Clinical review: Liberation from mechanical ventilation

Mechanical ventilation is the defining event of intensive care unit (ICU) management. Although it is a life saving intervention in patients with acute respiratory failure and other disease entities, a major goal of critical care clinicians should be to liberate patients from mechanical ventilation as early as possible to avoid the multitude of complications and risks associated with prolonged unnecessary mechanical ventilation, including ventilator induced lung injury, ventilator associated pneumonia, increased length of ICU and hospital stay, and increased cost of care delivery. This review highlights the recent developments in assessing and testing for readiness of liberation from mechanical ventilation, the etiology of weaning failure, the value of weaning protocols, and a simple practical approach for liberation from mechanical ventilation

Ultrarapid diagnosis, microscope imaging, genome sequencing, and culture isolation of SARS-CoV-2.

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Draft genome and description of Chryseobacterium phocaeense sp. nov.: a new bacterial species isolated from the sputum of a cystic fibrosis patient

International audienceStrain 6021061333 T was isolated from the sputum of 16-year-old girl with cystic fibrosis following a pulmonary exacerba-tion. This bacterial strain could not be identified by our systematic MALDI-TOF mass spectrometry screening on a Micro-Flex. This led to the sequencing of the 16S rRNA gene, which shows 97.83% sequence identity with Chryseobacterium kwangjuense strain KJ1R5 T , the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. Colonies are yellow, circular and 0.5-1 mm in diameter after cultivation at 28 °C for 24 h on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 28-37 °C (optimally at 28 °C). Strain 6021061333 T is Gram-negative, non-motile and strictly aerobic bacillus. It is catalase and oxidase positive. The 4,864,678 bp-long genome, composed of five contigs, has a G+C content of 38.86%. Out of the 4427 predicted genes, 4342 were protein-coding genes and 85 were RNAs. The major fatty acids are branched (13-methyl-tetradecanoic acid and 15-methyl-hexadecenoic acid). Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of the strain 6021061333 T against genomes of the type strains of related species ranged between 23.60 and 50.40% and between 79.31 and 93.06%, respectively. According to our taxonogenomics results, we propose the creation of Chryseobacterium phocaeense sp. nov. that contains the type strain 6021061333 T (= CSUR P2660, = CECT 9670)

Full-repertoire comparison of the microscopic objects composing the human gut microbiome with sequenced and cultured communities

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Draft genome and description of Cohnella massiliensis sp. nov., a new bacterial species isolated from the blood culture of a hemodialysis patient

International audienceStrain 6021052837T was isolated from the blood culture of a hemodialysis patient on Chocolat PolyViteX medium at 37 °C after 2 days of incubation. Colonies could not be identified by our systematic MALDI-TOF Mass Spectrometry screening. The16S rRNA gene sequencing showed that the strain had 96% sequence identity with Cohnella formosensis (Genbank accession number JN806384), the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The colonies cultivated on Columbia agar with 5% sheep blood medium at 37 °C after 24 h of incubation, are white pigmented, their size varied from 1.5 to 2 mm in diameter. Strain 6021052837T is an aerobic, Gram-negative, motile, spore forming rod, which cannot grow microaerophilically or under anaerobic conditions. The major fatty acids are branched saturated fatty acids: 14-methyl-pentadecanoic acid (34%) and 12-methyl-tetradecanoic acid (31%). The 6.328 Mb long genome, composed of 25 contigs, has a G+C content of 57.24%. Out of the 5710 predicted genes, 5646 were protein-coding genes and 64 were RNAs. A total of 3239 genes (57.37%) were assigned as putative function (by COGs) and 288 genes were identified as ORFans (5.1%). Average genomic identity of orthologous gene sequences (AGIOS) of strain 6021052837T against genomes of the type strains of related species ranged between 58.26 and 79.63%, respectively. According to our taxonogenomics results, we propose the creation of Cohnella massiliensis sp. nov. that contains the type strain 6021052837T (= CSUR P2659, =DSM103435)

Could the re-emerging practice of wild boar hunting linked to the recent economic crisis lead to new outbreaks of trichinellosis in Lebanon?

