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Primary biliary cholangitis (PBC) is a chronic progressive liver disease of unknown aetiology characterised by immune-mediated destruction of small and medium-sized intrahepatic bile ducts. There are few well-established risk factors and epidemiological studies are needed to further evaluate the pathogenesis of the disease.To evaluate the relationship between alcohol intake, smoking and marijuana use with PBC development.We conducted a prevalent case control study of 200 cases and 200 age (within a five year age band) and sex-matched controls, identified from the Victorian PBC prevalence study. We assessed lifetime alcohol intake and smoking behaviour (both tobacco and marijuana) prior to PBC onset and used conditional logistic regression for analyses.Alcohol intake consistently showed a dose-dependent inverse association with case status, and this was most substantial for 21-30 years and 31-40 years (Alcohol appears to have an inverse relationship with PBC. Smoking has been confirmed as an environmental risk factor for PBC. There was no association between marijuana use and PBC.

Background Clostridium is a genus of Gram-positive, spore-forming, anaerobic bacteria comprising approximately 100 species. Some Clostridium spp. (C. botulinum, C. perfringens, C. tetani, and C. difficile) have been recognized to cause acute food poisoning, botulism, tetanus, and diarrheal illness in humans. Thus, rapid identification of Clostridium spp. is critical for source-tracking of contaminated food and to understand the transmission dynamics of these foodborne pathogens. Objective This study was carried out to rapidly identify Clostridium-like isolates by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS and rRNA sequencing methods. Method Thirty-three Clostridium-like isolates were recovered from various baby food and surveillance samples. Species identification of these isolates was accomplished using the VITEK MS system. Sequence characterization of the 16S rRNA region was done on an ABI 3500xL Genetic Analyzer. Results The VITEK MS system identified 28 of the 33 Clostridium-like isolates with a high confidence value (99.9%); no identification was observed for the remaining five isolates. Nucleotide sequencing of the 16S rRNA region identified all 33 Clostridium-like isolates. Furthermore, while characterizing the 16S rRNA gene, 11 distinct Clostridium spp. (Clostridium aciditolerans, Clostridium aerotolerans, Clostridium argentinense, Clostridium beijerinckii, Clostridium bifermentans, Clostridium butyricum, Clostridium cochlearium, Clostridium difficile, Clostridium perfringens, Clostridium sporogenes, and Clostridium subterminale) were recognized among the 33 Clostridium-like isolates. One of the Clostridium-like isolates was identified as Citrobacter amalonaticus by both diagnostic methods. The generated 16S rRNA sequences matched completely (100%) with sequences available in GenBank for Clostridium and Citrobacter species. Species identification attained using the VITEK MS for the Clostridium-like isolates was comparable to that from the 16S rRNA sequencing-based data. Conclusions The VITEK MS and 16S rRNA sequence analysis can be implemented in the species identification of Clostridium spp. isolates of public health importance. Highlights MALDI-TOF MS and 16S rRNA sequencing can be used in the species identification of Clostridium species.

Background In September 2012, a multistate fungal meningitis outbreak started across 20 states in the United States. It affected 753 individuals and caused 64 deaths who received contaminated spinal injections. In a previous study, we analyzed 26 environmental samples collected from the manufacturing premises of a compounding company to determine the possible cause of an outbreak and identified 14 distinct fungal species. Objectives In this follow-up study, we have analyzed 198 environmental samples collected from three additional compounding company premises located in the United States for the presence of pathogenic fungi. Methods Environmental swab samples were initially examined by standard microbiological methods. Subsequently, DNA sequencing was performed on all of the 25 recovered fungal isolates at the D1–D2 domain of the large subunit (LSU) ribosomal RNA (rRNA) and the internal transcribed spacer (ITS) regions. Results Sequence analysis of the ITS1, ITS2, and LSU rRNA regions confirmed the presence of the following fungal species in the environmental samples analyzed: (i) Pestalotiopsis cocculi from the region Ia; (ii) Epicoccum nigrum and Trichaptum biforme from the region Ib; (iii) Nigrospora sphaerica and Fusarium sp. from the region II; and (iv) Curvularia sp., Fusarium sp., Penicillium sp., and Preussia sp. from the region III. Species identification of 25 recovered fungal isolates matched, in most cases, at 3 sequenced loci (ITS1, ITS2, and LSU). Highlights DNA sequencing of ITS1, ITS2, and LSU D1–D2 regions can be used to perform fungal typing and in implementing effective environmental monitoring programs of public health importance.

