Biophysical properties and microfilament assembly in neutrophils: modulation by cyclic AMP

The microfilament lattice, composed primarily of filamentous (F)-actin, determines in large part the mechanical (deformability) properties of neutrophils, and thus may regulate the ability of neutrophils to transit a microvascular bed. Circulating factors may stimulate the neutrophil to become rigid and therefore be retained in the capillaries. We hypothesized that cell stiffening might be attenuated by an increase in intracellular cAMP. A combination of cell filtration and cell poking (mechanical indentation) was used to measure cell deformability. Neutrophils pretreated with dibutyryl cAMP (db-cAMP) or the combination of prostaglandin E2 (PGE2, a stimulator of adenylate cyclase) and isobutylmethylxanthine (IBMX, an inhibitor of phosphodiesterase) demonstrated significant inhibition of the n-formyl-methionyl-leucyl-phenylalanine (fMLP)-inducing stiffening. The inhibition of cell stiffening was associated with an increase in intracellular cAMP as measured by enzyme-linked immunoassay (EIA) and an increase in the activity of the cAMP-dependent kinase (A-kinase). Treatment with PGE2 and IBMX also resulted in a decrease in the F-actin content of stimulated neutrophils as assayed by NBD-phallacidin staining and flow cytometry or by changes in right angle light scattering. Direct addition of cAMP to electropermeabilized neutrophils resulted in attenuation of fMLP-induced actin assembly. Neutrophils stimulated with fMLP demonstrated a rapid redistribution of F-actin from a diffuse cortical location to a peripheral ring as assessed by conventional and scanning confocal fluorescence microscopy. Pretreatment of neutrophils with the combination of IBMX and PGE2 resulted in incomplete development and fragmentation of the cortical ring. We conclude that assembly and redistribution of F-actin may be responsible for cell stiffening after exposure to stimulants and that this response was attenuated by agents that increase intracellular cAMP, by altering the amount and spatial organization of the microfilament component of the cytoskeleton.

Activation of MEKK by formyl-methionyl-leucyl-phenylalanine in human neutrophils. Mapping pathways for mitogen-activated protein kinase activation

Mechanisms of neutrophil activation in response to chemoattractants remain incompletely understood. We have recently reported a Ras-mediated c-Raf pathway leading to the activation of mitogen-activated protein (MAP) kinase in human neutrophils stimulated with the chemoattractant formyl-Met-Leu-Phe (FMLP). However, concern that Raf activation may not fully account for the early FMLP-mediated human neutrophil responses prompted us to investigate the activation of MAP kinase/ERK kinase (MEK) by MEK kinase (MEKK). In cell lysates we identified protein species at 180, 160, 110, 72, and 54 kDa with a monoclonal antibody to MEKK. Activation of MEKK was determined on immunoprecipitates from FMLP-stimulated neutrophils by in vitro kinase assay, which utilized both MEK1 and MEK2 as substrates. It was rapid, detectable at 30 s and reaching a plateau at 5 min, and it was inhibited in a dose-dependent fashion by a specific phosphatidylinositol 3-kinase inhibitor, wortmannin. Partial inhibition by pertussis toxin was observed. We were unable to show inhibition of the MEKK response by GF 109203X, a protein kinase C-specific inhibitor. These data indicate that in neutrophils activation of MEKK in addition to Raf may underlie stimulation of MAP kinase and other MAP kinase homologues by FMLP.

Aberrant wound healing and TGF-beta production in the autoimmune-prone MRL/+ mouse

Wound healing is a complex process that involves inflammation, apoptosis, growth, and tissue remodeling. The autoimmune-prone inbred mouse strain MRL/+ manifests accelerated and extensive healing to ear punch wounds, suggesting a link between immune defects and wound healing. Prior studies with lupus-prone mice have shown that hematopoietic cells of lupus-prone strains can transfer disease to otherwise non-autoimmune-prone recipients. In this study we performed reciprocal bone marrow transfers between MRL and the control strain B10.BR and found that radioresistant MRL/+ host cells, rather than hematopoietic cells, are required for the healing response. We have also made the novel observations that, compared to normal controls, MRL/+ hematopoietic cells overproduce TGF-beta1 and manifest impaired inflammatory responses to lipopolysaccharide challenge. These features suggest that the aberrant wound healing phenotype of MRL mice is independent of their propensity to develop autoimmunity.

