Bacterial Genomics and Epidemiology

Innovative technologies for Whole-Genome Sequencing (WGS) help to improve our understanding of the epidemiology and pathogenesis of bacterial infectious diseases and are becoming affordable for most microbiological laboratories [...

Salmonella enterica 4,5,12:b:- serotipo berriaren karakterizazioa eta etxeko dortokekin erlazionatutako arriskua

Salmonellosis, is one of the most common toxinfection caused by bacteria of the genus Salmonella in developed countries. In general, human salmonellosis is associated with contaminated food. However, contact with animals can be an important transmission route for Salmonella. Turtles have been shown to be reservoirs of different Salmonella serotypes. Considering that these reptiles are very common domestic pets, they can be a risk for public health, especially among children. In this work, a new monophasic serotype with the antigenic formula 4,5,12:b:- has been characterized. Most of the isolates analyzed have been isolated from children under 5 years of age in different regions of Spain. By means of different molecular techniques, it has been confirmed that 4,5,12:b:- isolates are genetically related to the biphasic isolates of Paratyphi B Java and that this serotype is their possible ancestor. The great homogeneity between the studied strains suggests that the origin of the turtles infected by these strains is closely related and that in Spain turtle shops have a common distribution point that contributes to the spread of this pathogen.; Salmonelosia, herrialde garatuetako toxiinfekzio ohikoenetariko bat da, Salmonella generoko bakterioek eragindakoa. Oro har, giza salmonelosia elikagai kutsatuekin lotzen da. Hala ere, animaliekin izandako kontaktua Salmonella generoaren transmisio bide garrantzitsua izan daiteke. Dortokak Salmonella serotipo desberdinen gordailuak direla frogatu da. Narrasti hauek etxeko maskota oso ohikoak direla kontuan izanda, osasun publikorako arriskutsuak izan daitezke, batez ere haurren artean. Horregatik, lan honetan 4,5,12:b:- formula antigenikoa duen serotipo monofasiko berri bat karakterizatu da. Aztertutako isolatu gehienak 5 urtetik beherako haurretan isolatu dira, Espainiako eskualde desberdinetan. Teknika molekular ezberdinen bidez, baieztatu da 4,5,12:b:- isolatuak Paratyphi B Javako iso- latu bifasikoekin genetikoki erlazionatuta daudela eta serotipo hori dela haren arbaso posiblea. Aztertutako anduien arteko homogeneotasun handiak iradokitzen du, andui horietaz infektatutako dortoken jatorria estuki lotuta dagoela, Espainian dortoken saltokiek banaketa-puntu komuna dutela, eta horrek patogeno honen sakabanaketan laguntzen duela

Molecular Epidemiology, Antimicrobial Surveillance, and PK/PD Analysis to Guide the Treatment of Neisseria gonorrhoeae Infections

The aim of this study was to apply molecular epidemiology, antimicrobial surveillance, and PK/PD analysis to guide the antimicrobial treatment of gonococci infections in a region of the north of Spain. Antibiotic susceptibility testing was performed on all isolates (2017 to 2019, n = 202). A subset of 35 isolates intermediate or resistant to at least two antimicrobials were selected to search for resistance genes and genotyping through WGS. By Monte Carlo simulation, we estimated the probability of target attainment (PTA) and the cumulative fraction of response (CFR) of the antimicrobials used to treat gonorrhea, both indicative of the probability of treatment success. In total, 2.0%, 6.4%, 5.4%, and 48.2% of the isolates were resistant to ceftriaxone, cefixime, azithromycin, and ciprofloxacin, respectively. Twenty sequence types were identified. Detected mutations were related to antibiotic resistance. PK/PD analysis showed high probability of treatment success of the cephalosporins. In conclusion, multiple populations of N. gonorrhoeae were identified. We can confirm that ceftriaxone (even at the lowest dose: 250 mg) and oral cefixime are good candidates to treat gonorrhea. For patients allergic to cephalosporins, ciprofloxacin should be only used if the MIC is known and ≤0.125 mg/L; this antimicrobial is not recommended for empirical treatment.This research was funded by the University of the Basque Country UPV/EHU (GIU20/048; PA20/03), Spain

Anianabacter salinae gen. nov., sp. nov. ASV31T, a Facultative Alkaliphilic and Extremely Halotolerant Bacterium Isolated from Brine of a Millennial Continental Saltern