Cerebral amyloid-β (Aβ) plaques are the hallmark biomarker of Alzheimer’s disease (AD) and are detectable decades before clinical symptoms. Modifying risk factors associated with Aβ accrual offers an opportunity for AD prevention. While midlife vascular health is linked to AD; there is minimal longitudinal evidence regarding the effect of midlife lipids on Aβ. We examined the association between midlife lipids and Aβ 20 years later. One hundred and twenty-two women had serum lipid profiles in midlife (1992, 45–57 years), and cerebral imaging, genotyping, and cognition measured 20 years later (2012/13, 66–77 years). Imaging was performed in 2012/13 via F-18 Florbetaben positron emission tomography (PET) and standard uptake value ratios (SUVR) were calculated. Lipid profiles and other predictors of high PET-SUVR levels (>1.2) were evaluated using multivariable logistic regression. Increases in low-density lipoprotein (LDL) cholesterol in midlife were associated with Aβ, adjusting for age, education, cholesterol medication, and cognition (AdjOR1.81, 95% CI 1.08–3.01, p = 0.024), but attenuated on adjustment for apolipoprotein E4 (APOE ɛ4). Aβ risk increased in women with APOE ɛ4 and midlife cholesterol >6.2 mmol/L (AdjOR9.59, 95% CI 2.94–31.31, p 3.3 mmol/L (AdjOR9.00, 95% CI 2.89–28.03, p

Cronobacter spp. are emerging infectious foodborne bacteria that can cause acute meningitis and necrotizing enterocolitis in neonates and immunocompromised individuals. Although, little is known about its reservoirs or transmission routes, it has been linked to powdered infant formula worldwide. Three Cronobacter spp. (C. sakazakii, C. malonaticus, and C. turicensis) have been described as more virulent, and isolated frequently from infant meningitis cases. The estimated mortality rates are as high as 80% in infants. Thus, surveillance and typing of Cronobacter spp. isolated from food and environmental samples is essential to prevent contamination and spread of this pathogen. In this study, we have characterized 83 Cronobacter isolates recovered from various environmental samples by conventional microbiologic protocols. Species identification was accomplished by VITEK 2 system and real-time PCR analysis. Subsequently, these isolates were analyzed using VITEK MS system. Single locus sequence typing (SLST) was achieved by characterizing the regions of 16S rRNA and rpoB genes. Multilocus sequence typing (MLST) was performed by sequence characterization of seven housekeeping genes (atpD, fusA, glnS, gltB, gyrB, infB, and pps) using ABI 3500XL Genetic Analyzer. VITEK MS system identified, the majority of isolates as Cronobacter sakazakii with a high confidence value (99.9%). MLST analysis ascertained 12 distinct clonal complexes (CC1, CC4, CC8, CC13, CC17, CC21, CC31, CC40, CC52, CC64, CC73, and CC83) for the recovered C. sakazakii isolates. The results suggest that the MALDI-TOF MS is a reliable diagnostic tool for rapid species identification whereas 7-loci MLST is a powerful technique to discriminate and differentiate Cronobacter spp. isolates.

