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Serratia sp. ATCC 39006 is a Gram-negative bacterium that has been used to study the function of phage defences, such as CRISPR–Cas, and phage counter-defence mechanisms. To expand our phage collection to study the phage–host interaction with Serratia sp. ATCC 39006, we isolated the T4-like myovirus LC53 in Ōtepoti Dunedin, Aotearoa New Zealand. Morphological, phenotypic and genomic characterization revealed that LC53 is virulent and similar to other Serratia , Erwinia and Kosakonia phages belonging to the genus Winklervirus. Using a transposon mutant library, we identified the host ompW gene as essential for phage infection, suggesting that it encodes the phage receptor. The genome of LC53 encodes all the characteristic T4-like core proteins involved in phage DNA replication and generation of viral particles. Furthermore, our bioinformatic analysis suggests that the transcriptional organization of LC53 is similar to that of Escherichia coli phage T4. Importantly, LC53 encodes 18 tRNAs, which likely compensate for differences in GC content between phage and host genomes. Overall, this study describes a newly isolated phage infecting Serratia sp. ATCC 39006 that expands the diversity of phages available to study phage–host interactions.

Contains fulltext : 290728.pdf (Publisher’s version ) (Closed access) BACKGROUND: Synkinesis is defined as involuntary movements accompanying by voluntary movements and can occur during the aftermath of peripheral facial palsy, causing functional, aesthetic and psychological problems in the patient. Botulinum toxin A (BTX-A) is frequently used as a safe and effective treatment; however, there is no standardized guideline for the use of BTX-A in synkinesis. The purpose of this article is to review and summarize studies about the BTX-A treatment of synkinesis in patients with a history of peripheral facial palsy; including given dosages, injection sites and time intervals between injections. MATERIALS AND METHODS: A multi-database systematic literature search was performed in October 2020 using the following databases: Pubmed, Embase, Medline, and The Cochrane Library. Two authors rated the methodological quality of the included studies independently using the 'Newcastle-Ottawa Quality Assessment Scale' for non-randomised studies' (NOS). RESULTS: Four-thousand-five-hundred-and-nineteen articles were found of which 34 studies met the inclusion criteria, in total comprising 1314 patients. Most studies were assessed to be of 'fair' to 'good' methodological quality. The Cohen's kappa (between author FJ and AS) was 0.78. Thirty-one studies investigated the reported dosage injected, 17 studies reported injection location and 17 studies investigated time intervals. A meta-analysis was performed for three studies comprising 106 patients, on the effects of BTX-A treatment on the Synkinesis Assessment Questionnaire (SAQ) scores. The mean difference was 11.599 (range 9.422-13.766), p

Background and Objective Ceftriaxone is a cornerstone antibiotic for critically ill children with severe infections. Despite its widespread use, information on the pharmacokinetics of ceftriaxone is lacking in this population. We aimed to determine ceftriaxone pharmacokinetics in critically ill children and to propose ceftriaxone dosing guidelines resulting in adequate target attainment using population pharmacokinetic modeling and simulation. Methods Critically ill children (aged 0–18 years) treated with intravenous ceftriaxone (100 mg/kg once daily, infused in 30 minutes) and a central or arterial line in place were eligible. Opportunistic blood sampling for total and unbound ceftriaxone concentrations was used. Population pharmacokinetic analysis was performed using non-linear mixed-effects modeling on NONMEM™ Version 7.4.3. Simulations were performed to select optimal doses using probability of target attainment for two pharmacokinetic targets of the minimum inhibitory concentration (MIC) reflecting the susceptibility of pathogens (f T > MIC 100% and fT > 4 × MIC 100%). Results Two hundred and five samples for total and 43 time-matched samples for unbound plasma ceftriaxone concentrations were collected from 45 patients, median age 2.5 (range 0.1–16.7) years. A two-compartment model with bodyweight as the co-variate for volume of distribution and clearance, and creatinine-based estimated glomerular filtration rate as an additional covariate for clearance, best described ceftriaxone pharmacokinetics. For a typical patient (2.5 years, 14 kg) with an estimated glomerular filtration rate of 80 mL/min/1.73 m2, the current 100-mg/kg once-daily dose results in a probability of target attainment of 96.8% and 60.8% for a MIC of 0.5 mg/L and 4 × MIC (2 mg/L), respectively, when using fT > MIC 100% as a target. For a 50-mg/kg twice-daily regimen, the probability of target attainment was 99.9% and 93.4%, respectively. Conclusions The current dosing regimen of ceftriaxone provides adequate exposure for susceptible pathogens in most critically ill children. In patients with an estimated glomerular filtration rate of > 80 mL/min/1.73 m2 or in areas with a high prevalence of less-susceptible pathogens (MIC ≥ 0.5 mg/L), a twice-daily dosing regimen of 50 mg/kg can be considered to improve target attainment. Clinical Trial Registration POPSICLE study (ClinicalTrials.gov, NCT03248349, registered 14 August, 2017), PERFORM study (ClinicalTrials.gov, NCT03502993, registered 19 April, 2018). Supplementary Information The online version contains supplementary material available at 10.1007/s40262-021-01035-9.

