New plasmids and putative virulence factors from the draft genome of an Australian clinical isolate of Photorhabdus asymbiotica

• Published in: FEMS microbiology letters Vol. 309; no. 2; pp. 136 - 143
• Main Authors: Wilkinson, Paul, Paszkiewicz, Konrad, Moorhouse, Alex, Szubert, Jan M, Beatson, Scott, Gerrard, John, Waterfield, Nicholas R, ffrench-Constant, Richard H
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.08.2010; Blackwell Publishing Ltd; Wiley-Blackwell; Oxford University Press
• Subjects: 454 pyrosequencing; Assembly; Australia; Bacteriology; bioinformatics; Biological and medical sciences; Bubonic plague; Cell culture; Clinical isolates; de novo sequence assembly; Enterobacteriaceae Infections - microbiology; Fundamental and applied biological sciences. Psychology; genome sequencing; Genome, Bacterial; Genomes; Humans; Illumina; Insects; Microbiology; Miscellaneous; Nucleotide sequence; Photorhabdus; Photorhabdus - genetics; Photorhabdus - isolation & purification; Photorhabdus - metabolism; Photorhabdus asymbiotica; Physical Chromosome Mapping; Plague; Plasmids; Plasmids - genetics; Plasmids - metabolism; Scaffolds; Sequence Analysis, DNA; Tissue culture; Virulence; Virulence factors; Virulence Factors - genetics; Virulence Factors - metabolism; Australia; United States > US; genome sequencing; 454 pyrosequencing; sequence assembly; Illumina; bioinformatics; de novo sequence assembly; Virulence; Plasmid; Photorhabdus; Photorhabdusasymbiotica; Bacteria; Genome; Clinical isolate; Enterobacteriaceae
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2010.02030.x

Clinical isolates of Photorhabdus asymbiotica have been recovered from patients in both the United States of America and Australia, and the full sequence of P. asymbiotica ATCC43949 from the United States has been reported recently. In contrast to other bacteria in the genus that only infect insects, P. asymbiotica strains are able to infect both insects and humans. Using a combination of Solexa (Illumina) and 454 Life Sciences (Roche) sequence data in different assembly pipelines, we report on a draft genome sequence of a strain of P. asymbiotica recovered from a patient from Kingscliff, Australia. The best assembly yielded an N50 scaffold size of 288 627 base pairs (bp) with >88.6% of the predicted genome covered by scaffolds over 100 000 bp. One of the central differences found between this Australian isolate and the US isolate is the presence of an additional plasmid, pPAA3. This plasmid is similar to pCRY from Yersinia pestis, the causative agent of bubonic plague, and the presence of pPAA3 may account for the increased virulence of Australian isolates both against tissue culture cells and infected patients. The genome of the Kingscliff strain also contains several genomic differences from the US isolate, whose potential significance in virulence against both humans and insects is discussed.