Analysis of high-throughput sequencing and annotation strategies for phage genomes

Background

Bacterial viruses (phages) play a critical role in shaping microbial populations as they influence both host mortality and horizontal gene transfer. As such, they have a significant impact on local and global ecosystem function and human health. Despite their importance, little is known about the genomic diversity harbored in phages, as methods to capture complete phage genomes have been hampered by the lack of knowledge about the target genomes, and difficulties in generating sufficient quantities of genomic DNA for sequencing. Of the approximately 550 phage genomes currently available in the public domain, fewer than 5% are marine phage.

Methodology/Principal Findings

To advance the study of phage biology through comparative genomic approaches we used marine cyanophage as a model system. We compared DNA preparation methodologies (DNA extraction directly from either phage lysates or CsCl purified phage particles), and sequencing strategies that utilize either Sanger sequencing of a linker amplification shotgun library (LASL) or of a whole genome shotgun library (WGSL), or 454 pyrosequencing methods. We demonstrate that genomic DNA sample preparation directly from a phage lysate, combined with 454 pyrosequencing, is best suited for phage genome sequencing at scale, as this method is capable of capturing complete continuous genomes with high accuracy. In addition, we describe an automated annotation informatics pipeline that delivers high-quality annotation and yields few false positives and negatives in ORF calling.

Conclusions/Significance

These DNA preparation, sequencing and annotation strategies enable a high-throughput approach to the burgeoning field of phage genomics.

Medium-chain-triglyceride lipid emulsion: metabolism and tissue distribution

The utilization and distribution of radioactively labeled lipid emulsions were evaluated in Sprague-Dawley rats. Animals received one of three lipid emulsions. Group 1 received [14C]medium-chain-triglyceride (MCT) lipid emulsion, group 2 received a 75%:25% (vol:vol) admixture of [14C]MCT: unlabeled long-chain-triglyceride (LCT) lipid emulsion, and group 3 received only [14C]LCT. The radioactive dose appearing in expired carbon dioxide and various body tissues was monitored over a 24-h period. Results indicate that MCT is oxidized more rapidly and completely than in LCT; approximately 90% of the MCT is converted to carbon dioxide with in 24 h compared with 45% for LCT. When MCT and LCT are administered together, the metabolism of MCT is slowed but remains more rapid than that of LCT. Removal of MCT from the blood was more rapid than was removal of LCT, and tissue radioactivity was lower.

Comparative genomics and transcriptomics of Pichia pastoris

Background

Pichia pastoris has emerged as an important alternative host for producing recombinant biopharmaceuticals, owing to its high cultivation density, low host cell protein burden, and the development of strains with humanized glycosylation. Despite its demonstrated utility, relatively little strain engineering has been performed to improve Pichia, due in part to the limited number and inconsistent frameworks of reported genomes and transcriptomes. Furthermore, the co-mingling of genomic, transcriptomic and fermentation data collected about Komagataella pastoris and Komagataella phaffii, the two strains co-branded as Pichia, has generated confusion about host performance for these genetically distinct species. Generation of comparative high-quality genomes and transcriptomes will enable meaningful comparisons between the organisms, and potentially inform distinct biotechnological utilies for each species.

Results

Here, we present a comprehensive and standardized comparative analysis of the genomic features of the three most commonly used strains comprising the tradename Pichia: K. pastoris wild-type, K. phaffii wild-type, and K. phaffii GS115. We used a combination of long-read (PacBio) and short-read (Illumina) sequencing technologies to achieve over 1000X coverage of each genome. Construction of individual genomes was then performed using as few as seven individual contigs to create gap-free assemblies. We found substantial syntenic rearrangements between the species and characterized a linear plasmid present in K. phaffii. Comparative analyses between K. phaffii genomes enabled the characterization of the mutational landscape of the GS115 strain. We identified and examined 35 non-synonomous coding mutations present in GS115, many of which are likely to impact strain performance. Additionally, we investigated transcriptomic profiles of gene expression for both species during cultivation on various carbon sources. We observed that the most highly transcribed genes in both organisms were consistently highly expressed in all three carbon sources examined. We also observed selective expression of certain genes in each carbon source, including many sequences not previously reported as promoters for expression of heterologous proteins in yeasts.