Leading state-of-the-art research facilities at the Universities of Edinburgh (UoE), Bristol (UoB), Lancaster (UoLan), King's College London (KCL) and Digital Catapult (DCAT) are interconnected through a dedicated JISC/JANET network infrastructure. Using Software Defined Networking (SDN) and Network Function Virtualisation (NFV) technologies, these distributed test-beds are integrated using a multi-domain NFV Orchestrator. This paper introduces a novel specialist distributed test-bed developed for facilitating the increasingly large and complex experimentation of future Internet system architectures, technologies, services, and applications between the geographically dispersed laboratories across the UK. The aim is to enable students, researchers, and enterprises to interconnect with and carry out remote experiments using these test-beds. Each one contributes a range of key capabilities for Internet research including optical networks, optical wireless and radio frequency communications, Internet of Things (IoT), SDN, NFV, as well as cloud computing technologies and services.

The increased use of mobile devices has prompted the need for efficient mobility management protocols to ensure continuity of communication sessions as users switch connection between available wireless access networks. Locator Identifier Separation Protocol Mobile Node (LISP-MN) was designed to enable such efficient mobility of nodes on the Internet. The protocol enables mobility by ensuring that the IP address used for creating data session is maintained throughout the lifetime of the communication session and the location of the mobile node (MN) is updated as the device moves. While session continuity is achieved during handover, we observed that LISP-MN records loss of packets in transit, long service disruption time, throughput degradation and increased rate of TCP retransmission as an MN conducts a handover from one access link to another. To mitigate the poor handover performance, we introduced a novel network node into the LISP-MN architecture, a loc-server that buffers the packets sent to an MN during handover and forwards to the device upon completion of the movement process. We analysed both qualitative features and quantitative measurements of vanilla LISP-MN against LISP-MN with loc-server support. Results show that the improved architecture significantly improved the performance of LISP-MN in all the investigated parameters.

Staphylococcus spp. is considered as one of the most common human-pathogenic bacteria, causing illnesses ranging from nonthreatening skin infections to lethal diseases, including sepsis, pneumonia, bloodstream infections, and food poisoning. The emergence of methicillin-resistant Staphylococcus aureus strains has increased morbidity and mortality and resulted in a major healthcare burden worldwide. Single and multilocus sequence typing have been extensively used in the identification of Staphylococcus species. Nevertheless, these assays are relatively time-consuming and require high-quality DNA. Matrix-assisted laser desorption ionization-time-of-flight has been used recently for the rapid identification of several bacterial species. In this study, we have examined 47 Staphylococcus isolates recovered from food, environment, clinical samples, cosmetic products, and a medical device and 3 American Type Culture Collection Staphylococcus reference isolates using bioMérieux VITEK MS and VITEK 2 systems to determine isolate identity. Sequencing of the 16S ribosomal RNA gene was performed to confirm and compare the species identification data generated by VITEK 2 and VITEK MS systems. Although the VITEK 2 system could not identify one of the isolates, VITEK MS identified all 50 Staphylococcus spp. isolates tested. Results of this study clearly suggest that VITEK MS can be used in the rapid identification of Staphylococcus isolates of public health importance.

Campylobacteriosis is an infectious gastrointestinal disease caused by Campylobacter spp. In most cases, it is either underdiagnosed or underreported due to poor diagnostics and limited databases. Several DNA-based molecular diagnostic techniques, including 16S ribosomal RNA (rRNA) sequence typing, have been widely used in the species identification of Campylobacter. Nevertheless, these assays are time-consuming and require a high quality of bacterial DNA. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS is an emerging diagnostic technology that can provide the rapid identification of microorganisms by using their intact cells without extraction or purification. In this study, we analyzed 24 American Type Culture Collection reference isolates of 16 Campylobacter spp. and five unknown clinical bacterial isolates for rapid identification utilizing two commercially available MADI-TOF MS platforms, namely the bioMérieux VITEK® MS and Bruker Biotyper systems. In addition, 16S rRNA sequencing was performed to confirm the species-level identification of the unknown clinical isolates. Both MALDI-TOF MS systems identified the isolates of C. jejuni, C. coli, C. lari, and C. fetus. The results of this study suggest that the MALDI-TOF MS technique can be used in the identification of Campylobacter spp. of public health importance.

