Low rate of bacterial co-infection in patients with COVID-19

We agree with Michael J Cox and colleagues1 that clinical management of COVID-19 would be enhanced by further characterisation of bacterial co-infections. A few case reports have described examples of such co-infections.2, 3, 4 However, national5 and international6 guidelines recommend empirical antibiotics for all patients who are severely ill with suspected COVID-19, and that cessation of therapy is left to the clinicians' discretion. Pending the widespread availability of metagenomic sequencing as envisaged by Cox and colleagues,1 we argue that traditional diagnostics still have a role

Ten-Year Analysis of Bacterial Colonisation and Outcomes of Major Burn Patients with a Focus on Pseudomonas aeruginosa

A retrospective descriptive study included patients admitted with severe burns over the course of 10 years (2008–2018). Across all patients, there were 39 different species of bacteria, with 23 species being Gram-negative and 16 being Gram-positive bacteria, with also five different species of fungi cultured. Pseudomonas aeruginosa was the most commonly isolated organism, with 57.45% of patients having a positive culture. There was a significant difference in the number of P. aeruginosa isolated from patients that acquired their burns at work, in a garden, inside a vehicle, in a garage or in a public place. In patients that were positive for P. aeruginosa, the number of operations was higher (2.4) and the length of stay was significantly increased (80.1 days). Patients that suffered from substance abuse demonstrated significantly higher numbers of isolated P. aeruginosa (14.8%). Patients that suffered from both mental health illness and substance abuse demonstrated significantly higher numbers of P. aeruginosa isolated (18.5%). In the P. aeruginosa-negative group, there were significantly fewer patients that had been involved in a clothing fire. Furthermore, in the P. aeruginosa-negative patient cohort, the mortality rate was significantly higher (p = 0.002). Since the incidence of P. aeruginosa was also associated with a decreased mortality rate, it may be that patients admitted to hospital for shorter periods of time were less likely to be colonised with P. aeruginosa. This study demonstrates novel factors that may increase the incidence of P. aeruginosa isolated from burn patients

Comparison of Control of Clostridium difficile Infection in Six English Hospitals Using Whole-Genome Sequencing

Background: Variation in Clostridium difficile infection (CDI) rates between healthcare institutions suggests overall incidence could be reduced if the lowest rates could be achieved more widely. Methods: We investigated whether whole-genome sequencing (WGS) of consecutive C. difficile isolates from six English hospitals over one year (2013-14) could be used to assess infection control performance. Fecal samples with a positive initial screen for C. difficile (GDH or toxin-PCR) were cultured and sequenced. Within each hospital, we estimated the proportion of cases plausibly acquired from previous cases, defined by an isolate ≤2 single nucleotide polymorphisms different from a previous isolate in the last 90-days. Results: 851/971(87.6%) sequenced culture-positive samples were toxigenic, and 451(46.4%) were fecal-toxin-positive. 128/652(20%,95%CI 17-23%) toxigenic isolates >90-days after the study started were genetically-linked to a prior patient’s isolate from the previous 90-days. Hospital-2 had the fewest linked isolates, 7/105(7%,3-13%), hospital-1 an intermediate proportion, 9/70(13%,6-23%), while hospitals 3-6 had similar proportions of linked isolates (22-26%) (p≤0.002 comparing hospital-2 vs 3-6). Results were similar adjusting for locally-circulating ribotypes. Adjusting for hospital, ribotype-027 had the highest proportion of linked isolates (57%, 95%CI 29-81%). Fecal-toxin-positive and toxin-negative patients were similarly infectious in terms of being a potential transmission donor, OR=1.01(0.68-1.49,p=0.97). There was no association between the estimated proportion of cases linked to a previous case within 90-days and testing rates (p=0.60). Conclusions: WGS can be used to identify varying rates of C. difficile transmission in different locations, and offers the potential to allow targeted efforts to reduce CDI incidence

ICAR: endoscopic skull‐base surgery

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Fungal diversity notes 253-366: taxonomic and phylogenetic contributions to fungal taxa