Conclusions

Our studies establish a foundation for understanding critical relationships between genome structure, cultivation conditions and gene expression. The resources we report here will inform and facilitate rational, organism-wide strain engineering for improved utility as a host for protein production.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2876-y) contains supplementary material, which is available to authorized users.

Analysis of the DNA sequence and duplication history of human chromosome 15

Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.

Paired-end sequencing of Fosmid libraries by Illumina

Eliminating the bacterial cloning step has been a major factor in the vastly improved efficiency of massively parallel sequencing approaches. However, this also has made it a technical challenge to produce the modern equivalent of the Fosmid- or BAC-end sequences that were crucial for assembling and analyzing complex genomes during the Sanger-based sequencing era. To close this technology gap, we developed Fosill, a method for converting Fosmids to Illumina-compatible jumping libraries. We constructed Fosmid libraries in vectors with Illumina primer sequences and specific nicking sites flanking the cloning site. Our family of pFosill vectors allows multiplex Fosmid cloning of end-tagged genomic fragments without physical size selection and is compatible with standard and multiplex paired-end Illumina sequencing. To excise the bulk of each cloned insert, we introduced two nicks in the vector, translated them into the inserts, and cleaved them. Recircularization of the vector via coligation of insert termini followed by inverse PCR generates a jumping library for paired-end sequencing with 101-base reads. The yield of unique Fosmid-sized jumps is sufficiently high, and the background of short, incorrectly spaced and chimeric artifacts sufficiently low, to enable applications such as mapping of structural variation and scaffolding of de novo assemblies. We demonstrate the power of Fosill to map genome rearrangements in a cancer cell line and identified three fusion genes that were corroborated by RNA-seq data. Our Fosill-powered assembly of the mouse genome has an N50 scaffold length of 17.0 Mb, rivaling the connectivity (16.9 Mb) of the Sanger-sequencing based draft assembly.

Evolutionary dynamics of the accessory genome of Listeria monocytogenes

Listeria monocytogenes, a foodborne bacterial pathogen, is comprised of four phylogenetic lineages that vary with regard to their serotypes and distribution among sources. In order to characterize lineage-specific genomic diversity within L. monocytogenes, we sequenced the genomes of eight strains from several lineages and serotypes, and characterized the accessory genome, which was hypothesized to contribute to phenotypic differences across lineages. The eight L. monocytogenes genomes sequenced range in size from 2.85-3.14 Mb, encode 2,822-3,187 genes, and include the first publicly available sequenced representatives of serotypes 1/2c, 3a and 4c. Mapping of the distribution of accessory genes revealed two distinct regions of the L. monocytogenes chromosome: an accessory-rich region in the first 65° adjacent to the origin of replication and a more stable region in the remaining 295°. This pattern of genome organization is distinct from that of related bacteria Staphylococcus aureus and Bacillus cereus. The accessory genome of all lineages is enriched for cell surface-related genes and phosphotransferase systems, and transcriptional regulators, highlighting the selective pressures faced by contemporary strains from their hosts, other microbes, and their environment. Phylogenetic analysis of O-antigen genes and gene clusters predicts that serotype 4 was ancestral in L. monocytogenes and serotype 1/2 associated gene clusters were putatively introduced through horizontal gene transfer in the ancestral population of L. monocytogenes lineage I and II.