During a prokaryotic diversity study in Añana Salt Valley, a new Rhodobacteraceae member, designated ASV31T, was isolated from Santa Engracia spring water. It was extremely halotolerant, tolerating up to 23% NaCl, and facultatively alkaliphilic, growing at pH 6.5–9.5 (optimum at 7.0–9.5). The isolate was a Gram-negative, rod-shaped, aerobic and non-motile bacterium that formed beige-to-pink colonies on marine agar. According to a 16S rRNA gene-based phylogenetic analysis, strain ASV31T forms a distinct branch of the family Rhodobacteraceae, with Thioclava pacifica DSM 10166T being its closest type strain (95.3%). This was confirmed with a phylogenomic tree and the values of ANI (73.9%), dDDH (19.3%), AAI (63.5%) and POCP (56.0%), which were below the genus/species level boundary. Additionally, an ability to degrade aromatic compounds and biosynthesise secondary metabolites was suggested by the genome of strain ASV31T. Distinguishing fatty acid profiles and polar lipid content were also observed. The genome size was 3.6 Mbp, with a DNA G+C content of 65.7%. Based on the data obtained, it was considered that strain ASV31T (=CECT 30309T = LMG 32242T) represents a new species of a new genus in the family Rhodobacteraceae, for which the name Anianabacter salinae gen. nov., sp. nov. is proposed.This research was funded by the University of the Basque Country UPV/EHU (grant number US19/01) and the Añana Salt Valley Foundation (specific agreement between the Añana Salt Valley Foundation and the University of the Basque Country UPV/EHU)

Fungal Diversity and Composition of the Continental Solar Saltern in Añana Salt Valley (Spain)

The Añana Salt Valley in Spain is an active continental solar saltern formed 220 million years ago. To date, no fungal genomic studies of continental salterns have been published, although DNA metabarcoding has recently expanded researchers’ ability to study microbial community structures. Accordingly, the aim of this present study was to evaluate fungal diversity using the internal transcribed spacer (ITS) metabarcoding at different locations along the saltern (springs, ponds, and groundwater) to describe the fungal community of this saline environment. A total of 380 fungal genera were detected. The ubiquity of Saccharomyces was observed in the saltern, although other halotolerant and halophilic fungi like Wallemia, Cladosporium, and Trimmatostroma were also detected. Most of the fungi observed in the saltern were saprotrophs. The fungal distribution appeared to be influenced by surrounding conditions, such as the plant and soil contact, cereal fields, and vineyards of this agricultural region.This research was funded by the University of the Basque Country UPV/EHU grant number US19/01 and the Añana Salt Valley Foundation (Specific Agreement between the Añana Salt Valley Foundation and the University of the Basque Country UPV/EHU)

Salmonella enterica espeziearen andui monofasikoen karakterizazio molekularra eta epidemiologikoa

Salmonellosis, is one of the most common food-poisoning disease caused by bacteria of the genus Salmonella in developed countries. More than 2,500 serotypes of Salmonella enterica species are described today, but a few serotypes have been re-ceived a harbor epidemiological monitoring. On the first decade of the 21th century, thanks to advances in molecular biology techniques, the Spanish National Center of Microbiology detected an emergence and increase of monophasic variants of Salmo-nella enterica. Typification methods allow us the analysis and characterization of 4 monophasic variants. As a result, it has been possible to determine their evolutionary origin and provide epidemiological markers designed for their detection, monitoring and control to facilitate the work in epidemiology of the health authorities.; Salmonelosia, herrialde garatuetako toxiinfekzio ohikoenetariko bat da, Salmonella generoko bakterioek eragindako elikagaien bidezkoa. Salmonella ente-ricaespeziearen barruan 2.500 serotipo baino gehiago deskribatuta daude gaur egun, baina serotipo gutxi batzuk izan dira jarraipen epidemiologiko sakonagoa jaso dutenak. XXI. mendearen lehenengo hamarkadan, biologia molekularreko tekniken aurrerakun-tzei esker, Salmonella enterica espeziearen aldaera monofasikoen gehikuntza detek-tatu zen Espainiako Mikrobiologiako Zentru Nazionalean. Lan honetan, aldaera mo-nofasiko horietako 4 aztertu eta karakterizatu dira tipikazio metodoen bidez. Ondorioz, posible izan da lau aldaeren eboluzio-jatorri zehaztea eta euren detekziorako, jarraipe-nerako eta kontrolerako diseinatu diren markatzaile epidemiologikoak eskaintzen dira, osasun agintariei epidemiologia esparruan lana erraztearren