Dendritic cell deficiencies persist seven months after SARS-CoV-2 infection.

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 infection induces an exacerbated inflammation driven by innate immunity components. Dendritic cells (DCs) play a key role in the defense against viral infections, for instance plasmacytoid DCs (pDCs), have the capacity to produce vast amounts of interferon-alpha (IFN-α). In COVID-19 there is a deficit in DC numbers and IFN-α production, which has been associated with disease severity. In this work, we described that in addition to the DC deficiency, several DC activation and homing markers were altered in acute COVID-19 patients, which were associated with multiple inflammatory markers. Remarkably, previously hospitalized and nonhospitalized patients remained with decreased numbers of CD1c+ myeloid DCs and pDCs seven months after SARS-CoV-2 infection. Moreover, the expression of DC markers such as CD86 and CD4 were only restored in previously nonhospitalized patients, while no restoration of integrin ß7 and indoleamine 2,3-dyoxigenase (IDO) levels were observed. These findings contribute to a better understanding of the immunological sequelae of COVID-19.

SARS-CoV-2 viral load in nasopharyngeal swabs is not an independent predictor of unfavorable outcome.

The aim was to assess the ability of nasopharyngeal SARS-CoV-2 viral load at first patient's hospital evaluation to predict unfavorable outcomes. We conducted a prospective cohort study including 321 adult patients with confirmed COVID-19 through RT-PCR in nasopharyngeal swabs. Quantitative Synthetic SARS-CoV-2 RNA cycle threshold values were used to calculate the viral load in log10 copies/mL. Disease severity at the end of follow up was categorized into mild, moderate, and severe. Primary endpoint was a composite of intensive care unit (ICU) admission and/or death (n = 85, 26.4%). Univariable and multivariable logistic regression analyses were performed. Nasopharyngeal SARS-CoV-2 viral load over the second quartile (≥ 7.35 log10 copies/mL, p = 0.003) and second tertile (≥ 8.27 log10 copies/mL, p = 0.01) were associated to unfavorable outcome in the unadjusted logistic regression analysis. However, in the final multivariable analysis, viral load was not independently associated with an unfavorable outcome. Five predictors were independently associated with increased odds of ICU admission and/or death: age ≥ 70 years, SpO2, neutrophils > 7.5 × 103/µL, lactate dehydrogenase ≥ 300 U/L, and C-reactive protein ≥ 100 mg/L. In summary, nasopharyngeal SARS-CoV-2 viral load on admission is generally high in patients with COVID-19, regardless of illness severity, but it cannot be used as an independent predictor of unfavorable clinical outcome.

Impact of Treating Asymptomatic Bacteriuria in Kidney Transplant Recipients: A Prospective Cohort Study.

This study aims to define the epidemiologic, clinical, and microbiological features of asymptomatic bacteriuria (AB) and cystitis in kidney transplantation recipients (KTRs), and to determine the impact of antimicrobial therapy of AB and the risk factors of cystitis. We conducted a prospective observational study of AB and cystitis in KTRs from January to June 2017. One-hundred ninety seven KTRs were included: 175 (88.8%) with AB and 22 (11.2%) with cystitis. The most frequent etiologies were Escherichia coli, Klebsiellapneumoniae, Enterococcusfaecalis, and Pseudomonas aeruginosa. No differences were observed regarding the etiologies, antimicrobial susceptibility patterns, and microbiologic outcomes in AB vs. cystitis. The treatment of AB diminished the microbiological cure and increased the rates of microbiologic relapses and reinfections; in addition, treated AB patients showed a trend of developing symptomatic urinary tract infection in the following six months. The analysis of the data identified the following independent risk factors for cystitis during the six months of follow-up: AB treatment, thymoglobulin induction, previous acute pyelonephritis, and time since transplantation < 1 year. In summary, considering the lack of clinical benefits of treating AB and its impact on cystitis development in the follow-up, we support the recommendation of not screening for or treating AB.

Impact of the COVID-19 Pandemic on Antimicrobial Consumption and Hospital-Acquired Candidemia and Multidrug-Resistant Bloodstream Infections.

