Single-cell RNA sequencing of SARS-CoV-2 cell entry factors in the preconceptional human endometrium.

STUDY QUESTION: Are SARS-CoV-2 canonical cell entry machinery, consisting of ACE2, TMPRSS2, NRP1 and LY6E, or alternative potential cell entry machinery, consisting of BSG, ANPEP, CD209, CLEC4G, TMPRSS4, TMPRSS11A, FURIN, CTSB, CTSL and IFITM1, expressed in the human endometrium across the menstrual cycle? SUMMARY ANSWER: Analysis of cell entry factors for SARS-CoV-2 by single-cell RNA-sequencing (scRNAseq) in the preconceptional human endometrium reveals low risk of infection. WHAT IS KNOWN ALREADY: Gene expression datasets from bulk endometrial tissue show no significant expression of the SARS-CoV-2 receptor ACE2 and TMPRSS2. This is in contrast to reported expression of ACE2 at the single-cell level in the decidua and trophoblast cells at the maternal-fetal interface in early pregnancy, as well as vertical transmission of SARS-CoV-2 during pregnancy. STUDY DESIGN, SIZE, DURATION: This analysis of SARS-CoV-2 cell entry machinery gene expression was conducted by scRNAseq in 73 181 human endometrial cells isolated from endometrial biopsies obtained from 27 donors across the menstrual cycle. PARTICIPANTS/MATERIALS, SETTING, METHODS: ScRNAseq examined the expression of genes encoding cell entry machinery for SARS-CoV-2. The raw data were from a previously published dataset. MAIN RESULTS AND THE ROLE OF CHANCE: ScRNAseq analysis showed no significant expression of ACE2 in stromal or unciliated epithelial cells in any phase of the menstrual cycle. TMPRSS2 was expressed in epithelial cells during the early proliferative and mid-secretory phases. Interestingly, the expression of NRP1 was observed in both stromal and epithelial cells across all phases of the menstrual cycle, and LY6E was highly expressed in stromal cells. In the mid-secretory phase, coexpression of ACE2 and TMPRSS2 was detected in 0.07% of luminal epithelial cells. No cells simultaneously expressed ACE2, NRP1 and TMPRSS2 at the time of embryo implantation. Focusing on non-canonical cell entry machinery, BSG was highly expressed in all cell types across the menstrual cycle and may interact with CTSB or CTSL proteases, but viral infection using this machinery has not yet been confirmed. LARGE SCALE DATA: All raw data in this study can be found at NCBI's Gene Expression Omnibus (series accession code GSE111976) and Sequence Read Archive (accession code SRP135922). LIMITATIONS, REASONS FOR CAUTION: Our findings at the single-cell level imply low efficiency of SARS-CoV-2 endometrial infection using canonical receptors in a cohort of healthy reproductive-age women; however, infection of endometrial cells can only be assessed in the presence of the virus. All samples were processed for scRNAseq, so no samples are remaining to analyze protein expression or spatial transcriptomics. WIDER IMPLICATIONS OF THE FINDINGS: Our results offer a useful resource to guide reproductive decisions when assessing risk of endometrial infection by SARS-CoV-2 during the preconceptional period in asymptomatic COVID-19 carriers. STUDY FUNDING/COMPETING INTEREST(S): This study was jointly supported by the March of Dimes, Chan Zuckerberg Biohub and MINECO/FEDER (SAF-2015-67164-R, to C.S.) (Spanish Government), and the European Union's Horizon 2020 Framework Programme for Research and Innovation (Grant agreement 874867). W.W. was supported by the Stanford Bio-X Graduate Bowes Fellowship and Chan Zuckerberg Biohub. F.V. was supported by the Miguel Servet Program Type II of ISCIII (CPII18/00020) and the FIS project (PI18/00957). A patent disclosure has been filed for the study with the title 'Methods for assessing endometrial transformation' and the global patent number 'EP 3807648 A2' under the inventors S.R.Q., C.S., W.W. and F.V. C.S. is the Founder and Head of the Scientific Advisory Board of Igenomix SL. S.R.Q is the Director of Mirvie. I.M. is partially employed by Igenomix SL. B.R. has no interests to declare.

Inappropriate prescribing in elderly people with diabetes admitted to hospital.

