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To develop a map of cell-cell communication mediated by extracellular RNA (exRNA), the NIH Extracellular RNA Communication Consortium created the exRNA Atlas resource (https://exrna-atlas.org). The Atlas version 4P1 hosts 5,309 exRNA-seq and exRNA qPCR profiles from 19 studies and a suite of analysis and visualization tools. To analyze variation between profiles, we apply computational deconvolution. The analysis leads to a model with six exRNA cargo types (CT1, CT2, CT3A, CT3B, CT3C, CT4), each detectable in multiple biofluids (serum, plasma, CSF, saliva, urine). Five of the cargo types associate with known vesicular and non-vesicular (lipoprotein and ribonucleoprotein) exRNA carriers. To validate utility of this model, we re-analyze an exercise response study by deconvolution to identify physiologically relevant response pathways that were not detected previously. To enable wide application of this model, as part of the exRNA Atlas resource, we provide tools for deconvolution and analysis of user-provided case-control studies.
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Comunicação Celular/fisiologia , RNA/metabolismo , Adulto , Líquidos Corporais/química , Ácidos Nucleicos Livres/metabolismo , MicroRNA Circulante/metabolismo , Vesículas Extracelulares/metabolismo , Feminino , Humanos , Masculino , Reprodutibilidade dos Testes , Análise de Sequência de RNA/métodos , SoftwareRESUMO
BACKGROUND: Staphylococcus aureus can infect and adapt to multiple host species. However, our understanding of the genetic and evolutionary drivers of its generalist lifestyle remains inadequate. This is particularly important when considering local populations of S. aureus, where close physical proximity between bacterial lineages and between host species may facilitate frequent and repeated interactions between them. Here, we aim to elucidate the genomic differences between human- and animal-derived S. aureus from 437 isolates sampled from disease cases in the northeast region of the United States. RESULTS: Multi-locus sequence typing revealed the existence of 75 previously recognized sequence types (ST). Our population genomic analyses revealed heterogeneity in the accessory genome content of three dominant S. aureus lineages (ST5, ST8, ST30). Genes related to antimicrobial resistance, virulence, and plasmid types were differentially distributed among isolates according to host (human versus non-human) and among the three major STs. Across the entire population, we identified a total of 1,912 recombination events that occurred in 765 genes. The frequency and impact of homologous recombination were comparable between human- and animal-derived isolates. Low-frequency STs were major donors of recombined DNA, regardless of the identity of their host. The most frequently recombined genes (clfB, aroA, sraP) function in host infection and virulence, which were also frequently shared between the rare lineages. CONCLUSIONS: Taken together, these results show that frequent but variable patterns of recombination among co-circulating S. aureus lineages, including the low-frequency lineages, that traverse host barriers shape the structure of local gene pool and the reservoir of host-associated genetic variants. Our study provides important insights to the genetic and evolutionary factors that contribute to the ability of S. aureus to colonize and cause disease in multiple host species. Our study highlights the importance of continuous surveillance of S. aureus circulating in different ecological host niches and the need to systematically sample from them. These findings will inform development of effective measures to control S. aureus colonization, infection, and transmission across the One Health continuum.
