Nanopore Sequencing Assessment of Bacterial Pathogens and Associated Antibiotic Resistance Genes in Environmental Samples

As seen in earlier and present pandemics, monitoring pathogens in the environment can offer multiple insights on their spread, evolution, and even future outbreaks. The present paper assesses the opportunity to detect microbial pathogens and associated antibiotic resistance genes, in relation to spe...

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Bibliographic Details
Published in:Microorganisms (Basel) 2023-11, Vol.11 (12), p.2834
Main Authors: Lobiuc, Andrei, Pavăl, Naomi-Eunicia, Dimian, Mihai, Covașă, Mihai
Format: Article
Language:English
Subjects:
16S
Antibiotic resistance
Antibiotics
Antigens
Antimicrobial agents
Bacteria
Bacteria, Pathogenic
Creeks & streams
Diversity indices
DNA sequencing
Drinking water
Drug resistance
Drug resistance in microorganisms
E coli
Environmental aspects
Environmental monitoring
Gastroenteritis
Genes
Genetic aspects
Health risk assessment
Health risks
Identification and classification
Infections
Meat processing
Methods
microbes
Microorganisms
Municipal wastewater
Neomycin
Nucleotide sequencing
Oxford Nanopore Technology
Pathogens
Public health
Risk factors
Streptomycin
Taxonomy
tetracycline
Tobramycin
treatment
wastewater
Water quality
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Summary:As seen in earlier and present pandemics, monitoring pathogens in the environment can offer multiple insights on their spread, evolution, and even future outbreaks. The present paper assesses the opportunity to detect microbial pathogens and associated antibiotic resistance genes, in relation to specific pathogen sources, by using nanopore sequencing in municipal waters and wastewaters in Romania. The main results indicated that waters collecting effluents from a meat processing facility exhibit altered communities' diversity and abundance, with reduced values (101-108 and 0.86-0.91) of Chao1 and, respectively, Simpson diversity indices and as main order, compared with other types of municipal waters where the same diversity index had much higher values of 172-214 and 0.97-0.98, and and were the most abundant families. Moreover, the incidence and type of antibiotic resistance genes were significantly influenced by the proximity of antibiotic sources, with either tetracycline (up to 45% of total reads) or neomycin, streptomycin and tobramycin (up to 3.8% total reads) resistance incidence being shaped by the sampling site. As such, nanopore sequencing proves to be an easy-to-use, accessible molecular technique for environmental pathogen surveillance and associated antibiotic resistance genes.
ISSN:2076-2607
2076-2607
DOI:10.3390/microorganisms11122834