AIMS: To assess inappropriate prescribing in older people with diabetes mellitus during the month prior to a hospitalization, using tools on potentially inappropriate medicines (PIMs) and potential prescribing omissions (PPOs) and comparing inappropriate prescribing in patients with without diabetes. METHODS: In an observational, prospective multicentric study, we assessed inappropriate prescribing in 672 patients aged 75 years and older during hospital admission. The Beers, Screening Tool of Older Person's Prescriptions (STOPP) and Screening Tool to Alert Doctors to Right Treatment (START) criteria and Assessing Care of Vulnerable Elders (ACOVE-3) medicine quality indicators were used. We analysed demographic and clinical factors associated with inappropriate prescribing. RESULTS: Of 672 patients, 249 (mean age 82.4 years, 62.9% female) had a diagnosis of diabetes mellitus. The mean number of prescribing drugs per patient with diabetes was 12.6 (4.5) vs. 9.4 (4.3) in patients without diabetes (P < 0.001). Of those patients with diabetes, 74.2% used 10 or more medications; 54.5% of patients with diabetes had at least one Beers-listed PIM, 68.1% had at least one STOPP-listed PIM, 64.6% had at least one START-listed PPO and 62.8% had at least one ACOVE-3-listed PPO. Except for the Beers criteria, these prevalences were significantly higher in patients with diabetes than in those without. After excluding diabetes-related items from these tools, only STOPP-listed PIMs remained significantly higher among patients with diabetes (P = 0.04). CONCLUSIONS: Polypharmacy is common among older patients with diabetes mellitus. Inappropriate prescribing is higher in older patients with diabetes, even when diabetes-related treatment is excluded from the inappropriate prescribing evaluation.

Factors associated with complications and mortality in adult patients hospitalized for infectious cellulitis.

The aim of this study was to analyze medical outcomes, including risks for complications and mortality, in 332 adult patients hospitalized for cellulitis. The infection was documented microbiologically in 128 cases (39%). Staphylococcus aureus (46 cases) and Streptococcus pyogenes (22 cases) were the most frequent causative pathogens. Overall, 63 patients (19%) were discharged early (< or =4 days) and 166 patients (50%) were hospitalized for more than 4 days without developing any complications. One hundred three patients (31%) had one or more complications or died. Of these, 78 required surgical debridement, 10 required plastic surgery, 7 underwent amputation, and 15 had shock on presentation. When comparing the three study groups (patients discharged early, patients hospitalized for < or =4 days without complications, and patients who developed 1 or more complication or who died), patients who were discharged early (low risk) were more frequently female and were less likely to have multiple comorbid conditions, hypoalbuminemia, renal insufficiency, and/or cutaneous necrosis at presentation. Overall mortality (<30 days) was 5% (16/332 patients). Factors associated with death were male sex, presence of multiple comorbid conditions, congestive heart failure, morbid obesity, hypoalbuminemia, renal insufficiency, shock, and Pseudomonas aeruginosa cellulitis. These findings can be used to stratify patients with acute cellulitis according to risks for complications and mortality and may be helpful when deciding the most appropriate means of care, i.e. outpatient treatment or hospitalization.

Efficacy and safety of sequential amoxicillin-clavulanate in the treatment of anaerobic lung infections.

In order to assess the efficacy and safety of amoxicillin-clavulanate for the treatment of anaerobic lung infection, 40 patients with lung abscess or necrotizing pneumonia were given sequential amoxicillin-clavulanate therapy. All patients received intravenous amoxicillin-clavulanate (2 g/200 mg/8 h), which was switched to oral form (1 g/125 mg/8 h) after clinical improvement. Mean duration of antibiotic therapy was 43.5 days. Microbiological documentation was obtained in 53% of cases. All but 1 of the 48 microorganisms isolated were susceptible to amoxicillin-clavulanate. The drug was well tolerated by the patients and no severe adverse effects were observed. At the end of treatment all patients were considered cured. The 35 patients assessed at long-term follow-up visit remained disease-free.

Etiology, reasons for hospitalization, risk classes, and outcomes of community-acquired pneumonia in patients hospitalized on the basis of conventional admission criteria.

We performed an observational analysis of prospectively collected data on 533 nonseverely immunosuppressed adult patients who were hospitalized for community-acquired pneumonia on the basis of conventional admission criteria. For this population, we correlated etiology, reasons for admission, and outcomes using the Pneumonia Severity Index (PSI), to identify major discrepancies between the PSI risk class and the conventional criteria for deciding the site of care. PSI classes and corresponding mortality rates were as follows: class I, 51 patients (0%); class II, 62 (2%); class III, 117 (3%); class IV, 198 (10%); and class V, 105 (29%). We identified significant discrepancies between both methods. Overall, 230 patients (40%) who were hospitalized according to conventional criteria were assigned to low-risk classes. Of these 230 patients, 137 (60%) needed supplementary oxygen or had pleural complications; for the remaining patients, there were no irrefutable reasons for admission. This latter group deserves prospective evaluation in randomized studies that compare ambulatory and in-hospital management.

Usefulness of betalactam therapy for community-acquired pneumonia in the era of drug-resistant Streptococcus pneumoniae: a randomized study of amoxicillin-clavulanate and ceftriaxone.

