scholarly journals Antibiotic treatment regimes as a driver of the global population dynamics of a major gonorrhea lineage

2020 ◽  
Author(s):  
Magnus N Osnes ◽  
Lucy van Dorp ◽  
Ola B Brynildsrud ◽  
Kristian Alfsnes ◽  
Thamarai Schneiders ◽  
...  
Keyword(s):  
Dual Therapy ◽  
Effective Population ◽  
Major Clade ◽  
Treatment Regimes ◽  
Fitness Advantage ◽  
Extended Spectrum ◽  
The Usa ◽  
Population Sizes ◽  
A Minor ◽  
Second Wave

Abstract The Neisseria gonorrhoeae multilocus sequence type (ST) 1901 is among the lineages most commonly associated with treatment failure. Here we analyze a global collection of ST-1901 genomes to shed light on the emergence and spread of alleles associated with reduced susceptibility to extended-spectrum cephalosporins (ESCs). The genetic diversity of ST-1901 falls into a minor and a major clade, both of which were inferred to have originated in East Asia. The dispersal of the major clade from Asia happened in two separate waves expanding from around 1987 and 1996, respectively. Both waves first reached North America, and from there spread to Europe and Oceania, with multiple secondary reintroductions to Asia. The ancestor of the second wave acquired the penA 34.001 allele, which significantly reduces susceptibility to extended-spectrum cephalosporins (ESCs). Our results suggest that the acquisition of this allele granted the second wave a fitness advantage at a time when ESCs became the key drug class used to treat gonorrhea. Following its establishment globally, the lineage has served as a reservoir for the repeated emergence of clones fully resistant to the ESC ceftriaxone, an essential drug for effective treatment of gonorrhea. We infer that the effective population sizes of both clades went into decline as treatment schemes shifted from fluoroquinolones via ESC monotherapy to dual therapy with ceftriaxone and azithromycin in Europe and the USA. Despite the inferred recent population size decline, the short evolutionary path from the penA 34.001 allele to alleles providing full ceftriaxone resistance is a cause of concern.

scholarly journals EFFECTS OF POPULATION SIZE AND SELECTION INTENSITY ON SHORT-TERM RESPONSE TO SELECTION FOR POSTWEANING GAIN IN MICE

Genetics ◽  
1973 ◽  
Vol 73 (3) ◽  
pp. 513-530
Author(s):  
J P Hanrahan ◽  
E J Eisen ◽  
J E Legates
Keyword(s):  
Population Size ◽  
Selection Response ◽  
Selection Intensity ◽  
Realized Heritability ◽  
Family Selection ◽  
Effective Population ◽  
Population Sizes ◽  
Selection For ◽  
Selection Intensities ◽  
Term Response

ABSTRACT The effects of population size and selection intensity on the mean response was examined after 14 generations of within full-sib family selection for postweaning gain in mice. Population sizes of 1, 2, 4, 8 and 16 pair matings were each evaluated at selection intensities of 100% (control), 50% and 25% in a replicated experiment. Selection response per generation increased as selection intensity increased. Selection response and realized heritability tended to increase with increasing population size. Replicate variability in realized heritability was large at population sizes of 1, 2 and 4 pairs. Genetic drift was implicated as the primary factor causing the reduced response and lowered repeatability at the smaller population sizes. Lines with intended effective population sizes of 62 yielded larger selection responses per unit selection differential than lines with effective population sizes of 30 or less.

Will Nurses’ Work Still be Valued after the COVID-19 Pandemic?

2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Pasquot L ◽  
◽  
Giorgetta S ◽  
Keyword(s):  
Public Health ◽  
Infection Rate ◽  
Health Sector ◽  
Risk Of Infection ◽  
Initial State ◽  
Public Places ◽  
The Public ◽  
High Infection ◽  
A Minor ◽  
Second Wave

Many are the aspects we should ponder on, after 17 months from the burst of the COVID-19 pandemic, especially as nurses. Due to the numerous cuts to the public health sector in the last decades in Italy, the sanitary emergency has been a great sacrifice for health professionals, as public health was completely unprepared to withstand it. The Italian government reacted to this lack of preparation with exceptionally urgent measures. Although, these measures were implemented long after the initial state of confusion and of inappropriate management, they brought about stability and led to a containment strategy for the spread of the virus across the nation [1]. The reduction in the number of COVID-19 diagnoses was mainly achieved through social distancing. At first this was only required to a small number of communities affected by high infection rates, but was eventually extended to the rest of the country from March 2020 [2]. The national lockdown during the first COVID-19 wave (from March to May 2020), was replaced by regional lockdowns in the second wave (from November 2020). As of now, regional lockdowns are integrated by the vaccine campaign and Green Pass enforcement. In November 2020 the Italian Prime Minister at the time, issued legislative measures to enforce regional lockdowns, limiting nonessential movements, cafes, restaurants and other public places opening hours. This legislation established to classify the national territory in different levels of restriction based on the infection rate: red zones - highest risk of infection, orange zones - medium high risk and yellow zones with a minor risk of infection. A later legislation introduced the white zone for territories with the lowest risk of infection (DPCM-14th January 2021). The infection rate has been important to establish a region’s tier status; however, it is not the defining parameter anymore. A new legislation from July 2021 (n.105 - 23rd July 2021), opted to classify a region’s tier status according to the hospital bed’s occupancy rate for COVID-19 patients in intensive care and other medical areas.