Notes on 113 fungal taxa are compiled in this paper, including 11 new genera, 89 new species, one new subspecies, three new combinations and seven reference specimens. A wide geographic and taxonomic range of fungal taxa are detailed. In the Ascomycota the new genera Angustospora (Testudinaceae), Camporesia (Xylariaceae), Clematidis, Crassiparies (Pleosporales genera incertae sedis), Farasanispora, Longiostiolum (Pleosporales genera incertae sedis), Multilocularia (Parabambusicolaceae), Neophaeocryptopus (Dothideaceae), Parameliola (Pleosporales genera incertae sedis), and Towyspora (Lentitheciaceae) are introduced. Newly introduced species are Angustospora nilensis, Aniptodera aquibella, Annulohypoxylon albidiscum, Astrocystis thailandica, Camporesia sambuci, Clematidis italica, Colletotrichum menispermi, C. quinquefoliae, Comoclathris pimpinellae, Crassiparies quadrisporus, Cytospora salicicola, Diatrype thailandica, Dothiorella rhamni, Durotheca macrostroma, Farasanispora avicenniae, Halorosellinia rhizophorae, Humicola koreana, Hypoxylon lilloi, Kirschsteiniothelia tectonae, Lindgomyces okinawaensis, Longiostiolum tectonae, Lophiostoma pseudoarmatisporum, Moelleriella phukhiaoensis, M. pongdueatensis, Mucoharknessia anthoxanthi, Multilocularia bambusae, Multiseptospora thysanolaenae, Neophaeocryptopus cytisi, Ocellularia arachchigei, O. ratnapurensis, Ochronectria thailandica, Ophiocordyceps karstii, Parameliola acaciae, P. dimocarpi, Parastagonospora cumpignensis, Pseudodidymosphaeria phlei, Polyplosphaeria thailandica, Pseudolachnella brevifusiformis, Psiloglonium macrosporum, Rhabdodiscus albodenticulatus, Rosellinia chiangmaiensis, Saccothecium rubi, Seimatosporium pseudocornii, S. pseudorosae, Sigarispora ononidis and Towyspora aestuari. New combinations are provided for Eutiarosporella dactylidis (sexual morph described and illustrated) and Pseudocamarosporium pini. Descriptions, illustrations and/or reference specimens are designated for Aposphaeria corallinolutea, Cryptovalsa ampelina, Dothiorella vidmadera, Ophiocordyceps formosana, Petrakia echinata, Phragmoporthe conformis and Pseudocamarosporium pini. The new species of Basidiomycota are Agaricus coccyginus, A. luteofibrillosus, Amanita atrobrunnea, A. digitosa, A. gleocystidiosa, A. pyriformis, A. strobilipes, Bondarzewia tibetica, Cortinarius albosericeus, C. badioflavidus, C. dentigratus, C. duboisensis, C. fragrantissimus, C. roseobasilis, C. vinaceobrunneus, C. vinaceogrisescens, C. wahkiacus, Cyanoboletus hymenoglutinosus, Fomitiporia atlantica, F. subtilissima, Ganoderma wuzhishanensis, Inonotus shoreicola, Lactifluus armeniacus, L. ramipilosus, Leccinum indoaurantiacum, Musumecia alpina, M. sardoa, Russula amethystina subp. tengii and R. wangii are introduced. Descriptions, illustrations, notes and / or reference specimens are designated for Clarkeinda trachodes, Dentocorticium ussuricum, Galzinia longibasidia, Lentinus stuppeus and Leptocorticium tenellum. The other new genera, species new combinations are Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis from Neocallimastigomycota, Phytophthora estuarina, P. rhizophorae, Salispina, S. intermedia, S. lobata and S. spinosa from Oomycota, and Absidia stercoraria, Gongronella orasabula, Mortierella calciphila, Mucor caatinguensis, M. koreanus, M. merdicola and Rhizopus koreanus in Zygomycota