Empirical antibiotic therapy of community-acquired pneumonia (CAP) has been complicated by the worldwide emergence of penicillin resistance among Streptococcus pneumoniae. The impact of this resistance on the outcome of patients hospitalized for CAP, empirically treated with betalactams, has not been evaluated in a randomized study. We conducted a prospective, randomized trial to assess the efficacy of amoxicillin-clavulanate (2 g/200 mg/8 hr) and ceftriaxone (1 g/24 hr) in a cohort of patients hospitalized for moderate-to-severe CAP. Three-hundred seventy-eight patients were randomized to receive amoxicillin-clavulanate (184 patients) or ceftriaxone (194 patients). Efficacy was assessed on Day 2, after completion of therapy and at long term follow-up. There were no significant differences in outcomes between treatment groups, both in intention-to-treat and per-protocol analysis. Overall mortality was 10.3% for amoxicillin-clavulanate and 8.8% for ceftriaxone (NS). There were 116 evaluable patients with proven pneumococcal pneumonia. Rates of high-level penicillin resistance (MIC of penicillin > or = 2 microg/mL) were similar in the two groups (8.2 and 10.2%). Clinical efficacy at the end of therapy was 90.6% for amoxicillin-clavulanate and 88.9% for ceftriaxone (95% C.I. of the difference: -9.3 to +12.7%). No differences in outcomes were attributable to differences in penicillin susceptibility of pneumococcal strains. Sequential i.v./oral amoxicillin-clavulanate and parenteral ceftriaxone were equally safe and effective for the empirical treatment of acute bacterial pneumonia, including penicillin and cephalosporin-resistant pneumococcal pneumonia. The use of appropriate betalactams in patients with penumococcal pneumonia and in the overall CAP population, is reliable at the current level of resistance.

Prospective study of the usefulness of sputum Gram stain in the initial approach to community-acquired pneumonia requiring hospitalization.

From February 1995 through May 1997, we prospectively studied 533 patients with community-acquired pneumonia requiring hospitalization in order to assess the current usefulness of sputum Gram stain in guiding the etiologic diagnosis and initial antibiotic therapy when applied routinely. Sputum samples of good quality were obtained in 210 (39%) patients, 175 of whom showed a predominant morphotype. Sensitivity and specificity of Gram stain for the diagnosis of pneumococcal pneumonia were 57% and 97%, respectively; the corresponding values for Haemophilus influenzae pneumonia were 82% and 99%. Patients with a predominant morphotype were more frequently treated with monotherapy than were patients without a demonstrative sputum sample (89% vs. 75%; P<.001). Analysis of our data shows that a good-quality sputum sample can be obtained from a substantial number of patients with community-acquired pneumonia. Gram stain was highly specific for the diagnosis of pneumococcal and H. influenzae pneumonia and may be useful in guiding pathogen-oriented antimicrobial therapy.

[Respiratory syncytial virus infection in adult patients hospitalized with community-acquired pneumonia]. / Infección por virus respiratorio sincitial en adultos ingresados per neumonía adquirida en la comunidad.

OBJECTIVE: To determine the incidence and distribution of infection caused by respiratory syncytial virus (RSV) in hospitalized adults with community-acquired pneumonia. PATIENTS AND METHODS: Patients were immunocompetent adults hospitalized with community-acquired pneumonia, who were prospectively studied in our hospital. As a part of the diagnostic protocol, we performed RSV serology with paired acute and convalescent phase sera of patients admitted between February 1995 and May 1997. Clinical and epidemiological characteristics of patients with and without acute infection were compared. RESULTS: Paired RSV serology was performed in 250 patients hospitalized with community-acquired pneumonia. 97% of them had presence of IgG antibodies but only 17 patients (6.8%) had serologic evidence of acute infection; of these, seroconversion was observed in eight and positive IgM in nine. Fourteen cases with acute infection (82%) occurred between November and May. Three patients had pneumococcal pneumonia, 2 Legionella pneumophila and 12 pneumonia of unknown etiology. There were no clinical differences between patients with and without RSV acute infection but those with acute infection had more frequently bilateral involvement in chest radiography and a greater proportion of pneumonias of unknown etiology. CONCLUSIONS: RSV is a cause of acute infection among adults hospitalized with community-acquired pneumonia, mainly between November and May. Further studies to assess the role of RSV as a causative agent of pneumonia in this population are needed.

Usefulness of PCR and antigen latex agglutination test with samples obtained by transthoracic needle aspiration for diagnosis of pneumococcal pneumonia.