scholarly journals The effect of life-history and mode of inheritance on neutral genetic variability

2001 ◽  
Vol 77 (2) ◽  
pp. 153-166 ◽  
Author(s):  
BRIAN CHARLESWORTH
Keyword(s):  
Sequence Variation ◽  
Adult Mortality ◽  
Structured Populations ◽  
Human Populations ◽  
Effective Population ◽  
Transmission Modes ◽  
Population Sizes ◽  
Age Structured ◽  
Infinite Sites Model ◽  
Site Diversity

Formulae for the effective population sizes of autosomal, X-linked, Y-linked and maternally transmitted loci in age-structured populations are developed. The approximations used here predict both asymptotic rates of increase in probabilities of identity, and equilibrium levels of neutral nucleotide site diversity under the infinite-sites model. The applications of the results to the interpretation of data on DNA sequence variation in Drosophila, plant, and human populations are discussed. It is concluded that sex differences in demographic parameters such as adult mortality rates generally have small effects on the relative effective population sizes of loci with different modes of inheritance, whereas differences between the sexes in variance in reproductive success can have major effects, either increasing or reducing the effective population size for X-linked loci relative to autosomal or Y-linked loci. These effects need to be accounted for when trying to understand data on patterns of sequence variation for genes with different transmission modes.

Contemporary and historical effective population sizes of Atlantic sturgeon Acipenser oxyrinchus oxyrinchus

2018 ◽  
Vol 20 (2) ◽  
pp. 167-184 ◽  
Author(s):  
John Waldman ◽  
S. Elizabeth Alter ◽  
Douglas Peterson ◽  
Lorraine Maceda ◽  
Nirmal Roy ◽  
...  
Keyword(s):  
Atlantic Sturgeon ◽  
Effective Population ◽  
Population Sizes ◽  
Acipenser Oxyrinchus

scholarly journals A comparative analysis of world health systems and Covid-19

2021 ◽  
Vol 38 (2) ◽  
pp. 115-120
Author(s):  
Ayşe İKİNCİ KELEŞ ◽  
Gökhan KELEŞ
Keyword(s):  
Health Systems ◽  
Social Life ◽  
Meta Analysis ◽  
Good Health ◽  
The United States ◽  
World Health ◽  
The Face ◽  
The Usa ◽  
Health Organization ◽  
Second Wave

Coronavirus disease 2019 (COVID-19), which causes severe airway problems, first emerged in the Chinese city of Wuhan. The virus led to a pandemic that affected the entire world. COVID-19 affects not only health, but also economic and social life. The emergence of this pandemic has led to health systems across the world being questioned. The aim of this study was to assess the adequacy of world health systems in the face of this pandemic. Twelve countries were selected and analyzed in the study. The choice of these countries was determined by the number of COVID-19 cases and deaths. Information concerning health systems and COVID-19 was obtained from Organization for Economic Co-operation and Development 2018, World Health Organization 2020 and Deep Knowledge Group data and was subjected to statistical analysis. According to the analysis, the country with the highest investment in health expenditures is the United States (10586 US dollars/capita), and Germany stands out as the best in health services. Another finding is the first and second wave of COVID-19 was identified as the USA with the highest case and death rate (First wave cases 1.942.363 and deaths 110.514; second wave cases at 7.419.230 and deaths 2.09.450). As a result of the meta-analysis, it is revealed that only socio-economic power is not enough, countries with good health systems are more successful in the pandemic. In addition, the analysis once again reveal how important health systems are in the face of such a pandemic.

scholarly journals The Genetic History of France

2019 ◽  
Author(s):  
Aude Saint Pierre ◽  
Joanna Giemza ◽  
Matilde Karakachoff ◽  
Isabel Alves ◽  
Philippe Amouyel ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Demographic History ◽  
Migration Routes ◽  
Effective Population ◽  
Genetic Studies ◽  
Independent Population ◽  
Genome Wide Data ◽  
Population Sizes ◽  
History Of ◽  
Exhaustive Study

