scholarly journals Evolution and Population Structure of Salmonella enterica Serovar Newport

2010 ◽  
Vol 192 (24) ◽  
pp. 6465-6476 ◽  
Author(s):  
Vartul Sangal ◽  
Heather Harbottle ◽  
Camila J. Mazzoni ◽  
Reiner Helmuth ◽  
Beatriz Guerra ◽  
...  
Keyword(s):  
Population Structure ◽  
North America ◽  
Salmonella Enterica ◽  
Health Concern ◽  
Global Public Health ◽  
Multiple Sequence ◽  
Monophyletic Lineage ◽  
Population Structures ◽  
Paratyphi B ◽  
Multiple Drugs

ABSTRACT Salmonellosis caused by Salmonella enterica serovar Newport is a major global public health concern, particularly because S. Newport isolates that are resistant to multiple drugs (MDR), including third-generation cephalosporins (MDR-AmpC phenotype), have been commonly isolated from food animals. We analyzed 384 S. Newport isolates from various sources by a multilocus sequence typing (MLST) scheme to study the evolution and population structure of the serovar. These were compared to the population structure of S. enterica serovars Enteritidis, Kentucky, Paratyphi B, and Typhimurium. Our S. Newport collection fell into three lineages, Newport-I, Newport-II, and Newport-III, each of which contained multiple sequence types (STs). Newport-I has only a few STs, unlike Newport-II or Newport-III, and has possibly emerged recently. Newport-I is more prevalent among humans in Europe than in North America, whereas Newport-II is preferentially associated with animals. Two STs of Newport-II encompassed all MDR-AmpC isolates, suggesting recent global spread after the acquisition of the bla CMY-2 gene. In contrast, most Newport-III isolates were from humans in North America and were pansusceptible to antibiotics. Newport was intermediate in population structure to the other serovars, which varied from a single monophyletic lineage in S. Enteritidis or S. Typhimurium to four discrete lineages within S. Paratyphi B. Both mutation and homologous recombination are responsible for diversification within each of these lineages, but the relative frequencies differed with the lineage. We conclude that serovars of S. enterica provide a variety of different population structures.

scholarly journals Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica

2020 ◽  
Author(s):  
Jingqiu Liao ◽  
Renato Hohl Orsi ◽  
Laura Carroll ◽  
Martin Wiedmann
Keyword(s):  
Population Structure ◽  
Comparative Genomics ◽  
Causative Agent ◽  
Salmonella Enterica ◽  
Geographic Origin ◽  
Health Concern ◽  
Ecological Niches ◽  
Evolutionary Forces ◽  
Geographic Origins ◽  
The Impact

SummaryGenetic variation in a pathogen, including the causative agent of salmonellosis, Salmonella enterica, can occur as a result of eco-evolutionary forces triggered by dissimilarities of ecological niches. Here, we applied comparative genomics to study 90 antimicrobial resistant (AMR) S. enterica isolates from bovine and human hosts in New York state and Washington state to understand host- and geographic-associated population structure. Results revealed distinct presence/absence profiles of functional genes and pseudogenes (e.g., virulence genes) associated with bovine and human isolates. Notably, bovine isolates contained significantly more transposase genes but fewer transposase pseudogenes than human isolates, suggesting the occurrence of large-scale transposition in genomes of bovine and human isolates at different times. The high correlation between transposase genes and AMR genes, as well as plasmid replicons, highlights the potential role of horizontally transferred transposons in promoting adaptation to antibiotics. By contrast, a number of potentially geographic-associated single-nucleotide polymorphisms (SNPs), rather than geographic-associated genes, were identified. Interestingly, 38% of these SNPs were in genes annotated as cell surface protein-encoding genes, including some essential for antibiotic resistance and host colonization. Overall, different evolutionary forces and limited recent inter-population transmission appear to shape AMR S. enterica population structure in different hosts and geographic origins.Originality/Significance StatementSalmonella enterica, which is the causative agent of salmonellosis, poses a growing public health concern due to the emergence and spread of antimicrobial resistant (AMR) strains. The mechanisms underlying the population structure associated with different hosts and geographic origins of AMR S. enterica are underexplored due to limited genome-wide studies assessing the impact of ecological niches on genetic variations. By employing comparative genomics, our study provided insights into the genomic profiles of AMR S. enterica associated with two distinct hosts and two distant geographic locations, improving the mechanistic understanding of how bacterial population structure is shaped by different ecological niches. Our findings have broad implications for elucidating the impact of ecological and evolutionary forces on the adaptation, antimicrobial resistance, and pathogenicity of bacteria. Also, specific genetic markers we identified may help predict host or geographic origin of AMR Salmonella isolates, which could benefit the source tracking (e.g., host and geographic origins) of human disease cases and contamination events caused by AMR S. enterica.

