Bioinformatics tools used for whole-genome sequencing analysis of <i>Neisseria gonorrhoeae</i>: a literature review

Singh, Reema; Kusalik, Anthony; Dillon, Jo-Anne R.

doi:10.1093/bfgp/elab028

Cited by 5 publications

(6 citation statements)

References 201 publications

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“…Because surveillance of antibiotic resistance requires a series of complex processes, including strain isolation, identification, culture, and AST, which take a long time, genotyping and genome analysis are well established for the investigation of gonococcal transmission and AMR prediction ( 20 ). Among them, MLST and ngSTAR are two simple methods to indicate phylogenetic relationships and antibiotic susceptibility.…”

Section: Discussionmentioning

confidence: 99%

Emergence and Genomic Characterization of Neisseria gonorrhoeae Isolates with High Levels of Ceftriaxone and Azithromycin Resistance in Guangdong, China, from 2016 to 2019

Lin

Chen

et al. 2022

Microbiol Spectr

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Here, we report five sporadic dual-resistant isolates, including FC428-related ceftriaxone-resistant clones with MICs of ≥0.5 mg/L and high-level azithromycin resistance with MICs of ≥1,024 mg/L. This study highlights that dual-resistant clones with the same evolutionary origin as FC428, A2735, and F89 have circulated in Guangdong, China, which suggests that the capacity for antibiotic resistance testing and genome analysis should be strengthened in daily epidemiological surveillance.

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Section: Discussionmentioning

confidence: 99%

Emergence and Genomic Characterization of Neisseria gonorrhoeae Isolates with High Levels of Ceftriaxone and Azithromycin Resistance in Guangdong, China, from 2016 to 2019

Lin

Chen

et al. 2022

Microbiol Spectr

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“…fr). Sequencing lays the foundation for emerging omics approaches such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, and panomics (Singh et al 2022). Moreover, the simple and often cost-free access to data repositories, bioinformatic algorithms, and computational systems enables the mutual comparison of genomes, transcriptomes, proteomes, and metabolomes (Li et al 2022).…”

Section: Introductionmentioning

confidence: 99%

In silico prediction of microRNA families involved in the biosynthesis of lignans and cyanogenic glycosides in flax (Linum usitatissimum L.)

Harenčár,

Ražná

2024

Plant Growth Regul

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Flaxseed (Linum usitatissimum L.) is renowned for having the highest concentration of lignans among all plant species worldwide. However, it also contains a notable amount of cyanogenic glycosides, prompting efforts to reduce their levels. MicroRNAs, recognized as significant epigenetic factors, hold the potential to serve as genetic markers in achieving this breeding goal. In this study, 44,885 mature microRNAs were utilized alongside one genome and four transcriptomes of flax. Twelve gene sequences were obtained for five lignan enzymes and three enzymes related to cyanogenic glycosides. Based on our in silico approach, we identified 15 microRNA families for the lignan metabolic pathway, 10 for the cyanogenic glycoside pathway, and 6 regulating both pathways. Additionally, we contributed to the annotation of the used transcriptomes and verified the functionality of the “Finding genes by keyword” algorithm available on Phytozome 13. The results obtained led to the design of a unique schema for microRNA mediated regulation in the biosynthetic pathways of lignans and cyanogenic glycosides. This research will enhance our understanding of the regulatory mechanisms of microRNA in these biosynthetic pathways, along with other specialized metabolites. The predicted microRNAs can be employed in marker-assisted selection with the breeding objective of optimizing the ratio of nutritional and antinutritional components in flaxseed while maintaining current physiological parameters.

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“…These NGS technologies can be exploited to provide information about the complete genome of an organism [ 19 , 20 ] and can detect many pathogens in clinical specimens simultaneously [ 21 , 22 ]. Data obtained from WGS can be analyzed by using a battery of bioinformatics tools [ 23 , 24 ], which provide information about the quality of sequenced genomes and identify species, strains, and genotypes of the infecting organisms, as well as predications about drug susceptibility/resistance and epidemiological investigations [ 25 – 30 ]. Such information is valuable for early diagnosis, effective treatment, and epidemiological investigations of known as well as unknown/new pathogens [ 31 , 32 ].…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing: Applications in Clinical Bacteriology

Mustafa

2024

Med Princ Pract

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The success in determining the whole genome sequence of a bacterial pathogen was first achieved in 1995 by determining the complete nucleotide sequence of Haemophilus influenzae Rd using the chain-termination method established by Sanger et al. in 1977 and automated by Hood et al. in 1987. However, this technology was laborious, costly, and time-consuming to obtain whole genome sequences. Since 2004, high-throughput next-generation sequencing technologies have been developed, which are highly efficient, require less time, and are cost-effective to perform whole genome sequencing (WGS) of all organisms, including bacterial pathogens. In recent years, the data obtained using WGS technologies coupled with bioinformatics analyses of the sequenced genomes have been projected to revolutionize clinical bacteriology practices. The WGS technologies have been used in the identification of bacterial species, strains, and genotypes from cultured organisms and directly from clinical specimens. WGS has also helped in determining resistance to antibiotics by the detection of antimicrobial resistance genes and point mutations. Furthermore, WGS data have helped in the epidemiological tracking and surveillance of pathogenic bacteria in healthcare settings as well as in communities. This review focuses on the above-mentioned applications of WGS in clinical bacteriology.

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Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review

Cited by 5 publications

References 201 publications

Emergence and Genomic Characterization of Neisseria gonorrhoeae Isolates with High Levels of Ceftriaxone and Azithromycin Resistance in Guangdong, China, from 2016 to 2019

Emergence and Genomic Characterization of Neisseria gonorrhoeae Isolates with High Levels of Ceftriaxone and Azithromycin Resistance in Guangdong, China, from 2016 to 2019

In silico prediction of microRNA families involved in the biosynthesis of lignans and cyanogenic glycosides in flax (Linum usitatissimum L.)

Whole Genome Sequencing: Applications in Clinical Bacteriology

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