Comparative genomics and evolutionary analysis of isolated from human endocarditis.

is a well-known pathogen of fish, but is rarely involved in infections in humans and other mammals. In humans, the main clinical manifestation of infections is endocarditis usually related to the ingestion of contaminated food, such as undercooked fish and shellfish. This study presents the first complete genomic sequence of a clinical strain isolated from a patient with endocarditis and its comparative analysis with other genomes.

The widespread presence of a family of fish virulence plasmids in stresses its relevance as a zoonotic pathogen linked to fish farms.

is a pathogen of public health concern that causes either primary septicemia after ingestion of raw shellfish or secondary septicemia after wound exposure to seawater. In consequence, shellfish and seawater are considered its main reservoirs. However, there is one aspect of its biology that is systematically overlooked: its association with fish in its natural environment.

Immunological response against SARS-CoV-2 following full-dose administration of Comirnaty® COVID-19 vaccine in nursing home residents.

Objectives: The current study was aimed at examining SARS-CoV-2 immune responses following two doses of Comirnaty® COVID-19 vaccine among elderly people in nursing homes.

Methods: A prospective cohort study in a representative sample from nursing homes in Valencia (n = 881; males: 271, females 610; median age, 86 years) recruited residents using a random one-stage cluster sampling approach. A lateral flow immunochromatography device (LFIC) (OnSite COVID-19 IgG/IgM Rapid Test; CTK BIOTECH, Poway, CA, USA) was used as the front-line test for detecting SARS-CoV-2-Spike (S)-specific antibodies in whole blood obtained using a fingerstick.

The first wave of the COVID-19 epidemic in Spain was associated with early introductions and fast spread of a dominating genetic variant.

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures.

Complete Analysis of the Epidemiological Scenario around a SARS-CoV-2 Reinfection: Previous Infection Events and Subsequent Transmission.

The first descriptions of reinfection by SARS-CoV-2 have been recently reported. However, these studies focus exclusively on the reinfected case, without considering the epidemiological context of the event. Our objectives were to perform a complete analysis of the sequential infections and community transmission events around a SARS-CoV-2 reinfection, including the infection events preceding it, the exposure, and subsequent transmissions.

Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2.

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.

Overlapping of Independent SARS-CoV-2 Nosocomial Transmissions in a Complex Outbreak.

SARS-CoV-2 nosocomial outbreaks in the first COVID-19 wave were likely associated with a shortage of personal protective equipment and scarce indications on control measures. Having covered these limitations, updates on current SARS-CoV-2 nosocomial outbreaks are required. We carried out an in-depth analysis of a 27-day nosocomial outbreak in a gastroenterology ward in our hospital, potentially involving 15 patients and 3 health care workers.

Poverty, social exclusion, and mental health: the role of the family context in children aged 7-11 years INMA mother-and-child cohort study.

Mental health problems are common in childhood and tend to be more frequent in populations at risk of poverty or social exclusion (AROPE). The family environment can play a role in reducing the impact of economic hardship on these problems. The aim of this study was to assess the effect of multidimensional poverty on the mental health of children aged 7-11 years and the role of the family environment in two areas of Spain.

Spread of a SARS-CoV-2 variant through Europe in the summer of 2020.

Following its emergence in late 2019, the spread of SARS-CoV-2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020.

Draft Genome Sequences of Vibrio vulnificus Strains Recovered from Moribund Tilapia.

Potentially zoonotic Vibrio vulnificus strains were isolated from vibriosis outbreaks occurring on eastern Mediterranean tilapia farms between 2016 and 2019. In this work, the draft genome sequences of three representative isolates are presented.

One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages.

The COVID-19 pandemic was officially declared on March 11, 2020. Since the very beginning, the spread of the virus has been tracked nearly in real-time by worldwide genome sequencing efforts. As of March 2021, more than 830,000 SARS-CoV-2 genomes have been uploaded in GISAID and this wealth of data allowed researchers to study the evolution of SARS-CoV-2 during this first pandemic year.

Epidemiological, clinical and genomic snapshot of the first 100 B.1.1.7 SARS-CoV-2 cases in Madrid.

We present clinical, genomic and epidemiological data on the first 106 cases with the SARS-CoV-2 B.1.1.

One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.

Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens).

Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020.

Following its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic resulting in unprecedented efforts to reduce transmission and develop therapies and vaccines (WHO Emergency Committee, 2020; Zhu et al., 2020). Rapidly generated viral genome sequences have allowed the spread of the virus to be tracked via phylogenetic analysis (Worobey et al.

Is there a widespread clone of Serratia marcescens producing outbreaks worldwide?

Background: Serratia marcescens frequently causes outbreaks in healthcare settings. There are few studies using high-throughput sequencing (HTS) that analyse S. marcescens outbreaks.

Genomic Epidemiology of Infantis in Ecuador: From Poultry Farms to Human Infections.

is one of the most important foodborne pathogens around the world. In the last years, . serovar Infantis has become an important emerging pathogen in many countries, often as multidrug resistant clones.

Yaws re-emergence and bacterial drug resistance selection after mass administration of azithromycin: a genomic epidemiology investigation.

Background: In a longitudinal study assessing the WHO strategy for yaws eradication using mass azithromycin treatment, we observed resurgence of yaws cases with dominance of a single JG8 sequence type and emergence of azithromycin-resistant Treponema pallidum subspecies pertenue (T p pertenue). Here, we analyse genomic changes in the bacterial population using samples collected during the study.

Methods: We did whole bacterial genome sequencing directly on DNA extracted from 37 skin lesion swabs collected from patients on Lihir Island, Papua New Guinea, between April 1, 2013, and Nov 1, 2016.

Ancient Bacterial Genomes Reveal a High Diversity of Treponema pallidum Strains in Early Modern Europe.

Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15 century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis' potential introduction into Europe from the Americas.

SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective.

In less than five months, COVID-19 has spread from a small focus in Wuhan, China, to more than 5 million people in almost every country in the world, dominating the concern of most governments and public health systems. The social and political distresses caused by this epidemic will certainly impact our world for a long time to come. Here, we synthesize lessons from a range of scientific perspectives rooted in epidemiology, virology, genetics, ecology and evolutionary biology so as to provide perspective on how this pandemic started, how it is developing, and how best we can stop it.

High-throughput sequencing (HTS) for the analysis of viral populations.

The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure.