Whole-Genome Sequencing of Pathogenic Bacteria—New Insights into Antibiotic Resistance Spreading

Abstract

In recent years, the acquisition of antimicrobial resistance (AMR) by both pathogenic and opportunistic bacteria has become a major problem worldwide, which was already noticed as a global healthcare threat by the World Health Organization [...]

Harnessing Genetic Code: Futuristic Approach of Next-Generation Sequencing for Sustainable Future

“…Examples of such superbugs are S. aureus [93], V. cholerae, C. difficile, K. pneumoniae, P. aeruginosa, P. mirabilis etc. [94,95]. NGS is now being extensively used to identify other superbugs so that proactive measures can be taken to stop their future outbreak [94].…”

ASGARD+: A New Modular Platform for Bacterial Antibiotic‐Resistant Analysis

“…The constant genetic variation in the different strains makes bacterial outbreak surveillance difficult, and although traditional techniques such as PCR‐based genotypic tests, multi‐locus sequence typing (MLST), and amplification fragment length polymorphism (AFLP) have provided robust results, they do not provide information on the mechanisms of antibiotic resistance acquisition and spreading among microbial communities (Carriço, Sabat, Friedrich, Ramirez, & ESCMID Study Group for Epidemiological Markers (ESGEM) 2013; Coolen et al., 2021). Nowadays, the use of genomic epidemiology through the application of whole‐genome sequencing (WGS) together with bioinformatics data analysis has facilitated the study of antimicrobial resistance on a large scale, allowing accurate, rapid, and cost‐effective genotyping of bacterial isolates and outbreak tracking (Shelenkov, 2021; Tümmler, 2020). In response to the increased use of next‐generation sequencing technologies, a large amount of WGS data has been generated, which in turn has led to the creation of public databases for microbiological typing where the information collected from epidemiological studies from all over the world is concentrated, accelerating the comparison and tracking of the different variants of species with resistance to antibiotics (Carriço et al., 2013).…”

“…One of the biggest challenges in public health surveillance today is antibiotic resistance in bacteria responsible for infectious diseases. This problem has been identified by the World Health Organization as a global healthcare threat, and it is predicted that it could cause at least 10 million deaths per year by 2050 (Barreiro & Barredo, 2021; Ding & Ya‐shuang, 2021; Shelenkov, 2021). The problem is aggravated due to the misuse and excessive use of broad‐spectrum antibiotics not only in the clinical field but also in husbandry, which is responsible for at least half of the use of antibiotics (He et al., 2020; Van Boeckel et al., 2017).…”

“…In response to these needs, bioinformatic methodologies have been developed to facilitate the efficient analysis of pathogens through the use of next‐generation sequencing (NGS) and whole‐genome sequencing (WGS) technologies (Van Camp, Haslam, & Porollo, 2020). The massive data generated from these technologies require substantial processing to obtain valuable information, which is why the need for the standardization of bioinformatic protocols has arisen, mainly for the effective analysis of big sample batches (Shelenkov, 2021). This article presents the ASGARD+ (Fig.…”

Quorum Sensing and Quorum Quenching with a Focus on Cariogenic and Periodontopathic Oral Biofilms

“…This feature of biofilms is becoming increasingly problematic because many chronic infections in humans are biofilm-related and are treated with antimicrobials [12]. Of particular concern is the indiscriminate overuse of antimicrobials which may result in the development of antimicrobial resistance (AMR) [13]. The rise of AMR is recognized as a major challenge currently faced by health care [13,14].…”