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Pool Gênico , Infecções Estafilocócicas , Animais , Tipagem de Sequências Multilocus , Staphylococcus aureus/genética , Evolução BiológicaRESUMO
BACKGROUND: The implementation of whole genome sequencing (WGS) by PulseNet, the molecular subtyping network for foodborne diseases, has transformed surveillance, outbreak detection, and public health laboratory practices in the United States. In 2017, the New Hampshire Public Health Laboratories, a member of PulseNet, commenced the use of WGS in tracking foodborne pathogens across the state. We present some of the initial results of New Hampshire's initiative to transition to WGS in tracking Salmonella enterica, a bacterial pathogen that is responsible for non-typhoidal foodborne infections and enteric fever. We characterize the population structure and evolutionary history of 394 genomes of isolates recovered from human clinical cases in New Hampshire from 2017 to 2020. RESULTS: The New Hampshire S. enterica population is phylogenetically diverse, consisting of 78 sequence types (ST) and 67 serotypes. Six lineages dominate the population: ST 11 serotype Enteritidis, ST 19 Typhimurium, ST 32 Infantis, ST 118 Newport, ST 22 Braenderup, and ST 26 Thompson. Each lineage is derived from long ancestral branches in the phylogeny, suggesting their extended presence in the region and recent clonal expansion. We detected 61 genes associated with resistance to 14 antimicrobial classes. Of these, unique genes of five antimicrobial classes (aminocoumarins, aminoglycosides, fluoroquinolones, nitroimidazoles, and peptides) were detected in all genomes. Rather than a single clone carrying multiple resistance genes expanding in the state, we found multiple lineages carrying different combinations of independently acquired resistance determinants. We estimate the time to the most recent common ancestor of the predominant lineage ST 11 serotype Enteritidis (126 genomes) to be 1965 (95% highest posterior density intervals: 1927-1982). Its population size expanded until 1978, followed by a population decline until 1990. This lineage has been expanding since then. Comparison with genomes from other states reveal lack of geographical clustering indicative of long-distance dissemination. CONCLUSIONS: WGS studies of standing pathogen diversity provide critical insights into the population and evolutionary dynamics of lineages and antimicrobial resistance, which can be translated to effective public health action and decision-making. We highlight the need to strengthen efforts to implement WGS-based surveillance and genomic data analyses in state public health laboratories.
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Salmonella enterica , Febre Tifoide , Animais , Antibacterianos/farmacologia , Genoma Bacteriano , Humanos , Laboratórios , New Hampshire , Filogenia , Saúde Pública , Estados Unidos , Sequenciamento Completo do Genoma/métodosRESUMO
OBJECTIVE: Surveillance tools for early cancer detection are suboptimal, including hepatocellular carcinoma (HCC), and biomarkers are urgently needed. Extracellular vesicles (EVs) have gained increasing scientific interest due to their involvement in tumour initiation and metastasis; however, most extracellular RNA (exRNA) blood-based biomarker studies are limited to annotated genomic regions. DESIGN: EVs were isolated with differential ultracentrifugation and integrated nanoscale deterministic lateral displacement arrays (nanoDLD) and quality assessed by electron microscopy, immunoblotting, nanoparticle tracking and deconvolution analysis. Genome-wide sequencing of the largely unexplored small exRNA landscape, including unannotated transcripts, identified and reproducibly quantified small RNA clusters (smRCs). Their key genomic features were delineated across biospecimens and EV isolation techniques in prostate cancer and HCC. Three independent exRNA cancer datasets with a total of 479 samples from 375 patients, including longitudinal samples, were used for this study. RESULTS: ExRNA smRCs were dominated by uncharacterised, unannotated small RNA with a consensus sequence of 20 nt. An unannotated 3-smRC signature was significantly overexpressed in plasma exRNA of patients with HCC (p<0.01, n=157). An independent validation in a phase 2 biomarker case-control study revealed 86% sensitivity and 91% specificity for the detection of early HCC from controls at risk (n=209) (area under the receiver operating curve (AUC): 0.87). The 3-smRC signature was independent of alpha-fetoprotein (p<0.0001) and a composite model yielded an increased AUC of 0.93. CONCLUSION: These findings directly lead to the prospect of a minimally invasive, blood-only, operator-independent clinical tool for HCC surveillance, thus highlighting the potential of unannotated smRCs for biomarker research in cancer.
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BACKGROUND: Bloodstream infections due to Staphylococcus aureus cause significant patient morbidity and mortality worldwide. Of major concern is the emergence and spread of methicillin-resistant S. aureus (MRSA) in bloodstream infections, which are associated with therapeutic failure and increased mortality. METHODS: We generated high quality draft genomes from 323 S. aureus blood culture isolates from patients diagnosed with bloodstream infection at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA in 2010-2018. RESULTS: In silico detection of antimicrobial resistance genes revealed that 133/323 isolates (41.18%) carry horizontally acquired genes conferring resistance to at least three antimicrobial classes, with resistance determinants for aminoglycosides, beta-lactams and macrolides being the most prevalent. The most common resistance genes were blaZ and mecA, which were found in 262/323 (81.11%) and 104/323 (32.20%) isolates, respectively. Majority of the MRSA (102/105 isolates or 97.14%) identified using in vitro screening were related to two clonal complexes (CC) 5 and 8. The two CCs emerged in the New Hampshire population at separate times. We estimated that the time to the most recent common ancestor of CC5 was 1973 (95% highest posterior density (HPD) intervals: 1966-1979) and 1946 for CC8 (95% HPD intervals: 1924-1959). The effective population size of CC8 increased until the late 1960s when it started to level off until late 2000s. The levelling off of CC8 in 1968 coincided with the acquisition of SCCmec Type IV in majority of the strains. The plateau in CC8 also coincided with the acceleration in the population growth of CC5 carrying SCCmec Type II in the early 1970s, which eventually leveled off in the early 1990s. Lastly, we found evidence for frequent recombination in the two clones during their recent clonal expansion, which has likely contributed to their success in the population. CONCLUSIONS: We conclude that the S. aureus population was shaped mainly by the clonal expansion, recombination and co-dominance of two major MRSA clones in the last five decades in New Hampshire, USA. These results have important implications on the development of effective and robust strategies for intervention, control and treatment of life-threatening bloodstream infections.
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Staphylococcus aureus Resistente à Meticilina/genética , Sepse/microbiologia , Infecções Estafilocócicas/tratamento farmacológico , Staphylococcus aureus/genética , Antibacterianos/uso terapêutico , Farmacorresistência Bacteriana , Genômica , Humanos , Staphylococcus aureus Resistente à Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Sepse/tratamento farmacológico , Sepse/virologia , Infecções Estafilocócicas/virologia , Staphylococcus aureus/efeitos dos fármacos , Staphylococcus aureus/isolamento & purificaçãoRESUMO
Deterministic lateral displacement (DLD) is a technique for size fractionation of particles in continuous flow that has shown great potential for biological applications. Several theoretical models have been proposed, but experimental evidence has demonstrated that a rich class of intermediate migration behavior exists, which is not predicted. We present a unified theoretical framework to infer the path of particles in the whole array on the basis of trajectories in a unit cell. This framework explains many of the unexpected particle trajectories reported and can be used to design arrays for even nanoscale particle fractionation. We performed experiments that verify these predictions and used our model to develop a condenser array that achieves full particle separation with a single fluidic input.
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Advances in colorectal cancer (CRC) diagnosis will be enhanced by development of more sensitive and reliable methods for early detection of the disease when treatment is more effective. Because many known disease biomarkers are membrane-bound glycoproteins with important biological functions, we chose to compare N-glycan profiles of membrane proteins from three phenotypically different CRC cell lines, LIM1215, LIM1899, and LIM2405, representing moderately differentiated metastatic, moderately differentiated primary, and poorly differentiated (aggressive) primary CRC cell lines, respectively. The N-glycan structures and their relative abundances were determined as their underivatized reduced forms, using porous graphitized carbon LC-ESI-MS/MS. A key observation was the similar N-glycan landscape in these cells with the dominance of high mannose type glycan structures (70-90%) in all three cell lines, suggesting an incomplete glycan processing. Importantly, unique glycan determinants such as bisecting N-acetylglucosamine were observed at a high level in the metastatic LIM1215 cells, with some expressed in the moderately differentiated LIM1899, while none were detected in the poorly differentiated LIM2405 cells. Conversely, α-2,3-sialylation was completely absent in LIM1215 and LIM1899 and present only in LIM2405. RNA-Seq and lectin immunofluorescence data correlated well with these data, showing the highest upregulation of Mgat3 and binding with PHA-E in LIM1215. Downregulation of Man1α1 and Mgat1 in LIM1215 also coincided with the higher degree of incomplete N-glycan processing and accumulation of high mannose type structures as well as bisecting N-glycans when compared to the other two cell lines. This study provides a comprehensive analysis of the membrane N-glycome in three CRC cell lines and identifies N-glycosylation differences that correlate with the histological and pathological features of the cell lines. The unique glycosylation phenotypes may therefore serve as a molecular feature to differentiate CRC disease stages.