In a large number of cases, the etiology of community-acquired pneumonia (CAP) is not established. Some cases are probably caused by Streptococcus pneumoniae. Transthoracic needle aspiration (TNA) culture has a limited sensitivity which might be improved by antigen detection or gene amplification techniques. We evaluated the capacity of a PCR assay and a latex agglutination test to detect S. pneumoniae in samples obtained by TNA from 95 patients with moderate-to-severe CAP. Latex agglutination and PCR had sensitivities of 52.2 and 91.3%, specificities of 88.7 and 83.3%, positive predictive values of 62.3 and 65.6%, and negative predictive values of 83.3 and 96.5%, respectively, when culture techniques were used as the "gold standard." When we considered expanded criteria for the diagnosis of pneumococcal pneumonia as a standard for our calculations, latex agglutination and PCR had sensitivities of 53.6 and 89.7%, specificities of 93.0 and 90.0%, positive predictive values of 78.9 and 81.3%, and negative predictive values of 80.3 and 94.7%, respectively. The additional diagnosis provided by the PCR assay compared to latex agglutination was 12.2% (95% confidence interval of the difference from 0.4 to 20. 1%). PCR was more sensitive than TNA culture, particularly in patients who had received prior antibiotic therapy (83.3 versus 33. 3%). Although PCR is a very sensitive and specific technique, it has not proved to be cost-effective in clinical practice. Conversely, latex agglutination is a fast and simple method whose results might have significant implications for initial antibiotic therapy.

Bacteremic pneumonia in neutropenic patients with cancer: causes, empirical antibiotic therapy, and outcome.

BACKGROUND: Bacteremic pneumonia is a major cause of death among neutropenic patients with cancer. METHODS: We analyzed the causes, empirical antibiotic therapy, and outcome of 40 consecutive cases of bacteremic pneumonia identified among 408 episodes of bacteremia in adult neutropenic patients with cancer, prospectively documented from 1986 to 1995. RESULTS: The most frequent causative organisms were Pseudomonas aeruginosa (17 cases), Streptococcus pneumoniae (12 cases), Escherichia coli (5 cases), and Streptococcus mitis (3 cases). Overall, P. aeruginosa and S. pneumoniae caused 72.5% of all episodes of bacteremic pneumonia, compared with 11.4% of bacteremic episodes from other sources (P< .001). Thirty patients received ceftazidime and 10 patients received imipenem as the beta-lactam component of the initial empirical treatment. All strains of P. aeruginosa were susceptible to both agents. Forty-seven percent of streptococcal strains were penicillin resistant and showed a decreased susceptibility to ceftazidime (minimum inhibitory concentration ranged from 1 to 64 microg/mL). Five patients (12.5%) were considered to have received inappropriate empirical antibiotic therapy. Attributable mortality in patients with bacteremic pneumonia was higher than in patients with bacteremia from other sources; 22 (55%) of the 40 patients with bacteremic pneumonia died, whereas 39 (10.6%) of the 368 patients with bacteremia from other sources died (P<.001). CONCLUSIONS: Our data suggest that bacteremic pneumonia in neutropenic cancer patients is associated with a poor outcome and that empirical antibiotic therapy for neutropenic patients with pneumonia should include agents active against both P. aeruginosa and cephalosporin-resistant streptococci.

Listeria monocytogenes empyema in an HIV infected patient.

Listeriosis in HIV infected patients is uncommon and usually presents as meningitis or bacteraemia. Pleural fluid infections caused by this organism are extremely rare. A case is described of empyema caused by Listeria monocytogenes in an HIV infected patient that was successfully treated with medical treatment only.

[Endocarditis caused by group B streptococci in adults]. / Endocarditis por estreptococo del grupo B en adultos.

OBJECTIVE: To evaluate clinical characteristics, treatment and outcome of group B streptococcal endocarditis in nonpregnant adults. METHODS: We included all cases of Streptococcus agalactiae endocarditis diagnosed according to the Duke criteria between 1980 and 1994 in a 1000-bed university hospital, where a prospective surveillance of all cases of bacteremia is regularly performed. RESULTS: There were 9 episodes of S. agalactiae endocarditis, that account for the 10.5% of 85 bacteremia caused by this organism and 2.6% of 336 infectious endocarditis (in non-drug abusers) during the study period. They occurred in 6 males and 3 females with an average age of 60 years (44-86 years). Three patients had underlying disease and three had been previously diagnosed of having valvulopathy. There were no cases of prosthetic valve endocarditis. The valves most frequently involved were the aortic and mitral valves. Only one patient had large vessel embolization. All isolates were penicillin-susceptible (MIC < 0.12 microgram/ml). Most of the patients were treated with penicillin plus an aminoglycoside and 6 patients also underwent surgery combined with the medical therapy after an average of 40 days (13-60 days). The overall mortality was 11%. CONCLUSIONS: S. agalactiae is a rare cause of infectious endocarditis. Combination of surgery with the antibiotic therapy might decrease mortality rates of this infection.