Skeletal CH3OH/NOx Kinetic Model for Simulating Spark-Ignition and Turbulent Jet Ignition Engines.

Methanol is a promising renewable fuel for achieving a better engine combustion efficiency and lower exhaust emissions. Under exhaust gas recirculation conditions, trace amounts of nitrogen oxides have been shown to participate in fuel oxidation and impact the ignition characteristics significantly. Despite numerous studies that analyzed the methanol/NOx interaction, no reliable skeletal kinetic mechanism is available for computational fluid dynamics (CFD) modeling. This work focuses on developing a skeletal CH3OH/NOx kinetic model consisting of 25 species and 55 irreversible and 27 reversible reactions, used for full-cycle engine combustion simulations. New experiments of methanol with the presence of 200 ppmv NO/NO2 were conducted in a rapid compression machine (RCM) at engine-relevant conditions (20-30 bar, 850-950 K). Experimental results indicate notable enhancement effects of the presence of NO/NO2 on methanol ignition under the conditions tested, which highlights the importance of including the CH3OH/NOx interactions in predicting combustion performance. The proposed skeletal mechanism was validated against the literature and new methanol and methanol/NOx experiments over a wide range of operating conditions. Furthermore, the skeletal mechanism was applied in three-dimensional (3D) CFD full-cycle simulations of spark-ignition (SI) and turbulent jet ignition (TJI) engine combustion using methanol. Simulation results demonstrate good agreement with experimental measurements of pressure traces and engine metrics, proving that the proposed skeletal mechanism is suitable and sufficient for CFD simulations.

Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas.

Chewie Nomenclature Server (chewie-NS, https://chewbbaca.online/) allows users to share genome-based gene-by-gene typing schemas and to maintain a common nomenclature, simplifying the comparison of results. The combination between local analyses and a public repository of allelic data strikes a balance between potential confidentiality issues and the need to compare results. The possibility of deploying private instances of chewie-NS facilitates the creation of nomenclature servers with a restricted user base to allow compliance with the strictest data policies. Chewie-NS allows users to easily share their own schemas and to explore publicly available schemas, including informative statistics on schemas and loci presented in interactive charts and tables. Users can retrieve all the information necessary to run a schema locally or all the alleles identified at a particular locus. The integration with the chewBBACA suite enables users to directly upload new schemas to chewie-NS, download existing schemas and synchronize local and remote schemas from chewBBACA command line version, allowing an easier integration into high-throughput analysis pipelines. The same REST API linking chewie-NS and the chewBBACA suite supports the interaction of other interfaces or pipelines with the databases available at chewie-NS, facilitating the reusability of the stored data.

Genome-wide identification of geographical segregated genetic markers in Salmonella enterica serovar Typhimurium variant 4,[5],12:i:.

Salmonella enterica ser. Typhimurium monophasic variant 4,[5],12:i:- has been associated with food-borne epidemics worldwide and swine appeared to be the main reservoir in most of the countries of isolation. However, the monomorphic nature of this serovar has, so far, hindered identification of the source due to expansion of clonal lineages in multiple hosts and food producing systems. Since geographically structured genetic signals can shape bacterial populations, identification of biogeographical markers in S. 1,4,[5],12:i:- genomes can contribute to improving source attribution. In this study, the phylogeographical structure of 148 geographically and temporally related Italian S. 1,4,[5],12:i:- has been investigated. The Italian isolates belong to a large population of clonal S. Typhimurium/1,4,[5],12:i:- isolates collected worldwide in two decades showing up to 2.5% of allele differences. Phylogenetic reconstruction revealed that isolates from the same geographical origin form highly supported monophyletic groups, suggesting discrete geographical segregation. These monophyletic groups are characterized by the gene content of a large sopE-containing prophage. Within this prophage, genome-wide comparison identified several genes overrepresented in strains of Italian origin. This suggests that certain lineages may be characterized by the acquisition of specific accessory genetic markers useful for improving identification of the source in ongoing epidemics.

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification.

Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. The chewBBACA software uses Python 3.4 or higher and can run on a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA.

Citrobacter portucalensis sp. nov., isolated from an aquatic sample.

A Gram-stain-negative strain, A60T, isolated from a water well sample in Portugal, was characterized phenotypically, genotypically and phylogenetically. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A60T belonged to the genus Citrobacter, and recN gene phylogeny revealed one strongly supported clade encompassing strain A60T and 13 other strains from public databases, distinct from currently recognized species of the genus Citrobacter. Furthermore, multilocus sequence analysis (MLSA) based on concatenated partial fusA, leuS, pyrG and rpoB sequences confirmed the classification obtained with the recN sequence. In silico genomic comparisons, including average nucleotide identity (ANI) and the genome-to-genome distance calculator (GGDC), showed 94.6 % and 58.4 % identity to the closest relative Citrobacter freundii ATCC 8090T, respectively. The ability to metabolize different compounds further discriminated strain A60T from other species of the genus Citrobacter. The G+C content of strain A60T is 52.0 %. The results obtained support the description of a novel species within the genus Citrobacter, for which the name Citrobacter portucalensis sp. nov. is proposed, with the type strain A60T (=DSM 104542T=CECT 9236T).

Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing.

High-Throughput Sequencing (HTS) technologies transformed the microbial typing and molecular epidemiology field by providing the cost-effective ability for researchers to probe draft genomes, not only for epidemiological markers but also for antibiotic resistance and virulence determinants. In this chapter, we provide protocols for the analysis of HTS data for the determination of multilocus sequence typing (MLST) information and for determining presence or absence of antibiotic resistance genes.

TypOn: the microbial typing ontology.

ABSTRACT: Bacterial identification and characterization at subspecies level is commonly known as Microbial Typing. Currently, these methodologies are fundamental tools in Clinical Microbiology and bacterial population genetics studies to track outbreaks and to study the dissemination and evolution of virulence or pathogenicity factors and antimicrobial resistance. Due to advances in DNA sequencing technology, these methods have evolved to become focused on sequence-based methodologies. The need to have a common understanding of the concepts described and the ability to share results within the community at a global level are increasingly important requisites for the continued development of portable and accurate sequence-based typing methods, especially with the recent introduction of Next Generation Sequencing (NGS) technologies. In this paper, we present an ontology designed for the sequence-based microbial typing field, capable of describing any of the sequence-based typing methodologies currently in use and being developed, including novel NGS based methods. This is a fundamental step to accurately describe, analyze, curate, and manage information for microbial typing based on sequence based typing methods.