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Acetilglucosamina/metabolismo , Neoplasias Colorretais/metabolismo , Proteínas de Membrana/metabolismo , Metástase Neoplásica , Polissacarídeos/metabolismo , Linhagem Celular Tumoral , Neoplasias Colorretais/patologia , HumanosRESUMO
Among the challenges hindering the integration of carbon nanotube (CNT) transistors in digital technology are the lack of a scalable self-aligned gate and complementary n- and p-type devices. We report CNT transistors with self-aligned gates scaled down to 20 nm in the ideal gate-all-around geometry. Uniformity of the gate wrapping the nanotube channels is confirmed, and the process is shown not to damage the CNTs. Further, both n- and p-type transistors were realized by using the appropriate gate dielectric-HfO2 yielded n-type and Al2O3 yielded p-type-with quantum simulations used to explore the impact of important device parameters on performance. These discoveries not only provide a promising platform for further research into gate-all-around CNT devices but also demonstrate that scalable digital switches with realistic technological potential can be achieved with carbon nanotubes.
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Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.
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As part of the genome-wide and chromosome-centric human proteomic project (C-HPP), we have integrated shotgun proteomics approach and a genome-wide transcriptomic approach (RNA-Seq) of a set of human colon cancer cell lines (LIM1215, LIM1899 and LIM2405) that were selected to represent a wide range of pathological states of colorectal cancer. The combination of a standard proteomics approach (1D-gel electrophoresis coupled to LC/ion trap mass spectrometry) and RNA-Seq allowed us to exploit the greater depth of the transcriptomics measurement (â¼ 9800 transcripts per cell line) versus the protein observations (â¼ 1900 protein identifications per cell line). Conversely, the proteomics data were helpful in identifying both cancer associated proteins with differential expression patterns as well as protein networks and pathways which appear to be deregulated in these cell lines. Examples of potential markers include mortalin, nucleophosmin, ezrin, LASP1, alpha and beta forms of spectrin, exportin, the carcinoembryonic antigen family, EGFR and MET. Interaction analyses identified the large intermediate filament family, the protein folding network and adapter proteins in focal adhesion networks, which included the CDC42 and RHOA signaling pathways that may have potential for identifying phenotypic states representing poorly and moderately differentiated states of CRC, with or without metastases.
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Neoplasias do Colo/genética , Neoplasias do Colo/metabolismo , Proteoma/análise , Proteômica/métodos , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Diferenciação Celular , Linhagem Celular Tumoral , Neoplasias do Colo/patologia , Regulação Neoplásica da Expressão Gênica , Humanos , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Mapeamento de Interação de Proteínas , Proteoma/genética , Proteoma/metabolismo , RNA Mensageiro/análise , Transdução de Sinais , Proteína cdc42 de Ligação ao GTP/metabolismo , Proteína rhoA de Ligação ao GTP/metabolismoRESUMO
In this manuscript, we describe a shotgun proteomics approach for a comprehensive proteomic analysis of samples including total lysates, membrane, secretome, and exosome fractions from a panel of colorectal cancer cell lines. We will present an analysis of our proteomics data in two alternative formats. First we will discuss a traditional analysis of our data, in which we identify a number of cancer-associated proteins using various proteomic data analysis tools. In a second approach, we use a chromosome format to organize the proteomic data on chromosome 7, allowing the identification of clusters of cancer-associated genes with boundaries defined by physical proximity on different chromosomes.
