Genetic structure of four plasmids found in Acinetobacter baumannii isolate D36 belonging to lineage 2 of global clone 1

© 2018 Hamidian, Hall.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Four plasmids ranging in size from 4.7 to 44.7 kb found in the extensively antibiotic resistant Acinetobacter baumannii isolate D36 that belongs to lineage 2 of global clone 1 were examined. D36 includes two cryptic plasmids and two carrying antibiotic resistance genes. The smallest plasmid pD36-1 (4.7 kb) carries no resistance genes but includes mobA and mobC mobilisation genes related to those found in pRAY∗(pD36-2, 6,078 bp) that also carries the aadB gentamicin, kanamycin and tobramycin resistance gene cassette. These two plasmids do not encode a Rep protein. Plasmid pRAY∗ was found to be mobilised at high frequency by the large conjugative plasmid pA297-3 but a pRAY∗ derivative lacking the mobA and mobC genes was not. The two larger plasmids, pD36-3 and pD36-4, encode Rep3 family proteins (Pfam1051). The cryptic plasmid pD36-3 (6.2 kb) has RepAci1 and pD36-4 (44.7 kb) encodes two novel Rep3 family proteins suggesting a co-integrate. Plasmid pD36-4 includes the sul2 sulfonamide resistance gene, the aphA1a kanamycin/neomycin resistance gene in Tn4352::ISAba1 and a mer module in a hybrid Tn501/Tn1696 transposon conferring resistance to mercuric ions. New examples of dif modules flanked by pdif sites (XerC-XerD binding sites) that are part of many A. baumannii plasmids were also identified in pD36-3 and pD36-4 which carry three and two dif modules, respectively. Homologs of three dif modules, the sup sulphate permease module in pD36-3, and of the abkAB toxin-antitoxin module and the orf module in pD36-4, were found in different contexts in diverse Acinetobacter plasmids, consistent with module mobility. A novel insertion sequence named ISAba32 found next to the pdif site in the abkAB dif module is related to members of the ISAjo2 group which also are associated with the pdif sites of dif modules. Plasmids found in D36 were also found in some other members of GC1 lineage 2

Dissemination of novel Tn<i>7</i> family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among <i>Acinetobacter baumannii</i> isolates.

Acinetobacter baumannii is a successful opportunistic pathogen that can compete for iron under iron-limiting conditions. Here, large novel transposons that carry genes for synthesis and transport of the fimsbactin siderophores present in some A. baumannii strains were examined. Tn6171, originally found in the A. baumannii global clone 1 (GC1) lineage 2 isolate D36, includes tns genes encoding proteins related to the TnsA, TnsB, TnsC transposition proteins (50-59 % identity), TnsD targeting protein (43 % identity) and TnsE (31 % identity) of Tn7, and is found in the chromosome downstream of the glmS gene, the preferred location for Tn7, flanked by a 5 bp target site duplication. Tn6171 is bounded by 29 bp inverted repeats and, like Tn7, includes additional TnsB binding sites at each end. Tn6171 or minor variants were detected in the equivalent location in complete or draft genomes of several further A. baumannii isolates belonging to GC1 [sequence type (ST) 1, ST81, ST94, ST328, ST623, ST717], GC2 (ST2) and ST10. However, in some of these isolates the surrounding glmS region was clearly derived from a different A. baumannii lineage, indicating that the transposon may have been acquired by replacement of a segment of the chromosome. A recombination-free phylogeny revealed that there were several transposon acquisition events in GC1. The GC1 isolates were mainly lineage 2, but a potential third lineage was also detected. A related transposon, designated Tn6552, was detected in ATCC 17978 (ST437) and other ST437 isolates. However, the Tn6552 tnsD targeting gene was interrupted by an ISAba12, and Tn6552 is not downstream of glmS

Concentration and size distribution data of silicon nitride nanoparticles measured using nanoparticle tracking analysis

This article refers to the paper “A novel method for isolation and recovery of ceramic nanoparticles and metal wear debris from serum lubricants at ultra-low wear rates” (Lal et al., 2016) [1] and describes the concentration and size distribution data of silicon nitride nanoparticles measured using nanoparticle tracking analysis (NTA). A NanoSight LM10 instrument was used to capture the video data of silicon nitride nanoparticles moving under Brownian motion in the water. The video data was then analyzed using the NanoSight NTA software. This article also describes a methodology for calculating the percentage recovery of a nanoparticle isolation process

