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Francisella
Published in Dongyou Liu, Handbook of Foodborne Diseases, 2018
In recent years, a modern global phylogenetic framework based on genome-wide canonical single nucleotide SNPs (canSNPs) has been established for F. tularensis.51–55 The F. tularensis type B strains are divided into the genetic clades B.4, B.6, B.12, and B.16.56–59 Clade B.12 is the most geographically successful clade and dominates in Scandinavia, East Europe, and a large part of Eurasia.51,55–58,60 There is a perfect correlation between biovar II strains (EryR) and the clade B.12.60 Another geographically successful genetic entity is a subclade of B.6, which is found over a large area of western and central Europe.57,61–65 The B.4 clade is dominant in the United States, and also found in Europe. Strains of the B.16 clade mainly represent biovar japonica strains,51,58 which originally were thought to be confined to the Japanese islands only, but these strains have more recently been identified also in Australia, Turkey, and China.66–68
Emergence and Pathogenesis of Avian Influenza in Humans
Published in Sunit K. Singh, Human Respiratory Viral Infections, 2014
Jennifer R. Plourde, Kevin S. Harrod
Although H5N1 has continued to diversify since the H5 HA gene was sequenced in 1997, the HA has remained relatively unchanged allowing it to be used as the basis for comparing emerging strains. This has also permitted the development of a standard nomenclature system based on clades that group H5 isolates by their HA sequence.39 This system has formally identified 20 distinct clades of viruses since 2008.40,41 Clades are defined by a viral isolate meeting these specific criteria: (1) the viruses share a common clade-defining node in the phylogenetic tree, (2) the clade grouping is monophyletic with a bootstrap of >60 at the node (after 1000 neighbor-joining bootstrap replicates), and (3) the average percentage pair-wise nucleotide distances between and within clades is >1.5% and <1.5%, respectively. Sublineages, or subclades, are added as the viruses evolve within these identified clades until they meet the three criteria for forming a new clade. While 20 clades have been identified, 13 of these have been considered inactive and have not been detected since 2008.39 The eradication of the 13 strains could have been the result of limited or reduced fitness, or high mortality exhibited in the host that prohibited efficient transmission.
Order Lefavirales
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
Yang et al. (2007) constructed an influenza vaccine, where the histidine-tagged hemagglutinin of the H5N2 subtype was linked to the cytoplasmic domain derived gp64. The product was efficiently incorporated into baculovirus and demonstrated strong immunogenicity. In fact, this was the first report demonstrating the potential of the hemagglutinin-pseudotyped baculovirus as an avian influenza vaccine. Tang et al. (2010) engineered another influenza vaccines, where chimeric hemagglutinins were provided with different segments of gp64. The signal peptide and cytoplasmic tail domains of gp64 enhanced the hemagglutinin display the baculovirus surface, while the transmembrane domain of gp64 impaired the display. The baculovirus simultaneously displaying four hemagglutinins derived from four subclades of H5N1 influenza viruses was constructed. This tetravalent H5N1 vaccine provided 100% protection against lethal doses of homologous H5N1 viruses (Tang et al. 2010). Lin W et al. (2011) combined the characteristics of baculovirus as a gene delivery vehicle (which is described later) and surface display system and constructed a Baculovirus Dual Expression System (BV-Dual), which was capable of displaying the H9N2 hemagglutinin on the surface of the viral envelope and expressing it upon transduction in mammalian cells. The results showed that stronger immune responses were induced in a mouse model immunized with BV-Dual-HA than in those vaccinated with a DNA vaccine encoding the same antigen. Moreover, the BV-Dual-HA vaccine candidate ensured complete protection of mice against lethal challenge with H9N2 virus (Lin W et al. 2011).