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Cromossomos Humanos Par 7 , Neoplasias do Colo , Proteínas , Proteoma , Carcinoma/genética , Carcinoma/metabolismo , Linhagem Celular Tumoral , Deleção Cromossômica , Cromossomos Humanos Par 7/genética , Cromossomos Humanos Par 7/metabolismo , Neoplasias do Colo/genética , Neoplasias do Colo/metabolismo , Bases de Dados de Proteínas , Genoma Humano , Projeto Genoma Humano , Humanos , Proteínas/classificação , Proteínas/genética , Proteínas/metabolismoRESUMO
Carbapenem-resistant Enterobacterales (CRE) are important pathogens that can develop resistance via multiple molecular mechanisms, including hydrolysis or reduced antibiotic influx. Identifying these mechanisms can improve pathogen surveillance, infection control, and patient care. We investigated how resistance mechanisms influence the carbapenem inoculum effect (IE), a phenomenon where inoculum size affects antimicrobial susceptibility testing (AST). We demonstrated that seven different carbapenemases impart a meropenem IE in Escherichia coli. Across 110 clinical CRE isolates, the carbapenem IE strictly depended on resistance mechanism: all carbapenemase-producing CRE (CP-CRE) exhibited a strong IE, whereas porin-deficient CRE displayed none. Concerningly, 50% and 24% of CP-CRE isolates changed susceptibility classification to meropenem and ertapenem, respectively, across the allowable inoculum range in clinical guidelines. The meropenem IE, and the ratio of ertapenem to meropenem minimal inhibitory concentration (MIC) at standard inoculum, reliably identified CP-CRE. Understanding how resistance mechanisms affect AST could improve diagnosis and guide therapies for CRE infections.
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Appropriately controlling the properties of the Si shell in Ge/Si core/shell nanowires permits not only passivation of the Ge surface states, but also introduces new interface phenomena, thereby enabling novel nanoelectronics concepts. Here, we report a rational synthesis of Ge/Si core/shell nanowires with doped Si shells. We demonstrate that the morphology and thickness of Si shells can be controlled for different dopant types by tuning the growth parameters during synthesis. We also present distinctly different electrical characteristics that arise from nanowire field-effect transistors fabricated using the synthesized Ge/Si core/shell nanowires with different shell morphologies. Furthermore, a clear transition in the modification of device characteristics is observed for crystalline shell nanowires following removal of the shell using a unique trimming process of successive native oxide formation/etching. Our results demonstrate that the preferred transport path through the nanowire structure can be modulated by appropriately tuning the growth conditions.
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Germânio/química , Nanoestruturas/química , Nanoestruturas/ultraestrutura , Silício/química , Cristalização/métodos , Condutividade Elétrica , Transporte de Elétrons , Substâncias Macromoleculares/química , Teste de Materiais , Conformação Molecular , Tamanho da Partícula , Propriedades de SuperfícieRESUMO
Staphylococcus aureus is a multi-host pathogen that causes infections in animals and humans globally. The specific genetic loci-and the extent to which they drive cross-species switching, transmissibility, and adaptation-are not well understood. Here, we conducted a population genomic study of 437 S. aureus isolates to identify bacterial genetic variation that determines infection of human and animal hosts through a genome-wide association study (GWAS) using linear mixed models. We found genetic variants tagging φSa3 prophage-encoded immune evasion genes associated with human hosts, which contributed ~99.9% of the overall heritability (~88%), highlighting their key role in S. aureus human infection. Furthermore, GWAS of pairs of phylogenetically matched human and animal isolates confirmed and uncovered additional loci not implicated in GWAS of unmatched isolates. Our findings reveal the loci that are critical for S. aureus host transmissibility, infection, switching, and adaptation and how their spread alters the specificity of host-adapted clones.
