Nationwide Assessment of Water Quality in Rivers across Lebanon by Quantifying Fecal Indicators Densities and Profiling Antibiotic Resistance of Escherichia coli

The use of contaminated water has been associated with severe disease outbreaks. Due to widespread pollution with untreated sewage, concerns have been raised over water quality in Lebanon, a country with well-documented challenges in infrastructure. Here, we evaluated the water quality of major rivers in Lebanon by quantifying the densities of fecal indicator bacteria (fecal coliforms and Escherichia coli). Additionally, we assessed the dissemination of antibiotic-resistant E. coli in river water. Composite water samples (n = 132) were collected from fourteen rivers, and 378 E. coli were isolated and analyzed. Fecal coliforms and E. coli were detected in 96.29% and 95.5% of the samples, respectively. Additionally, 73.48–61.3% and 31.81% of the samples exceeded the microbiological acceptability standards for irrigation and the fecal coliform limit for recreational activities, respectively. The E. coli exhibited resistance to ampicillin (40% of isolates), amoxicillin + clavulanic acid (42%), cefepime (4%), cefotaxime (14%), cefalexin (46%), cefixime (17%), doripenem (0.3%), imipenem (0.5%), gentamicin (6%), kanamycin (9%), streptomycin (35%), tetracycline (35%), ciprofloxacin (10%), norfloxacin (7%), trimethoprim-sulfamethoxazole (32%), and chloramphenicol (13%). Notably, 45.8% of the isolates were classified as multidrug resistant (MDR). Our results highlight the need to urgently address fecal pollution and the dissemination of antibiotic resistance in Lebanese rivers

First report of the mobile colistin resistance gene, mcr-1.26, in multidrug-resistant Escherichia coli isolated from retail chicken meat

ABSTRACT: Objectives: We isolated a highly colistin-resistant Escherichia coli, strain 58, from fresh chicken wings in Lebanon. Here, we performed in-depth phenotypic and genomic analyses to identify the resistome of the isolate, focusing on the determinants that encoded colistin resistance. Methods: The minimum inhibitory concentration (MIC) of colistin and resistance to other antibiotics were determined using the broth microdilution method and the Kirby-Bauer disk diffusion assay, respectively. Whole-genome sequencing (WGS) and different software available at the Center of Genomic Epidemiology were used to predict the resistome, the sequence type (ST), and the presence of virulence genes and plasmid replicon types. Results: Susceptibility testing revealed that E. coli 58 exhibited multidrug resistance, including against colistin (MIC = 32 µg/mL). Whole-genome sequencing analyses showed that E. coli 58 carried 26 antimicrobial resistance genes associated with resistance to polymyxins (mcr-1.26), β-lactams (blaTEM-1b and blaCMY-2), fosfomycin (fosA4), aminoglycosides (aac(3)-IId, aadA2b, aadA5, partial aadA1, aph(3′')-Ia, aph(3′)-Ia, and aph(6)-Id), tetracyclines (tetA and tetM), quinolones (qnrS1), sulphonamides (sul2 and sul3), trimethoprim (dfrA14, dfrA17, and dfrA5), phenicols (floR and cmlA1), macrolides (mphA), lincosamides (lnu(F)), quaternary ammonium compounds (partial qacL and qacE), and peroxides (sitABCD). mcr-1.26 was located on an IncX4 plasmid and induced colistin resistance in otherwise naïve E. coli and Salmonella Enteritidis. Escherichia coli 58 was predicted to be a human pathogen and belonged to ST3107. Conclusion: To our knowledge, this is the first report of mcr-1.26 in poultry meat worldwide. We previously reported mcr-1.26 in an MDR E. coli (ST2207) isolated from a pigeon in Lebanon, which suggests that it might be spreading in different animal hosts and genetic backgrounds

Annotated Assembled Genomes - Georgia, USA

The draft genomes of antibiotic-resistant bacteria isolated from imported fresh produce in Georgia, USA.</p

Multidrug-resistant pathogens contaminate river water used in irrigation in disenfranchised communities

ABSTRACT: Objectives: The contamination of fresh surface waters poses a significant burden on human health and prosperity, especially in marginalized communities with limited resources and inadequate infrastructure. Here, we performed in-depth genomic analyses of multidrug-resistant bacteria (MDR-B) isolated from Al-Oueik river water that is used for irrigation of agricultural fields in a disenfranchised area that also hosts a makeshift Syrian refugee camp. Methods: A composite freshwater sample was filtered. Faecal coliforms were counted and extended spectrum cephalosporins and/or ertapenem resistant bacteria were screened. Isolates were identified using MALDI-TOF-MS and analysed using whole-genome sequencing (WGS) to identify the resistome, sequence types, plasmid types, and virulence genes. Results: Approximately 106 CFU/100 mL of faecal coliforms were detected in the water. Four drug-resistant Gram-negative bacteria were identified, namely Escherichia coli, Klebsiella pneumoniae, Enterobacter hormaechei, and Pseudomonas otitidis. Notably, the E. coli isolate harboured blaNDM-5 and a YRIN-inserted PBP3, representing an emerging public health challenge. The K. pneumoniae isolate carried blaSHV-187 as well as mutations in the gene encoding the OmpK37 porin. Enterobacter hormaechei and P. otitidis harboured blaACT-16 and blaPOM-1, respectively. Conclusion: This report provides comprehensive genomic analyses of MDR-B in irrigation water in Lebanon. Our results further support that irrigation water contaminated with faecal material can be a reservoir of important MDR-B, which can spread to adjacent agricultural fields and other water bodies, posing both public health and food safety issues. Therefore, there is an urgent need to implement effective water quality monitoring and management programs to control the proliferation of antibiotic-resistant pathogens in irrigation water in Lebanon