Characterization of antibiotic resistance and virulence genes of ocular methicillin-resistant Staphylococcus aureus strains through complete genome analysis

Kandasamy, Kathirvel; Rudhra, O.; Rajapandian, Siva Ganesa Karthikeyan; Prajna, Namperumalsamy Venkatesh; Lalitha, Prajna; Devarajan, Bharanidharan

doi:10.1016/j.exer.2021.108764

Cited by 5 publications

(5 citation statements)

References 77 publications

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“…Kirstahler et al [60] studied the application of NGS technology supported by WGS in the disease management of endophthalmitis after cataract or intravitreal injection, pointing out that this technology may better distinguish infectious from sterile endophthalmitis. In the case of a very high coverage depth of metagenomic sequencing, it can also reveal valuable functional information, such as antibiotic resistance and virulence-related genes [82] .…”

Section: Prophylaxis Treatment and Prognosis Of Endophthalmitismentioning

confidence: 99%

Nanopore techniques as a potent tool in the diagnosis and treatment of endophthalmitis: a literature review

Li¹,

Jin²

2022

Int J Ophthalmol

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Endophthalmitis is a serious ophthalmic disease characterized by changes in the eye’s posterior segment, such as hypopyon and intraocular inflammation, vitritis being a hallmark. Infection-caused endophthalmitis can lead to irreversible vision loss, accompanied by eye pain or eye distention, and in the most severe cases the removal of the eyeball. Microorganisms such as bacteria, fungi, viruses, and parasites typically account for the disease and the entry pathways of the microbial can be divided into either endogenous or exogenous approaches, according to the origin of the etiological agents. Exogenous endophthalmitis can be derived from various occasions (such as post-operative complications or trauma) while endogenous endophthalmitis results from the bloodstream which carries pathogens to the eye. This review aims to summarize the application of new technology in pathogen identification of endophthalmitis so as to prevent the disease and better guide clinical diagnosis and treatment.

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Section: Prophylaxis Treatment and Prognosis Of Endophthalmitismentioning

confidence: 99%

Nanopore techniques as a potent tool in the diagnosis and treatment of endophthalmitis: a literature review

Li¹,

Jin²

2022

Int J Ophthalmol

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“…Short-read sequencing [such as from Illumina and MGI next-generation sequencing (NGS) technologies] has high base-calling accuracy, but the nature of the short reads means that only fragmented draft genomes can be obtained from such data. Instead, scientists would prefer to receive correct, complete genomes as their study advances ( Cohen et al, 2019 ; Kathirvel et al, 2021 ). Shortly after the introduction of NGS, third-generation sequencing technologies (TGS) emerged, presented by two platforms, Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), giving long and ultra-long sequencing reads, respectively, and enabling coverage of highly repetitive regions and structural variants.…”

Section: Introductionmentioning

confidence: 99%

Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing

et al. 2023

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IntroductionGenome-based analysis is crucial in monitoring antibiotic-resistant bacteria (ARB)and antibiotic-resistance genes (ARGs). Short-read sequencing is typically used to obtain incomplete draft genomes, while long-read sequencing can obtain genomes of multidrug resistance (MDR) plasmids and track the transmission of plasmid-borne antimicrobial resistance genes in bacteria. However, long-read sequencing suffers from low-accuracy base calling, and short-read sequencing is often required to improve genome accuracy. This increases costs and turnaround time.MethodsIn this study, a novel ONT sequencing method is described, which uses the latest ONT chemistry with improved accuracy to assemble genomes of MDR strains and plasmids from long-read sequencing data only. Three strains of Salmonella carrying MDR plasmids were sequenced using the ONT SQK-LSK114 kit with flow cell R10.4.1, and de novo genome assembly was performed with average read accuracy (Q > 10) of 98.9%.Results and DiscussionFor a 5-Mb-long bacterial genome, finished genome sequences with accuracy of >99.99% could be obtained at 75× sequencing coverage depth using Flye and Medaka software. Thus, this new ONT method greatly improves base-calling accuracy, allowing for the de novo assembly of high-quality finished bacterial or plasmid genomes without the need for short-read sequencing. This saves both money and time and supports the application of ONT data in critical genome-based epidemiological analyses. The novel ONT approach described in this study can take the place of traditional combination genome assembly based on short- and long-read sequencing, enabling pangenomic analyses based on high-quality complete bacterial and plasmid genomes to monitor the spread of antibiotic-resistant bacteria and antibiotic resistance genes.

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“…This dearth represents a crucial gap to fill for the advancement of risk assessment on antimicrobial resistance. Furthermore, based on emerging sequencing technologies such as Oxford Nanopore, 154 in the near future long read metagenomic sequencing will become more common. These sequences will eventually be able to be read in near real-time, meaning that within hours of sampling the MGEs, ARGs, and their host organisms could be known.…”

Section: Environmental Science: Water Research and Technology Perspec...mentioning

confidence: 99%

Targeting current and future threats: recent methodological trends in environmental antimicrobial resistance research and their relationships to risk assessment

Burch

Newton

Kimbell

et al. 2022

Environ. Sci.: Water Res. Technol.

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Characterization of antibiotic resistance and virulence genes of ocular methicillin-resistant Staphylococcus aureus strains through complete genome analysis

Cited by 5 publications

References 77 publications

Nanopore techniques as a potent tool in the diagnosis and treatment of endophthalmitis: a literature review

Nanopore techniques as a potent tool in the diagnosis and treatment of endophthalmitis: a literature review

Oxford nanopore long-read sequencing enables the generation of complete bacterial and plasmid genomes without short-read sequencing

Targeting current and future threats: recent methodological trends in environmental antimicrobial resistance research and their relationships to risk assessment

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