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Rapid whole genome characterization of antimicrobial-resistant pathogens using long-read sequencing to identify potential healthcare transmission

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INFECTION CONTROL & HOSPITAL EPIDEMIOLOGY 2025年第2期46卷 129-135页

作者： Wu, Chin-Ting Shropshire, William C. Bhatti, Micah M. Cantu, Sherry Glover, Israel K. Anand, Selvalakshmi Selvaraj Liu, Xiaojun Kalia, Awdhesh Treangen, Todd J. Chemaly, Roy F. Spallone, Amy Shelburne, Samuel Univ Texas MD Anderson Canc Ctr Sch Hlth Profess Grad Program Diagnost Genet & Genom Houston TX USA Univ Texas MD Anderson Canc Ctr Dept Infect Dis Infect Control & Employee Hlth Houston TX 77030 USA Univ Texas MD Anderson Canc Ctr Dept Lab Med Houston TX USA Univ Texas MD Anderson Canc Ctr Infect Control Chief Qual Off Houston TX USA Univ Texas MD Anderson Canc Ctr Dept Genom Med Houston TX 77030 USA Rice Univ PhD Program Synthet Biol Inst Syst Synthet & Phys Houston TX USA Rice Univ Dept Comp Sci Houston TX USA Rice Univ Dept Bioengn Houston TX USA

Objective: Whole genome sequencing (WGS) can help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time intensive. Given recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource approach providing accurate WGS-pathogen comparison within a time frame allowing for infection prevention and control (IPC) interventions. Methods: WGS was prospectively performed on pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecaller. Potential transmission was assessed via Ridom SeqSphere & thorn;for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cutoff values. The accuracy of our ONT pipeline was determined relative to Illumina. Results: Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold standard, our ONT pipeline achieved a mean identity score of Q60 for assembled genomes, even with a coverage rate as low as 40x. The mean time from initiating DNA extraction to complete analysis was 2 days (IQR 2-3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of sequenced strains). Integrating ONT with epidemiological data, > 70% (15/21) of putative transmission cluster isolates originated from patients with potential healthcare transmission links. Conclusions: Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in IPC efforts. (Received 27 August 2024;accepted 1 November 2024)

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Assessment of regulating ecosystem services generated by green infrastructure: A case study of Bolzano, Italy

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URBAN CLIMATE 2025年 60卷

作者： Sokolova, Milena, V Fath, Brian D. Buonocore, Elvira Franzese, Pier Paolo Parthenope Univ Naples UNESCO Chair Environm Resources & Sustainable Dev Dept Sci & Technol Int PhD Programme Naples Italy Int Inst Appl Syst Anal Adv Syst Anal Program Laxenburg Austria Towson Univ Dept Biol Sci Towson MD USA Masaryk Univ Dept Environm Studies Brno Czech Republic

Sustainable cities is one of the key topics of the United Nations 2030 Agenda for Sustainable Development. SDG 11 promotes the goal that cities should be inclusive, safe, resilient and sustainable human settlements. In this context, urban ecosystems, namely, Green Infrastructure (GI) can play a key role to enhance ecosystem services. GI improves ecosystem functioning and resilience, protects biodiversity, promotes societal health and well-being. The concept of GI in cities is becoming increasingly important in the development of urban policies since it improves the quality of life while mitigating the adverse effects of climate change. In this paper, we integrate biophysical method and monetary methods using i-Tree Eco software with about 12,000 trees within Bolzano, Italy. Model results are given for five assessed ecosystem services: 1) carbon storage, 2) carbon sequestration, 3) oxygen production, 4) avoided runoff, and 5) air pollution removal. Thus, our results show the significance of urban trees as a key element for better urban planning considering specific species contribution. The findings of this study will increase the awareness on the important role GIs play in urban systems to improve human well-being, informing policy-makers in charge of developing strategies to achieve impelling conservation actions and sustainability goals.

