In vivo evaluation of T-Scan in quantifying occlusal contact.

BACKGROUND: The T-scan system has been used previously to analyse occlusion, but the quantitative analysis of occlusal contact by T-Scan system has yet to be reported. OBJECTIVES: To evaluate the reliability and validity of T-Scan system for quantitatively measuring occlusal contact area and occlusal contact number. METHODS: Twenty-two individuals with normal occlusion, 11 men and 11 women, were recruited for the study. Two occlusal analysis methods, including silicone transmission analysis method (STA) and T-Scan occlusion analysis method (TSO), were used to make quantitative analysis to measure occlusal contact area (OCA) and occlusal contact number (OCN). A test-retest check was performed with an interval of 2 weeks. The values of intraclass correlation coefficients (ICC) between test-retest of each method were calculated for reliability evaluation. Pearson correlations analysis, paired t-tests, regression analysis and Bland-Altman analysis were performed for validity evaluation. RESULTS: The ICC values of STA were greater than those of TSO for OCA while for OCN, ICC values of TSO were greater than STA. The higher OCA and OCN values were found in TSO compared with STA. Pearson's correlation coefficient indicated strong relations between TSO and STA (0.730-0.812) for OCA, while good relations between then (0.569-0.583) for OCN. Paired t-test showed a significant difference between the OCA and OCN values between TSO and STA. Bland-Altman analysis showed good agreement between OCA and OCN values of TSO and STA both in men and women. Regression analysis identified a linear correlation between OCA values obtained from these two methods. CONCLUSIONS: T-Scan method showed strong reliability for measuring OCA and OCN quantitatively. Strong correlations were found between OCA values from TSO and STA method, but the validity of TSO for measuring OCN needs to be promoted. CLINICAL SIGNIFICANCE: T-Scan system demonstrates good potential in quantitative analysis of occlusion, which will expand its clinical application.

Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host.

In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However, transmission analysis cannot rely solely on a phylogeny of the genomes but must account for the within-host evolution of the pathogen, which blurs the relationship between phylogenetic and transmission trees. When only a single genome is sampled for each host, the uncertainty about who infected whom can be quite high. Consequently, transmission analysis based on multiple genomes of the same pathogen per host has a clear potential for delivering more precise results, even though it is more laborious to achieve. Here, we present a new methodology that can use any number of genomes sampled from a set of individuals to reconstruct their transmission network. Furthermore, we remove the need for the assumption of a complete transmission bottleneck. We use simulated data to show that our method becomes more accurate as more genomes per host are provided, and that it can infer key infectious disease parameters such as the size of the transmission bottleneck, within-host growth rate, basic reproduction number, and sampling fraction. We demonstrate the usefulness of our method in applications to real datasets from an outbreak of Pseudomonas aeruginosa amongst cystic fibrosis patients and a nosocomial outbreak of Klebsiella pneumoniae.

GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach.

BACKGROUND: Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interactive functionalities for easy data exploration. RESULTS: GraphSNP is an interactive visualisation tool running in a web browser that allows users to rapidly generate pairwise SNP distance networks, investigate SNP distance distributions, identify clusters of related organisms, and reconstruct transmission routes. The functionality of GraphSNP is demonstrated using examples from recent multi-drug resistant bacterial outbreaks in healthcare settings. CONCLUSIONS: GraphSNP is freely available at https://github.com/nalarbp/graphsnp . An online version of GraphSNP, including demonstration datasets, input templates, and quick start guide is available for use at https://graphsnp.fordelab.com .

Screening for Clostridioides difficile colonization at admission to the hospital: a multi-centre study.

OBJECTIVES: To assess the value of screening for Clostridioides difficile colonization (CDC) at hospital admission in an endemic setting. METHODS: A multi-centre study was conducted at four hospitals located across the Netherlands. Newly admitted patients were screened for CDC. The risk of development of Clostridioides difficile infection (CDI) during admission and 1-year follow-up was assessed in patients with and without colonization. C. difficile isolates from patients with colonization were compared with isolates from incident CDI cases using core genome multi-locus sequence typing to determine whether onwards transmission had occurred. RESULTS: CDC was present in 108 of 2211 admissions (4.9%), whereas colonization with a toxigenic strain (toxigenic Clostridoides difficile colonization [tCDC]) was present in 68 of 2211 admissions (3.1%). Among these 108 patients with colonization, diverse PCR ribotypes were found and no 'hypervirulent' PCR ribotype 027 (RT027) was detected (95% CI, 0-0.028). None of the patients with colonization developed CDI during admission (0/49; 95% CI, 0-0.073) or 1-year follow-up (0/38; 95% CI, 0-0.93). Core genome multi-locus sequence typing identified six clusters with genetically related isolates from patients with tCDC and CDI; however, in these clusters, only one possible transmission event from a patient with tCDC to a patient with CDI was identified based on epidemiological data. CONCLUSION: In this endemic setting with a low prevalence of 'hypervirulent' strains, screening for CDC at admission did not detect any patients with CDC who progressed to symptomatic CDI and detected only one possible transmission event from a patient with colonization to a patient with CDI. Thus, screening for CDC at admission is not useful in this setting.

