The identification of filamentous fungi by matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI–TOF MS) represents a challenge due to their complex taxonomy and the lack of comprehensive databases. The aim of this study was to evaluate the current status of available MALDI–TOF MS databases for the identification of dermatophytes, including commercial, in-house, and web-based databases. We collected 289 dermatophyte strains from different centers and analyzed them using four databases and a combination of them. The combination of commercial and in-house databases was shown to improve the identification rate and accuracy at the species level. For Trichophyton rubrum, the concordance among all databases was above 90.0%. For the T. mentagrophytes group, correct identification at the species level ranged from 30.0 to 78.9%, depending on the database, and showed very low agreement among them. The addition of the novel species T. japonicum to our in-house database resulted in the successful identification of this species. On the other hand, T. interdigitale and T. tonsurans were the species most frequently misidentified by MALDI–TOF MS. Through deep spectra analysis of both species, up to 29 protein peaks were found to be suitable for their differentiation, demonstrating the potential of peak analysis in differentiating closely related species. In conclusion, improvements of the databases with new strains resulted in increased identification accuracy at the species level. This, combined with peak analysis, could improve the overall identification of dermatophytes by MALDI–TOF MS in clinical laboratories.

The monophasic 4,[5],12:i:-variant of Salmonella enterica serovar Typhimurium with sequence type ST34 has become one of the most prevalent non-typhoidal salmonellae worldwide. In the present study, we thoroughly characterized seven isolates of this variant detected in a Spanish hospital and selected based on cefotaxime resistance and cefoxitin susceptibility, mediated by bla_CTX-M-9. For this, conventional microbiological techniques, together with whole genome sequencing performed with the Illumina platform, were applied. All selected isolates carried the resistance region RR or variants therein, and most also contained the SGI-4 genomic island. These chromosomal elements, typically associated with monophasic S. Typhimurium ST34, confer resistance to traditional antibiotics (ampicillin, streptomycin, sulfonamides, and tetracycline) and tolerance to heavy metals (mercury, silver, and copper). In addition, each isolate carried a large IncHI2-ST1 conjugative plasmid containing additional or redundant resistance genes. All harbored the bla_CTX-M-9 gene responsible for cefotaxime resistance, whereas the qnrA1 gene mediating fluoroquinolone resistance was detected in two of the plasmids. These genes were embedded in ISCR1-bearing complex class 1 integrons, specifically In60-like and In36-like. The mcr-9 gene was present in all but one of the IncHI2-ST1 plasmids found in the analyzed isolates, which were nevertheless susceptible to colistin. Most of the resistance genes of plasmid origin clustered within a highly complex and variable region. The observed diversity results in a wide range of resistance phenotypes, enabling bacterial adaptation to selective pressure posed by the use of antimicrobials.

Hard ticks are vectors of a wide range of pathogens, with tick-borne bacteria being among the most frequently detected. This study presents a first approach to the identification of human-biting ticks in the Basque Country (northern Iberian Peninsula), where previous research has mainly focused on ticks from vegetation and domestic and wild animals. The aim of this study was (i) to identify tick species collected in hospitals and health centres and (ii) to determine the presence and identify of pathogenic bacteria that they may carry using PCR, RLB and sequencing methods. A total of 181 ticks were collected and grouped in pools of one, two or three specimens, resulting in 157 samples. Morphological and molecular identification of collected ticks revealed that most specimens belonged to Ixodes ricinus (88.5%). Additionally, Rhipicephalus bursa, Haemaphysalis punctata, Dermacentor reticulatus and Dermacentor marginatus were also identified. A total of 25 samples (15.9%) tested positive for DNA from the targeted pathogens. The most prevalent vector-borne bacteria were Borrelia spp. (6.4%), followed by Rickettsia spp. (5.1%), Anaplasma phagocytophilum (2.5%) and Coxiella spp. (1.9%). Species identified included B. afzelii, B. garinii, B. miyamotoi, B. valaisiana, B. burgdorferi s. s., R. monacensis, “Candidatus R. rioja”, R. helvetica and R. massiliae. This study highlights the usefulness of combining molecular diagnostics with passive surveillance of human-attached ticks as an effective tool for regional monitoring of ticks and tick-borne pathogens.

Cyclospora cayetanensis is an emerging cause of prolonged diarrhoea that remains underdiagnosed in Europe because routine laboratory testing is uncommon and conventional diagnostic methods have limited sensitivity. We retrospectively reviewed laboratory-confirmed cases of cyclosporiasis diagnosed following the implementation of routine multiplex GI PCR panel at a tertiary-care hospital in northern Spain between 2016 and 2025. Among 97,116 stool specimens screened, 52 infections were identified. Most patients had recently travelled to endemic regions, predominantly Mexico, whereas nine had no recent travel history. One of these patients reported habitual consumption of imported food, although exposure during the relevant period could not be established. Routine multiplex PCR improves the detection of cyclosporiasis in non-endemic settings and enables the identification of infections beyond the classical travel-associated pattern, supporting the inclusion of C. cayetanensis in routine gastrointestinal molecular diagnostic panels, not only for travel-associated diarrhoea but also for sporadic infections without recent travel.