关键词： Green infrastructure Ecosystem services i-Tree Eco software SDG 11 Bolzano Urban ecosystems

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Pharmacogenetic activation of parvalbumin interneurons in the prefrontal cortex rescues cognitive deficits induced by adolescent MK801 administration

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NEUROPSYCHOPHARMACOLOGY 2023年第9期48卷 1267-1276页

作者： Chamberlin, Linda A. Yang, Sha-Sha McEachern, Erin P. Lucas, Joshua T. M. McLeod Ii, Owen W. Rolland, Claire A. Mack, Nancy R. Ferguson, Brielle R. Gao, Wen-Jun Drexel Univ Dept Neurobiol & Anat Coll Med Philadelphia PA 19129 USA Drexel Univ MD PhD program Coll Med Philadelphia PA USA Fudan Univ Inst Translat Brain Res Dept Neurol Shanghai 200032 Peoples R China Drexel Univ MD program Coll Med Philadelphia PA USA Drexel Univ Interdisciplinary Hlth Sci Program Coll Med Philadelphia PA USA 2 Blackfan circle Cetern Life Sci Boston MA 02115 USA

The cognitive symptoms of schizophrenia (SZ) present a significant clinical burden. They are treatment resistant and are the primary predictor of functional outcomes. Although the neural mechanisms underlying these deficits remain unclear, pathological GABAergic signaling likely plays an essential role. Perturbations with parvalbumin (PV)-expressing fast-spiking (FS) interneurons in the prefrontal cortex (PFC) are consistently found in post-mortem studies of patients with SZ, as well as in animal models. Our studies have shown decreased prefrontal synaptic inhibition and PV immunostaining, along with working memory and cognitive flexibility deficits in the MK801 model. To test the hypothesized association between PV cell perturbations and impaired cognition in SZ, we activated prefrontal PV cells by using an excitatory DREADD viral vector with a PV promoter to rescue the cognitive deficits induced by adolescent MK801 administration in female rats. We found that targeted pharmacogenetic upregulation of prefrontal PV interneuron activity can restore E/I balance and improve cognition in the MK801 model. Our findings support the hypothesis that the reduced PV cell activity levels disrupt GABA transmission, resulting in the disinhibition of excitatory pyramidal cells. This disinhibition leads to an elevated prefrontal excitation/inhibition (E/I) balance that could be causal for cognitive impairments. Our study provides novel insights into the causal role of PV cells in cognitive function and has clinical implications for understanding the pathophysiology and management of SZ.

关键词： Schizophrenia

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Characterization of a Novel Thermostable DNA Lyase Used To Prepare DNA for Next-Generation Sequencing

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CHEMICAL RESEARCH IN TOXICOLOGY 2023年第2期36卷 162-176页

作者： Baljinnyam, Tuvshintugs Conrad, James W. Sowers, Mark L. Chang-Gu, Bruce Herring, Jason L. Hackfeld, Linda C. Zhang, Kangling Sowers, Lawrence C. Univ Texas Med Branch Dept Pharmacol & Toxicol Galveston TX 77555 USA Univ Texas Med Branch MD PhD Combined Degree Program Galveston TX 77555 USA Univ Texas Med Branch Dept Internal Med Galveston TX 77555 USA

Recently, we constructed a hybrid thymine DNA glycosylase (hyTDG) by linking a 29-amino acid sequence from the human thymine DNA glycosylase with the catalytic domain of DNA mismatch glycosylase (MIG) from M. thermoautotrophicum, increasing the overall activity of the glycosylase. Previously, it was shown that a tyrosine to lysine (Y126K) mutation in the catalytic site of MIG could convert the glycosylase activity to a lyase activity. We made the corresponding mutation to our hyTDG to create a hyTDGlyase (Y163K). Here, we report that the hybrid mutant has robust lyase activity, has activity over a broad temperature range, and is active under multiple buffer conditions. The hyTDG-lyase cleaves an abasic site similar to endonuclease III (Endo III). In the presence of beta-mercaptoethanol (beta-ME), the abasic site unsaturated aldehyde forms a beta-ME adduct. The hyTDG-lyase maintains its preference for cleaving opposite G, as with the hyTDG glycosylase, and the hyTDG-lyase and hyTDG glycosylase can function in tandem to cleave T:G mismatches. The hyTDG-lyase described here should be a valuable tool in studies examining DNA damage and repair. Future studies will utilize these enzymes to quantify T:G mispairs in cells, tissues, and genomic DNA using next-generation sequencing.

