Rapid Whole-Genome Sequencing for Investigation of a Neonatal MRSA Outbreak

Abstract

Whole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care. The need for automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation. (Funded by the U.K. Clinical Research Collaboration Translational Infection Research Initiative and others.).

MLST revisited: the gene-by-gene approach to bacterial genomics

“…A popular method has been to construct phylogenies on the basis of SNPs (single-nucleotide differences among samples) that have been identified either by the mapping of short-read sequence data to a reference genome, or by aligning de novo-assembled sequences to a reference genome 37,40 . This approach has been used successfully to investigate the epidemiology and evolution of a number of single-clone pathogens or members of the same lineage [41][42][43][44][45][46][47][48][49][50][51][52] , but it is limited by its requirement for a reference sequence or whole-genome alignment 40 . The analysis of diverse or highly recombining organisms in this way will prove challenging because the number of total polymorphisms increases as the number of polymorphisms conforming to a clonal model of descent decreases (BOX 1).…”

“…Consequently, staphylococci have been subjected to many molecular epidemiology studies 80 , including WGS analyses [41][42][43][44][45][46]82 . Many areas of the biology and pathology of these organisms have been investigated, including their evolution (particularly the origins of MRSA) in hospitals and communities 83,84 , the spread of clones among animals and humans 85 , the dynamics of colonization and infection 86 , and outbreak detection and control 87 .…”

“…The detection and control of S. aureus outbreaks remains a high priority in health care systems [41][42][43] . The gene-by-gene approach described above can rapidly establish very highresolution relationships among isolates, as demonstrated by an analysis of isolate data from a study that described an MRSA outbreak in a special-care baby unit 43 .…”

“…Furthermore, an allele-based rMLST analysis of 669 S. aureus isolates identified 229 unique rSTs based on 51 rps loci (two para logous loci, rpsN and rpmG, were excluded for the purposes of this analysis) and resolved the isolates into lineages that corresponded to previously described clonal complexes 83,90 , also indicating genealogical relationships among the clonal complexes (FIG. 3b).The detection and control of S. aureus outbreaks remains a high priority in health care systems [41][42][43] . The gene-by-gene approach described above can rapidly establish very highresolution relationships among isolates, as demonstrated by an analysis of isolate data from a study that described an MRSA outbreak in a special-care baby unit 43 .…”

Making the genomic leap in HCT: application of second-generation sequencing to clinical advances in hematopoietic cell transplantation

“…53 A similar strategy has also been efficacious in using SGS to identify MRSA, influenza, or specific pathogenic E. coli strains from related, but benign strains. 54,55 FROM RESEARCH FINDINGS TO CLINICAL DELIVERABLES Since the first draft human genome was completed, requiring $3 billion USD over 13 years, the technological and scientific advances that have been made in human genetics have exponentially accelerated. Indeed, SGS can now accomplish the equivalent task in o30 h for the cost of a magnetic resonance imaging scan (B2-3000 USD).…”