SARS-COV2 virus and Coronavirus disease (COVID-19)

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 977-982
Author(s):  
Mohamed J. Saadh ◽  
Bashar Haj Rashid M ◽  
Roa’a Matar ◽  
Sajeda Riyad Aldibs ◽  
Hala Sbaih ◽  
...  
Keyword(s):  
Close Contact ◽  
Antiviral Agents ◽  
Health Concern ◽  
The Novel ◽  
Global Public Health ◽  
Fatal Disease ◽  
Mild Disease ◽  
Life Threatening ◽  
Novel Coronavirus

SARS-COV2 virus causes Coronavirus disease (COVID-19) and represents the causative agent of a potentially fatal disease that is of great global public health concern. The novel coronavirus (2019) was discovered in 2019 in Wuhan, the market of the wet animal, China with viral pneumonia cases and is life-threatening. Today, WHO announces COVID-19 outbreak as a pandemic. COVID-19 is likely to be zoonotic. It is transmitted from bats as intermediary animals to human. Also, the virus is transmitted from human to human who is in close contact with others. The computerized tomographic chest scan is usually abnormal even in those with no symptoms or mild disease. Treatment is nearly supportive; the role of antiviral agents is yet to be established. The SARS-COV2 virus spreads faster than its two ancestors, the SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), but has lower fatality. In this article, we aimed to summarize the transmission, symptoms, pathogenesis, diagnosis, treatment, and vaccine to control the spread of this fatal disease.

Surnames and population structure in the Doctrine of Belén, Altos de Arica, Viceroyalty of Peru (1750–1813)

2021 ◽  
pp. 1-13
Author(s):  
Emma Alfaro ◽  
Xochitl Inostroza ◽  
José E. Dipierri ◽  
Daniela Peña Aguilera ◽  
Jorge Hidalgo ◽  
...  
Keyword(s):  
Population Structure ◽  
Indigenous Population ◽  
Random Mating ◽  
Quantitative Information ◽  
Geographic Space ◽  
Documentary Sources ◽  
Cultural Variables ◽  
The Social ◽  
Population Structures ◽  
And Migration

Abstract The analysis of multiple population structures (biodemographic, genetic and socio-cultural) and their inter-relations contribute to a deeper understanding of population structure and population dynamics. Genetically, the population structure corresponds to the deviation of random mating conditioned by a limited number of ancestors, by restricted migration in the social or geographic space, or by preference for certain consanguineous unions. Through the isonymic method, surname frequency and distribution across the population can supply quantitative information on the structure of a human population, as they constitute universal socio-cultural variables. Using documentary sources to undertake the Doctrine of Belén’s (Altos de Arica, Chile) historical demography reconstruction between 1763 and 1820, this study identified an indigenous population with stable patronymics. The availability of complete marriage, baptism and death records, low rates of migration and the significant percentage of individuals registered and constantly present in this population favoured the application of the isonymic method. The aim of this work was to use given names and surnames recorded in these documentary sources to reconstruct the population structure and migration pattern of the Doctrine of Belén between 1750 and 1813 through the isonymic method. The results of the study were consistent with the ethno-historical data of this ethnic space, where social cohesion was, in multiple ways, related to the regulation of daily life in colonial Andean societies.