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Staphylococcus aureus causes a variety of debilitating and life-threatening diseases, and thus remains a challenging global health threat. S. aureus is remarkably diverse, yet only a minority of methicillin-resistant S. aureus (MRSA) clones have caused pandemic proportions of diseases. The genetic drivers of the successful dissemination of some clones across wide geographical expanses remain poorly understood. We analyzed 386 recently published MRSA genomes from bloodstream infections sampled in North, Central, and South America from 2011 to 2018. Here, we show that MRSA-associated bloodstream infections were attributable to two genetically distinct lineages. One lineage consisted almost exclusively of sequence type (ST) 8, which emerged in 1964. A second lineage emerged in 1986 and consisted of STs 5, 105, and 231. The two lineages have simultaneously disseminated across geographically distant sites. Sublineages rapidly diverged within locations in the early 2000s. Their diversification was associated with independent acquisitions of unique variants of the mobile mecA-carrying chromosomal cassette and distinct repertoires of antimicrobial resistance genes. We show that the evolution and spread of invasive multidrug-resistant MRSA in the Americas was driven by transcontinental dissemination, followed by more recent establishment and divergence of local pathogen populations. Our study highlights the need for continued international surveillance of high-risk clones to control the global health threat of multidrug resistance. IMPORTANCE Bloodstream infections due to S. aureus cause significant patient morbidity and mortality worldwide, exacerbated by the emergence and spread of methicillin resistant S. aureus (MRSA). This study provides important insights on the evolution and long-distance geographic expansion of two distinct MRSA lineages that predominate in bloodstream infections in the past 5 decades. The success of these two lineages partly lies on their acquisition of a diverse set of antimicrobial resistance genes and of unique variants of the mobile genetic element SCCmec that carries the gene mecA conferring resistance to beta-lactams. High-risk antimicrobial resistant clones can therefore rapidly disseminate across long distances and establish within local communities within a short period of time. These results have important implications for global initiatives and local epidemiological efforts to monitor and control invasive MRSA infections and transcontinental spread of multidrug resistance.
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Staphylococcus aureus Resistente à Meticilina , Sepse , Infecções Estafilocócicas , América/epidemiologia , Antibacterianos/farmacologia , Evolução Molecular , Humanos , Staphylococcus aureus Resistente à Meticilina/genética , Infecções Estafilocócicas/epidemiologia , Staphylococcus aureus/genéticaRESUMO
The emergence of methicillin-resistant Staphylococcus aureus (MRSA) poses an important threat in human and animal health. In this study, we ask whether resistance and virulence genes in S. aureus are homogeneously distributed or constrained by different animal hosts. We carried out whole genome sequencing of 114 S. aureus isolates from ten species of animals sampled from four New England states (USA) in 2017-2019. The majority of the isolates came from cats, cows and dogs. The maximum likelihood phylogenetic tree based on the alignment of 89,143 single nucleotide polymorphisms of 1173 core genes reveal 31 sequence types (STs). The most common STs were ST5, ST8, ST30, ST133 and ST2187. Every genome carried at least eight acquired resistance genes. Genes related to resistance found in all genomes included norA (fluoroquinolone), arlRS (fluoroquinolone), lmrS (multidrug), tet(38) (tetracycline) and mepAR (multidrug and tigecycline resistance). The most common superantigen genes were tsst-1, sea and sec. Acquired antibiotic resistance (n = 10) and superantigen (n = 9) genes of S. aureus were widely shared between S. aureus lineages and between strains from different animal hosts. These analyses provide insights for considering bacterial gene sharing when developing strategies to combat the emergence of high-risk clones in animals.