Wear simulation of a polyethylene-on-metal cervical total disc replacement under different concentrations of bovine serum lubricant

Metal-on-polyethylene total disc replacements have been an alternative to spinal fusion in the lumbar spine under certain indications for more than a decade. Recently, cervical total disc replacement has also become an alternative to cervical fusion. Knowledge acquired from years of in vitro simulator studies on other joint replacements has highlighted the risks associated with premature wear due to unforeseen adverse clinical conditions and the effect of particulate debris on surrounding natural tissues. Having no evidence of the type and composition of the lubricating fluid that will result after spinal arthroplasty, a study on the effects of lubricant serum concentration was undertaken. The wear rate was shown to be inversely proportional to protein content of the serum over a range of 50%–3% bovine serum to water concentration

A Novel Method for Isolation and Recovery of Ceramic Nanoparticles and Metal Wear Debris from Serum Lubricants at Ultra-low Wear Rates

Ceramics have been used to deliver significant improvements in the wear properties of orthopaedic bearing materials, which has made it challenging to isolate wear debris from simulator lubricants. Ceramics such as silicon nitride, as well as ceramic-like surface coatings on metal substrates have been explored as potential alternatives to conventional implant materials. Current isolation methods were designed for isolating conventional metal, UHMWPE and ceramic wear debris. In this paper, we describe a methodology for isolation and recovery of ceramic or ceramic-like coating particles and metal wear particles from serum lubricants under ultra-low and low wear performance. Enzymatic digestion was used to digest the serum proteins and sodium polytungstate was used as a novel density gradient medium to isolate particles from proteins and other contaminants by ultracentrifugation. This method demonstrated over 80% recovery of particles and did not alter the size or morphology of ceramic and metal particles during the isolation process

A novel method for isolation and recovery of ceramic nanoparticles and metal wear debris from serum lubricants at ultra-low wear rates.

UNLABELLED: Ceramics have been used to deliver significant improvements in the wear properties of orthopaedic bearing materials, which has made it challenging to isolate wear debris from simulator lubricants. Ceramics such as silicon nitride, as well as ceramic-like surface coatings on metal substrates have been explored as potential alternatives to conventional implant materials. Current isolation methods were designed for isolating conventional metal, UHMWPE and ceramic wear debris. In this paper, we describe a methodology for isolation and recovery of ceramic or ceramic-like coating particles and metal wear particles from serum lubricants under ultra-low and low wear performance. Enzymatic digestion was used to digest the serum proteins and sodium polytungstate was used as a novel density gradient medium to isolate particles from proteins and other contaminants by ultracentrifugation. This method demonstrated over 80% recovery of particles and did not alter the size or morphology of ceramic and metal particles during the isolation process. STATEMENT OF SIGNIFICANCE: Improvements in resistance to wear and mechanical damage of the articulating surfaces have a large influence on longevity and reliability of joint replacement devices. Modern ceramics have demonstrated ultra-low wear rates for hard-on-hard total hip replacements. Generation of very low concentrations of wear debris in simulator lubricants has made it challenging to isolate the particles for characterisation and further analysis. We have introduced a novel method to isolate ceramic and metal particles from serum-based lubricants using enzymatic digestion and novel sodium polytungstate gradients. This is the first study to demonstrate the recovery of ceramic and metal particles from serum lubricants at lowest detectable in vitro wear rates reported in literature

IncM Plasmid R1215 Is the Source of Chromosomally Located Regions Containing Multiple Antibiotic Resistance Genes in the Globally Disseminated Acinetobacter baumannii GC1 and GC2 Clones.

