@article {811, title = {Genotypic characterization and antimicrobial susceptibility of human isolates in Southern Spain.}, journal = {Microbiol Spectr}, volume = {12}, year = {2024}, month = {2024 Oct 03}, pages = {e0102824}, abstract = {

is the main cause of bacterial gastroenteritis and a public health problem worldwide. Little information is available on the genotypic characteristics of human in Spain. This study is based on an analysis of the resistome, virulome, and phylogenetic relationship, antibiogram prediction, and antimicrobial susceptibility of 114 human isolates of from a tertiary hospital in southern Spain from October 2020 to June 2023. The isolates were sequenced using Illumina technology, and a bioinformatic analysis was subsequently performed. The susceptibility of isolates to ciprofloxacin, tetracycline, and erythromycin was also tested. The resistance rates for each antibiotic were 90.3\% for ciprofloxacin, 66.7\% for tetracycline, and 0.88\% for erythromycin. The fluoroquinolone resistance rate obtained is well above the European average (69.1\%). CC-21 ( = 23), ST-572 ( = 13), and ST-6532 ( = 13) were the most prevalent clonal complexes (CCs) and sequence types (STs). In the virulome, the , and genes were detected in all the isolates. A prevalence of 20.1\% was obtained for the genes and , which are related to the pathogenesis of Guillain-Barr{\'e} syndrome (GBS). The prevalence of the main antimicrobial resistance markers detected were CmeABC (92.1\%), RE-cmeABC (7.9\%), the T86I substitution in (88.9\%), (72.6\%) (65.8\%), and (17.1\%). High antibiogram prediction rates (>97\%) were obtained, except for in the case of the erythromycin-resistant phenotype. This study contributes significantly to the knowledge of genomics for the prevention, treatment, and control of infections caused by this pathogen.IMPORTANCEDespite being the pathogen with the greatest number of gastroenteritis cases worldwide, remains a poorly studied microorganism. A sustained increase in fluoroquinolone resistance in human isolates is a problem when treating infections. The development of whole genome sequencing (WGS) techniques has allowed us to better understand the genotypic characteristics of this pathogen and relate them to antibiotic resistance phenotypes. These techniques complement the data obtained from the phenotypic analysis of isolates. The zoonotic transmission of through the consumption of contaminated poultry supports approaching the study of this pathogen through "One Health" approach. In addition, due to the limited information on the genomic characteristics of in Spain, this study provides important data and allows us to compare the results with those obtained in other countries.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, Anti-Bacterial Agents, Campylobacter Infections, Campylobacter jejuni, Child, Child, Preschool, Ciprofloxacin, Drug Resistance, Bacterial, Erythromycin, Female, Genotype, Humans, Infant, Male, Microbial Sensitivity Tests, Middle Aged, Phylogeny, Spain, Tetracycline, Young Adult}, issn = {2165-0497}, doi = {10.1128/spectrum.01028-24}, author = {Fern{\'a}ndez-Palacios, Pablo and Gal{\'a}n-S{\'a}nchez, F{\'a}tima and Casimiro-Soriguer, Carlos S and Jurado-Tarifa, Estefan{\'\i}a and Arroyo, Federico and Lara, Mar{\'\i}a and Chaves, J Alberto and Dopazo, Joaquin and Rodriguez-Iglesias, Manuel A} } @article {762, title = {Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival.}, journal = {Viruses}, volume = {14}, year = {2022}, month = {2022 Aug 27}, abstract = {

OBJECTIVES: More than two years into the COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations for which the impact on COVID-19 severity and patient survival is uncertain.

METHODS: A total of 764 SARS-CoV-2 genomes, sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30 April 2021, along with their clinical data, were used for survival analysis.

RESULTS: A significant association of B.1.1.7, the alpha lineage, with patient mortality (log hazard ratio (LHR) = 0.51, C.I. = [0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome revealed 27 of them were significantly associated with higher mortality of patients. Most of these mutations were located in the genes coding for the S, ORF8, and N proteins.

CONCLUSIONS: This study illustrates how a combination of genomic and clinical data can provide solid evidence for the impact of viral lineage on patient survival.

}, keywords = {COVID-19, Genome, Viral, Humans, mutation, Pandemics, Phylogeny, SARS-CoV-2}, issn = {1999-4915}, doi = {10.3390/v14091893}, author = {Loucera, Carlos and Perez-Florido, Javier and Casimiro-Soriguer, Carlos S and Ortuno, Francisco M and Carmona, Rosario and Bostelmann, Gerrit and Mart{\'\i}nez-Gonz{\'a}lez, L Javier and Mu{\~n}oyerro-Mu{\~n}iz, Dolores and Villegas, Rom{\'a}n and Rodr{\'\i}guez-Ba{\~n}o, Jes{\'u}s and Romero-G{\'o}mez, Manuel and Lorusso, Nicola and Garcia-Le{\'o}n, Javier and Navarro-Mar{\'\i}, Jose M and Camacho-Martinez, Pedro and Merino-Diaz, Laura and Salazar, Adolfo de and Vi{\~n}uela, Laura and Lepe, Jose A and Garc{\'\i}a, Federico and Dopazo, Joaquin} } @article {744, title = {Highly accurate whole-genome imputation of SARS-CoV-2 from partial or low-quality sequences.}, journal = {Gigascience}, volume = {10}, year = {2021}, month = {2021 12 02}, abstract = {

BACKGROUND: The current SARS-CoV-2 pandemic has emphasized the utility of viral whole-genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and, therefore, useless sequences. Viral sequences evolve in the context of a complex phylogeny and different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.

RESULTS: We have developed the impuSARS application, which takes advantage of the enormous number of SARS-CoV-2 genomes available, using a reference panel containing 239,301 sequences, to produce missing data imputation in viral genomes. ImpuSARS was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing), showing great fidelity when reconstructing the original sequences, recovering the lineage with a 100\% precision for almost all the lineages, even in very poorly covered genomes (<20\%).

CONCLUSIONS: Imputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. ImpuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole-genome sequencing.

}, keywords = {Genome, Viral, Phylogeny, SARS-CoV-2, Whole Genome Sequencing}, issn = {2047-217X}, doi = {10.1093/gigascience/giab078}, author = {Ortuno, Francisco M and Loucera, Carlos and Casimiro-Soriguer, Carlos S and Lepe, Jose A and Camacho Martinez, Pedro and Merino Diaz, Laura and de Salazar, Adolfo and Chueca, Natalia and Garc{\'\i}a, Federico and Perez-Florido, Javier and Dopazo, Joaquin} }