Advantages of long- and short-reads sequencing for the hybrid investigation of the Mycobacterium tuberculosis genome.

Introduction: In the fight to limit the global spread of antibiotic resistance, computational challenges associated with sequencing technology can impact the accuracy of downstream analysis, including drug resistance identification, transmission, and genome resolution. About 10% of Mycobacterium tuberculosis (MTB) genome is constituted by the PE/PPE family, a GC-rich repetitive genome region. Although sequencing using short read technology is widely used, it is well recognized its limit in the PE/PPE regions due to the unambiguously mapping process onto the reference genome. The aim of this study was to compare the performances of short-reads (SRS), long-reads (LRS) and hybrid-reads (HYBR) based analysis over different common investigative tasks: genome coverage estimation, variant calling and cluster analysis, drug resistance detection and de novo assembly. Methods: For the study 13 model MTB clinical isolates were sequenced with both SRS and LRS. HYBR were produced correcting the long reads with the short reads. The fastq from the three approaches were then processed using a customized version of MTBseq for genome coverage estimation and variant calling and using two different assemblers for de novo assembly evaluation. Results: Estimation of genome coverage performances showed lower 8X breadth coverage for SRS respect to LRS and HYBR: considering the PE/PPE genes, SRS showed low results for the PE_PGRS family, while obtained acceptable coverage in PE and PPE genes; LRS and HYBR reached optimal coverages in PE/PPE genes. For variant calling HYBR showed the highest resolution, detecting the highest percentage of uniquely identified mutations compared to LRS and SRS. All three approaches agreed on the identification of two major clusters, with HYBR identifying an higher number of SNPs between the two clusters. Comparing the quality of the assemblies, HYBR and LRS obtained better results than SRS. Discussion: In conclusion, depending on the aim of the investigation, both SRS and LRS present complementary advantages and limitations implying that for a full resolution of MTB genomes, where all the mentioned analyses and both technologies are needed, the use of the HYBR approach represents a valid option and a well-rounded strategy.

Early evolution and transmission of GII.P16-GII.2 norovirus in China.

Norovirus is the most common cause of acute gastroenteritis worldwide. During 2016-2017, a novel recombinant GII.P16-GII.2 genotype of norovirus suddenly appeared and over the next several years became the predominant strain in both China and worldwide. To better understand the origin and diffusion of the GII.P16-GII.2 genotype in China, we conducted molecular evolutionary analyses, including phylodynamics and phylogeography. Moreover, to trace person-to-person transmission of GII.P16-GII.2 norovirus, we applied the novel method, TransPhylo, to a historical phylogeny using sequences obtained from a publicly available database. A time-scaled phylogenetic tree indicated that the time to the most recent common ancestor of the GII.P16-GII.2 major capsid protein (VP1) gene diverged from the GII.P2-GII.2 VP1 gene at 2,001.03 with an evolutionary rate of 3.32 × 10-3 substitutions/site/year. The time to the most recent common ancestor of the GII.P16-GII.2 RNA-dependent RNA polymerase region diverged from the GII.P16-GII.4 RNA-dependent RNA polymerase region at 2,013.28 with an evolutionary rate of 9.44 × 10-3 substitutions/site/year. Of these 2 genomic regions, VP1 gene sequence variations were the most influenced by selective pressure. A phylogeographic analysis showed that GII.P16-GII.2 strains in China communicated most frequently with those in the United States, Australia, Thailand, and Russia, suggesting import from Australia to Taiwan and from the United States to Guangdong. TransPhylo analyses indicated that the basic reproductive number (R0) and sampling proportion (pi) of GII.P16-GII.2 norovirus were 1.99 (95% confidence interval: 1.58-2.44) and 0.76 (95% confidence interval: 0.63-0.88), respectively. Strains from the United States and Australia were responsible for large spread during the evolution and transmission of the virus. Coastal cities and places with high population densities should be closely monitored for norovirus.

Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo.

Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo. © 2021 The Authors. Basic Protocol 1: First steps with TransPhylo Basic Protocol 2: Simulation of outbreak data Basic Protocol 3: Inference of transmission Basic Protocol 4: Exploring the results of inference.

Evaluation of Thermal Optical Analysis (TOA) using an aqueous binary mixture.