ABSTRACTThe study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2 184 individuals born in France who were enrolled in two independent population cohorts. Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe. In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

scholarly journals dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

2014 ◽  
Author(s):  
Jonathan Puritz ◽  
Christopher M. Hollenbeck ◽  
John R. Gold
Keyword(s):  
Population Genomics ◽  
De Novo ◽  
Variant Calling ◽  
Population Level ◽  
Model Organisms ◽  
Effective Population ◽  
Reduction Techniques ◽  
Indel Polymorphisms ◽  
Indel Calling ◽  
Population Sizes

Restriction-site associated DNA sequencing (RADseq) has become a powerful and useful approach for population genomics. Currently, no software exists that utilizes both paired-end reads from RADseq data to efficiently produce population-informative variant calls, especially for organisms with large effective population sizes and high levels of genetic polymorphism but for which no genomic resources exist. dDocent is an analysis pipeline with a user-friendly, command-line interface designed to process individually barcoded RADseq data (with double cut sites) into informative SNPs/Indels for population-level analyses. The pipeline, written in BASH, uses data reduction techniques and other stand-alone software packages to perform quality trimming and adapter removal, de novo assembly of RAD loci, read mapping, SNP and Indel calling, and baseline data filtering. Double-digest RAD data from population pairings of three different marine fishes were used to compare dDocent with Stacks, the first generally available, widely used pipeline for analysis of RADseq data. dDocent consistently identified more SNPs shared across greater numbers of individuals and with higher levels of coverage. This is most likely due to the fact that dDocent quality trims instead of filtering and incorporates both forward and reverse reads in assembly, mapping, and SNP calling, thus enabling use of reads with Indel polymorphisms. The pipeline and a comprehensive user guide can be found at (http://dDocent.wordpress.com).

scholarly journals The alpha/B.1.1.7 SARS-CoV-2 variant exhibits significantly higher affinity for ACE-2 and requires lower inoculation doses to cause disease in K18-hACE2 mice

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Rafael Bayarri-Olmos ◽  
Laust Bruun Johnsen ◽  
Manja Idorn ◽  
Line S Reinert ◽  
Anne Rosbjerg ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
United Kingdom ◽  
Disease Progression ◽  
Low Dose ◽  
Transmission Rate ◽  
Functional Characterization ◽  
Fitness Advantage ◽  
The United Kingdom ◽  
A Minor

The alpha/B.1.1.7 SARS-CoV-2 lineage emerged in autumn 2020 in the United Kingdom and transmitted rapidly until winter 2021 when it was responsible for most new COVID-19 cases in many European countries. The incidence domination was likely due to a fitness advantage that could be driven by the RBD residue change (N501Y), which also emerged independently in other Variants of Concern such as the beta/B.1.351 and gamma/P.1 strains. Here we present a functional characterization of the alpha/B.1.1.7 variant and show an eight-fold affinity increase towards human ACE-2. In accordance with this, transgenic hACE-2 mice showed a faster disease progression and severity after infection with a low dose of B.1.1.7, compared to an early 2020 SARS-CoV-2 isolate. When challenged with sera from convalescent individuals or anti-RBD monoclonal antibodies, the N501Y variant showed a minor, but significant elevated evasion potential of ACE-2/RBD antibody neutralization. The data suggest that the single asparagine to tyrosine substitution remarkable rise in affinity may be responsible for the higher transmission rate and severity of the B.1.1.7 variant.

scholarly journals Fitness Trade-Offs in blaTEM Evolution

2008 ◽  
Vol 52 (7) ◽  
pp. 2340-2345 ◽  
Author(s):  
Joanna E. Mroczkowska ◽  
Miriam Barlow
Keyword(s):  
Microbial Populations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bacterial Populations ◽  
Real Time Quantitative Pcr ◽  
Fitness Effects ◽  
Fitness Advantage ◽  
Extended Spectrum ◽  
Trade Offs ◽  
Pcr Method

ABSTRACT bla TEM-1 expression results in penicillin resistance, whereas expression of many bla TEM-1 descendants, called extended-spectrum β-lactamases (ESBLs), results simultaneously in resistance to penicillins and extended-spectrum cephalosporins. Despite the expanded resistance phenotypes conferred by many ESBLs, bla TEM-1 is still the most abundant bla TEM allele in many microbial populations. This study examines the fitness effects of the two amino acid substitutions, R164S and E240K, that have occurred repeatedly among ESBL bla TEM-1 descendants. Using a single-nucleotide polymorphism-specific real-time quantitative PCR method, we analyzed the fitness of strains expressing bla TEM-1, bla TEM-10, and bla TEM-12. Our results show that bacteria expressing the ancestral bla TEM-1 allele have a fitness advantage over those expressing either bla TEM-10 or bla TEM-12 when exposed to ampicillin. This observation, combined with the fact that penicillins are the most prevalent antimicrobials prescribed worldwide, may explain why bla TEM-1 has persisted as the most frequently encountered bla TEM allele in bacterial populations.

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