Source Attribution of Human Campylobacteriosis Using Whole-Genome Sequencing Data and Network Analysis

Campylobacter spp. are a leading and increasing cause of gastrointestinal infections world-wide. Source attribution, which apportions human infection cases to different animal species and food reservoirs, has been instrumental in control-and evidence-based intervention efforts. The rapid increase in whole-genome sequencing data provides an opportunity for higher-resolution source attribution models. Important challenges, including the high dimension and complex structure of WGS data, have inspired concerted research efforts to develop new models. We propose network analysis models as an accurate, high-resolution source attribution approach for the sources of human campylobacteriosis. A weighted network analysis approach was used in this study for source attribution comparing different WGS data inputs. The compared model inputs consisted of cgMLST and wgMLST distance matrices from 717 human and 717 animal isolates from cattle, chickens, dogs, ducks, pigs and turkeys. SNP distance matrices from 720 human and 720 animal isolates were also used. The data were collected from 2015 to 2017 in Denmark, with the animal sources consisting of domestic and imports from 7 European countries. Clusters consisted of network nodes representing respective genomes and links representing distances between genomes. Based on the results, animal sources were the main driving factor for cluster formation, followed by type of species and sampling year. The coherence source clustering (CSC) values based on animal sources were 78%, 81% and 78% for cgMLST, wgMLST and SNP, respectively. The CSC values based on Campylobacter species were 78%, 79% and 69% for cgMLST, wgMLST and SNP, respectively. Including human isolates in the network resulted in 88%, 77% and 88% of the total human isolates being clustered with the different animal sources for cgMLST, wgMLST and SNP, respectively. Between 12% and 23% of human isolates were not attributed to any animal source. Most of the human genomes were attributed to chickens from Denmark, with an average attribution percentage of 52.8%, 52.2% and 51.2% for cgMLST, wgMLST and SNP distance matrices respectively, while ducks from Denmark showed the least attribution of 0% for all three distance matrices. The best-performing model was the one using wgMLST distance matrix as input data, which had a CSC value of 81%. Results from our study show that the weighted network-based approach for source attribution is reliable and can be used as an alternative method for source attribution considering the high performance of the model. The model is also robust across the different Campylobacter species, animal sources and WGS data types used as input

Outbreak of Salmonella manhattan associated with a ready-to-eat pork product in Denmark in 1998

Salmonella Manhattan is rarely found in Denmark. Since 1980, only 0-3 human cases have been registered annually. However, in the first 4 weeks of 1998, 19 cases of this serotype were registered suggesting an outbreak. S. Manhattan isolates from 18 human cases were typed using pulsedfield gel electrophoresis. Twelve of these isolates were identical and 3 were closely related, whereas the remaining isolates from humans in 1997 were clearly different. This indicated an outbreak with a common source. Further typing of S. Manhattan isolates collected as a part of the routine surveillance of domestic animals and food suggested a link to pork. Of 17 isolates from broilers, pigs and imported poultry, 6 isolates from breeder pigs imported from an internationally operating pig-production company were indistinguishable from the outbreak strain, whereas the remaining were different. A matched case-control study of 16 cases and 45 controls was carried out. The results suggested that cured and smoked ready-to-eat fillet of pork was the most likely source. Ten of 16 cases had consumed this product within three days before onset of disease, compared with 4 of 45 matched controls (OR 17,

Many-particle entanglement with Bose--Einstein condensates

We propose a method to produce entangled states of several particles starting from a Bose-Einstein condensate. In the proposal, a single fast $\pi/2$ pulse is applied to the atoms and due to the collisional interaction, the subsequent free time evolution creates an entangled state involving all atoms in the condensate. The created entangled state is a spin-squeezed state which could be used to improve the sensitivity of atomic clocks.Comment: 4 pages. Minor modification

Entanglement and Extreme Spin Squeezing

For any mean value of a cartesian component of a spin vector we identify the smallest possible uncertainty in any of the orthogonal components. The corresponding states are optimal for spectroscopy and atomic clocks. We show that the results for different spin J can be used to identify entanglement and to quantity the depth of entanglement in systems with many particles. With the procedure developed in this letter, collective spin measurements on an ensemble of particles can be used as an experimental proof of multi-particle entanglementComment: 4 pages, 2 figures, minor changes in the presentatio

Polarization squeezing of intense pulses with a fiber Sagnac interferometer

We report on the generation of polarization squeezing of intense, short light pulses using an asymmetric fiber Sagnac interferometer. The Kerr nonlinearity of the fiber is exploited to produce independent amplitude squeezed pulses. The polarization squeezing properties of spatially overlapped amplitude squeezed and coherent states are discussed. The experimental results for a single amplitude squeezed beam are compared to the case of two phase-matched, spatially overlapped amplitude squeezed pulses. For the latter, noise variances of -3.4dB below shot noise in the S0 and the S1 and of -2.8dB in the S2 Stokes parameters were observed, which is comparable to the input squeezing magnitude. Polarization squeezing, that is squeezing relative to a corresponding polarization minimum uncertainty state, was generated in S1.Comment: v4: 2 small typos corrected v3: misc problems with Tex surmounted - mysteriously missing text returned to results - vol# for Korolkova et al. PRA v2: was a spelling change in author lis