Improved Limits on Scattering of Weakly Interacting Massive Particles from Reanalysis of 2013 LUX Data

We present constraints on weakly interacting massive particles (WIMP)-nucleus scattering from the 2013 data of the Large Underground Xenon dark matter experiment, including 1.4×10^{4}  kg day of search exposure. This new analysis incorporates several advances: single-photon calibration at the scintillation wavelength, improved event-reconstruction algorithms, a revised background model including events originating on the detector walls in an enlarged fiducial volume, and new calibrations from decays of an injected tritium β source and from kinematically constrained nuclear recoils down to 1.1 keV. Sensitivity, especially to low-mass WIMPs, is enhanced compared to our previous results which modeled the signal only above a 3 keV minimum energy. Under standard dark matter halo assumptions and in the mass range above 4  GeV c^{-2}, these new results give the most stringent direct limits on the spin-independent WIMP-nucleon cross section. The 90% C.L. upper limit has a minimum of 0.6 zb at 33  GeV c^{-2} WIMP mass.

DNA sequence and analysis of human chromosome 18

Chromosome 18 appears to have the lowest gene density of any human chromosome and is one of only three chromosomes for which trisomic individuals survive to term. There are also a number of genetic disorders stemming from chromosome 18 trisomy and aneuploidy. Here we report the finished sequence and gene annotation of human chromosome 18, which will allow a better understanding of the normal and disease biology of this chromosome. Despite the low density of protein-coding genes on chromosome 18, we find that the proportion of non-protein-coding sequences evolutionarily conserved among mammals is close to the genome-wide average. Extending this analysis to the entire human genome, we find that the density of conserved non-protein-coding sequences is largely uncorrelated with gene density. This has important implications for the nature and roles of non-protein-coding sequence elements.

Dissociation between emotional and endocrine responses preceding an academic examination in male medical students

A study was made in 2 consecutive years of the emotional states and morning and afternoon serum levels of prolactin, cortisol and testosterone of male medical students during a 4- to 5-week period preceding a major university examination. 'Distress', 'anxiety' and, to a lesser degree, 'depression' increased during the 2 weeks immediately preceding the examination and were positively correlated with personality anxiety or neuroticism traits. Group means for hormones showed no consistent change over the same period. Neither was there evidence for a correlation between endocrine and emotional changes within individual students during the pre-examination period. A restricted study showed that there were significant increments in cortisol in samples taken during the examination itself. Changes in emotional state before an examination occurred in the absence of equally dramatic changes in levels of the three hormones studied, though this relationship may have altered during the examination itself. This suggests that the factors controlling the two categories of response may relate differently, in some way, to the imminence of this stressful event.

The relations between temperament and empathy in 2-year-olds

The role of infant and toddler temperament in the prediction of empathy in 2-year-old children was examined. Assessments of temperament included reactivity and affect observed at 4 months of age, as well as inhibition at Age 2. Empathy was measured in 2-year-old children's responses to simulations of distress performed by their mothers and by an unfamiliar person. Children showed relatively more concern for the mother's distress, but they were also responsive to unfamiliar victims. Infants who were unreactive and showed little affect also showed less empathy toward the unfamiliar adult almost 2 years later. Inhibition toward an unfamiliar adult (but not toward the mother) at 2 years of age was negatively related to empathy. Inhibited temperament may thus have a major impact on young children's empathy in unfamiliar contexts. Findings also highlight the need to consider early underarousal as another dimension of temperament that may dampen expressions of empathic concern.

Engineering design of vascular prostheses

The replacement and bypass of arteries of diameter greater than 6 mm with textile vascular prostheses has proved very successful since they were first introduced forty years ago. Although manufacturers continue to improve their products and make them of consistent quality for increased safety and performance and to facilitate their use by surgeons, most of the research work in this area is concerned with the development of small-diameter prostheses. Current expanded PTFE and textile prostheses do not perform satisfactorily when their diameters are reduced to less than 6 mm. For the small-diameter prostheses it will be necessary to develop less thrombogenic materials and to design the structure of the prostheses more closely to match the mechanical properties of the natural arteries. The purpose of this paper is to discuss the design requirements and to review the development of large- and small-diameter vascular prostheses.