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Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Animais , Antibacterianos/farmacologia , Bovinos , Cães , Resistência Microbiana a Medicamentos , Feminino , Fluoroquinolonas , Staphylococcus aureus Resistente à Meticilina/genética , Testes de Sensibilidade Microbiana , Filogenia , Infecções Estafilocócicas/microbiologia , Staphylococcus aureus , Superantígenos , Virulência/genética , Fatores de Virulência/genéticaRESUMO
Staphylococcus pseudintermedius is a major bacterial colonizer and opportunistic pathogen in dogs. Methicillin-resistant S. pseudintermedius (MRSP) continues to emerge as a significant challenge to maintaining canine health. We sought to determine the phylogenetic relationships of S. pseudintermedius across five states in the New England region of the United States and place them in a global context. The New England dataset consisted of 125 previously published S. pseudintermedius genomes supplemented with 45 newly sequenced isolates. The core genome phylogenetic tree revealed many deep branching lineages consisting of 142 multi-locus sequence types (STs). In silico detection of the mecA gene revealed 40 MRSP and 130 methicillin-susceptible S. pseudintermedius (MSSP) isolates. MRSP were derived from five structural types of SCCmec, the mobile genetic element that carries the mecA gene conferring methicillin resistance. Although many genomes were MSSP, they nevertheless harbored genes conferring resistance to many other antibiotic classes, including aminoglycosides, macrolides, tetracyclines and penams. We compared the New England genomes to 297 previously published genomes sampled from five other states in the United States and 13 other countries. Despite the prevalence of the clonally expanding ST71 found worldwide and in other parts of the United States, we did not detect it in New England. We next sought to interrogate the combined New England and global datasets for the presence of coincident gene pairs linked to antibiotic resistance. Analysis revealed a large co-circulating accessory gene cluster, which included mecA as well as eight other resistance genes [aac (6')-Ie-aph (2â³)-Ia, aad (6), aph (3')-IIIa, sat4, ermB, cat, blaZ, and tetM]. Furthermore, MRSP isolates carried significantly more accessory genes than their MSSP counterparts. Our results provide important insights to the evolution and geographic spread of high-risk clones that can threaten the health of our canine companions.
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Importance: Alcohol withdrawal syndrome (AWS) is a common inpatient diagnosis managed primarily with benzodiazepines. Concerns about the adverse effects associated with benzodiazepines have spurred interest in using benzodiazepine-sparing treatments. Objective: To evaluate changes in outcomes after implementation of a benzodiazepine-sparing AWS inpatient order set that included adjunctive therapies (eg, gabapentin, valproic acid, clonidine, and dexmedetomidine). Design, Setting, and Participants: This difference-in-differences quality improvement study was conducted among 22â¯899 AWS adult hospitalizations from October 1, 2014, to September 30, 2019, in the Kaiser Permanente Northern California integrated health care delivery system. Data were analyzed from September 2020 through November 2021. Exposures: Implementation of the benzodiazepine-sparing AWS order set on October 1, 2018. Main Outcomes and Measures: Adjusted rate ratios for medication use, inpatient mortality, length of stay, intensive care unit admission, and nonelective readmission within 30 days were calculated comparing postimplementation and preimplementation periods among hospitals with and without order set use. Results: Among 904â¯540 hospitalizations in the integrated health care delivery system during the study period, AWS was present in 22â¯899 hospitalizations (2.5%), occurring among 16â¯323 unique patients (mean [SD] age, 57.1 [14.8] years; 15â¯764 [68.8%] men). Of these hospitalizations, 12â¯889 (56.3%) used an order set for alcohol withdrawal. Among hospitalizations with order set use, any benzodiazepine use decreased after implementation from 6431 hospitalizations (78.1%) to 