The primary mission of the U.S. Food and Drug Administration is to enforce the Food, Drug, and Cosmetic Act and regulate food, drug, and cosmetic products. Thus, this agency monitors the presence of pathogenic microorganisms in these products, including canned foods, as one of the regulatory action criteria and also ensures that these products are safe for human consumption. This study was carried out to investigate the effectiveness of pathogen control and integrity of ready-to-eat canned food containing Black Bean Corn Poblano Salsa. A total of nine unopened and recalled canned glass jars from the same lot were examined initially by conventional microbiologic protocols that involved a two-step enrichment, followed by streaking on selective agar plates, for the presence of gram-positive and gram-negative bacteria. Of the eight subsamples examined for each sample, all subsamples of one of the containers were found positive for the presence of slow-growing rod-shaped, gram-positive, facultative anaerobic bacteria. The recovered isolates were subsequently sequenced at rRNA and gyrB loci. Afterward, multilocus sequence typing (MLST) was performed characterizing 11 additional known MLST loci (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). Analyses of the nucleotide sequences of rRNA, gyrB, and 11 MLST loci confirmed these gram-positive bacteria recovered from canned food to be Lactobacillus fermentum . Thus, the DNA sequencing of housekeeping MLST genes can provide species identification of L. fermentum and can be used in the canned food monitoring program of public health importance.

NFV-MANO has become the de-facto standard for network service orchestration in future programmable network infrastructures. Relevant standards define an architecture and a data model that allows an orchestration entity to deploy, dynamically configure and monitor virtual and physical network functions across virtualized datacenters. Although the model offers extensive details for network function management and host-level network configuration, end-to-end connectivity management beyond the datacenter remains limited. The responsibility for cross-site connectivity is delegated to a control abstraction, the WAN Infrastructure Manager (WIM), which is partially defined in relevant standards. The reference implementation of the NFVMANO standards, Open Source MANO (OSM), has recently released a reference WIM driver model, but no open-source WIM implementation is currently available, thus restricting the ability of researchers to experiment with multi-site service deployments. In this paper, we present the DataPlane Broker (DPB), the first open-source WIM implementation for software-defined networks. Using an extensive data model, DPB seamlessly translates NFVMANO requirements into SDN configuration, supporting point-to-point and multipoint connectivity with strong bandwidth guarantees. DPB is integrated with OSM FIVE via a WIM plugin. Initial experiments highlight that path computation can scale to large network topologies and a large number of services, with negligible computational overheads, while DPB increases by less than 10% the overall deployment delay of an OSM service.

Background: Campylobacter is a genus of Gram-negative bacteria. It is considered one of the leading cause of diarrheal illness worldwide. Incidence of human campylobacteriosis has increased significantly during recent decades; the increase has been directly linked with the advancement made in Campylobacter detection methods. C. jejuni and C. coli are the two major human-pathogenic species that can colonize poultry and cause foodborne illness and outbreak. Objective: This study was carried out to rapidly identify Campylobacter-like isolates recovered from raw poultry products by matrix-assisted laser desorption ionization (MALDI)–time-of-flight (TOF) MS and DNA sequencing of 16S and 23S ribosomal RNA (rRNA) regions. Methods: Twenty-seven isolates of Campylobacter-like organisms were isolated from raw poultry products and cultured on blood agars for MALDI–TOF MS analysis and DNA isolation. For each isolate, one to two colonies were directly spotted on the VITEK MS analysis. Genomic DNA was extracted from overnight bacterial culture. Afterward, two-directional Sanger sequencing of rRNA gene was performed to confirm species identification on an ABI 3500xL Genetic Analyzer. Results: The VITEK MS could provide species-level identification for all 27 Campylobacter-like bacterial isolates (including 13 isolates as C. jejuni and 14 isolates as C. coli). Species identification attained by the VITEK MS matched completely with the rRNA sequence characterization data. Conclusions: Based on the restricted number of target strains and agar plates, MALDI–TOF MS and rRNA sequence analysis can be used for rapid identification of C. jejuni and C. coli isolates. Highlights: MALDI–TOF MS and rRNA sequencing can provide species identification of C. jejuni and C. coli isolates.