tRNAs in bacteriophage genomes are widespread across bacterial genera, but their exact function has remained unclear for more than 50 years. Multiple hypotheses have been proposed, with the most established being codon compensation, where codons more rarely used by the host but necessary for the phage are supplemented by tRNAs encoded by the phage. Here, we combine several observations and propose a new hypothesis that phage-encoded tRNAs are a means to counteract the tRNA-depleting strategies of the host to defend from viral infection. Based on mutational patterns of tRNA anticodon loops, we predict that phage tRNAs are insensitive to the host tRNAses. For tRNAs targeted in the anticodon itself, we observe phage counter-selection of targeted isoacceptor tRNAs, further supporting the hypothesis that phage tRNAs are selected to be insensitive to host anticodon nucleases. Importance The presence of tRNAs in phages was discovered more than 50 years ago and their function has been debated ever since. Here, we propose that phage tRNAs counteract the tRNAse activities of the host, which may represent a depletion strategy of essential cellular components to stop translation and thereby phage infection.

There has been an increased interest in the role of preoperative posterior tilt, as measured on lateral radiographs, on the outcomes of internal fixation of non-displaced femoral neck fractures (FNF). The goal was to assess the available evidence for this in the literature.PRISMA guidelines were followed. PubMed, Embase and Cochrane were searched on June 10th, 2020 for studies assessing the role of posterior tilt on outcomes of internal fixation of non-displaced FNF. Primary outcomes were non-union and fixation failure, avascular necrosis (AVN), treatment failure, and reoperation (excluding symptomatic hardware removal). Outcomes were reported in Odds Ratio (OR) with 95% confidence intervals [CI].Fourteen studies and 3729 patients were included (mean age 76 years, 72% female, mean follow-up 25 months). Moderate evidence was noted for the following: patients with greater preoperative posterior tilt had an increased risk of non-union and fixation failure (OR 2.4 [1.3 - 4.3]; p = 0.006), no increased risk of AVN (p = 0.550), an increased risk of treatment failure (OR 6.0 [2.2 - 15.9]; p0.001) and reoperation (OR 2.5 [1.4 - 4.4]; p = 0.002). Furthermore, a greater preoperative tilt of 9.0° [4.1° - 13.9°] for treatment failure and 6.1° [3.7° - 8.5°] (p0.001) for reoperation were noted in the unsuccessfully treated groups when compared to the successfully treated groups. Four studies found a threshold for posterior tilt ranging from 7° to 20° CONCLUSION: There is moderate evidence that patients with non-displaced FNF and greater tilt have an increased risk of unsuccessful outcomes following internal fixation. Older patients with a preoperative tilt of ≥20° might benefit from arthroplasty surgery, although studies assessing the optimal threshold are needed.

Protein cages, such as viruses, are well-defined biological nanostructures which are highly symmetrical and monodisperse. They are found in various shapes and sizes and can encapsulate or template non-native materials. Furthermore, the proteins can be chemically or genetically modified giving them new properties. For these reasons, these protein structures have received increasing attention in the field of polymer–protein hybrid materials over the past years, however, advances are still to be made. This Viewpoint highlights the different ways polymers and protein cages or their subunits have been combined to understand self-assembly and create functional materials.