Spiteful interactions between sympatric natural isolates of Xenorhabdus bovienii benefit kin and reduce virulence

Spite occurs when an individual harms itself in the act of harming others. Spiteful behaviour may be more pervasive in nature than commonly thought. One of the clearest examples of spite is the costly production and release of bacteriocins, antimicrobial toxins noted for their ability to kill conspecifics. A key question is to what extent these toxins provide a fitness advantage to kin of the producer cell, especially in natural communities. Additionally, when bacteria are involved in parasitic relationships, spiteful interactions are predicted to lower bacterial densities within a host, causing a reduction in parasite-induced virulence. Using five sympatric, field-collected genotypes of the insect pathogen Xenorhabdus bovienii, we experimentally demonstrate that bacteriocin production benefits kin within the host, and that it slows the mortality rate of the host. These results confirm that spite among naturally coexisting bacterial clones can be a successful kin-selected strategy that has emergent effects on virulence.

In vivo delivery of recombinant human growth hormone from genetically engineered human fibroblasts implanted within Baxter immunoisolation devices

Continuous delivery of therapeutic peptide to the systemic circulation would be the optimal treatment for a variety of diseases. The Baxter TheraCyte system is a membrane encapsulation system developed for implantation of tissues, cells such as endocrine cells or cell lines genetically engineered for therapeutic peptide delivery in vivo. To demonstrate the utility of this system, cell lines were developed which expressed human growth hormone (hGH) at levels exceeding 1 microgram per million cells per day. These were loaded into devices which were then implanted into juvenile nude rats. Significant levels of hGH of up to 2.5 ng/ml were detected in plasma throughout the six month duration of the study. In contrast, animals implanted with free cells showed peak plasma levels of 0.5 to 1.2 ng four days after implantation with no detectable hGH beyond 10 days. Histological examination of explanted devices showed they were vascularized and contained cells that were viable and morphologically healthy. After removal of the implants, no hGH could be detected which confirmed that the source of hGH was from cells contained within the device. The long term expression of human growth hormone as a model peptide has implications for the peptide therapies for a variety of human diseases using membrane encapsulated cells.

Congenital epulis (gingival granular cell tumor): ultrastructural evidence of origin from pericytes

The congenital epulis (gingival granular cell tumor) is a rare lesion of unknown origin found only in newborn infants. Remarkable similarities are noted between this lesion and the adult granular cell tumor (myoblastoma) by both light and electron microscopy. An electron microscopic study of a lesion from the anterior mandibular ridge in a newborn male infant was performed. No Schwann cells, axon fibers, odontogenic elements, or any muscle cells could be found. Cytoplasmic features were similar to those in adult granular cell tumors. Cells which appeared to be in a transitional state, not yet true granular cells, were found juxtaposed to the vessels in the position of pericytes. Fine-structure details of these cells were consistent with pericytes. Cells of this type found farther from the vessels appeared more like the typical granular cells. The cells were filled with structures of the autophagic type devoid of normal cell organelles. These findings support the theory that these are nonneoplastic, degenerative, or reactive lesions arising from a mesenchymal cell, possibly the pericyte.

Linkage to the mating-type locus across the genus Microbotryum: insights into nonrecombining chromosomes

Parallels have been drawn between the evolution of nonrecombining regions in fungal mating-type chromosomes and animal and plant sex chromosomes, particularly regarding the stages of recombination cessation forming evolutionary strata of allelic divergence. Currently, evidence and explanations for recombination cessation in fungi are sparse, and the presence of evolutionary strata has been examined in a minimal number of fungal taxa. Here, the basidiomycete genus Microbotryum was used to determine the history of recombination cessation for loci on the mating-type chromosomes. Ancestry of linkage with mating type for 13 loci was assessed across 20 species by a phylogenetic method. No locus was found to exhibit trans-specific polymorphism for alternate alleles as old as the mating pheromone receptor, indicating that ages of linkage to mating type varied among the loci. The ordering of loci in the ancestry of linkage to mating type does not agree with their previously proposed assignments to evolutionary strata. This study suggests that processes capable of influencing divergence between alternate alleles may act at loci in the nonrecombining regions (e.g., gene conversion) and encourages further work to dissect the evolutionary processes acting upon genomic regions that determine mating compatibility.