The cnf1 gene is associated with an expanding Escherichia coli ST131 H30Rx/C2 subclade and confers a competitive advantage for gut colonization
Published in Gut Microbes, 2022
Landry L. Tsoumtsa Meda, Luce Landraud, Serena Petracchini, Stéphane Descorps-Declere, Emeline Perthame, Marie-Anne Nahori, Laura Ramirez Finn, Molly A. Ingersoll, Rafael Patiño-Navarrete, Philippe Glaser, Richard Bonnet, Olivier Dussurget, Erick Denamur, Amel Mettouchi, Emmanuel Lemichez
We next analyzed the temporal distribution of cnf1-positive strains within clades and subclades. Using a Generalized Linear Models (GLM) approach, we first verified within our dataset the increase of fimH30-positive isolates over time (clade C) in E. coli ST131 that was maximal in H30Rx/C2 (P < 2.2 10−16, Chi-square association test) (Figure 4a). We also noted a significant increase in the proportion of cnf1-positive strains over time in E. coli ST131 (Figure 4b, top panel). The GLM was then fitted on years, clades, and subclades. We tested the significance of the year effect and P-values were corrected for multiple comparisons using Tukey’s method. The year effect was not significant for clade A, B, or subclade H30R/C1 (Figure 4b). Instead, we observed a significant increase of the proportion of cnf1-positive strains within H30Rx/C2 over time (P = 1.25 10−11). In addition, the GLM fitted curves predicted that the prevalence of cnf1-positive strains within H30Rx/C2 subclade would be approximately 50% (confidence interval of 95% [43% to 58%] in 2018; [47% to 64%] in 2019). Predictive values were compared to the prevalence of cnf1 in ST131 strains isolated in 2018 or 2019 in a second independent dataset up-loaded from EnteroBase in September 2020. The prevalence of cnf1-positive strains within the subclade H30Rx/C2 was 45% in 2018 and 48% in 2019, confirming the prediction of a dominant expansion of cnf1-positive strains within ST131-H30Rx/C2.
The genetic landscape of Mediterranean North African populations through complete mtDNA sequences
Published in Annals of Human Biology, 2018
Neus Font-Porterias, Neus Solé-Morata, Gerard Serra-Vidal, Asmahan Bekada, Karima Fadhlaoui-Zid, Pierre Zalloua, Francesc Calafell, David Comas
In North Africa, H1 is the most frequent West-European haplogroup (Coudray et al., 2009), with an east to west frequency gradient (Hernández et al., 2017). It has an estimated coalescence age of 8000–9000 years (Ottoni et al., 2010) and, as previously reported, this supports the post-glacial radiation from the Iberian Peninsula to the African continent (Achilli et al., 2004; Roostalu et al., 2007), the Northwestern African coast being the nucleus for the dispersion of the H1 haplogroup (Ennafaa et al., 2009; Ottoni et al., 2010). Within this region, new H1 sub-clades progressively appeared (H1w, H1x and H1v) (Ottoni et al., 2010). Our results show that the H1v sub-branch includes Berber sequences from Tunisia (basal H1v), Tahala (H1v1a) and Al Awaynat (H1v1b), Tuareg groups from Libya and the novel mitochondrial lineage H1v2 is supported by four Mozabite sequences from Algeria. Our coalescence age estimation of H1v is found between 1900 and 6100 years, which agrees with previous time estimations (Behar et al., 2012; Ottoni et al., 2010); and it might be correlated with an ancestral split of a North African nomadic population (Hernández et al., 2017; Ottoni et al., 2010).
Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool
Published in Gut Microbes, 2022
Vita Rozman, Petra Mohar Lorbeg, Primož Treven, Tomaž Accetto, Majda Golob, Irena Zdovc, Bojana Bogovič Matijašić
The phylogeny of the 53 E. faecium strains confirmed two major clades, A and B (Supplementary Figure S3B). As expected, the commensal strain clustered into clade B, whereas the animal and pathogenic isolates clustered into clade A.16 The epidemic hospital strains clustered into a subclade that was genetically more distant from other clade strains of clade A, mainly nonstarter isolates. Interestingly, the ARGs were enriched in a subclade with pathogenic isolates. Commercial strains were generally not found in a subclade with pathogenic strains and did not contain ARGs.