Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
Highlights
Human genomics is inseparably linked to the genomics of bacteria
What does the future hold for wholegenome sequencing (WGS)? we showed that WGS may be well poised to make a decisive impact on the study and control of MDR in pathogenic bacteria (Table 1) [126]
Not reviewed here, studies have shown that WGS can contribute to the investigation of various pathogenic and beneficial resistant microorganisms: bacteria [70, 155], fungi (Candida spp., Cryptococcus neoformans, Pneumocystis spp., and Aspergillus spp.) [208], and viruses (HIV virus, hepatitis B, hepatitis C, influenza, herpes viruses) [144, 255]
Summary
Human genomics is inseparably linked to the genomics of bacteria. Bacteria share a long history with humans and play a major role in our life [152, 200]. Future investigations of pathogen resistance mechanisms together with establishment of robust links between genetic components and phenotypic traits in MDR bacteria will help the development of successful WGS-based antibiotic resistance tests.
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