Background: Documented trichinellosis outbreaks in Lebanon date back to the late 19th century. The first published outbreaks were attributed to the consumption of wild boar meat, while those that followed incriminated pork. The practice of hunting wild boar is currently re-emerging in Lebanon given the recent economic crisis that has limited the purchase of livestock meat. Results: In Lebanon, at least 15 outbreaks of trichinellosis have been reported since 1870. We report an outbreak in January 2019, where five of the fifteen people present at a barbecue party were diagnosed with trichinellosis after wild boar meat consumption. Two subspecies of wild boar, Sus scrofa libycus and Sus scrofa scrofa, are commonly targeted by hunters. Hunters and consumers are sometimes unaware of the ineffectiveness of freezing meat and cooking over a wood fire to avoid trichinellosis. Unexpectedly, the National Center for Zoonosis Control receives every year 4 samples of wild boar meat, all free of Trichinella sp. larvae. Conclusion: Trichinellosis, a zoonosis typically unrecognized or undeclared, still represents a risk linked to the consumption of meat from wild animals, especially wild boar. Consumers, hunters, veterinarians, and butchers need to be further educated. Government regulation of wild boar hunting should be implemented to prevent further outbreaks

Emergence of Mycobacterium simiae: A retrospective study from a tertiary care center in Lebanon.

The objective of this study is to describe the clinical significance of Mycobacterium simiae at a major tertiary care center in Lebanon.This is a retrospective study of patients with positive cultures for M. simiae isolated between 2004 and 2016 at the American University of Beirut Medical Center.This study included 103 M. simiae isolates recovered from 51 patients. Their mean age was 62.7 years. The majority were males and smokers. Specimens were mostly from respiratory sources (97%). Common comorbidities included chronic lung disease (such as chronic obstructive pulmonary disease), solid tumor, systemic disease, and diabetes mellitus. Productive cough and dyspnea were the most common symptoms. Frequent radiographic findings were infiltrates and nodules on chest X-ray and nodules, infiltrates, and bronchiectasis on chest computed tomography scan. Among 18 tested isolates, 5.8% were resistant to clarithromycin, 11.7% to amikacin, and 70-100% to other antimicrobials. Out of 13 patients receiving early treatment, 5 noted improvement, one had recurrence of symptoms, two received alternative diagnosis, and five died. Two of those deaths were related to M. simiae. Common treatment regimens included clarithromycin in different combinations with trimethoprim-sulfamethoxazole, moxifloxacin, and amikacin. Moreover, clofazimine was used in only two patients whose isolates were resistant to all but one agent. Duration of treatment ranged from 6-24 months.In Lebanon, M. simiae is increasingly encountered with true infection rates of at least 47%. Furthermore, the prevalence of multidrug resistance among the Lebanese M. simiae isolates is very high limiting the treatment options

Developmental Cycle and Genome Analysis of ``Rubidus massiliensis,'' a New Vermamoeba vermiformis Pathogen

International audienceThe study of amoeba-associated Chlamydiae is a dynamic field in which new species are increasingly reported. In the present work, we characterized the developmental cycle and analyzed the genome of a new member of this group associated with Vermarnoeba vermiforrnis, we propose to name ``Rubidus rnassiliensis.'' This bacterium is well-adapted to its amoeba host and do not reside inside of inclusion vacuoles after phagocytosis. It has a developmental cycle typical of this family of bacteria, with a transition from condensed elementary bodies to hypodense replicative reticulate bodies. Multiplication occurs through binary fission of the reticulate bodies. The genome of ``R. massiliensis'' consists of a 2.8 Mbp chromosome and two plasmids (pRml, pRm2) consisting of 39,075 bp and 80,897 bp, respectively, a feature that is unique within this group. The Re-analysis of the Chlamydiales genomes including the one of ``R. massiliensis'' slightly modified the previous phylogeny of the tic gene encoding the ADP/ATP translocase. Our analysis suggested that the tic gene could have been transferred to plant and algal plastids before the transfer to Rickettsiales, and that this gene was probably duplicated several times

High Content Screening, a reliable system for Coxiella burnetii isolation from clinical samples

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