Rapid bacterial genome sequencing: methods and applications in clinical microbiology

Abstract

The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for large clinical microbiology laboratories. Indeed, the continuing reduction in sequencing costs and the shortening of the 'time to result' makes it an attractive strategy in both research and diagnostics. Here, we review how high-throughput sequencing is revolutionizing clinical microbiology and the promise that it still holds. We discuss major applications, which include: (i) identification of target DNA sequences and antigens to rapidly develop diagnostic tools; (ii) precise strain identification for epidemiological typing and pathogen monitoring during outbreaks; and (iii) investigation of strain properties, such as the presence of antibiotic resistance or virulence factors. In addition, recent developments in comparative metagenomics and single-cell sequencing offer the prospect of a better understanding of complex microbial communities at the global and individual levels, providing a new perspective for understanding host-pathogen interactions. Being a high-resolution tool, high-throughput sequencing will increasingly influence diagnostics, epidemiology, risk management, and patient care.

Los laboratorios de microbiología del mundo pueden convertirse en una red de detección microbiana

“…These have generally been sufficiently stable on repeated isolates of the same genus/species from the same patient to infer sufficient identity of that strain in another patient to detect most such transfers (30,48,51,52). They have also been shown to greatly increase sensitivity of detection of clusters of cases in trials of the SaTScan program (53,54).…”

“…Other subtyping technologies are coming into increasing use, such as multi-locus sequence typing (MLST), polymerase chain reaction (PCR), including that for 18s ribosomal RNA, and ultimately full genome nucleotide sequencing (46)(47)(48)(49). These may be done selectively for problems of a patient or a hospital's infection control, but informatics to capture, integrate and compare their results across hospitals will amplify their value.…”

Metagenomic approach to study biofilm in medical context

“…Currently, it is known that infectious diseases may be caused not only by one single potential pathogenic microorganism but instead by a personalized combination of complex interactions of distinct microbial species (2). Such a combination can be organized as biofilm (microorganisms encased in extracellular matrix) ( Figure 1).…”

Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A

“…biosynthesis | drug discovery | genome mining S ince the first genome of the bacterial pathogen Haemophilus influenzae Rd was revealed by shotgun sequencing in 1995 (1), the number of deposited genome sequences has grown exponentially, with >700 in the year 2012 alone (2). This rapid expansion of genomic information has benefited from increased throughput, improved fidelity, and lower costs associated with next-generation sequencing technologies (2,3).…”

“…This rapid expansion of genomic information has benefited from increased throughput, improved fidelity, and lower costs associated with next-generation sequencing technologies (2,3). Whereas initial genome sequencing efforts focused on microbial pathogens, bacterial genome sequencing projects have since increasingly involved industrial and environmental microbes.…”