ABSTRACT
Bacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Oxford Nanopore Technologies (ONT) sequencing in the genotyping of Listeria monocytogenes and Salmonella enterica serovar Enteritidis. Our results indicated that ONT sequences, generated with the R10.4.1 flow cell and basecalled using the Dorado 0.5.0 Super Accurate 4.3 model, exhibited comparable accuracy to Illumina sequences, effectively discriminating among bacterial strains from outbreaks. These findings suggest that ONT sequencing has the potential to be a promising tool for rapid whole-genome sequencing of bacterial pathogens in public health laboratories for epidemiological investigations. IMPORTANCE: This study unveils that Oxford Nanopore Technologies sequencing, by itself, holds the potential to serve as a whole-genome sequencing-based genotyping tool in public health laboratories, enabling routine subtyping of bacterial isolates for disease surveillance and outbreak investigations.
Subject(s)
Genome, Bacterial , Listeria monocytogenes , Nanopore Sequencing , Salmonella enteritidis , Whole Genome Sequencing , Listeria monocytogenes/genetics , Listeria monocytogenes/classification , Listeria monocytogenes/isolation & purification , Salmonella enteritidis/genetics , Salmonella enteritidis/classification , Salmonella enteritidis/isolation & purification , Whole Genome Sequencing/methods , Nanopore Sequencing/methods , Genome, Bacterial/genetics , Humans , Listeriosis/microbiology , Genotype , Disease Outbreaks , Genotyping Techniques/methods , Salmonella Infections/microbiologyABSTRACT
Objectives: Salmonella, a zoonotic pathogen, significantly impacts global human health. Understanding its serotype distribution and antimicrobial resistance is crucial for effective control measures and medical interventions. Methods: We collected Salmonella isolates and demographic data from Taiwanese hospitals between 2004 and 2022, analyzing their serotypes and antimicrobial susceptibility. Results: Among 40,595 isolates, salmonellosis predominated in children aged 0-4 (61.2%) years and among males (55.2%). Males also showed higher rates of extraintestinal infections (18.1% vs 16.0%, P <0.001), particularly, in the ≥65 years age group (52.4%). The top five serovars were S. Enteritidis (32.8%), S. Typhimurium (21.7%), S. Newport (6.2%), S. Stanley (4.7%), and S. Anatum (4.0%). Notably, S. Enteritidis prevalence increased from 23.9% (2004-2005) to 43.6% (2021-2022). Antimicrobial resistance was high, with a 51.6% multidrug resistance (MDR) rate. Disturbingly, MDR rates exceeded 90% in serovars Albany, Schwarzengrund, Choleraesuis, and Goldcoast. Resistance to key therapeutic agents, azithromycin, cefotaxime, and ciprofloxacin, exhibited concerning upward trends, and the surge in cefotaxime and ciprofloxacin resistance was closely linked to the emergence and spread of MDR S. Anatum and S. Goldcoast clones. Conclusions: Prioritizing control measures against S. Enteritidis and closely monitoring the prevalence and spread of MDR clones are imperative to mitigate Salmonella infections in Taiwan.