04049nas a2200517   4500008004100000022001400041245010200055210006900157260001600226300001300242490000700255520251300262653001502775653001002790653000902800653002202809653002602831653002902857653002502886653001002911653002102921653001802942653003102960653001702991653001103008653001303019653001103032653001103043653000903054653003203063653001603095653001403111653001003125653001703135653001603152100003103168700002903199700003303228700003003261700002103291700001703312700002003329700002003349700003403369856012803403       2024                        eng d  a2165-049700aGenotypic characterization and antimicrobial susceptibility of human  isolates in Southern Spain.0 aGenotypic characterization and antimicrobial susceptibility of h  c2024 Oct 03  ae01028240 v123 a<p> 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-Barré 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.</p>10aAdolescent10aAdult10aAged10aAged, 80 and over10aAnti-Bacterial Agents10aCampylobacter Infections10aCampylobacter jejuni10aChild10aChild, Preschool10aCiprofloxacin10aDrug Resistance, Bacterial10aErythromycin10aFemale10aGenotype10aHumans10aInfant10aMale10aMicrobial Sensitivity Tests10aMiddle Aged10aPhylogeny10aSpain10aTetracycline10aYoung Adult1 aFernández-Palacios, Pablo1 aGalán-Sánchez, Fátima1 aCasimiro-Soriguer, Carlos, S1 aJurado-Tarifa, Estefanía1 aArroyo, Federico1 aLara, María1 aChaves, Alberto1 aDopazo, Joaquin1 aRodriguez-Iglesias, Manuel, A  uhttp://clinbioinfosspa.es/content/genotypic-characterization-and-antimicrobial-susceptibility-human-isolates-southern-spain03334nas a2200445   4500008004100000022001400041245013500055210006900190260001600259300001000275490000700285520187800292653001202170653003102182653002202213653001302235653001102248653001502259653002202274653002802296100003302324700002602357700002302383700001702406700001902423700003302442700001802475700002202493700002702515700002202542700002602564700002002590700001902610700002002629700002802649700002302677700002002700700002002720856014802740       2024                        eng d  a2045-232200aThe integrated genomic surveillance system of Andalusia (SIEGA) provides a One Health regional resource connected with the clinic.0 aintegrated genomic surveillance system of Andalusia SIEGA provid  c2024 Aug 19  a192000 v143 a<p>The One Health approach, recognizing the interconnectedness of human, animal, and environmental health, has gained significance amid emerging zoonotic diseases and antibiotic resistance concerns. This paper aims to demonstrate the utility of a collaborative tool, the SIEGA, for monitoring infectious diseases across domains, fostering a comprehensive understanding of disease dynamics and risk factors, highlighting the pivotal role of One Health surveillance systems. Raw whole-genome sequencing is processed through different species-specific open software that additionally reports the presence of genes associated to anti-microbial resistances and virulence. The SIEGA application is a Laboratory Information Management System, that allows customizing reports, detect transmission chains, and promptly alert on alarming genetic similarities. The SIEGA initiative has successfully accumulated a comprehensive collection of more than 1900 bacterial genomes, including Salmonella enterica, Listeria monocytogenes, Campylobacter jejuni, Escherichia coli, Yersinia enterocolitica and Legionella pneumophila, showcasing its potential in monitoring pathogen transmission, resistance patterns, and virulence factors. SIEGA enables customizable reports and prompt detection of transmission chains, highlighting its contribution to enhancing vigilance and response capabilities. Here we show the potential of genomics in One Health surveillance when supported by an appropriate bioinformatic tool. By facilitating precise disease control strategies and antimicrobial resistance management, SIEGA enhances global health security and reduces the burden of infectious diseases. The integration of health data from humans, animals, and the environment, coupled with advanced genomics, underscores the importance of a holistic One Health approach in mitigating health threats.