scholarly journals CO0005 C-C CHEMOKINE RECEPTOR TYPE 5 AND ITS LIGANDS CCL4, 8 AND 11 CAN LINK COVID-19, RHEUMATOID ARTHRITIS AND HYDROXYCHLOROQUINE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 213.3-214
Author(s):  
M. Y. Hachim ◽  
S. Hannawi
Keyword(s):  
Rheumatoid Arthritis ◽  
Mechanism Of Action ◽  
Immune Cells ◽  
Health Concern ◽  
Healthy Controls ◽  
Global Public Health ◽  
Ccr5 Expression ◽  
Disease Modifying Drugs ◽  
Link Type ◽  
Disease Modifying

Background:Coronavirus disease (COVID-19) caused by SARS-COV2 represents an unprecedented global public health concern with a particular burden on patients with chronic diseases and those on immune-modulating drugs. It is especially worrisome to patients with rheumatoid arthritis (RA) who are on immune suppression regimens[1]. On the other side, many reports showed and recommended the use of some Disease-Modifying Drugs commonly used to treat rheumatic diseases like hydroxychloroquine. However, the general understanding of COVID-19 characteristics in this population and the mechanism of action of these drugs in COVID-19 is still unknown[2].Objectives:Explore publicly available transcriptomic dataset of patients infected with SARS-COV2 compared to uninfected to identify differentially expressed genes (DEGs) related to the immune system that might be pathogenic in RA synovium. Then explore the effect of Disease-Modifying Drugs on their local expression that might give hints about their possible mechanism of action.Methods:RNAseq dataset (GSE147507) were retrieved using the Gene Expression Omnibus (GEO) and used to identify DEGs between infected and uninfected lung samples using BioJupies tools [3]. The DEGs were explored for common pathways using Metascape online tool (http://metascape.org) [10], as shown in figure (1). The chemokines genes were filtered out, and their common receptor (CR) was identified. The immune cells that express a higher level of the identified receptor were explored using DICE project tool (https://dice-database.org/). The expression of CR was searched in a microarray dataset (GSE77298) of synovial biopsies of RA and healthy controls. RNAseq dataset (GSE97165) of synovial biopsies taken from 19 early RA patients at baseline and after six months of Triple Disease-Modifying Anti-rheumatic drugs (tDMARD; methotrexate, sulfasalazine, and hydroxychloroquine) treatment.Results:84 DEGs were identified between uninfected and COVID-19 infected lung samples. These DEGs were enriched in pathways specific to (response to the virus, response to interferon, leukocyte activation, and chemotaxis). Interestingly, SARS-COV-2 infected lungs express more CCL4, CCL8, and CCL11; the three ligands shared the same receptor, which is CCR5. Top immune cells that express CCR5 were CD4 T memory T reg cells, Th17, Th1, and monocytes. CCR5 was significantly upregulated in RA compared to healthy controls synovium (p=0.04) and was dramatically downregulated after six months of tDMARD treatment (p=0.004), as shown in figure (2).Conclusion:Using publicly available transcriptomic datasets properly highlighted the possible beneficiary effect of DMARDs in patients with COVID-19, which can block CCR5 rich immune cells recruitment.References:[1]Favalli, E.G., et al.,COVID-19 infection and rheumatoid arthritis: Faraway, so close!Autoimmun Rev, 2020. 19(5): p. 102523.[2]Gianfrancesco, M.A., et al.,Rheumatic disease and COVID-19: initial data from the COVID-19 Global Rheumatology Alliance provider registries.The Lancet Rheumatology, 2020. 2(5): p. e250-e253.[3]Torre, D., A. Lachmann, and A. Ma’ayan,BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud.Cell Systems, 2018. 7(5): p. 556-561.e3.Figure 1.Flowchart of transcriptomic analysisFigure 2.(A) Top immune cells that express CCR5 (B) CCR5 expression in synovial biopsies of RA and control (C) CCR5 expression at baseline and after 6 months of tDMARD treatment.Disclosure of Interests:None declared

scholarly journals Virulence and Antimicrobial Resistance Profiles of Salmonella enterica Serovars Isolated from Chicken at Wet Markets in Dhaka, Bangladesh

