Fast and accurate read mapping with approximate seeds and multiple backtracking

We present Masai, a read mapper representing the state-of-the-art in terms of speed and accuracy. Our tool is an order of magnitude faster than RazerS 3 and mrFAST, 2-4 times faster and more accurate than Bowtie 2 and BWA. The novelties of our read mapper are filtration with approximate seeds and a method for multiple backtracking. Approximate seeds, compared with exact seeds, increase filtration specificity while preserving sensitivity. Multiple backtracking amortizes the cost of searching a large set of seeds by taking advantage of the repetitiveness of next-generation sequencing data. Combined together, these two methods significantly speed up approximate search on genomic data sets. Masai is implemented in C++ using the SeqAn library. The source code is distributed under the BSD license and binaries for Linux, Mac OS X and Windows can be freely downloaded from http://www.seqan.de/projects/masai

Bacterial fecal microbiota is only minimally affected by a standardized weight loss plan in obese cats

Background: Research in humans and mice suggests that obesity influences the abundance and diversity of gastrointestinal (GI) microbiota, and that an "obese microbiome" influences energy metabolism and fat storage in the host. Microbiota membership and composition have been previously assessed in healthy cats. However, research investigating the effects of obesity and weight loss on the cat's fecal microbiota is limited. Therefore, this study's objective was to evaluate differences in fecal microbial abundance and biodiversity, as well as serum cobalamin and folate concentrations in obese cats, before and after weight loss, and compare to lean cats. Fourteen lean and 17 obese healthy client-owned cats were fed a veterinary therapeutic weight loss food at maintenance energy requirement for 4 weeks. At the end of week 4, lean cats finished the study, whereas obese cats continued with a 10-week weight loss period on the same food, fed at individually-tailored weight loss energy requirements. Body weight and body condition score were recorded every 2 weeks throughout the study. At the end of each period, a fecal sample and food-consumption records were obtained from the owners, and serum cobalamin and folate concentrations were analysed. DNA was extracted from fecal samples, polymerase chain reaction (PCR) was performed, and products were sequenced using next-generation sequencing (Illumina MiSeq). Results: No significant differences in the relative abundance of taxa and in biodiversity indices were observed between cats in either group (P > 0.05 for all tests). Nevertheless, some significantly enriched taxa, mainly belonging to Firmicutes, were noted in linear discriminant analysis effect size test in obese cats before weight loss compared to lean cats. Serum cobalamin concentrations were significantly higher in lean compared to obese cats both before and after weight loss. Serum folate concentrations were higher in obese cats before weight loss compared to after. Conclusions: The association between feline obesity and the fecal bacterial microbiota was demonstrated in enriched taxa in obese cats compared to lean cats, which may be related to enhanced efficiency of energy-harvesting. However, in obese cats, the fecal microbial abundance and biodiversity were only minimally affected during the early phase of a standardized weight loss plan

Evolutionary game of coalition building under external pressure

We study the fragmentation-coagulation (or merging and splitting) evolutionary control model as introduced recently by one of the authors, where $N$ small players can form coalitions to resist to the pressure exerted by the principal. It is a Markov chain in continuous time and the players have a common reward to optimize. We study the behavior as $N$ grows and show that the problem converges to a (one player) deterministic optimization problem in continuous time, in the infinite dimensional state space

Autonomic Nervous System Dysfunction in Pediatric Sepsis

The autonomic nervous system (ANS) plays a major role in maintaining homeostasis through key adaptive responses to stress, including severe infections and sepsis. The ANS-mediated processes most relevant during sepsis include regulation of cardiac output and vascular tone, control of breathing and airway resistance, inflammation and immune modulation, gastrointestinal motility and digestion, and regulation of body temperature. ANS dysfunction (ANSD) represents an imbalanced or maladaptive response to injury and is prevalent in pediatric sepsis. Most of the evidence on ANSD comes from studies of heart rate variability, which is a marker of ANS function and is inversely correlated with organ dysfunction and mortality. In addition, there is evidence that other measures of ANSD, such as respiratory rate variability, skin thermoregulation, and baroreflex and chemoreflex sensitivity, are associated with outcomes in critical illness. The relevance of understanding ANSD in the context of pediatric sepsis stems from the fact that it might play an important role in the pathophysiology of sepsis, is associated with outcomes, and can be measured continuously and noninvasively. Here we review the physiology and dysfunction of the ANS during critical illness, discuss methods for measuring ANS function in the intensive care unit, and review the diagnostic, prognostic, and therapeutic value of understanding ANSD in pediatric sepsis

