Nasopharyngeal Microbial Communities of Patients Infected With SARS-CoV-2 That Developed COVID-19.

BACKGROUND: SARS-CoV-2 is an RNA virus causing COVID-19. The clinical characteristics and epidemiology of COVID-19 have been extensively investigated, however, only one study so far focused on the patient's nasopharynx microbiota. In this study we investigated the nasopharynx microbial community of patients that developed different severity levels of COVID-19. We performed 16S ribosomal DNA sequencing from nasopharyngeal swab samples obtained from SARS-CoV-2 positive (56) and negative (18) patients in the province of Alicante (Spain) in their first visit to the hospital. Positive SARS-CoV-2 patients were observed and later categorized in mild (symptomatic without hospitalization), moderate (hospitalization), and severe (admission to ICU). We compared the microbiota diversity and OTU composition among severity groups and built bacterial co-abundance networks for each group. RESULTS: Statistical analysis indicated differences in the nasopharyngeal microbiome of COVID19 patients. 62 OTUs were found exclusively in SARS-CoV-2 positive patients, mostly classified as members of the phylum Bacteroidota (18) and Firmicutes (25). OTUs classified as Prevotella were found to be significantly more abundant in patients that developed more severe COVID-19. Furthermore, co-abundance analysis indicated a loss of network complexity among samples from patients that later developed more severe symptoms. CONCLUSION: Our study shows that the nasopharyngeal microbiome of COVID-19 patients showed differences in the composition of specific OTUs and complexity of co-abundance networks. Taxa with differential abundances among groups could serve as biomarkers for COVID-19 severity. Nevertheless, further studies with larger sample sizes should be conducted to validate these results.

Azole and Amphotericin B MIC Values against Aspergillus fumigatus: High Agreement between Spectrophotometric and Visual Readings Using the EUCAST EDef 9.3.2 Procedure.

The EUCAST EDef 9.3.2 procedure recommends visual readings of azole and amphotericin B MICs against Aspergillus spp. Visual determination of MICs may be challenging. In this work, we aim to obtain and compare visual and spectrophotometric MIC readings of azoles and amphotericin B against Aspergillus fumigatussensu lato isolates. A total of 847 A. fumigatussensu lato isolates (A. fumigatus sensu stricto [n = 828] and cryptic species [n = 19]) were tested against amphotericin B, itraconazole, voriconazole, posaconazole, and isavuconazole using the EUCAST EDef 9.3.2 procedure. Isolates were classified as susceptible or resistant/non-wild type according to the 2020 updated breakpoints. The area of technical uncertainty for the azoles was defined in the updated breakpoints. Visual and spectrophotometric (fungal growth reduction of >95% compared to the control, read at 540 nm) MICs were compared. Essential (±1 2-fold dilution) and categorical agreements were calculated. Overall, high essential (97.1%) and categorical (99.6%) agreements were found. We obtained 100% categorical agreements for amphotericin B, itraconazole, and posaconazole, and consequently, no errors were found. Categorical agreements were 98.7 and 99.3% for voriconazole and isavuconazole, respectively. Most of the misclassifications for voriconazole and isavuconazole were found to be associated with MIC results falling either in the area of technical uncertainty or within one 2-fold dilution above the breakpoint. The resistance rate was slightly lower when the MICs were obtained by spectrophotometric readings. However, all relevant cyp51A mutants were correctly classified as resistant. Spectrophotometric determination of azole and amphotericin B MICs against A. fumigatussensu lato isolates may be a convenient alternative to visual endpoint readings.

Infección por Rothia mucilaginosa. ¿Un patógeno respiratorio? / Infection due to Rothia mucilaginosa. A respiratory pathogen?

INTRODUCCIÓN: Describir el espectro de las infecciones causadas por Rothia mucilaginosa. Métodos Estudio retrospectivo de 20 casos de infección por R. mucilaginosa entre los años 2009 y 2012.ResultadosLa infección pulmonar fue la forma clínica más frecuente (n = 14; 70%): bronquiectasias sobreinfectadas (10), empiema pleural (2), neumonía (1) y bronquitis aguda (1). Dos episodios fueron digestivos: colangitis bacteriémica y peritonitis secundaria. Dos bacteriemias afectaron a pacientes con neoplasia hematológica. Hubo una infección bacteriémica de herida quirúrgica y otra infección urinaria bacteriémica en portador de nefrostomía. Discusión R. mucilaginosa puede ser responsable de infecciones de vías respiratorias bajas en pacientes con bronquiectasias pulmonares

INTRODUCTION: To describe the spectrum of infections caused by Rothia mucilaginosa. METHODS: Retrospective study of 20 cases diagnosed with R. mucilaginosa from 2009 to 2012.RESULTS: Pulmonary infection was the most frequent clinical presentation (n = 14, 70%): bronchiectasis infected (10), followed by pleural empyema (2), pneumonia (1) and acute bronchitis (1). Two episodes were of gastrointestinal origin: cholangitis secondary to biliary drainage and secondary peritonitis. Two episodes included bacteremia in patients with hematological malignancy. One patient had a surgical wound infection with bacteremia, and another had a bacteremic urinary tract infection in a patient withnephrostomy. DISCUSSION: R. mucilaginosa may be responsible for infections of the lower respiratory tract in predisposed Patients

[Infection due to Rothia mucilaginosa. A respiratory pathogen?]. / Infección por Rothia mucilaginosa. ¿Un patógeno respiratorio?

INTRODUCTION: To describe the spectrum of infections caused by Rothia mucilaginosa. METHODS: Retrospective study of 20 cases diagnosed with R. mucilaginosa from 2009 to 2012. RESULTS: Pulmonary infection was the most frequent clinical presentation (n=14, 70%): bronchiectasis infected (10), followed by pleural empyema (2), pneumonia (1) and acute bronchitis (1). Two episodes were of gastrointestinal origin: cholangitis secondary to biliary drainage and secondary peritonitis. Two episodes included bacteremia in patients with hematological malignancy. One patient had a surgical wound infection with bacteremia, and another had a bacteremic urinary tract infection in a patient with nephrostomy. DISCUSSION: R. mucilaginosa may be responsible for infections of the lower respiratory tract in predisposed patients.