For several decades antibiotics are used to combat against pathogenic bacteria, but their misuse and overuse have caused the emergence of resistant bacteria. The scarcities of effective antibiotics along with unavailability of alternative solutions have exacerbated bacterial infections and mortality rate. This review provides the concept of bacterial resistome and mechanisms of resistance. It has also described the utility of whole genome sequencing in identifying resistance and its dissemination in association with available bioinformatics tools and databases. Moreover, the whole genome sequencing methodology described in this review will help to select effective antibiotics, maintain unparalleled surveillance of resistance and provide early diagnosis during resistance outbreaks. The provided information could be used to control infection caused by resistant microorganisms.
BackgroundEmergence of carbapenem resistant Escherichia coli pathovars and their environmental dissemination are alarming problems. E. coli isolated from sewage water of hospital setting conferred a high resistance towards β-lactams, particularly towards carbapenem. This prompted us to perform whole genome sequence analysis to investigate the antimicrobial determinants, pathogenicity status and mobile genetic elements associated with resistance genes.ResultsTo the best of our knowledge this is the first report of ST 315 carrying NDM-4 from India. The genome analysis has revealed the unknown characteristics associated with this sequence type (ST 315) like resistance and virulence factors. Based on virulence markers, its pathotype was identified as ExPEC. Furthermore, a mobile plasmid with multiple β-lactamases genes and clinically relevant resistance markers was detected. Phylogenetic analysis of Inc F plasmids sequences carrying ESBLs and NDM variants, revealed un-relatedness in these plasmids due to their varying size and backbone sequences.ConclusionsPresence of carbapenem resistant E. coli ST 315 with high level antibiotic resistance, near hospital environment is an alarming situation in context to its spread. WGS based analyses have provided details on virulence and resistance status which could overcome the lack of information available on ST 315, globally. This could further help in its quick detection and control in clinical settings.Electronic supplementary materialThe online version of this article (10.1186/s13099-018-0247-8) contains supplementary material, which is available to authorized users.
Pseudomonas aeruginosa
is inextricably linked with chronic lung infections. In this study, the well-conserved Fap operon was found to be essential for pathoadaptation in pulmonary infection in a rat lung model.
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