2021 ◽  
Vol 9 (5) ◽  
pp. 952
Author(s):  
Nure Alam Siddiky ◽  
Md Samun Sarker ◽  
Md. Shahidur Rahman Khan ◽  
Ruhena Begum ◽  
Md. Ehsanul Kabir ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Salmonella Enterica ◽  
Virulence Genes ◽  
Health Concern ◽  
Production Cycle ◽  
Salmonella Spp ◽  
Native Chicken ◽  
Resistance Patterns ◽  
Research Findings ◽  
Native Chickens

Virulent and multi drug resistant (MDR) Salmonellaenterica is a foremost cause of foodborne diseases and had serious public health concern globally. The present study was undertaken to identify the pathogenicity and antimicrobial resistance (AMR) profiles of Salmonellaenterica serovars recovered from chicken at wet markets in Dhaka, Bangladesh. A total of 870 cecal contents of broiler, sonali, and native chickens were collected from 29 wet markets. The overall prevalence of S. Typhimurium, S. Enteritidis, and untyped Salmonella spp., were found to be 3.67%, 0.57%, and 1.95% respectively. All isolates were screened by polymerase chain reaction (PCR) for eight virulence genes, namely invA, agfA, IpfA, hilA, sivH, sefA, sopE, and spvC. S. Enteritidis isolates carried all virulence genes whilst S. Typhimurium isolates carried six virulence genes except sefA and spvC. A diverse phenotypic and genotypic AMR pattern was found. Harmonic descending trends of resistance patterns were observed among the broiler, sonali, and native chickens. Interestingly, virulent and MDR Salmonella enterica serovars were found in native chicken, although antimicrobials were not used in their production cycle. The research findings anticipate that virulent and MDR Salmonella enterica are roaming in the wet markets which can easily anchor to the vendor, consumers, and in the food chain.

scholarly journals Optimized and Non-Optimized Personal Protective Equipment Use during the COVID-19 Pandemic in Thailand: A National Cross-Sectional Survey in a Resource-Limited Setting

2021 ◽  
Vol 15 ◽  
pp. 117863022110135
Author(s):  
Visal Moolasart ◽  
Weerawat Manosuthi ◽  
Varaporn Thienthong ◽  
Uajai Jaemsak ◽  
Winnada Kongdejsakda ◽  
...  
Keyword(s):  
Personal Protective Equipment ◽  
Negative Pressure ◽  
Symptom Severity ◽  
Univariate Analysis ◽  
Education Level ◽  
Health Concern ◽  
Protective Equipment ◽  
Global Public Health ◽  
Cross Sectional ◽  
Infection Control Program

Introduction: Coronavirus disease (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-COV2). COVID-19 is highly contagious, potentially fatal, and a global public health concern. Combining optimized personal protective equipment (PPE) use and hand hygiene is the best strategy for preventing COVID-19 in health care workers (HCWs). Methods: We conducted a national cross-sectional web-based survey of HCWs in the infection control program (IPC) in Thailand between May 5, 2020 and May 15, 2020. The primary objective was the prevalence of optimized PPE use amongst HCWs. The secondary objective was identification of the independent predictors of optimized PPE use. Results: We received a response from 46% of HCWs (756/1650), and all those who responded were nurse or HCWs who were registered in the IPC network. Five HCWs were excluded because of missing data, and 751 were included in the final analysis. The prevalences of PPE use were 22% (168/751) for optimized PPE use, 78% (583/751) for non-optimized PPE use, 35% (263/751) for PPE overuse, and 43% (320/751) for PPE underused. In univariate analysis, optimized PPE use was significantly associated with age, education level, knowledge of appropriate negative pressure room selection, and knowledge of apparently milder symptom severity in children than adults. In multivariate analysis, independent predictors of optimized PPE use were knowledge of appropriate negative pressure room selection (aOR = 1.95, 95% CI = 1.18-3.22), the difference in symptom severity between children and adults (aOR = 0.55, 95% CI = 0.37-0.81), and education level (aOR = 1.54, 95% CI = 1.04-2.27). Conclusion: The prevalence of optimized PPE use amongst HCWs was 22%. Independent predictors of optimized PPE use were COVID-19 knowledge-based factors and education level. Therefore, the continued education training program should be implemented to ensure maintenance of appropriate practices during the COVID-19 pandemic.

