Genetic factors related to the widespread dissemination of ST11 extensively drug-resistant carbapenemase-producing Klebsiella pneumoniae strains within hospital

Background:Carbapenemase-producing Klebsiella pneumoniae(CP-Kp)poses distinct clinical challenges due to extensively drug resistant(XDR)phenotype,and sequence type(ST)11 is the most dominant blaKPC-2-bearing CP-Kp clone in China.The purpose of this current retrospective study was to explore the genetic factors associated with the success of XDR CP-Kp ST11 strains circulated in the intensive care unit(ICU)of a Chinese tertiary hospital.Methods:Six ST11 XDR CP-Kp strains were identified between May and December 2014 and validated by minimum inhibitory concentration examination,polymerase chain reaction,and pyrosequencing.The six ST11 XDR CP-Kp,as well as three multi-drug resistant(MDR)and four susceptible strains,were sequenced using single-molecule real-time method.Comprehensively structural and functional analysis based on comparative genomics was performed to identify genomic characteristics of the XDR ST11 CP-Kp strains.Results:We found that ST11 XDR blaKPC-2-bearing CP-Kp strains isolated from inpatients spread in the ICU of the hospital.Functionally,genes associated with information storage and processing of the ST11 XDR CP-Kp strains were more abundant than those of MDR and susceptible strains,especially genes correlative with mobile genetic elements(MGEs)such as transposons and prophages.Structurally,eleven large-scale genetic regions taken for the unique genome in these ST11 XDR CP-Kp strains were identified as MGEs including transposons,integrons,prophages,genomic islands,and integrative and conjugative elements.Three of them were located on plasmids and eight on chromosomes;five of them were with antimicrobial resistance genes and eight with adaptation associated genes.Notably,a new blaKPC-2-bearingΔΔTn1721-blaKPC-2 transposon,probably transposed and truncated fromΔTn1721-blaKPC-2 by IS903D and ISKpn8,was identified in all six ST11 XDR CP-Kp strains.Conclusion:Our findings suggested that together with clonal spread,MGEs identified uniquely in the ST11 XDR CP-Kp strains might contribute to their formidable adaptability,which facilitated their widespread dissemination in hospital.

Comparative analysis of the Monochamus alternatus immune system

The pine sawyer beetle, Monochamus alternatus, is regarded as a notorious for- est pest in Asia, vectoring an invasive pathogenic nematode, Bursaphelenchus xylophilus, which is known to cause pine wilt disease. However, little sequence information is available for this vector beetle. This hampered the research on its immune system. Based on the transcriptome of M. alternatus, we have identified and characterized 194 immunity-related genes in M. alternatus, and compared them with homologues molecules from other species known to exhibit immune responses against invading microbes. The lower number of puta- tive immunity-related genes in M. alternatus were attributed to fewer C-type lectin, serine protease （SP） and anti-microbial peptide （AMP） genes. Phylogenetic analysis revealed that M. alternatus had a unique recognition gene, galectin3, orthologues of which were not identified in Tribolium castaneum, Drosophila melanogastor, Anopheles gambiae and Apis mellifera. This suggested a lineage-specific gene evolution for coleopteran insects. Our study provides the comprehensive sequence resources of the immunity-related genes ofM. alternatus, presenting valuable information for better understanding of the molecular mechanism of innate immunity processes in M. alternatus against B. xylophilus.

A large-scale gene discovery for the red palm weevil Rhynchophorus ferrugineus （Coleoptera： Curculionidae）

The red palm weevil （RPW; Rhynchophorusferrugineus） is a devastating pest of palms, prevalent in the Middle East as well as many other regions of the world. Here, we report a large-scale de novo complementary DNA （cDNA） sequencing effort that acquired ~5 million reads and assembled them into 26 765 contigs from 12 libraries made from samples of different RPW developmental stages based on the Roche/454 GS FLX platform. We annotated these contigs based on the publically available known insect genes and the Tribolium castaneum genome assembly. We find that over 80% of coding sequences （CDS） from the RPW contigs have high-identity homologs to known proteins with complete CDS. Gene expression analysis shows that the pupa and larval stages have the highest and lowest expression levels, respectively. In addition, we also identified more than 60 000 single nucleotide polymorphisms and 1 200 simple sequence repeat markers. This study provides the first large-scale eDNA dataset for RPW, a much-needed resource for future molecular studies.