Epidemiology of companion animal AMR in the United States of America: filling a gap in the one health approach

IntroductionAntimicrobial resistance (AMR) is a global health concern that affects all aspects of the One Health Triad, including human, animal, and environmental health. Companion animals, such as cats and dogs, may contribute to the spread of AMR through their close contact with humans and the frequent prescription of antimicrobials. However, research on AMR in companion animals is limited, and there are few surveillance measures in place to monitor the spread of resistant pathogens in the United States.MethodsThis study aims to explore the practicality of using data from commercial laboratory antimicrobial susceptibility testing (AST) services for epidemiological analyses of AMR in companion animals in the United States.ResultsThe study analyzed 25,147,300 individual AST results from cats and dogs submitted to a large commercial diagnostic laboratory in the United States between 2019 and 2021, and found that resistance to certain antimicrobials was common in both E. coli and S. pseudintermedius strains.ConclusionThere has been a paucity of information regarding AMR in companion animals in comparison to human, environmental and other animal species. Commercial AST datasets may prove beneficial in providing more representation to companion animals within the One Health framework for AMR

Methicillin-resistant Staphylococcus aureus Colonization in Veterinary Personnel

TOC Summary: Prevalence of colonization was 6.5%, and employment within a large-animal practice was a significant risk factor

Infection prevention and control interventions in the first outbreak of methicillin-resistant Staphylococcus aureus infections in an equine hospital in Sweden

<p>Abstract</p> <p>Background</p> <p>The first outbreak of methicillin-resistant <it>Staphylococcus aureus </it>(MRSA) infection in horses in Sweden occurred in 2008 at the University Animal Hospital and highlighted the need for improved infection prevention and control. The present study describes interventions and infection prevention control in an equine hospital setting July 2008 - April 2010.</p> <p>Method</p> <p>This descriptive study of interventions is based on examination of policy documents, medical records, notes from meetings and cost estimates. MRSA cases were identified through clinical sampling and telephone enquiries about horses post-surgery. Prospective sampling in the hospital environment with culture for MRSA and genotyping of isolates by <it>spa</it>-typing and pulsed-field gel electrophoresis (PFGE) were performed.</p> <p>Results</p> <p>Interventions focused on interruption of indirect contact spread of MRSA between horses via staff and equipment and included: Temporary suspension of elective surgery; and identification and isolation of MRSA-infected horses; collaboration was initiated between authorities in animal and human public health, human medicine infection control and the veterinary hospital; extensive cleaning and disinfection was performed; basic hygiene and cleaning policies, staff training, equipment modification and interior renovation were implemented over seven months.</p> <p>Ten (11%) of 92 surfaces sampled between July 2008 and April 2010 tested positive for MRSA <it>spa</it>-type 011, seven of which were from the first of nine sampling occasions. PFGE typing showed the isolates to be the outbreak strain (9 of 10) or a closely related strain. Two new cases of MRSA infection occurred 14 and 19 months later, but had no proven connections to the outbreak cases.</p> <p>Conclusions</p> <p>Collaboration between relevant authorities and the veterinary hospital and formation of an infection control committee with an executive working group were required to move the intervention process forward. Support from hospital management and the dedication of staff were essential for the development and implementation of new, improved routines. Demonstration of the outbreak strain in the environment was useful for interventions such as improvement of cleaning routines and interior design, and increased compliance with basic hygienic precautions. The interventions led to a reduction in MRSA-positive samples and the outbreak was considered curbed as no new cases occurred for over a year.</p