CRISPR-Cas defence is a combination of adaptation to new invaders by spacer acquisition, and interference by targeted nuclease activity. While these processes have been studied on a population level, the individual cellular variability has remained unknown. Here, using a microfluidic device combined with time-lapse microscopy, we monitor invader clearance in a population of Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we show large cell-to-cell variability of clearance times, which originates from primed CRISPR adaptation. Faster growth and cell division, as well as higher levels of Cascade, increase the chance of clearance by interference. In contrast, faster growth is associated with decreased chances of clearance by priming. A mathematical model explains the experimental findings, and identifies Cascade binding to the mutated invader DNA, rather than spacer integration, as the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond to invading threats in a timely manner. We conjecture that CRISPR-Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.

CRISPR–Cas systems require discriminating self from non-self DNA during adaptation and interference. Yet, multiple cases have been reported of bacteria containing self-targeting spacers (STS), i.e. CRISPR spacers targeting protospacers on the same genome. STS has been suggested to reflect potential auto-immunity as an unwanted side effect of CRISPR–Cas defense, or a regulatory mechanism for gene expression. Here we investigated the incidence, distribution, and evasion of STS in over 100 000 bacterial genomes. We found STS in all CRISPR–Cas types and in one fifth of all CRISPR-carrying bacteria. Notably, up to 40% of I-B and I-F CRISPR–Cas systems contained STS. We observed that STS-containing genomes almost always carry a prophage and that STS map to prophage regions in more than half of the cases. Despite carrying STS, genetic deterioration of CRISPR–Cas systems appears to be rare, suggesting a level of escape from the potentially deleterious effects of STS by other mechanisms such as anti-CRISPR proteins and CRISPR target mutations. We propose a scenario where it is common to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition in type I systems, without detrimental autoimmunity effects as mechanisms of auto-immunity evasion create tolerance to STS-targeted prophages.

BACKGROUND The alpha-defensin lateral flow (ADLF) test is a new diagnostic tool for periprosthetic joint infection (PJI). Test accuracy for combined cohorts of hip and knee PJI has been reported to be good. AIM To assess the accuracy of the ADLF test for hip PJI, and to compare three different diagnostic criteria for PJI. METHODS A cohort of 52 patients was identified, with a painful or poorly functioning total hip- or hemi-arthroplasty, that underwent aspiration and a subsequent ADLF test. PJI was diagnosed with Musculoskeletal Infection Society (MSIS) criteria, and sensitivity, specificity, overall accuracy, positive predictive value and negative predictive value were calculated. Furthermore, test specifics were compared with the European Bone and Joint Infection Society (EBJIS) and 2018 International Consensus Meeting (ICM) criteria for PJI. RESULTS Using MSIS criteria, sensitivity was 100% (CI: 54%-100%) and specificity was 89% (CI: 76%-96%). Six true positives and 5 false positives were found, including one case of metallosis. Using EBJIS criteria, more PJIs were found (11 vs 6), sensitivity was lower (71%, CI: 42%-92%) and specificity was higher (97%, CI: 86%-100%), with 4 false negatives and one false positive result. Using 2018 ICM criteria, sensitivity was 91% (62%-100%) and specificity 100% (91%-100%). The results in this cohort are comparable to previous studies. CONCLUSION Overall test accuracy of the ADLF test was good in this cohort, with a sensitivity of 100% and specificity of 89%. Using different PJI definition criteria, sensitivity and specificity changed slightly but overall accuracy remained around 90%. Using the ADLF test in metallosis cases can result in false positive results and should be performed with caution.

