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July 7, 2019

Characterization of an IncA/C multidrug resistance plasmid in Vibrio alginolyticus.

Cephalosporin-resistant Vibrio alginolyticus were firstly isolated from food products with ß-lactamases, blaPER-1, blaVEB-1 and blaCMY-2, being the major mechanisms mediating cephalosporin resistance. The complete sequence of a multidrug resistance plasmid, pVAS3-1, harboring the blaCMY-2 and qnrVC4 genes was decoded in this study. Its backbone exhibited genetic homology to known IncA/C plasmids recoverable from Enterobacteriaceae species, suggesting its possible origin from Enterobacteriaceae. Copyright © 2016, American Society for Microbiology. All Rights Reserved.


July 7, 2019

Genome sequences of five nonvirulent Listeria monocytogenes serovar 4 strains.

We present the complete genome sequences of five nonpathogenicListeria monocytogenesserovar 4 strains: WSLC 1018 (4e), 1019 (4c), 1020 (4a), 1033 (4d), and 1047 (4d). These sequences may help to uncover genes involved in the synthesis of the serovar antigens-phenotypic determinants of virulence deemed clinically relevant. Copyright © 2016 Sumrall et al.


July 7, 2019

First report of cfr-encoding plasmids in the pandemic sequence type (ST) 22 methicillin-resistant Staphylococcus aureus Staphylococcal cassette chromosome mec type-IV clone.

Linezolid is often the drug of last resort for serious methicillin-resistant Staphylococcus aureus (MRSA) infections. Linezolid resistance is mediated by mutations in 23S rRNA and genes for ribosomal proteins, cfr encoding phenicol, lincosamide, oxazolidinone, pleuromutilin and streptogramin A (PhLOPSA) resistance, its homolgue cfr(B) or optrA conferring oxazolidinone and phenicol resistance. Linezolid resistance is rare in S. aureus, and cfr even rarer. This study investigated the clonality and linezolid resistance mechanisms of two MRSA isolates from patients in separate Irish hospitals. Isolates were subjected to cfr PCR, PhLOPSA susceptibility testing, 23S rRNA PCR and sequencing, DNA microarray profiling, spa typing, pulsed-field gel electrophoresis (PFGE), plasmid curing and conjugative transfer. Whole-genome sequencing was used for single nucleotide variant (SNV) analysis, multilocus-sequence typing, L-protein mutation identification, cfr-plasmid sequence analysis and optrA and cfr(B) detection. Isolates M12/0145 and M13/0401 exhibited linezolid MICs of 64 and 16 mg/liter, respectively, and harbored identical 23S rRNA and L22 mutations, but M12/0145 exhibited the mutation in 2/6 23S rRNA alleles compared to 1/5 in M13/0401. Both isolates were ST22-MRSA-IV/t032, harbored cfr, exhibited the PhLOPSA phenotype and lacked optrA and cfr(B). They differed by five PFGE bands and 603 SNVs. Isolate M12/0145 harbored cfr and fexA on a 41-kb conjugative pSCFS3-type plasmid, whereas M13/0401 harbored cfr and lsa(B) on a novel 27-kb plasmid. This is the first report of cfr in the pandemic ST22-MRSA-IV clone. Different cfr plasmids and mutations associated with linezolid resistance in genotypically distinct ST22-MRSA-IV isolates highlights that prudent management of linezolid use is essential. Copyright © 2016 Shore et al.


July 7, 2019

Detection of translocatable units in a blaCTX-M-15 extended-spectrum ß-lactamase-producing ST131 Escherichia coli isolate using a hybrid sequencing approach.

Sir,Escherichia coli sequence type 131 (ST131) producing CTX- M-type [3-lactamases are the most common extended-spectrum [3-lactamase (ESBL)-producing strains and are of high virulence potential. In particular, the blal-;X.M.[5 gene is often encoded on a conjugative plasmid and less frequently on the chromo- some. The presence of identical bluCTX.M.[5 alleles on both the chromosome and on a plasmid in the same strain has been reported [1], suggesting transfer ofthese genes between these two locations.


July 7, 2019

Dissemination of the mcr-1 colistin resistance gene.

Since our first report on plasmid- mediated colistin resistance gene mcr-1,1 strains previously collected in seven countries (Denmark, the Netherlands, Laos, Nigeria, Thailand, France, and the UK) have been found to carry mcr-1.2–6 Furthermore, the sequences in GenBank show that mcr-1 might also be circulating in Portugal and Malaysia. The earliest mcr-1- positive strain was collected from cattle in France in 2008 (GenBank accession number LMBK01000308). These findings confirm our initial concern that mcr-1 could have already disseminated worldwide.


July 7, 2019

Complete genome sequences of Aerococcus christensenii CCUG 28831T, Aerococcus sanguinicola CCUG 43001T, Aerococcus urinae CCUG 36881T, Aerococcus urinaeequi CCUG 28094T, Aerococcus urinaehominis CCUG 42038 BT, and Aerococcus viridans CCUG 4311T.

Strains belonging to the genus Aerococcusare causative agents of human and animal infections, including urogenital infections, bacteremia/septicemia, and infective endocarditis. This study reports the first fully closed and complete genome sequences of six type strains belonging to the genus Aerococcususing a combination of Illumina HiSeq and PacBio sequencing technologies. Copyright © 2016 Carkaci et al.


July 7, 2019

Complete genome sequence of Salmonella enterica serovar Typhimurium strain SO3 (sequence type 302) isolated from a baby with meningitis in Mexico.