Desmoplastic fibroma of the mandible in a child: report of a case

A 6-year-old girl was seen with a history of progressive trismus and expansion of the right mandible over a 9-month period. Desmoplastic fibroma was diagnosed on biopsy. This report reviews the diagnostic criteria and surgical management of this uncommon primary bone tumor of the maxillofacial region.

Factors related to failure of structural bone grafts in acetabular reconstruction of total hip arthroplasty

Structural bone grafts in acetabular reconstruction of total hip arthroplasty have come into more common usage with the increasing number of revision arthroplasties. The authors present the outcome of 40 bone grafts with follow-up periods of 2-8 years. Primary and revision arthroplasties with both cemented and noncemented fixation are included. Factors that had a statistically significant relationship to failure of the bone graft included fit and fixation of bone graft to host, fit and fixation of prosthesis to host, union of bone graft to host, and the presence or absence of the confluence of the anterior and posterior columns of the acetabulum. Other findings of interest were a higher failure rate of multiple grafts as compared to a single graft and freeze-dried femoral heads. Migration of the socket of more than 3 mm is statistically related to failure of the socket.

Induction of Th1 cytokine responses by mycobacterial antigens in leprosy

Twelve mycobacterial antigens were compared for induction of gamma interferon (IFN-gamma) secretion by human blood mononuclear cells of patients with leprosy. Fractionated Mycobacterium leprae antigens containing cell wall proteins or cytosolic and membrane proteins induced good IFN-gamma responses in tuberculoid leprosy patients. Lipoarabinomannan from M. tuberculosis Erdman and M. leprae mycolylarabinogalactan peptidoglycan were the poorest IFN-gamma inducers.

Type four fracture of the medial epicondyle: a true indication for surgical intervention

Fourteen consecutive cases with type 4 fracture of the medial epicondyle were evaluated following open reduction and internal fixation of the displaced medial epicondyle. The mean age was 9.7 years (range 6-16) and the mean follow-up was 17.2 months (range 12-24). Operative treatment yielded excellent results with no loss of functional range of motion, residual deformity or instability. There were three cases with pre-operative symptoms of ulnar nerve injury which made a good recovery following neurolysis of the ulnar nerve. Type 4 fractures are commonly associated with intra-articular entrapment of the ulnar nerve and result from serious damage to the soft tissues on the medial side of the elbow. Assessing instability is therefore of key importance, as is the intra-operative gravity stress-valgus test in assessing instability.

Control of bleeding in cemented arthroplasty

Bleeding from cancellous bone causes lamination within bone cement and at its prosthetic interfaces, and weakens the fixation of joint replacements. We examined the effects of anaesthesia and blood pressure on bleeding in human cancellous bone, and investigated the local response to freezing saline, 1:200,000 adrenaline and hydrogen peroxide. Spinal anaesthesia reduced cancellous bleeding by an average of 44%, local freezing saline by 24%. Saline at room temperature, adrenaline solution and hydrogen peroxide each reduced it by 14%. The effects of spinal anaesthesia and of freezing saline were additive: used together they reduced bleeding by 56%. The reduction of blood contamination of cement and its interfaces should contribute to better prosthetic fixation.

Intravascular angiomatosis

For 55 years much has been written about a peculiar benign intravascular process which can be misdiagnosed as angiosarcoma unless careful attention is paid by the pathologist to its benign cellular morphology and growth pattern. The cases reported in the literature demonstrate an increased incidence in the extremities and the head and neck, with a propensity for the subcutaneous tissues of the perioral region. Four cases are presented to further point out the perioral incidence and emphasize the differential diagnostic criteria for benignancy, including intravascular proliferation without atypical mitotic activity and necrosis in areas devoid of vascular differentiation.

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

BACKGROUND

Carbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole-genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms.

METHODS

To overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem-susceptible Enterobacterales, isolated from patients from four US hospitals over nearly 5 years.

RESULTS

Our CRE collection comprised a diverse range of species, lineages, and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment.

CONCLUSIONS

Collectively, the framework we developed provides a clearer, high-resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.