2823 hospitalizations (60.7%) (P < .001), with concomitant decreases in the mean (SD) total dosage of lorazepam before vs after implementation (19.7 [38.3] mg vs 6.0 [9.1] mg; P < .001). There were also significant changes from before to after implementation in the use of adjunctive medications, including gabapentin (2413 hospitalizations [29.3%] vs 2814 hospitalizations [60.5%]; P < .001), clonidine (1476 hospitalizations [17.9%] vs 2208 hospitalizations [47.5%]; P < .001), thiamine (6298 hospitalizations [76.5%] vs 4047 hospitalizations [87.0%]; P < .001), valproic acid (109 hospitalizations [1.3%] vs 256 hospitalizations [5.5%]; P < .001), and phenobarbital (412 hospitalizations [5.0%] vs 292 hospitalizations [6.3%]; P = .003). Compared with AWS hospitalizations without order set use, use of the benzodiazepine-sparing order set was associated with decreases in intensive care unit use (adjusted rate ratio [ARR], 0.71; 95% CI, 0.56-0.89; P = .003) and hospital length of stay (ARR, 0.71; 95% CI, 0.58-0.86; P < .001). Conclusions and Relevance: This study found that implementation of a benzodiazepine-sparing AWS order set was associated with decreased use of benzodiazepines and favorable trends in outcomes. These findings suggest that further prospective research is needed to identify the most effective treatments regimens for patients hospitalized with alcohol withdrawal.
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Benzodiazepinas/uso terapêutico , Etanol/efeitos adversos , Síndrome de Abstinência a Substâncias/tratamento farmacológico , Adulto , Idoso , Alcoolismo , Benzodiazepinas/administração & dosagem , Benzodiazepinas/efeitos adversos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Melhoria de Qualidade , Estudos Retrospectivos , Resultado do TratamentoRESUMO
A retrospective cohort study. Studies to quantify the breadth of antibiotic exposure across populations remain limited. Therefore, we applied a validated method to describe the breadth of antimicrobial coverage in a multicenter cohort of patients with suspected infection and sepsis. We conducted a retrospective cohort study across 21 hospitals within an integrated healthcare delivery system of patients admitted to the hospital through the ED with suspected infection or sepsis and receiving antibiotics during hospitalization from January 1, 2012, to December 31, 2017. We quantified the breadth of antimicrobial coverage using the Spectrum Score, a numerical score from 0 to 64, in patients with suspected infection and sepsis using electronic health record data. Of 364,506 hospital admissions through the emergency department, we identified 159,004 (43.6%) with suspected infection and 205,502 (56.4%) with sepsis. Inpatient mortality was higher among those with sepsis compared to those with suspected infection (8.4% vs 1.2%; P < .001). Patients with sepsis had higher median global Spectrum Scores (43.8 [interquartile range IQR 32.0-49.5] vs 43.5 [IQR 26.8-47.2]; P < .001) and additive Spectrum Scores (114.0 [IQR 57.0-204.5] vs 87.5 [IQR 45.0-144.8]; P < .001) compared to those with suspected infection. Increased Spectrum Scores were associated with inpatient mortality, even after covariate adjustments (adjusted odds ratio per 10-point increase in Spectrum Score 1.31; 95%CI 1.29-1.33). Spectrum Scores quantify the variability in antibiotic breadth among individual patients, between suspected infection and sepsis populations, over the course of hospitalization, and across infection sources. They may play a key role in quantifying the variation in antibiotic prescribing in patients with suspected infection and sepsis.
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Antibacterianos , Sepse , Antibacterianos/uso terapêutico , Serviço Hospitalar de Emergência , Mortalidade Hospitalar , Hospitalização , Humanos , Estudos Retrospectivos , Sepse/diagnóstico , Sepse/tratamento farmacológicoRESUMO
Mammaliicoccus sciuri (previously Staphylococcus sciuri) is a frequent colonizer of mammals. We report the draft genomes of a methicillin-resistant strain (2254A) isolated from an armadillo and a methicillin-susceptible strain (6942A) from a cow. Genomes were sequenced using long-read Nanopore sequencing.