During the COVID-19 pandemic, the implementation of antimicrobial stewardship strategies has been recommended. This study aimed to assess the impact of the COVID-19 pandemic in a tertiary care Spanish hospital with an active ongoing antimicrobial stewardship programme (ASP). For a 20-week period, we weekly assessed antimicrobial consumption, incidence density, and crude death rate per 1000 occupied bed days of candidemia and multidrug-resistant (MDR) bacterial bloodstream infections (BSI). We conducted a segmented regression analysis of time series. Antimicrobial consumption increased +3.5% per week (p = 0.016) for six weeks after the national lockdown, followed by a sustained weekly reduction of -6.4% (p = 0.001). The global trend for the whole period was stable. The frequency of empirical treatment of patients with COVID-19 was 33.7%. No change in the global trend of incidence of hospital-acquired candidemia and MDR bacterial BSI was observed (+0.5% weekly; p = 0.816), nor differences in 14 and 30-day crude death rates (p = 0.653 and p = 0.732, respectively). Our work provides quantitative data about the pandemic effect on antimicrobial consumption and clinical outcomes in a centre with an active ongoing institutional and education-based ASP. However, assessing the long-term impact of the COVID-19 pandemic on antimicrobial resistance is required.

Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. Emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996.

A comparative taxonomic study of Halorubrum distributum, Halorubrum terrestre, Halorubrum arcis and Halorubrum litoreum was carried out using different approaches, 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), phylogenomic analysis based on the comparison of the core genome, orthologous average nucleotide identity (OrthoANI), Genome-to-Genome Distance Calculator (GGDC), synteny plots and polar lipid profile (PLP). The MLSA study, using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB', and the phylogenomic analysis based on 1347 core translated gene sequences obtained from their genomes showed that Halorubrum distributum JCM 9100T, Halorubrum terrestre JCM 10247T, Halorubrum arcis JCM 13916T and Halorubrum litoreum JCM 13561T formed a robust cluster, clearly separated from the rest of species of the genus Halorubrum. The OrthoANI and digital DDH values, calculated by the GGDC, showed percentages among Hrr. distributum JCM 9100T, Hrr. terrestre JCM 10247T, Hrr. arcis JCM 13916T and Hrr. litoreum JCM 13561T that ranged from 98.1 to 97.5 %, and 84.0 to 78.0 %, respectively, while these values among those strains and the type strains of their most related species of Halorubrum were equal or lower than 90.8 and 41.2 %, respectively. Moreover, degree of synteny across the four genomes was very high, especially between the genomes of Halorubrum litoreum JCM 13561T and Halorubrum arcis JCM 13916T. In addition, the PLP is quite similar among the four strains studied, showing a common pattern typical of the neutrophilic species of the genus Halorubrum. Overall, these data show that Hrr. distributum, Hrr. terrestre, Hrr. arcis and Hrr. litoreum constitute a single species. Thus, the latter three should be considered as later, heterotypic synonyms of Hrr. distributum based on the rules for priority of names. We propose an emended description of Hrr. distributum, including the features of Hrr. terrestre, Hrr. arcis and Hrr. litoreum.

Efficacy and safety of a comprehensive educational antimicrobial stewardship program focused on antifungal use.

OBJECTIVE: Few data exist regarding the impact of antimicrobial stewardship programs on antifungal use. We evaluated the efficacy and safety of a comprehensive long-term antimicrobial stewardship program (ASP) focused on antifungal use. METHODS: During a 9-year period, we quarterly assessed antifungal consumption, incidence density of hospital-acquired candidemia, Candida spp. distribution, antifungal resistance, and crude death rate per 1000 occupied bed days (OBDs) of hospital-acquired candidemia. We performed segmented regression analysis of interrupted time series. RESULTS: A significant change in trend was observed for antifungal consumption, with a sustained reduction of -0.87% per quarter (95% confidence interval [CI], -1.36 -0.38, p < 0.001), accounting for a final reduction of -38.4%. The main reduction was produced in fluconazole, with a sustained reduction of -1.37% per quarter (95%CI, -1.96 -0.68, p<0.001). The incidence density of hospital-acquired candidemia decreased, with a change in slope of -5.06% cases per 1000 OBDs per year (95%CI, -8.23 -1.77, p = 0.009). The 14-day crude death rate per 1000 OBDs dropped from 0.044 to 0.017 (-6.36% deaths per 1000 OBDs per year; 95%CI, -13.45 -1.31, p = 0.09). CONCLUSIONS: This ASP has succeeded in optimizing the use of antifungal with a long-lasting reduction without increasing the incidence, neither the mortality, of hospital-acquired candidemia.

