Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex.

Members of the Burkholderia cepacia complex (Bcc) have been isolated from various environmental and clinical samples and reportedly pose a threat to human health. Here we examine the draft genome sequence of Burkholderia sp. LS-044, an antibiotic-resistant endophytic strain affiliated to the Bcc (ST895) inhabiting rice (Oryza sativa ssp. japonica cv. Tainung 71) root. Antimicrobial susceptibility of LS-044 was evaluated comparatively with other Burkholderia sp. (CC-Al74 and CC-3XP9) using commercial ATB PSE 5 test strips. The genome of LS-044 was sequenced using an Illumina MiSeq platform. Plant probiotic and antimicrobial resistance genes were screened by Rapid Annotation using Subsystem Technology (RAST), CARD 2017, NCBI and/or UniProt. Plant-associated members of Bcc (LS-044 and CC-Al74) exhibited greater resistance to the majority of antibiotics tested. The draft genome sequence of LS-044 contained 8.78 Mbp in 62 contigs having a G + C content of 66.5%, 8868 coding sequences and 75 RNAs. The genome harboured genes coding for LysR-type β-lactamase transcription regulator, classes A, C and D β-lactamases, several metal-dependent β-lactamases, antibiotic efflux proteins, and proteins conferring resistance to colistin, streptothricin, colicin and fluoroquinolones. Similarly, it also possessed genes for copper homeostasis, copper-cobalt-zinc-cadmium-chromium resistance and reduction of mercury. Genes involved in flagellar motility, hydrolysis of murein and chitin, production of siderophore and auxin, and metabolism of aromatic compounds were also found. Genome sequence data revealed an interlinked occurrence of plant probiotic traits and antimicrobial resistance in the rice root endophyte LS-044.

Hameed A ，Shahina M ，Lai WA ，Stothard P ，Young LS ，Lin SY ，Young CC ... -  《-》

Hormesis of glyphosate on ferulic acid metabolism and antifungal volatile production in rice root biocontrol endophyte Burkholderia cepacia LS-044.

Glyphosate (GP, N-phosphonomethyl glycine) is one of the most popular organophosphate herbicides widely used in agricultural practices worldwide. There have been extensive reports on the biohazard attributes and hormetic impacts of GP on plant and animal systems. However, the effects of GP on plant growth-promoting microbes and its ecological relevance remain unknown. Here, we show that GP does exert a hormetic impact on Burkholderia cepacia LS-044, a rice (Oryza sativa ssp. japonica cv. Tainung 71) root endophytic isolate. We used increasing doses of ferulic acid (FA, 1-25 mM) and GP (0.5-5 mM) to test the growth and antifungal volatile production in LS-044 by electrochemical, liquid chromatographic, gas chromatographic and spectrophotometric means. GP treatment at a low dose (0.5 mM) increased FA utilization and significantly (P < 0.0001) enhanced antifungal volatile activity in LS-044. Although FA (1 mM) was rapidly utilized by LS-044, no chromatographically detectable utilization of GP was observed at tested doses (0.5-5 mM). LS-044 emitted predominant amounts of tropone in addition to moderate-to-minor amounts of diverse ketones and/or their derivatives (acetone, acetophenone, 2-butanone, 1-propanone, 1-(2-furanyl-ethanone, 1-phenyl-1-propanone and 1-(3-pyridinyl)-1-propanone), d-menthol, 2-methoxy-3-(1-methylethyl)-pyrazine, dimethyl disulfide, pyridine and ammonium carbamate when grown under GP supplement. GP hormesis on LS-044 induced phenotypic variations in O. sativa ssp. japonica cv. Tainan 11 as evident through seed germination assay. Genes involved in the transformation of FA, and a key gene encoding 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) with Gly-94 and Tyr-95 residues localized at active site most likely rendering EPSPS sensitivity to GP, were detected in LS-044. This is the first report on the GP hormesis influencing morphological and metabolic aspects including volatile emission in a biocontrol bacterium that could modulate rice plant phenotype.