The complete genome of Salmonella entericaserovar Typhimurium strain SO3 (sequence type 302), isolated from a fatal meningitis infection in Mexico, was determined using PacBio technology. The chromosome hosts six complete prophages and is predicted to harbor 51 genomic islands, including 13 pathogenicity islands (SPIs). It carries the Salmonella virulence plasmid (pSTV). Copyright © 2016 Vinuesa et al.


July 7, 2019

First complete genome sequence of the Dutch veterinary Coxiella burnetii strain NL3262, originating from the largest global Q fever outbreak, and draft genome sequence of its epidemiologically linked chronic human isolate NLhu3345937

The largest global Q fever outbreak occurred in The Netherlands during 2007 to 2010. Goats and sheep were identified as the major sources of disease. Here, we report the first complete genome sequence of Coxiella burnetiigoat outbreak strain NL3262 and that of an epidemiologically linked chronic human strain, both having the outbreak-related CbNL01multilocus variable-number tandem-repeat analysis (MLVA) genotype. Copyright © 2016 Kuley et al.


July 7, 2019

Mechanisms involved in acquisition of blaNDM genes by IncA/C2 and IncFIIY plasmids.

blaNDM genes confer carbapenem resistance and have been identified on transferable plasmids belonging to different incompatibility (Inc) groups. Here we present the complete sequences of four plasmids carrying a blaNDM gene, pKP1-NDM-1, pEC2-NDM-3, pECL3-NDM-1 and pEC4-NDM-6, from four clinical samples originating from four different patients. Different plasmids carry segments that align to different parts of the blaNDM region found on Acinetobacter plasmids. pKP1-NDM-1 and pEC2-NDM-3, from Klebsiella pneumoniae and Escherichia coli, respectively, were identified as type 1 IncA/C2 plasmids with almost identical backbones. Different regions carrying blaNDM are inserted in different locations in the antibiotic resistance island known as ARI-A and ISCR1 may have been involved in acquisition of blaNDM-3 by pEC2-NDM-3. pECL3-NDM-1 and pEC4-NDM-6, from Enterobacter cloacae and E. coli, respectively, have similar IncFIIY backbones but different regions carrying blaNDM are found in different locations. Tn3-derived Inverted-repeat Transposable Elements (TIME) appear to have been involved in acquisition of blaNDM-6 by pEC4-NDM-6 and the rmtC 16S rRNA methylase gene by IncFIIY plasmids. Characterisation of these plasmids further demonstrates that even very closely related plasmids may have acquired blaNDM genes by different mechanisms. These findings also illustrate the complex relationships between antimicrobial resistance genes, transposable elements and plasmids and provide insights into the possible routes for transmission of blaNDM genes amongst species of the Enterobacteriaceae family. Copyright © 2016, American Society for Microbiology. All Rights Reserved.


July 7, 2019

Prediction of putative resistance islands in a carbapenem-resistant Acinetobacter baumannii global clone 2 clinical isolate.

We investigated the whole genome sequence (WGS) of a carbapenem-resistant Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance islands using a software tool.A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively.The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following resistance genes: four ß-lactamase genes bla(ADC-30), bla(OXA-66), bla(OXA-23), and bla(TEM-1); armA, aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6′)Ib-cr for fluoroquinolone resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed two copies of Tn2009 carrying bla(OXA-23), and PRI5 carried two copies of a class I integron carrying sul1 and armA genes.By prediction of resistance islands in the carbapenem-resistant A. baumannii YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed Tn2009 and class I integrons. The prediction of resistance islands using software tools was useful for analysis of the WGS.


July 7, 2019

Complete genome sequence of the larvicidal bacterium Lysinibacillus sphaericus strain OT4b.25.

Lysinibacillus sphaericus OT4b.25 is a native Colombian strain isolated from coleopteran larvae in an oak forest near Bogotá D.C.; this strain has shown high levels of pathogenic activity against Culex quinquefasciatus larvae in laboratory assays compared to that of other members of the same species. Using Pacific Biosciences sequencing technology, we propose a chromosomal contig of 4,665,775 bp that, according to comparative analysis, is highly similar to that of reference strain L. sphaericus C3-41. Copyright © 2016 Rey et al.


July 7, 2019

Complete nucleotide sequence of pH11, an IncHI2 plasmid conferring multi-antibiotic resistance and multi-heavy metal resistance genes in a clinical Klebsiella pneumoniae isolate.

The complete 284,628bp sequence of pH11, an IncHI2 plasmid, was determined through single-molecule, real-time (SMRT) sequencing. Harbored by a clinical Klebsiella pneumoniae strain H11, and isolated in Beijing, this plasmid contains multiple antibiotic resistance genes, including catA2, aac(6′)-Ib, strB, strA, dfrA19, blaTEM-1, blaSHV-12, sul1, qacE delta 1, ereA, arr2, and aac3. The aac(6′)-Ib is carried by a class I integron. Plasmid pH11 also carries several genes associated with resistance to heavy metals, such as tellurium, mercury, cobalt, zinc, nickel, copper, lead and cadmium. This plasmid exhibits numerous characteristics, including HipBA and RelBE toxin-antitoxin systems, two major transfer (Tra) regions closely related to those of Salmonella enterica serovar plasmid pRH-R27, a type II restriction modification system (EcoRII R-M system), several methyltransferases and methylases and genes encoding Hha and StpA. These characteristics suggest that pH11 may adapt to various hosts and environments. Multiple insertion sequence elements, transposases, recombinases, resolvases and integrases are scattered throughout pH11. The presence of these genes may indicate that horizontal gene transfer occurs frequently in pH11 and thus may facilitate the dissemination of antimicrobial resistance determinants. Our data suggest that pH11 is a chimera gradually assembled through the integration of different horizontally acquired DNA segments via transposition or homologous recombination. Copyright © 2016 Elsevier Inc. All rights reserved.


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