We used metagenomics to analyze one sputum sample from a patient with symptoms of a respiratory infection that yielded negative results for all pathogens tested. We detected two viral genomes that could be assembled and showed sequence similarity to redondoviruses, a recently described group within the CRESS-DNA viruses. One hundred sputum samples were screened for the presence of these viruses using specific primers. One sample was positive for the same two viruses, and another was positive for one of them. These findings raise questions about a possible role of redondoviruses in respiratory infections in humans.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in Madrid, Spain, on 25 February 2020. It increased in frequency very fast and by the end of May more than 70,000 cases had been confirmed by reverse transcription-polymerase chain reaction (RT-PCR). To study the lineages and the diversity of the viral population during this first epidemic wave in Madrid we sequenced 224 SARS-CoV-2 viral genomes collected from three hospitals from February to May 2020. All the known major lineages were found in this set of samples, though B.1 and B.1.5 were the most frequent ones, accounting for more than 60% of the sequences. In parallel with the B lineages and sublineages, the D614G mutation in the Spike protein sequence was detected soon after the detection of the first coronavirus disease 19 (COVID-19) case in Madrid and in two weeks became dominant, being found in 80% of the samples and remaining at this level during all the study periods. The lineage composition of the viral population found in Madrid was more similar to the European population than to the publicly available Spanish data, underlining the role of Madrid as a national and international transport hub. In agreement with this, phylodynamic analysis suggested multiple independent entries before the national lockdown and air transportation restrictions.

(1) Background: We determined the relevance of intestinal dominance by Serratia spp. during a neonatal outbreak over 13 weeks. (2) Methods: Rectal swabs (n = 110) were obtained from 42 neonates. Serratia spp. was cultured from swabs obtained from 13 neonates (Group 1), while the other 29 neonates were culture-negative (Group 2). Total DNA was extracted from rectal swabs, and quantitative PCRs (qPCRs) using Serratia- and 16SrRNA-gene-specific primers were performed. relative intestinal loads (RLs) were determined using ΔΔC_t. Clonality was investigated by random amplified polymorphic DNA analysis and whole-genome sequencing. (3) Results: The outbreak was caused by Serratia marcescens during the first eight weeks and Serratia ureilytica during the remaining five weeks. Serratia spp. were detected by qPCR in all Group 1 neonates and eleven Group 2 neonates. RLs of Serratia spp. were higher in Group 1 as compared to Group 2 (6.31% vs. 0.09%, p < 0.05) and in the first swab compared to the last (26.9% vs. 4.37%, p < 0.05). Nine neonates had extraintestinal detection of Serratia spp.; eight of them were infected. RLs of the patients with extraintestinal spread were higher than the rest (2.79% vs. 0.29%, p < 0.05). (4) Conclusions: Intestinal dominance by Serratia spp. plays a role in outbreaks and extraintestinal spread.

The poxtA gene is a transferable linezolid-resistance gene that encodes an ATP-binding cassette F protein that prevents linezolid from inhibiting protein synthesis. In enterococci, the presence of the poxtA gene does not consistently imply resistance to linezolid. The objective of this work was to analyze the role of the poxtA gene in linezolid susceptibility in a cohort of five poxtA⁺ clinical isolates of Enterococcus faecium. Three of the isolates were linezolid-resistant and two were linezolid-susceptible. The genomes of all five isolates were sequenced using short and long read sequencing. The genomes were assembled to identify the location of the poxtA gene. The presence and relative amount of the PoxtA protein was determined with a proteomics approach. One of the linezolid-resistant isolates harbored a deletion in the poxtA gene promoter and a mutation in the ribosomal protein L4. Another exhibited two sets of tandem repeats of the poxtA gene within the chromosome, and the third displayed an increased copy number of the plasmid carrying the poxtA gene. Proteomic analysis detected the PoxtA protein and confirmed increased expression levels in the three resistant mutants. The highest expression was seen in the promoter deletion mutant. The presence of the poxtA gene in clinical isolates of E. faecium does not imply resistance to linezolid, but it should be considered a significant risk factor for the development of resistance. Active molecular surveillance for intestinal poxtA gene carriers could be important to prevent dissemination.