关键词： Biopolymers Crystal cleavage Genetics Monomers Peptides and proteins

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Retrospective Comparison of Upper and Lower Extremity Intraosseous Access During Out-of-Hospital Cardiac Arrest Resuscitation

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PREHOSPITAL EMERGENCY CARE 2024年第6期28卷 779-786页

作者： Smida, Tanner Crowe, Remle Jarvis, Jeffrey Ratcliff, Taylor Goebel, Mat West Virginia Univ MD PhD Program Morgantown WV 26506 USA ESO Solut Austin TX USA Metropolitan Area EMS Author Ft Worth TX USA Texas A&M Coll Med Dept Emergency Med Bryan TX USA Univ Massachusetts Chan Med Sch Baystate Springfield MA USA

ObjectiveIntraosseous (IO) access is frequently utilized during the resuscitation of out-of-hospital cardiac arrest (OHCA) patients. Due to proximity to the heart and differential flow rates, the anatomical site of IO access may impact patient outcomes. Using a large dataset, we aimed to compare the outcomes of OHCA patients who received upper or lower extremity IO access during *** ESO Data Collaborative public use research datasets were used for this retrospective study. All adult (>= 18 years of age) OHCA patients with successful IO access in an upper or lower extremity were evaluated for inclusion. Patients were excluded if they had intravenous (IV) access prior to IO access, or if they had a Do Not Resuscitate order documented. Our primary outcome was return of spontaneous circulation (ROSC). Secondary outcomes included survival to discharge and survival to discharge to home. Mixed-effects multivariable logistic regression models adjusted for age, sex, etiology, witnessed status, pre-first responder cardiopulmonary resuscitation (CPR), initial electrocardiogram (ECG) rhythm, location [private/residential, public, or assisted living/institutional], and response time in addition to the primary airway management strategy (endotracheal intubation, supraglottic device, surgical airway, no advanced airway) were used to compare the outcomes of patients with upper extremity IO access to the outcomes of patients with lower extremity IO *** application of exclusion criteria, 155,884 patients who received IO access during resuscitation remained (76% lower extremity, 24% upper extremity). Upper extremity IO access was associated with greater adjusted odds of ROSC (1.11 [1.08, 1.15]), and this finding was consistent across multiple patient subgroups. Secondary analyses suggested that upper extremity access was associated with increased survival to discharge (1.18 [1.00, 1.39]) and survival to discharge to home (1.23 [1.02, 1.48]) in comp

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Alterations in facial expressions in individuals at risk for psychosis: a facial electromyography approach using emotionally evocative film clips

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PSYCHOLOGICAL MEDICINE 2023年第12期53卷 5829-5838页

作者： Gupta, Tina Osborne, K. Juston Nadig, Ajay Haase, Claudia M. Mittal, Vijay A. Univ Pittsburgh Dept Psychiat Pittsburgh PA 15213 USA Northwestern Univ Dept Psychol Evanston IL USA Harvard Med Sch Harvard MIT MD PhD Program Boston MA 02115 USA Northwestern Univ Sch Educ & Social Policy Evanston IL USA

Background Negative symptoms such as blunted facial expressivity are characteristic of schizophrenia. However, it is not well-understood if and what abnormalities are present in individuals at clinical high-risk (CHR) for psychosis. Methods This experimental study employed facial electromyography (left zygomaticus major and left corrugator supercilia) in a sample of CHR individuals (N = 34) and healthy controls (N = 32) to detect alterations in facial expressions in response to emotionally evocative film clips and to determine links with symptoms. Results Findings revealed that the CHR group showed facial blunting manifested in reduced zygomatic activity in response to an excitement (but not amusement, fear, or sadness) film clip compared to controls. Reductions in zygomatic activity in the CHR group emerged in response to the emotionally evocative peak period of the excitement film clip. Lower zygomaticus activity during the excitement clip was related to anxiety while lower rates of change in zygomatic activity during the excitement video clip were related to higher psychosis risk conversion scores. Conclusions Together, these findings inform vulnerability/disease driving mechanisms and biomarker and treatment development.