Halorubrum chaoviator Mancinelli et al. 2009 is a later, heterotypic synonym of Halorubrum ezzemoulense Kharroub et al. 2006. Emended description of Halorubrum ezzemoulense Kharroub et al. 2006.

A polyphasic comparative taxonomic study of Halorubrum ezzemoulense Kharroub et al. 2006, Halorubrum chaoviator Mancinelli et al. 2009 and eight new Halorubrum strains related to these haloarchaeal species was carried out. Multilocus sequence analysis using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB', and phylogenetic analysis based on the 757 core protein sequences obtained from their genomes showed that Hrr. ezzemoulense DSM 17463T, Hrr. chaoviator Halo-G*T (=DSM 19316T) and the eight Halorubrum strains formed a robust cluster, clearly separated from the remaining species of the genus Halorubrum. The orthoANI value and digital DNA-DNA hybridization value, calculated by the Genome-to-Genome Distance Calculator (GGDC), showed percentages among Hrr. ezzemoulense DSM 17463T, Hrr. chaoviator DSM 19316T and the eight Halorubrum strains ranging from 99.4 to 97.9 %, and from 95.0 to 74.2 %, respectively, while these values for those strains and the type strains of the most closely related species of Halorubrum were 88.7-77.4 % and 36.1-22.3 %, respectively. Although some differences were observed, the phenotypic and polar lipid profiles were quite similar for all the strains studied. Overall, these data show that Hrr. ezzemoulense, Hrr. chaoviator and the eight new Halorubrum isolates constitute a single species. Thus, Hrr. chaoviator should be considered as a later, heterotypic synonym of Hrr. ezzemoulense. We propose an emended description of Hrr. ezzemoulense, including the features of Hrr. chaoviator and those of the eight new isolates.

Genotypic and Lipid Analyses of Strains From the Archaeal Genus Halorubrum Reveal Insights Into Their Taxonomy, Divergence, and Population Structure.

To gain a better understanding of how divergence occurs, and how taxonomy can benefit from studying natural populations, we isolated and examined 25 closely related Halorubrum strains obtained from different hypersaline communities and compared them to validly named species and other reference strains using five taxonomic study approaches: phylogenetic analysis using the 16S rRNA gene and multilocus sequencing analysis (MLSA), polar lipid profiles (PLP), average nucleotide identity (ANI) and DNA-DNA hybridization (DDH). 16S rRNA gene sequence could not differentiate the newly isolated strains from described species, while MLSA grouped strains into three major clusters. Two of those MLSA clusters distinguished candidates for new species. The third cluster with concatenated sequence identity equal to or greater than 97.5% was comprised of strains from Aran-Bidgol Lake (Iran) and solar salterns in Namibia and Spain, and two previously described species isolated from Mexico and Algeria. PLP and DDH analyses showed that Aran-Bidgol strains formed uniform populations, and that strains isolated from other geographic locations were heterogeneous and divergent, indicating that they may constitute different species. Therefore, applying only sequencing approaches and similarity cutoffs for circumscribing species may be too conservative, lumping concealed diversity into a single taxon. Further, our data support the interpretation that local populations experience unique evolutionary homogenization pressures, and once relieved of insular constraints (e.g., through migration) are free to diverge.

Halovenus salina sp. nov., an extremely halophilic archaeon isolated from a saltern.

An extremely halophilic archaeon was isolated from a water sample of Isla Bacuta saltern in Huelva, Spain. Strain ASP54(T) is a novel red-pigmented, motile, rod-shaped, Gram-stain-negative and strictly aerobic haloarchaeon. Strain ASP54(T) grew in media containing 15-30% (w/v) salts and optimally with 25% (w/v) salts. It grew between pH 5.0 and 9.0 (optimally at pH 7.5) and at 20-40 °C (optimally at 37 °C). Phylogenetic analysis based on multi-locus sequence analysis (MLSA) and the comparison of 16S rRNA gene sequences revealed that strain ASP54(T) is most closely related to the genus Halovenus. The closest relatives were Halovenus aranensis EB27(T) (92.1% 16S rRNA gene sequence similarity), Halorientalis regularis TNN28(T) (92.1%), and Halorientalis persicus D108(T) (92.0%). The polar lipid pattern of strain ASP54(T) consisted of biphosphatidylglycerol, phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl glucosyl diether and a minor-phospholipid. The predominant respiratory quinone was menaquinone-8 (MK-8) (83%), and a minor amount of MK-8(VIII-H2) (17%) was also detected. The G+C content of the genomic DNA of this strain was 63.1 mol%. Based on the phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain ASP54(T) represents a novel species of the genus Halovenus, for which the name Halovenus salina sp. nov. is proposed. The type strain is ASP54(T) ( = CEC(T) 8749(T) = IBRC-M 10946(T) = JCM 30072(T)).

