The Taxonomy Dictionary: a resource for correct spelling of taxa.

This article describes 'The Taxonomy Dictionary', a resource that can enhance the spelling engine of a text editor such as Word, so that it can correctly spell every taxon described and listed in the largest taxonomy databases. It contains around 1.4 million unique words, and once installed an incorrectly spelled taxon will be marked by the spelling engine and it will suggest possible correct spellings. Installation instructions for Firefox, LibreOffice and Microsoft Word can be found on the GitHub repository. The software is licensed with a GPL3 licence.

Estimated Roles of the Carrier and the Bacterial Strain When Methicillin-Resistant Staphylococcus aureus Decolonization Fails: a Case-Control Study.

Methicillin-resistant Staphylococcus aureus (MRSA) is a common bacterial pathogen that frequently colonizes healthy individuals, with potential to cause invasive infection. In Denmark, to keep the prevalence low, MRSA carriers are recommended to undergo decolonization treatments, but achieving decolonization is challenging. Knowledge about the factors contributing to decolonization is scarce. We aimed to identify bacterial genome and clinical factors influencing MRSA decolonization. We identified all new MRSA patients above 2 years of age within the Hvidovre catchment area, Copenhagen, Denmark, in 2017 and 2018. Carriers were defined as chronic carriers (cases) if they were MRSA positive after two or more treatments and as nonchronic carriers (controls) if they were MRSA free after the first or second treatment. Using whole-genome sequencing (WGS), we constructed a pangenome of bacterial strains. With the incorporation of bacterial genome and clinical patient data, machine learning and multivariate analyses were performed to determine the factors associated with decolonization. A total of 477 MRSA carriers were included. An age of ≥13 years was significantly associated with nonchronic carriage. We identified 278 bacterial genetic features that were statistically significantly associated with chronic carriage (P < 0.05 by Fisher's exact test). Chronic MRSA carriage was predicted with 68% accuracy using a combination of bacterial genome data and patient clinical data. Decolonization success is multifactorial. Apart from the 68% predicted accuracy found in this study, we estimate that the remaining 32% is a result of host factors and microbiome composition. IMPORTANCE Carriage of methicillin-resistant Staphylococcus aureus (MRSA) and other multiresistant bacteria is a prerequisite for infection and transmission. Successful decolonization treatment removes these risks. We aimed to identify bacterial genome and host clinical factors that influence MRSA decolonization to estimate the roles of the carrier and the bacterial strain, respectively, when decolonization fails. The long-term goal, beyond this study, is to optimize decolonization success, minimize MRSA transmission, and, ultimately, improve the quality of life of MRSA carriers.

Antibiotic treatment in acute exacerbation of COPD: patient outcomes with amoxicillin vs. amoxicillin/clavulanic acid-data from 43,636 outpatients.

BACKGROUND: For antibiotic treatment of Acute exacerbations of COPD (AECOPD) the National guidelines in Denmark recommend either first choice amoxicillin 750 mg TID (AMX) or amoxicillin with clavulanic acid 500 mg/125 mg TID (AMC). Addition of clavulanic acid offers a broader spectrum; opposite, AMX alone in a higher dose may offer more time above MIC. The aim of this study was to determine which of these regimens is associated with better outcome. METHODS: The Danish Registry of COPD (DrCOPD), a nationwide outpatient COPD registry, was crosslinked with medication data and hospital contacts. The first prescription of AMX or AMC after inclusion in DrCOPD was used as exposure variable. Adjusted Cox proportional hazards models were used to analyze the risk of hospitalization or death (combined) within 30 days and other endpoints. RESULTS: For the first treatment of AECOPD 12,915 received AMX, and 30,721 patients received AMC. AMX was associated with a decreased risk of pneumonia hospitalization or death (aHR 0.6, 95% CI 0.5-0.7; p < 0.0001) compared to AMC. CONCLUSION: In AECOPD, empirically adding clavulanic acid to amoxicillin is not associated with a better outcome; it seems safe for these patients to be treated with amoxicillin alone.

Streptococcal toxic shock syndrome in a patient with community-acquired pneumonia. Impact of rapid diagnostics on patient management.

Here we describe a community-acquired pneumonia with Streptococcus pyogenes , group A following a common cold caused by human metapneumovirus. The patient, a 58-year-old woman with no prior medical history, developed respiratory failure and multi-organ dysfunction caused by streptococcal toxic shock syndrome. The patient was admitted to the intensive care unit and treated with supportive care. The definitive diagnosis was made by BioFire FilmArray by Biomerieux (multiplex PCR) 12 h before positive blood culture, thus enabling the clinician to add clindamycin and intravenous immunoglobulin to the treatment. The patient was discharged fully recovered after 23 days. Streptococci group A is a rare pathogen of severe pneumonia and rapid diagnostics by syndromic testing, potentially performed in a near patient setting, is crucial for early implementation of targeted antimicrobial treatment.

Eradicating MRSA carriage: the impact of throat carriage and Panton-Valentine leukocidin genes on success rates.

In Denmark, eradication treatment is recommended for methicillin-resistant Staphylococcus aureus (MRSA) carriers. Here, we analyze factors associated with eradication outcome. MRSA carriers referred to the MRSA Knowledge Center at Hvidovre Hospital in 2013 were included. Carriers were sampled from nose, throat, and perineum. Eradication regimen was 5 days of mupirocin nasal ointment and chlorhexidine whole-body wash. Oral antibiotics were sometimes added. Factors associated with eradication after the first eradication attempt were analyzed by logistic regression and expressed as odds ratio (OR) with 95% confidence interval (95% CI). Of 164 individuals, 143 completed 1- and 6-month follow-up after 1st treatment. Eradication was achieved in 63 (38.4%) patients after one treatment and 101 (61.6%) individuals became MRSA free after up to 4 eradication treatments. Throat carriage was associated with a higher failure rate (OR 0.29 (0.10-0.80)), while the presence of Panton-Valentine leukocidin (PVL) genes (37%) was associated with higher success rate (OR 3.52 (1.44-8.57)). Other factors analyzed were not significantly associated with eradication outcome. None of the 26 patients lost to follow-up developed later MRSA infections. This study estimates the efficacy of treatment of MRSA carriage with an eradication rate of 38.4% after the first treatment and a total eradication rate of 61.6% after several treatments. Throat carriers had a lower eradication success rate. Adding oral antibiotics to the first treatment did not increase success. The finding of a significant higher success rate when having a PVL-positive clone should be further investigated.

[Brain abscesses caused by Nocardia farcinica in a kidney transplanted man].

Nocardiosis is primarily an opportunistic infection caused by aerobic Gram-positive bacteria of the genus Nocardia. In this case report we describe a male patient who previously received a kidney transplant and was admitted to hospital with chills, headache and pain in the neck and left eye, tremor and coordination problems. A magnetic resonance scan of the brain showed multiple abscesses, and blood culture was positive for Nocardia farcinica. Nocardiosis of the central nervous system is a rare, but serious differential diagnosis in immunosuppressed patients with signs of high intracranial pressure.