh

Fluro(quinolones) is an important class of antibiotic used widely in both human and veterinary medicine. Resistance to fluro(quinolones) can be acquired by either chromosomal point mutations or plasmid-mediated quinolone resistance (PMQR). There is a lack of studies on the prevalence of PMQR in organisms from environmental sources in Bangladesh. In this study, we investigated the occurrence of PMQR genes in E. coli from various water sources and analysed associations between multi-drug resistance (MDR) and resistance to extended spectrum β-lactam antibiotics. We analysed 300 E. coli isolates from wastewaters of urban live-bird markets (n = 74) and rural households (n = 80), rural ponds (n = 71) and river water samples (n = 75) during 2017–2018. We isolated E. coli by filtering 100 ml of water samples through a 0.2μm cellulose membrane and incubating on mTEC agar media followed by identification of isolated colonies using biochemical tests. We selected one isolate per sample for detection of PMQR genes by multiplex PCR and tested for antibiotic susceptibility by disc diffusion. Clonal relatedness of PMQR-positive isolates was evaluated by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR). About 66% (n = 199) of E. coli isolates harbored PMQR-genes, predominantly qnrS (82%, n = 164) followed by aac(6’)-lb-cr (9%, n = 17), oqxAB (7%, n = 13), qnrB (6%, n = 11) and qepA (4%, n = 8). Around 68% (n = 135) of PMQR-positive isolates were MDR and 92% (n = 183) were extended spectrum β-lactamase (ESBL)-producing of which the proportion of positive samples was 87% (n = 159) for blaCTX-M-1’ 34% (n = 62) for blaTEM, 9% (n = 16) for blaOXA-1, blaOXA-47 and blaCMY-2, and 2% (n = 4) for blaSHV. Further, 16% (n = 32) of PMQR-positive isolates were resistant to carbapenems of which 20 isolates carried blaNDM-1. Class 1 integron (int1) was found in 36% (n = 72) of PMQR-positive E. coli isolates. PMQR genes were significantly associated with ESBL phenotypes (p≤0.001). The presence of several PMQR genes were positively associated with ESBL and carbapenemase encoding genes such as qnrS with blaCTXM-1 (p<0.001), qnrB with blaTEM (p<0.001) and blaOXA-1 (p = 0.005), oqxAB and aac(6’)-lb-cr with blaSHV and blaOXA-1 (p<0.001), qnrB with blaNDM-1 (p<0.001), aac(6’)-lb-cr with blaOXA-47 (p<0.001) and blaNDM-1 (p = 0.002). Further, int1 was found to correlate with qnrB (p<0.001) and qepA (p = 0.011). ERIC-PCR profiles allowed identification of 84 of 199 isolates with 85% matching profiles which were further grouped into 33 clusters. Only 5 clusters had isolates (n = 11) with identical ERIC-PCR profiles suggesting that PMQR-positive E. coli isolates are genetically heterogeneous. Overall, PMQR-positive MDR E. coli were widely distributed in aquatic environments of Bangladesh indicating poor wastewater treatment and highlighting the risk of transmission to humans and animals

Characteristics of patients according to their age, sex and urine culture status.

Characteristics of patients according to their age, sex and urine culture status.</p

Prevalence of MDR community-acquired UTI among patients according to different age and sex groups.

Prevalence of MDR community-acquired UTI among patients according to different age and sex groups.</p

Distribution of the prevalence of major pathogens causing CA-UTI among patients by age and sex.

Distribution of the prevalence of major pathogens causing CA-UTI among patients by age and sex.</p

Spatiotemporal distribution of antimicrobial resistant organisms in different water environments in urban and rural settings of Bangladesh

The spatial distribution of clinically important antibiotic resistant bacteria (ARB) and associated genes is important to identify the environmental distribution of contamination and ‘hotspots’ of antimicrobial resistance (AMR). We conducted an integrated survey of AMR in drinking water, wastewater and surface water (rivers and ponds) in three settings in Bangladesh: rural households, rural poultry farms, and urban food markets. Spatial mapping was conducted via geographic information system (GIS) using ArcGIS software. Samples (n = 397) were analyzed for the presence of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec), carbapenem-resistant E. coli (CR-Ec) and resistance genes (blaCTX-M-1, blaNDM-1). In rural households, 5% of drinking water supply samples tested positive for ESBL-Ec, and a high proportion of wastewater, pond and river water samples were positive for ESBL-Ec (90%, 76%, and 85%, respectively). In poultry farms, 10% of drinking water samples tested positive for ESBL-Ec compared to a high prevalence in wastewater, pond and river water (90%, 68%, and 85%, respectively). CR-Ec prevalence in household wastewater and pond water was relatively low (8% and 5%, respectively) compared to river water (33%). In urban areas, 38% of drinking water samples and 98% of wastewater samples from food markets tested positive for ESBL-Ec while 30% of wastewater samples tested positive for CR-Ec. Wastewaters had the highest concentrations of ESBL-Ec, CR-Ec, blaCTXM-1 and blaNDM-1 and these were significantly higher in urban compared to rural samples (p < 0.05). ESBL-Ec is ubiquitous in drinking water, wastewater and surface water bodies in both rural and urban areas of Bangladesh. CR-Ec is less widespread but found at a high prevalence in wastewater discharged from urban food markets and in rural river samples. Surveillance and monitoring of antibiotic resistant organisms and genes in waterbodies is an important first step in addressing environmental dimensions of AMR