Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain

Abstract

BackgroundPhotorhabdus luminescens is an enteric bacterium, which lives in mutualistic association with soil nematodes and is highly pathogenic for a broad spectrum of insects. A complete genome sequence for the type strain P. luminescens subsp. laumondii TT01, which was originally isolated in Trinidad and Tobago, has been described earlier. Subsequently, a rifampicin resistant P. luminescens strain has been generated with superior possibilities for experimental characterization. This strain, which is widely used in research, was described as a spontaneous rifampicin resistant mutant of TT01 and is known as TT01-RifR.ResultsUnexpectedly, upon phenotypic comparison between the rifampicin resistant strain and its presumed parent TT01, major differences were found with respect to bioluminescence, pigmentation, biofilm formation, haemolysis as well as growth. Therefore, we renamed the strain TT01-RifR to DJC. To unravel the genomic basis of the observed differences, we generated a complete genome sequence for strain DJC using the PacBio long read technology. As strain DJC was supposed to be a spontaneous mutant, only few sequence differences were expected. In order to distinguish these from potential sequencing errors in the published TT01 genome, we re-sequenced a derivative of strain TT01 in parallel, also using the PacBio technology. The two TT01 genomes differed at only 30 positions. In contrast, the genome of strain DJC varied extensively from TT01, showing 13,000 point mutations, 330 frameshifts, and 220 strain-specific regions with a total length of more than 300 kb in each of the compared genomes.ConclusionsAccording to the major phenotypic and genotypic differences, the rifampicin resistant P. luminescens strain, now named strain DJC, has to be considered as an independent isolate rather than a derivative of strain TT01. Strains TT01 and DJC both belong to P. luminescens subsp. laumondii.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5121-z) contains supplementary material, which is available to authorized users.

Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC‐1

“…The chromosome comparison strategy used here is the same as previously developed and applied to strains of P. laumondii (Zamora‐Lagos et al, ). The sequence alignment program MAFFT (Katoh & Standley, ) was used to delineate matching segments (matchSEGs) which are common to both strains and divergent segments (divSEGs) which represent strain‐specific genome regions (see the legend to Table for details).…”

“…We recently described the comparison of two closely related strains of Photorhabdus laumondii (Zamora‐Lagos et al, ) and adopted the same analysis strategy for Halobacterium . Briefly, matching segments (matchSEGs) were identified by an initial pairwise MAFFT (Katoh & Standley, ) alignment in chunks of 400 kb.…”

The Genome Sequence of the Halobacterium salinarum Type Strain Is Closely Related to That of Laboratory Strains NRC-1 and R1

“…The chromosomes of strains 91-R6 and R1 were compared in detail by methods we previously described for strain comparisons of Haloquadratum walsbyi and Photorhabdus laumondii (9, 10). They showed very high DNA sequence similarity (99.63% sequence identity covering 84.9% of 2.17 Mb in strain 91-R6 and 92.5% of 2.00 Mb in strain R1) and complete colinearity.…”

Characterization of bacterial community changes and antibiotic resistance genes in lamb manure of different incidence

“…The use of antibiotics can effectively kill pathogenic microorganisms, but at the same time, it also leads to the spread of antibiotic resistance genes (ARGs) 25 . Some ARGs have been shown to exist in transposons, integrons, or plasmids, which are mobilizable elements that can be transferred among bacteria The migration and transformation of ARGs in the enteric microorganism is potentially more harmful, it can cause pathogens to become resistant to antibiotics.…”