关键词： Clinical high-risk electromyography evocative film clips facial expressions negative symptoms schizophrenia

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Estimating highest capacity propulsion performance using backward-directed force during walking evaluation for individuals with acquired brain injury

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JOURNAL OF NEUROENGINEERING AND REHABILITATION 2024年第1期21卷 134页

作者： Lacroix, Kelli Horelka, Lauren Hung, Clif Brown, David A. Univ Texas Med Branch Dept Rehabil Sci MD PhD Combined Degree Program 301 Univ Blvd Galveston TX 77555 USA Moody Neurorehabil Inst Galveston 1528 PO St Galveston TX USA Univ Texas Med Branch Sch Hlth Profess 301 Univ Blvd Galveston TX USA

There are over 5.3 million Americans who face acquired brain injury (ABI)-related disability as well as almost 800,000 who suffer from stroke each year. To improve mobility and quality of life, rehabilitation professionals often focus on walking recovery soon after hospital discharge for ABI. Reduced propulsion capacity (force output of the lower limbs to counteract ground reaction forces) negatively impacts walking ability and complicates recovery during rehabilitation for brain injured people. We describe a method, using backward-directed resistance (BDR) in a robotic-based treadmill device, to allow measurement of maximum walking propulsion force (MWPF) that is not otherwise possible during overground walking assessment. Our objective was to test the construct validity of a maximum walking propulsion force (MWPF) measure that reflects a person's propulsive strength against applied BDR, while walking on a robotic treadmill-based device for participants with acquired brain injury (ABI). Our study enrolled 14 participants with ABI at an in inpatient rehabilitation in Galveston, TX from 8/1/21 - 4/31/22. The range of weight-adjusted MWPF was 2.6-27.1% body weight (%BW), mean 16.5 +/- 8.4%BW, reflecting a wide range of propulsive force capability. The strongest correlation with overground tests was between the 6-minute walk test (6-MWT) distance and the MWPF values (r = 0.83, p < 0.001) with moderate correlations between the 10-meter walk tests at comfortable (CWS) and fast speeds (FWS). The Five Times Sit-to-Stand (used as a standard clinical measure of functional lower extremity strength) and MWPF tests were poorly correlated (r = 0.26, p = 0.4). Forward model selection included 6-MWT distance, age, and overground CWS as significant partial predictors of MWPF. We conclude that this novel MWPF measure is a valid representation of maximum propulsive force effort during walking for people post-ABI. Additional research could help determine the impact of interventions de

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How medical learners and educators decide what counts as mistreatment: A qualitative study

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MEDICAL EDUCATION 2023年第10期57卷 910-920页

作者： Vanstone, Meredith Cavanagh, Alice Molinaro, Monica Connelly, Catherine E. Bell, Amanda Mountjoy, Margo Whyte, Robert Grierson, Lawrence McMaster Univ Dept Family Med Hamilton ON Canada McMaster Program Educ Res Innovat & Theory Hamilton ON Canada McMaster Univ Michael G DeGroote Sch Med MD PhD Program Hamilton ON Canada McMaster Univ Michael G DeGroote Sch Business Hamilton ON Canada McMaster Univ Michael G DeGroote Sch Med Undergraduate MD Program Hamilton ON Canada McMaster Univ Dept Anesthesia Hamilton ON Canada McMaster Univ Dept Family Med DBHSC 5001F100 Main St W Hamilton ON Canada