</p>10aAnimals10aDrug Resistance, Bacterial10aGenome, Bacterial10aGenomics10aHumans10aOne Health10aVirulence Factors10aWhole Genome Sequencing1 aCasimiro-Soriguer, Carlos, S1 aPerez-Florido, Javier1 aRobles, Enrique, A1 aLara, María1 aAguado, Andrea1 aIglesias, Manuel, A Rodrígu1 aLepe, Jose, A1 aGarcía, Federico1 aPérez-Alegre, Mónica1 aAndújar, Eloísa1 aJiménez, Victoria, E1 aCamino, Lola, P1 aLoruso, Nicola1 aAmeyugo, Ulises1 aVazquez, Isabel, María1 aLozano, Carlota, M1 aChaves, Alberto1 aDopazo, Joaquin  uhttp://clinbioinfosspa.es/content/integrated-genomic-surveillance-system-andalusia-siega-provides-one-health-regional-resource-connected-clinic02738nas a2200313   4500008004100000022001400041245009700055210006900152260001300221300001000234490000600244520172000250100003301970700002602003700001702029700002802046700002302074700002602097700002302123700001702146700002002163700002002183700002802203700002002231700001802251700002002269700002202289856011302311       2024                        eng d  a2398-883500aMolecular and phylogenetic characterization of the monkeypox outbreak in the South of Spain.0 aMolecular and phylogenetic characterization of the monkeypox out  c2024 Mar  ae19650 v73 a<p><b>BACKGROUND AND AIM: </b>Until the May 2022 Monkeypox (MPXV) outbreak, which spread rapidly to many non-endemic countries, the virus was considered a viral zoonosis limited to some African countries. The Andalusian circuit of genomic surveillance was rapidly applied to characterize the MPXV outbreak in the South of Spain.</p><p><b>METHODS: </b>Whole genome sequencing was used to obtain the genomic profiles of samples collected across the south of Spain, representative of all the provinces of Andalusia. Phylogenetic analysis was used to study the relationship of the isolates and the available sequences of the 2022 outbreak.</p><p><b>RESULTS: </b>Whole genome sequencing of a total of 160 MPXV viruses from the different provinces that reported cases were obtained. Interestingly, we report the sequences of MPXV viruses obtained from two patients who died. While one of the isolates bore no noteworthy mutations that explain a potential heightened virulence, in another patient the second consecutive genome sequence, performed after the administration of tecovirimat, uncovered a mutation within the A0A7H0DN30 gene, known to be a prime target for tecovirimat in its Vaccinia counterpart. In general, a low number of mutations were observed in the sequences reported, which were very similar to the reference of the 2022 outbreak (OX044336), as expected from a DNA virus. The samples likely correspond to several introductions of the circulating MPXV viruses from the last outbreak. The virus sequenced from one of the two patients that died presented a mutation in a gene that bears potential connections to drug resistance. This mutation was absent in the initial sequencing before treatment.</p>1 aCasimiro-Soriguer, Carlos, S1 aPerez-Florido, Javier1 aLara, María1 aCamacho-Martinez, Pedro1 aMerino-Diaz, Laura1 aPupo-Ledo, Inmaculada1 ade Salazar, Adolfo1 aFuentes, Ana1 aViñuela, Laura1 aChueca, Natalia1 aMartinez-Martinez, Luis1 aLorusso, Nicola1 aLepe, Jose, A1 aDopazo, Joaquin1 aGarcía, Federico  uhttp://clinbioinfosspa.es/content/molecular-and-phylogenetic-characterization-monkeypox-outbreak-south-spain02368nas a2200337   4500008004100000022001400041245017900055210006900234260001600303490000700319520115700326100002601483700003301509700002201542700002901564700001901593700001701612700002101629700003401650700002801684700002301712700002601735700002301761700002001784700001701804700002001821700002201841700002001863700001801883856012901901       2023                        eng d  a1422-006700aDetection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia.0 aDetection of High Level of CoInfection and the Emergence of Nove  c2023 Jan 260 v243 a<p>Recombination is an evolutionary strategy to quickly acquire new viral properties inherited from the parental lineages. The systematic survey of the SARS-CoV-2 genome sequences of the Andalusian genomic surveillance strategy has allowed the detection of an unexpectedly high number of co-infections, which constitute the ideal scenario for the emergence of new recombinants. Whole genome sequence of SARS-CoV-2 has been carried out as part of the genomic surveillance programme. Sample sources included the main hospitals in the Andalusia region. In addition to the increase of co-infections and known recombinants, three novel SARS-CoV-2 delta-omicron and omicron-omicron recombinant variants with two break points have been detected. Our observations document an epidemiological scenario in which co-infection and recombination are detected more frequently. Finally, we describe a family case in which co-infection is followed by the detection of a recombinant made from the two co-infecting variants. This increased number of recombinants raises the risk of emergence of recombinant variants with increased transmissibility and pathogenicity.</p>1 aPerez-Florido, Javier1 aCasimiro-Soriguer, Carlos, S1 aOrtuno, Francisco1 aFernandez-Rueda, Jose, L1 aAguado, Andrea1 aLara, María1 aRiazzo, Cristina1 aRodriguez-Iglesias, Manuel, A1 aCamacho-Martinez, Pedro1 aMerino-Diaz, Laura1 aPupo-Ledo, Inmaculada1 ade Salazar, Adolfo1 aViñuela, Laura1 aFuentes, Ana1 aChueca, Natalia1 aGarcía, Federico1 aDopazo, Joaquin1 aLepe, Jose, A  uhttp://clinbioinfosspa.es/content/detection-high-level-co-infection-and-emergence-novel-sars-cov-2-delta-omicron-and-omicron