Clear similarities between antibiotic resistance islands in the chromosomes of extensively antibiotic-resistant isolates from the two dominant, globally distributed Acinetobacter baumannii clones, GC1 and GC2, suggest a common origin. A close relative of the likely progenitor of both of these regions was found in R1215, a conjugative IncM plasmid from a Serratia marcescens strain isolated prior to 1980. The 37.8-kb resistance region in R1215 lies within the mucB gene and includes aacC1, aadA1, aphA1b, bla TEM, catA1, sul1, and tetA(A), genes that confer resistance to gentamicin, streptomycin and spectinomycin, kanamycin and neomycin, ampicillin, chloramphenicol, sulfamethoxazole, and tetracycline, respectively. The backbone of this region is derived from Tn1721 and is interrupted by a hybrid Tn2670 (Tn21)-Tn1696-type transposon, Tn6020, and an incomplete Tn1. After minor rearrangements, this R1215 resistance island can generate AbGRI2-0*, the predicted earliest form of the IS26-bounded AbGRI2-type resistance island of GC2 isolates, and to the multiple antibiotic resistance region (MARR) of AbaR0, the precursor of this region in AbaR-type resistance islands in the GC1 group. A 29.9-kb circle excised by IS26 has been inserted into the A. baumannii chromosome to generate AbGRI2-0*. To create the MARR of AbaR0, a different circular form, again generated by IS26 from an R1215 resistance region variant, has been opened at a different point by recombination with a copy of the sul1 gene already present in the AbaR precursor. Recent IncM plasmids related to R1215 have a variant resistance island containing a bla SHV gene in the same location. IMPORTANCE Two lineages of extensively antibiotic-resistant A. baumannii currently plaguing modern medicine each acquired resistance to all of the original antibiotics (ampicillin, tetracycline, kanamycin, and sulfonamides) by the end of the 1970s and then became resistant to antibiotics from newer families after they were introduced in the 1980s. Here, we show that, in both of the dominant globally disseminated A. baumannii clones, a related set of antibiotic resistance genes was acquired together from the same resistance region that had already evolved in an IncM plasmid. In both cases, the action of IS26 was important in this process, but homologous recombination was also involved. The findings highlight the fact that complex regions carrying several resistance genes can evolve in one location or organism and all or part of the evolved region can then move to other locations and other organisms, conferring resistance to several antibiotics in a single step

Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2

© 2019 The Authors. The Acinetobacter baumannii global clone 1 isolate AB307-0294, recovered in the USA in 1994, and the global clone 2 (GC2) isolate ACICU, isolated in 2005 in Italy, were among the first A. baumannii isolates to be completely sequenced. AB307-0294 is susceptible to most antibiotics and has been used in many genetic studies, and ACICU belongs to a rare GC2 lineage. The complete genome sequences, originally determined using 454 pyrosequencing technology, which is known to generate sequencing errors, were re-determined using Illumina MiSeq and MinION (Oxford Nanopore Technologies) technologies and a hybrid assembly generated using Unicycler. Comparison of the resulting new high-quality genomes to the earlier 454-sequenced versions identified a large number of nucleotide differences affecting protein coding sequence (CDS) features, and allowed the sequences of the long and highly repetitive bap and blp1 genes to be properly resolved for the first time in ACICU. Comparisons of the annotations of the original and revised genomes revealed a large number of differences in the protein CDS features, underlining the impact of sequence errors on protein sequence predictions and core gene determination. On average, 400 predicted CDSs were longer or shorter in the revised genomes and about 200 CDS features were no longer present

Benthic foraminifera show some resilience to ocean acidification in the northern Gulf of California, Mexico.

The version on PEARL: Corrected proofs are Articles in Press that contain the authors' corrections. Final citation details, e.g., volume/issue number, publication year and page numbers, still need to be added and the text might change before final publication. Although corrected proofs do not have all bibliographic details available yet, they can already be cited using the year of online publication and the DOI , as follows: author(s), article title, journal (year), DOIExtensive CO2 vents have been discovered in the Wagner Basin, northern Gulf of California, where they create large areas with lowered seawater pH. Such areas are suitable for investigations of long-term biological effects of ocean acidification and effects of CO2 leakage from subsea carbon capture storage. Here, we show responses of benthic foraminifera to seawater pH gradients at 74-207m water depth. Living (rose Bengal stained) benthic foraminifera included Nonionella basispinata, Epistominella bradyana and Bulimina marginata. Studies on foraminifera at CO2 vents in the Mediterranean and off Papua New Guinea have shown dramatic long-term effects of acidified seawater. We found living calcareous benthic foraminifera in low pH conditions in the northern Gulf of California, although there was an impoverished species assemblage and evidence of post-mortem test dissolution