Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

<p>Abstract</p> <p>Background</p> <p>The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.</p> <p>Results</p> <p>We sequenced the complete flagellin gene <it>(flaA</it>) in 18 different species and subspecies of <it>Aeromonas</it>. Sequences ranged in size from 870 (<it>A. allosaccharophila</it>) to 921 nucleotides (<it>A. popoffii</it>). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze <it>flaA </it>sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an ω ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.</p> <p>Conclusion</p> <p>The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the <it>flaA </it>gene in <it>Aeromonas</it>, suggesting that this gene have probably been evolving independently in the two groups of <it>Aeromonas </it>species since the divergence of a distant common ancestor after one or several episodes of positive selection.</p> <p>Reviewers</p> <p>This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).</p

2018 consensus statement by the Spanish Society of Pathology and the Spanish Society of Medical Oncology on the diagnosis and treatment of cancer of unknown primary

Cancer of unknown primary (CUP) is defined as a heterogeneous group of tumours that present with metastasis, and in which attempts to identify the original site have failed. They differ from other primary tumours in their biological features and how they spread, which means that they can be considered a separate entity. There are several hypotheses regarding their origin, but the most plausible explanation for their aggressiveness and chemoresistance seems to involve chromosomal instability. Depending on the type of study done, CUP can account for 2-9% of all cancer patients, mostly 60-75years old. This article reviews the main clinical, pathological, and molecular studies conducted to analyse and determine the origin of CUP. The main strategies for patient management and treatment, by both clinicians and pathologists, are also addressed

Accuracy and Survival Outcomes after National Implementation of Sentinel Lymph Node Biopsy in Early Stage Endometrial Cancer

Background. Sentinel lymph node (SLN) biopsy has recently been accepted to evaluate nodal status in endometrial cancer at early stage, which is key to tailoring adjuvant treatments. Our aim was to evaluate the national implementation of SLN biopsy in terms of accuracy to detect nodal disease in a clinical setting and oncologic outcomes according to the volume of nodal disease. Patients and Methods. A total of 29 Spanish centers participated in this retrospective, multicenter registry including patients with endometrial adenocarcinoma at preoperative early stage who had undergone SLN biopsy between 2015 and 2021. Each center collected data regarding demographic, clinical, histologic, therapeutic, and survival characteristics. Results. A total of 892 patients were enrolled. After the surgery, 12.9% were suprastaged to FIGO 2009 stages III-IV and 108 patients (12.1%) had nodal involvement: 54.6% macrometastasis, 22.2% micrometastases, and 23.1% isolated tumor cells (ITC). Sensitivity of SLN biopsy was 93.7% and false negative rate was 6.2%. After a median follow up of 1.81 years, overall surivial and disease-free survival were significantly lower in patients who had macrometastases when compared with patients with negative nodes, micrometastases or ITC. Conclusions. In our nationwide cohort we obtained high sensitivity of SLN biopsy to detect nodal disease. The oncologic outcomes of patients with negative nodes and low-volume disease were similar after tailoring adjuvant treatments. In total, 22% of patients with macrometastasis and 50% of patients with micrometastasis were at low risk of nodal metastasis according to their preoperative risk factors, revealing the importance of SLN biopsy in the surgical management of patients with early stage EC

Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process

Potential pathogenicity of Aeromonas hydrophila complex strains isolated from clinical, food and environmental sources

Aeromonas are autochthonous inhabitants of aquatic environments including chlorinated and polluted waters, although they can also be isolated from a wide variety of environmental and clinical sources. They cause infections in vertebrates and invertebrates and are considered to be an emerging pathogen in humans, producing intestinal and extra-intestinal diseases. Most of the clinical isolates correspond to A. hydrophila, A. caviae, and A. veronii bv. Sobria, which are described as the causative agents of wound infections, septicaemia and meningitis in immunocompromised people, and diarrhoea and dysenteric infections in the elderly and children. The pathogenic factors associated with Aeromonas are multifactorial and involve structural components, siderophores, quorum sensing mechanisms, secretion systems, extracellular enzymes and exotoxins. In this study, we analysed a representative number of clinical and environmental strains belonging to the A. hydrophila species complex to evaluate their potential pathogenicity. We thereby detected their enzymatic activities and antibiotic susceptibility pattern, and the presence of virulence genes (aer, alt, ast and ascV). The notably high prevalence of these virulence factors, even in environmental strains, indicated a potential pathogenic capacity. Additionally, we determined the adhesion capacity and cytopathic effects of this group of strains in Caco-2 cells, most strains exhibiting adherence and causing complete lysis.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Violin plots of the tmrca distribution for Bayes and MLA simulated trees.

<p>The plots show the kernel density estimation of the data (mirrored curves) with a box and whiskers plot overlaid. The plots are scaled so each one has the same total area. The internal box plots indicate the range (whiskers), interquartile range (boxes), median (horizontal black lines) and mean (circles) of the data. The grey points on the plot tails indicate the outliers. See text for more details.</p

Diversification rates and model of speciation for the major clades of <i>Aeromonas.</i>

a<p>clade numbers appear in the MLA chronogram in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088805#pone-0088805-g002" target="_blank">Figure 2</a>.</p><p>Clades 7 and 8 were not analysed due to their low number of species (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088805#pone-0088805-g002" target="_blank">Fig. 2</a>).</p><p>Abbreviations: N, clade size; se, standard error.</p

Age estimates (Ma) of all strains and the major clades of <i>Aeromonas.</i>

a<p>clade numbers appear in the MLA chronogram in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088805#pone-0088805-g002" target="_blank">Figure 2</a>.</p><p>Abbreviations: N, clade size; HPD, the highest posterior density interval; CI, confidence interval.</p

<i>Aeromonas</i> species maximum likelihood phylogenetic tree.

<p><i>E.coli</i> and <i>S. enterica</i> were used as the outgroup. Nodes supported by bootstrap values ≥70% are indicated. The scale bar represents 20% sequence divergence.</p