Aquisalimonas lutea sp. nov., a moderately halophilic bacterium from a saltern.

A yellow-pigmented, motile, Gram-stain-negative, moderately halophilic and strictly aerobic bacterium, designated BA42AL-1(T), was isolated from water of a saltern of Santa Pola, Alicante, Spain. Strain BA42AL-1(T) grew in media containing 5-20% (w/v) salts (optimum 7.5% salts). It grew between pH 6.0 and 9.0 (optimally at pH 7.5) and at 15-45 °C (optimally at 37 °C). Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain BA42AL-1(T) is a member of the genus Aquisalimonas . The closest relatives to this strain were Aquisalimonas halophila YIM 95345(T) and Aquisalimonas asiatica CG12(T) with sequence similarities of 99.4% and 97.0%, respectively. DNA-DNA hybridization between the novel isolate and Aquisalimonas halophila YIM 95345(T) revealed a relatedness of 54%. The major fatty acids of strain BA42AL-1(T) were C(18 : 1)ω6c/C(18 : 1)ω7c, C(19 : 0) cyclo ω8c and C(16 : 0), and lower contents of C12 : 0 and C18 : 0. The polar lipid pattern of strain BA42AL-1(T) consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, two glycolipids, a lipid and four unknown phospholipids. The G+C content of the genomic DNA of this strain was 65.0 mol%. Based on the DNA-DNA hybridization, phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain BA42AL-1(T) is proposed as a novel species of the genus Aquisalimonas , for which the name Aquisalimonas lutea sp. nov. is suggested. The type strain is BA42AL-1(T) ( = CCM 8472(T) = CECT 8326(T) = LMG 27614(T)).

Fodinicurvata halophila sp. nov., a moderately halophilic bacterium from a marine saltern.

A Gram-stain-negative, rod-shaped, facultatively anaerobic, moderately halophilic bacterium, designated strain BA45AL(T), was isolated from water of a saltern located in Santa Pola, Alicante, Spain. Cells were motile, and catalase- and oxidase-positive. Strain BA45AL(T) grew at temperatures in the range 14-45 °C (optimally at 37 °C), at pH 5.0-9.0 (optimally at pH 7.5), and in media containing 5-20 % (w/v) salts [optimally in media containing 10 % (w/v) salts]. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain BA45AL(T) is a member of the genus Fodinicurvata. The closest relatives to the novel strain were Fodinicurvata fenggangensis YIM D812(T) and Fodinicurvata sediminis YIM D82(T) with sequence similarities of 98.2 % and 97.4 %, respectively. DNA-DNA hybridization between the novel isolate and these phylogenetically related species revealed relatedness values of 30 % and 15 %, respectively, with respect to the aforementioned species. The major cellular fatty acids of strain BA45AL(T) were C18 : 1ω7c, C16 : 0 and iso-C15 : 0. The G+C content of the genomic DNA of strain BA45AL(T) was 58.0 mol%, and the polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylmethylethanolamine and a number of unknown phospholipids and lipids. Based on phenotypic, chemotaxonomic and phylogenetic data presented in this study, strain BA45AL(T) constituted a novel species of the genus Fodinicurvata, for which the name Fodinicurvata halophila sp. nov. is suggested. The type strain is BA45AL(T) ( = CCM 8504(T) = CECT 8472(T) = JCM 19075(T) = LMG 27945(T)).

Draft Genome Sequence of the Moderately Halophilic Bacterium Marinobacter lipolyticus Strain SM19.

Marinobacter lipolyticus strain SM19, isolated from saline soil in Spain, is a moderately halophilic bacterium belonging to the class Gammaproteobacteria. Here, we report the draft genome sequence of this strain, which consists of a 4.0-Mb chromosome and which is able to produce the halophilic enzyme lipase LipBL.