IntroductionThe mistreatment or abuse (maltreatment) of medical learners by their peers and supervisors has been documented globally for decades, and there is significant research about the prevalence, sequelae and strategies for intervention. However, there is evidence that learners experience maltreatment as being less clear cut than do researchers, educators and administrators. This definitional ambiguity creates problems for understanding and addressing this issue. The objective of this study was to understand how medical learners and educators make sense of less-than-ideal interactions in the clinical learning environment, and to describe which factors influenced their perception that the encounter constituted maltreatment. MethodsUsing constructivist grounded theory, we interviewed 16 medical students, 15 residents or fellows, and 18 educators associated with a single medical school (n = 49). Data collection began with the most junior learners, iterating with analysis as we progressed through the project. Constant comparative analysis was used to gather and compare stories of 'definitely', 'maybe' and 'definitely not' maltreatment across a variety of axes including experience level, clinical setting and type of interaction. ResultsOur data show that learners and educators have difficulty classifying their experiences of negative interpersonal interaction, except in the most severe and concrete cases. While there was tremendous variation in the way they categorised similar experiences, there was consistency in the elements drawn upon to make sense of those experiences. Participants interpreted negative interpersonal interactions on an individual basis by considering factors related to the interaction, initiator and recipient. ConclusionsOnly the most negative behaviour is consistently understood as maltreatment;a complex process of individual sense-making is required to determine the acceptability of each interaction. The differences between how individuals jud

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Thymidine nucleotide metabolism controls human telomere length (vol 55, pg 568, 2023)

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NATURE GENETICS 2023年第7期55卷 1251-1251页

作者： Mannherz, William Agarwal, Suneet Boston Childrens Hosp Oncol & Stem Cell Program Div Hematol Boston MA 02115 USA Dana Farber Canc Inst Pediat Oncol Boston MA 02215 USA Harvard Med Sch Harvard Stem Cell Inst Harvard Initiat RNA Med Biol & Biomed Sci Program Boston MA 02115 USA Harvard Med Sch Harvard MIT MD PhD Program Dept Pediat Boston MA 02115 USA

Telomere length in humans is associated with lifespan and severe diseases, yet the genetic determinants of telomere length remain incompletely defined. Here we performed genome-wide CRISPR–Cas9 functional telomere length screening and identified thymidine (dT) nucleotide metabolism as a limiting factor in human telomere maintenance. Targeted genetic disruption using CRISPR–Cas9 revealed multiple telomere length control points across the thymidine nucleotide metabolism pathway: decreasing dT nucleotide salvage via deletion of the gene encoding nuclear thymidine kinase (TK1) or de novo production by knockout of the thymidylate synthase gene (TYMS) decreased telomere length, whereas inactivation of the deoxynucleoside triphosphohydrolase-encoding gene SAMHD1 lengthened telomeres. Remarkably, supplementation with dT alone drove robust telomere elongation by telomerase in cells, and thymidine triphosphate stimulated telomerase activity in a substrate-independent manner in vitro. In induced pluripotent stem cells derived from patients with genetic telomere biology disorders, dT supplementation or inhibition of SAMHD1 promoted telomere restoration. Our results demonstrate a critical role of thymidine metabolism in controlling human telomerase and telomere length, which may be therapeutically actionable in patients with fatal degenerative diseases.

关键词： Genetic engineering Haematological diseases High-throughput screening Stem-cell research

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Canine Conundrum: Non-Bite Transmission Leading to Pasteurella multocida Epicardial Abscess

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AMERICAN JOURNAL OF MEDICINE 2024年第1期137卷 E3-E5页

作者： McPherson, David F. V. Menghani, Sanjay Bhalodi, Rina G. Roesch, Torey A. St Lukes Univ Hosp Network SLUHN Bethlehem PA USA St Lukes Univ Hosp Network SLUHN St Luke's Family Med Residency Easton PA USA Univ Arizona Coll Med Tucson AZ USA Univ Arizona Coll Med Tucson Med Scientist Training MD PhD Program Tucson AZ USA St Lukes Univ Hosp Network SLUHN St Luke's Psychiat Residency Anderson Bethlehem PA USA St Lukes Infect Dis Associates Bethlehem PA USA UA Coll Med MD PhD Program 1295 North Martin AveDrachman HallRoom B207POB Tucson AZ 85721 USA

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