Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs

Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact

Host ecology regulates interspecies recombination in bacteria of the genus Campylobacter

Horizontal gene transfer (HGT) can allow traits that have evolved in one bacterial species to transfer to another. This has potential to rapidly promote new adaptive trajectories such as zoonotic transfer or antimicrobial resistance. However, for this to occur requires gaps to align in barriers to recombination within a given time frame. Chief among these barriers is the physical separation of species with distinct ecologies in separate niches. Within the genus there are species with divergent ecologies, from rarely isolated single host specialists to multi-host generalist species that are among the most common global causes of human bacterial gastroenteritis. Here, by characterising these contrasting ecologies, we can quantify HGT among sympatric and allopatric species in natural populations. Analysing recipient and donor population ancestry among genomes from 30 species we show that cohabitation in the same host can lead to a 6-fold increase in HGT between species. This accounts for up to 30% of all SNPs within a given species and identifies highly recombinogenic genes with functions including host adaptation and antimicrobial resistance. As described in some animal and plant species, ecological factors are a major evolutionary force for speciation in bacteria and changes to the host landscape can promote partial convergence of distinct species through HGT. [Abstract copyright: © 2022, Mourkas et al.

Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance

Campylobacter is the most common cause of bacterial gastroenteritis worldwide, and diarrhoeal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries. Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we aimed to quantify the extent of gene sharing in local and global populations. We characterized the genetic diversity and accessory-genome content of a collection of Campylobacter isolates from the Cairo metropolitan area, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24), and patients suffering from gastroenteritis (n=57). Among the most common sequence types (STs), we identified the globally disseminated host generalist ST-21 clonal complex (CC21) and the poultry specialists CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented, with a total absence of CC61. Core- and accessory-genome sharing was compared among isolates from Egypt and a comparable collection from the UK (Oxford). Lineage-specific accessory-genome sharing was significantly higher among isolates from the same country, particularly CC21, which demonstrated greater local geographical clustering. In contrast, no geographical clustering was noted in either the core or accessory genome of CC828, suggesting a highly admixed population. A greater proportion of Campylobacter coli isolates were multidrug resistant compared to Campylobacter jejuni. Our results suggest that there is more horizontal transfer of accessory genes between strains in Egypt. This has strong implications for controlling the spread of antimicrobial resistance among this important pathogen

Multi-Function Tribometer Design

ME450 Capstone Design and Manufacturing Experience: Winter 2010Friction and wear properties of many material combinations are becoming increasingly important as engineers look to create more durable and reduced-friction materials. Currently, there is no tribometer which can measure real world complex 2D wear patterns at speeds required by our sponsor. Because of this, our team has been asked to design a tribometer which will measure friction and wear in complex two-dimensional wear patterns to better model and test real world applications. Key design characteristics will include both closed-loop environmental control and closed-loop normal force application. A successful prototype must have each of the aforementioned functionalities among others.http://deepblue.lib.umich.edu/bitstream/2027.42/109387/1/me450w10project5_report.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/109387/2/me450w10project5_photo.jp

Substitutability of Fishmeal in Diets for Salmon: An Optimisation by Simulation Approach

The world’s output of farmed fish has grown steadily over the past two decades or so. Most notably in the UK, since the mid 1980’s, a rapid increase in farmed salmon production has taken place. Given that many of the world’s oceans are overfished, many see aquaculture as a method of feeding the world's growing population. However, the production of salmon relies heavily on marine raw materials as inputs in compound feed. Consequently, the demand for fishmeal is, therefore, increasing, although the production of fishmeal has remained relatively stable over the past decade or so suggesting that fishmeal has reached a production limit, with most industrial fisheries classified as fully or over exploited. Therefore, given the stagnant production from industrial fisheries and the rapid increase in aquaculture production, fishmeal can pose a biological constraint on production and thus aquacultures contribution to world supplies. In this study, the economic feasibility of substituting fishmeal in diets for salmon was analysed through an optimisation by simulation approach using @Risk to derive range of combinations stochastically. The results indicate that there are cost combinations of alternative ingredients that can substitute fishmeal producing market size salmon for a similar price to traditional fishmeal diets

Large Sequence Diversity within the Biosynthesis Locus and Common Biochemical Features of Campylobacter coli Lipooligosaccharides

Despite the importance of lipooligosaccharides (LOS) in the pathogenicity of campylobacteriosis, little is known about the genetic and phenotypic diversity of LOS in C. coli. In this study, we investigated the distribution of LOS locus classes among a large collection of unrelated C. coli isolates sampled from several different host species. Furthermore, we paired C. coli genomic information and LOS chemical composition for the first time to identify mechanisms consistent with the generation of LOS phenotypic heterogeneity. After classifying three new LOS locus classes, only 85% of the 144 isolates tested were assigned to a class, suggesting higher genetic diversity than previously thought. This genetic diversity is at the basis of a completely unexplored LOS structure heterogeneity. Mass spectrometry analysis of the LOS of nine isolates, representing four different LOS classes, identified two features distinguishing C. coli LOS from C. jejuni's. GlcN-GlcN disaccharides were present in the lipid A backbone in contrast to the GlcN3N-GlcN backbone observed in C. jejuni. Moreover, despite that many of the genes putatively involved in Qui3pNAcyl were absence in the genomes of various isolates, this rare sugar was found in the outer core of all C. coli. Therefore, regardless the high genetic diversity of LOS biosynthesis locus in C. coli, we identified species-specific phenotypic features of C. coli LOS which might explain differences between C. jejuni and C. coli in terms of population dynamics and host adaptation

Impact of skipper characteristics and technology on individual fisher technical efficiency

Differences in technical efficiency of fishing vessels are often attributed to skipper skill and differences in technology. While the later can be defined in terms of the technology employed, the former is more difficult to quantify. In this paper, the contribution of technology and skipper characteristics (e.g. level of education, experience, training) to technical efficiency are examined using a stochastic production frontier. Three types of fishing activities are examined: mobile gear (e.g. trawl), potters and netter-liners. The results suggest that technology and skipper characteristics can affect the level of efficiency, although these effects differ by gear type used. Traditional measures of labour skill (education and experience) are found to be less relevant when trying to measure skipper skill.Keywords: Technical efficiency, fisheries, Fisheries Economics, stochastic production frontier, Theoretical and Empirical Bio-Economic Modellin