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BackgroundOptical mapping is an emerging technology that complements sequencing-based methods in genome analysis. It is widely used in improving genome assemblies and detecting structural variations by providing information over much longer (up to 1 Mb) reads. Current standards in optical mapping analysis involve assembling optical maps into contigs and aligning them to a reference, which is limited to pairwise comparison and becomes bias-prone when analyzing multiple samples.FindingsWe present a new method, OMMA, that extends optical mapping to the study of complex genomic features by simultaneously interrogating optical maps across many samples in a reference-independent manner. OMMA captures and characterizes complex genomic features, e.g., multiple haplotypes, copy number variations, and subtelomeric structures when applied to 154 human samples across the 26 populations sequenced in the 1000 Genomes Project. For small genomes such as pathogenic bacteria, OMMA accurately reconstructs the phylogenomic relationships and identifies functional elements across 21 Acinetobacter baumannii strains.ConclusionsWith the increasing data throughput of optical mapping system, the use of this technology in comparative genome analysis across many samples will become feasible. OMMA is a timely solution that can address such computational need. The OMMA software is available at https://github.com/TF-Chan-Lab/OMTools.

Methicillin-resistant Staphylococcus lugdunensis (MRSL) is increasingly recognized in healthcare and community settings. To obtain a better understanding of the emergence of MRSL, this study characterized the structure and content of the SCC mec elements harboured by 36 MRSL isolates obtained from diverse sources in Hong Kong from 2008 to 2017. The isolates were investigated by whole-genome sequencing. SCC mec types and subtypes were assigned according to the guidelines from the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements. The sequence type (ST)-SCC mec combinations in the 36 MRSL isolates were as follows: ST3-SCC mec IV ( n =2), ST3-SCC mec V ( n =28), ST27-SCC mec V ( n =5) and ST42-SCC mec V ( n =1). The two SCC mec IV elements were highly similar to the SCC mec IV element harboured by the community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain, JCSC6668. The J3 -mec complex-J2 regions in the SCC mec V elements were highly similar to the corresponding regions in the CA-MRSA strains PM1 ( n =13) or WIS ( n =21). Based on the J1 to J3 sequences, the SCC mec V elements can be categorized into nine different subtypes. Our findings highlight the diversified structures of SCC mec elements among MRSL strains and their close relationship with SCC mec elements harboured by CA-MRSA.