Thermal-Optical Analysis (TOA), a commonly implemented technique used to measure the amount of particulate carbon in the atmosphere or deposited on a filter substrate, distinguishes organic carbon (OC) from elemental carbon (EC) through the monitoring of laser light, heating, and measuring evolved carbon. Here, we present a method to characterize the TOA transmission method with an aqueous binary mixture containing EC and OC that can easily be deposited onto a filter at low volumes. Known amounts of EC and OC were deposited onto a quartz-fiber filter and analyzed with different temperature protocols. Results with the NIST-EPA-C temperature protocol agreed with the reference values to better than 2 % for EC, OC, total carbon (TC), and EC/TC. Indicated TC for all temperature protocols was within 5 % of the reference value while all protocols reproduced EC/TC ratios with an uncertainty less than 10 %.

Patterns of recognition of Arabic consonants by non-native children with cochlear implants and normal hearing.

OBJECTIVE: This study examined the patterns of recognition of Arabic consonants, via information transmission analysis for phonological features, in a group of Malay children with normal hearing (NH) and cochlear implants (CI). METHOD: A total of 336 and 616 acoustic tokens were collected from six CI and 11 NH Malay children, respectively. The groups were matched for hearing age and duration of exposure to Arabic sounds. All the 28 Arabic consonants in the form of consonant-vowel /a/ were presented randomly twice via a loudspeaker at approximately 65 dB SPL. The participants were asked to repeat verbally the stimulus heard in each presentation. RESULTS: Within the native Malay perceptual space, the two groups responded differently to the Arabic consonants. The dispersed uncategorized assimilation in the CI group was distinct in the confusion matrix (CM), as compared to the NH children. Consonants /h/, /tˁ/, /sˁ/ and /ʁ/ were difficult for the CI children, while the most accurate item was /k/ (84%). The CI group transmitted significantly reduced information, especially for place feature transmission, then the NH group (p < 0.001). Significant interactions between place-hearing status and manner-hearing status were also obtained, suggesting there were information transmission differences in the pattern of consonants recognition between the study groups. CONCLUSION: CI and NH Malay children may be using different acoustic cues to recognize Arabic sounds, which contribute to the different assimilation categories' patterns within the Malay perceptual space.

Animal health and price transmission along livestock supply chains.

Animal health diseases can severely affect the food supply chain by causing variations in prices and market demand. Price transmission analysis reveals in what ways price variations are transmitted along the supply chain, and how supply chains of substitute products and different regional markets are also affected. In perfect markets, a price variation would be completely and instantaneously transmitted across the different levels of the supply chain: producers, the processing industry, retailers and consumers. However, empirical studies show that food markets are often imperfect, with anomalies or asymmetries in price transmission and distortions in the distribution of market benefits. This means, for instance, that a price increase at the consumer level may not be transmitted from retailers to processors and producers; yet, on the other hand, price falls may rapidly affect the upstream supply chain. Market concentration and the consequent exertion of market power in key segments of the supply chain can explain price transmission asymmetries and their distributional effects, but other factors may also be involved, such as transaction costs, scale economies, and imperfect information. During the bovine spongiform encephalopathy (BSE) crisis, asymmetric price transmission in the beef supply chain and related meat markets determined distributional effects among sectors. After the spread of the BSE food scare, the fall in demand marginally affected the price paid to retailers, but producers and wholesalers suffered much more, in both price reductions and the time needed to recover to precrisis demand. Price transmission analysis investigates how animal health crises create different economic burdens for various types of stakeholder, and provides useful socioeconomic insights when used with other tools.

Les maladies animales peuvent avoir de graves répercussions sur la filière agroalimentaire en occasionnant une instabilité des prix et de la demande. L'analyse de la transmission des prix met en lumière la manière dont les variations de prix se transmettent tout au long de la chaîne d'approvisionnement et leurs conséquences sur les productions de substitution et sur les différents marchés régionaux. Dans un marché parfait, toute variation de prix se répercute de manière intégrale et instantanée à chaque niveau de la chaîne d'approvisionnement : producteurs, transformateurs, détaillants et consommateurs. Des études empiriques ont toutefois montré que les marchés de l'agroalimentaire sont souvent imparfaits, avec des anomalies ou des asymétries dans la transmission des prix ainsi que des distorsions dans la répartition des bénéfices commerciaux. Ainsi, par exemple, une hausse du prix payé par le consommateur ne se transmet pas nécessairement du détaillant aux transformateurs et aux producteurs, tandis qu'une baisse des prix affecte très rapidement la filière en amont. Si les asymétries de la transmission des prix et leur impact distributif peuvent s'expliquer par la concentration des marchés et par la puissance commerciale exercée par des segments clés de la chaîne d'approvisionnement, d'autres facteurs entrent également en jeu, tels les coûts de transaction, les économies d'échelle et les failles de l'information. Lors de la crise due à l'encéphalopathie spongiforme bovine (ESB), l'asymétrie de la transmission des prix au sein de la filière viande bovine et des marchés connexes de la viande a eu pour conséquence un impact distributif parmi les secteurs concernés. Suite à la panique causée par l'ESB, la chute de la demande a eu des répercussions marginales sur le prix payé aux détaillants, tandis que les producteurs et les grossistes ont été beaucoup plus affectés, non seulement par la chute des prix mais aussi par le temps qu'il leur a fallu attendre avant que la demande retrouve son niveau d'avant la crise. L'analyse de la transmission des prix permet de comprendre la diversité des répercussions économiques d'une crise de santé animale en fonction des parties prenantes concernées et fournit un éclairage socio-économique précieux lorsqu'elle est utilisée parallèlement à d'autres outils.