Hameed A ，Nguyen DH ，Lin SY ，Stothard P ，Neelakandan P ，Young LS ，Young CC ... -  《-》

Genomic insights into an extensively drug-resistant and hypervirulent Burkholderia dolosa N149 isolate of a novel sequence type (ST2237) from a Vietnamese patient hospitalised for stroke.

Burkholderia dolosa is a clinically important opportunistic pathogen in inpatients. Here we characterised an extensively drug-resistant and hypervirulent B. dolosa isolate from a patient hospitalised for stroke. Resistance to 41 antibiotics was tested with the agar disc diffusion, minimum inhibitory concentration, or broth microdilution method. The complete genome was assembled using short-reads and long-reads and the hybrid de novo assembly method. Allelic profiles obtained by multilocus sequence typing were analysed using the PubMLST database. Antibiotic-resistance and virulence genes were predicted in silico using public databases and the 'baargin' workflow. B. dolosa N149 phylogenetic relationships with all available B. dolosa strains and Burkholderia cepacia complex strains were analysed using the pangenome obtained with Roary. B. dolosa N149 displayed extensive resistance to 31 antibiotics and intermediate resistance to 4 antibiotics. The complete genome included three circular chromosomes (6 338 630 bp in total) and one plasmid (167 591 bp). Genotypic analysis revealed various gene clusters (acr, amr, amp, emr, ade, bla and tet) associated with resistance to 35 antibiotic classes. The major intrinsic resistance mechanisms were multidrug efflux pump alterations, inactivation and reduced permeability of targeted antibiotics. Moreover, 91 virulence genes (encoding proteins involved in adherence, formation of capsule, biofilm and colony, motility, phagocytosis inhibition, secretion systems, protease secretion, transmission and quorum sensing) were identified. B. dolosa N149 was assigned to a novel sequence type (ST2237) and formed a mono-phylogenetic clade separated from other B. dolosa strains. This study provided insights into the antimicrobial resistance and virulence mechanisms of B. dolosa.

Nguyen QH ，Nguyen CL ，Nguyen TS ，Do BN ，Tran TTT ，Le TTH ，Bui TT ，Le HS ，Quyen DV ，Hayer J ，Bañuls AL ，Bui TS ... -  《-》

Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards.

Khan A ，Asif H ，Studholme DJ ，Khan IA ，Azim MK ... -  《-》

Draft genome sequence of an NDM-5, CTX-M-15 and OXA-1 co-producing Escherichia coli ST167 clinical strain isolated from a urine sample.

Escherichia coli is the leading cause of urinary tract infections worldwide. Carbapenemase-producing clinical isolates leave few therapeutic options. Here we report the draft genome sequence of an NDM-5, CTX-M-15, and OXA-1 co-producing E. coli sequence type 167 (ST167) multidrug-resistant clinical strain (ECWJ1) isolated from a urine sample of a hospitalised male patient diagnosed with intracranial injury from a road traffic accident. The genome of E. coli ECWJ1 was sequenced using an Illumina HiSeq™ 4000 platform. The generated sequence reads were assembled using CLC Genomics Workbench. The draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server, and further bioinformatics analysis was performed. Escherichia coli ECWJ1 belongs to ST167. The total genome length of the isolate is 4992753bp, with 4890 protein-coding sequences. The presence of blaNDM-5, blaCTX-M-15 and blaOXA-1 genes was detected in addition to other antimicrobial resistance genes conferring resistance to aminoglycosides, fluoroquinolones, sulphonamides, trimethoprim and tetracyclines. Antimicrobial susceptibility testing revealed, that besides tigecycline and colistin, this isolate is resistant to all antimicrobials tested. To our knowledge, this is the first report of an E. coli ST167 strain co-producing NDM-5, CTX-M-15 and OXA-1 isolated from urine sample in China. It may help us to understand the genomic features, molecular characteristics and resistance gene diversity of this bacterial pathogen. The genome sequence of E. coli ECWJ1 can be used as a reference sequence for comparative analysis of NDM-5-producing E. coli, aiming to reveal the mechanism of NDM-5 dissemination in this pathogen.

Sun L ，Xu J ，He F 《-》