scholarly journals Probiotics as a Possible Strategy for the Prevention and Treatment of Allergies. A Narrative Review

Foods ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 701
Author(s):  
Aroa Lopez-Santamarina ◽  
Esther Gonzalez Gonzalez ◽  
Alexandre Lamas ◽  
Alicia del Carmen Mondragon ◽  
Patricia Regal ◽  
...  
Keyword(s):  
Allergic Diseases ◽  
Urban Environments ◽  
Probiotic Bacteria ◽  
Health Concern ◽  
Global Public Health ◽  
Cytokine Release ◽  
Public Health Concern ◽  
Beneficial Effects ◽  
Opportunistic Bacteria

Allergies are an increasing global public health concern, especially for children and people living in urban environments. Allergies impair the quality of life of those who suffer from them, and for this reason, alternatives for the treatment of allergic diseases or reduction in their symptoms are being sought. The main objective of this study was to compile the studies carried out on probiotics as a possible therapy for allergies. The most studied allergies on which probiotics have been shown to have a beneficial effect are rhinitis, asthma, and atopic dermatitis. Most studies have studied the administration of Lactobacillus and Bifidobacterium spp. in children and have shown beneficial effects, such as a reduction in hyperreactivity and inflammation caused by allergens and a decrease in cytokine release, among other beneficial effects. In the case of children, no clear beneficial effects were found in several studies, and the potential risk from the use of some opportunistic bacteria, such as probiotics, seems controversial. In the studies that reported beneficial results, these effects were found to make allergy symptoms less aggressive, thus reducing morbidity in allergy sufferers. The different effects of the same probiotic bacteria on different patients seem to reinforce the idea that the efficacy of probiotics is dependent on the microbial species or strain, its derived metabolites and byproducts, and the gut microbiota eubiosis of the patient. This study is relevant in the context of allergic diseases, as it provides a broader understanding of new alternatives for the treatment of allergies, both in children, who are the main sufferers, and adults, showing that probiotics, in some cases, reduce the symptoms and severity of such diseases.

Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia

2011 ◽  
Vol 38 (7) ◽  
pp. 1368-1380 ◽  
Author(s):  
Sarah A. Sonsthagen ◽  
Sandra L. Talbot ◽  
Kim T. Scribner ◽  
Kevin G. McCracken
Keyword(s):  
Population Structure ◽  
North America ◽  
Common Eiders

scholarly journals Non-Homogeneous Markov Set Systems

Mathematics ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 471
Author(s):  
P.-C.G. Vassiliou
Keyword(s):  
Asymptotic Behavior ◽  
Population Structure ◽  
Confidence Intervals ◽  
Limit Set ◽  
Stroke Patients ◽  
Relative Population ◽  
Set Systems ◽  
Population Structures ◽  
Basic Parameters ◽  
Initial Distributions

A more realistic way to describe a model is the use of intervals which contain the required values of the parameters. In practice we estimate the parameters from a set of data and it is natural that they will be in confidence intervals. In the present study, we study Non-Homogeneous Markov Systems (NHMS) processes for which the required basic parameters are in intervals. We call such processes Non-Homogeneous Markov Set Systems (NHMSS). First we study the set of the relative expected population structure of memberships and we prove that under certain conditions of convexity of the intervals of the parameters the set is compact and convex. Next, we establish that if the NHMSS starts with two different initial distributions sets and allocation probability sets under certain conditions, asymptotically the two expected relative population structures coincide geometrically fast. We continue proving a series of theorems on the asymptotic behavior of the expected relative population structure of a NHMSS and the properties of their limit set. Finally, we present an application for geriatric and stroke patients in a hospital and through it we solve problems that surface in an application.

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