Las enfermedades de los animales pueden resultar muy perjudiciales para la cadena de suministro alimentario por las oscilaciones que provocan en los precios y la demanda del mercado. El análisis de la transmisión de precios revela de qué manera las variaciones de precios se transmiten a lo largo de la cadena de suministro y cómo afectan también a las cadenas de suministro de productos sustitutorios y a mercados regionales diferentes. En un mercado perfecto, la variación de un precio se transmitiría de forma completa e instantánea a los distintos eslabones de la cadena de suministro: productores, industria transformadora, minoristas y consumidores. Sin embargo, los estudios empíricos demuestran que los mercados agroalimentarios suelen ser imperfectos y presentar anomalías o asimetrías en la transmisión de los precios, así como distorsiones en la distribución de los beneficios comerciales. Ello significa, por ejemplo, que un aumento de precio a nivel del consumidor puede no transmitirse de los minoristas a los transformadores y productores. Por otro lado, en cambio, las caídas de precios pueden afectar rápidamente a los primeros eslabones de la cadena de suministro. La concentración del mercado y el consiguiente ejercicio del poder de mercado en segmentos clave de la cadena de suministro pueden explicar las asimetrías de la transmisión de precios y sus efectos en la distribución, aunque también es posible que intervengan otros factores, como los costos de transacción, las economías de escala o las imperfecciones de la información. Durante la crisis causada por la encefalopatía espongiforme bovina (EEB), la transmisión asimétrica de los precios en la cadena de suministro de carne vacuna y en los mercados cárnicos conexos trajo consigo una serie de efectos distributivos entre los sectores. Cuando cundió la alarma causada por la EEB, la caída de la demanda afectó solo de manera marginal al precio pagado a los minoristas, pero en cambio productores y mayoristas sufrieron mucho más, tanto por la caída de precios como por el tiempo necesario para que la demanda recuperara los niveles previos a la crisis. El análisis de la transmisión de precios estudia cómo las crisis zoosanitarias imponen una carga económica variable a las distintas partes interesadas y proporciona información socioeconómica de utilidad cuando se emplea en combinación con otras herramientas.

Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks.

Genomic data are increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom-a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by coloring the branches of a phylogeny according to which host those branches were in. Here we extend this approach and show that it can be applied to partially sampled and ongoing outbreaks. This requires computing the correct probability of an observed transmission tree and we herein demonstrate how to do this for a large class of epidemiological models. We also demonstrate how the branch coloring approach can incorporate a variable number of unique colors to represent unsampled intermediates in transmission chains. The resulting algorithm is a reversible jump Monte-Carlo Markov Chain, which we apply to both simulated data and real data from an outbreak of tuberculosis. By accounting for unsampled cases and an outbreak which may not have reached its end, our method is uniquely suited to use in a public health environment during real-time outbreak investigations. We implemented this transmission tree inference methodology in an R package called TransPhylo, which is freely available from https://github.com/xavierdidelot/TransPhylo.

Analysis of a long-term outbreak of XDR Pseudomonas aeruginosa: a molecular epidemiological study.

OBJECTIVES: Here we report on a long-term outbreak from 2009 to 2012 with an XDR Pseudomonas aeruginosa on two wards at a university hospital in southern Germany. METHODS: Whole-genome sequencing was performed on the outbreak isolates and a core genome was constructed for molecular epidemiological analysis. We applied a time-place-sequence algorithm to improve estimation of transmission probabilities. RESULTS: By using conventional infection control methods we identified 49 P. aeruginosa strains, including eight environmental isolates that belonged to ST308 (by MLST) and carried the metallo-ß-lactamase IMP-8. Phylogenetic analysis on the basis of a non-recombinant core genome that contained 22 outbreak-specific SNPs revealed a pattern of four dominant clades with a strong phylogeographic structure and allowed us to determine the potential temporal origin of the outbreak to July 2008, 1 year before the index case was diagnosed. Superspreaders at the root of clades exhibited a high number of probable and predicted transmissions, indicating their exceptional position in the outbreak. CONCLUSIONS: Our results suggest that the initial expansion of dominant sublineages was driven by a few superspreaders, while environmental contamination seemed to sustain the outbreak for a long period despite regular environmental control measures.