Background Pharmacokinetics (PK) are severely altered in critically ill patients due to changes in volume of distribution (Vd) and/or drug clearance (Cl). This affects the target attainment of antibiotics in critically ill children. We aimed to identify gaps in current knowledge and to compare published PK parameters and target attainment of antibiotics in critically ill children to healthy children and critically ill adults. Methods Systematic literature search in PubMed, EMBASE and Web of Science. Articles were labelled as relevant when they included information on PK of antibiotics in critically ill, non-neonatal, pediatric patients. Extracted PK-parameters included Vd, Cl, (trough) concentrations, AUC, probability of target attainment, and elimination half-life. Results 50 relevant articles were identified. Studies focusing on vancomycin were most prevalent (17/50). Other studies included data on penicillins, cephalosporins, carbapenems and aminoglycosides, but data on ceftriaxone, ceftazidime, penicillin and metronidazole could not be found. Critically ill children generally show a higher Cl and larger Vd than healthy children and critically ill adults. Reduced target-attainment was described in critically ill children for multiple antibiotics, including amoxicillin, piperacillin, cefotaxime, vancomycin, gentamicin, teicoplanin, amikacin and daptomycin. 38/50 articles included information on both Vd and Cl, but a dosing advice was given in only 22 articles. Conclusion The majority of studies focus on agents where TDM is applied, while other antibiotics lack data altogether. The larger Vd and higher Cl in critically ill children might warrant a higher dose or extended infusions of antibiotics in this patient population to increase target-attainment. Studies frequently fail to provide a dosing advice for this patient population, even if the necessary information is available. Our study shows gaps in current knowledge and encourages future researchers to provide dosing advice for special populations whenever possible. Electronic supplementary material The online version of this article (10.1007/s40262-019-00813-w) contains supplementary material, which is available to authorized users.

Contains fulltext : 225119.pdf (Publisher’s version ) (Open Access) BACKGROUND: The Dutch Pediatric Formulary (DPF) increasingly bases its guidelines on model-based dosing simulations from pharmacokinetic studies. This resulted in nationwide dose changes for vancomycin, gentamicin, and tobramycin in 2015. OBJECTIVE: We aimed to evaluate target attainment of these altered, model-based doses in critically ill neonates and children. METHODS: This was a retrospective cohort study in neonatal intensive care unit (NICU) and pediatric ICU (PICU) patients receiving vancomycin, gentamicin, or tobramycin between January 2015 and March 2017 in two university hospitals. The first therapeutic drug monitoring concentration for each patient was collected, as was clinical and dosing information. Vancomycin and tobramycin target trough concentrations were 10-15 and ≤ 1 mg/L, respectively. Target gentamicin trough and peak concentrations were

Objectives Acute kidney injury (AKI) is common in critically ill children, but current biomarkers are suboptimal. Proenkephalin A 119–159 (PENK) is a promising new biomarker for AKI in adults, but pediatric data is lacking. We determined PENK reference intervals for healthy children, crucial for clinical implementation, and explored concentrations in critically ill infants aged under 1 year. Methods Observational cohort study in healthy infants and critically ill children aged 0–1 years. Reference values were determined using generalized additive models. Plasma PENK concentrations between healthy children and critically ill children with and without AKI, were compared using linear mixed modelling. The performance of PENK as AKI biomarker was compared to cystatin C (CysC) and β-trace protein (BTP) using receiver-operating-characteristic (ROC) analysis. Results PENK concentrations in 100 healthy infants were stable during the first year of life (median 517.3 pmol/L). Median PENK concentrations in 91 critically ill children, were significantly higher in those with AKI (n=40) (KDIGO Stage 1 507.9 pmol/L, Stage 2 704.0 pmol/L, Stage 3 930.5 pmol/L) than non-AKI patients (n=51, 432.2 pmol/L) (p Conclusions PENK reference values are much higher in young infants than adults, but clearly discriminate between children with and without AKI, with comparable or better performance than CysC and BTP. Our results illustrate the importance of establishing age-normalized reference values and indicate PENK as a promising pediatric AKI biomarker.

While CRISPR-Cas defence mechanisms have been studied on a population level, their temporal dynamics and variability in indi- vidual cells have remained unknown. Using a microfluidic device, time-lapse microscopy and mathematical modelling, we studied invader clearance in Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distri- bution of clearance times. In contrast, for invaders with escaping PAM mutations we found large cell-to-cell variability, which origi- nates from primed CRISPR adaptation. Faster growth and cell divi- sion and higher levels of Cascade increase the chance of clearance by interference, while slower growth is associated with increased chances of clearance by priming. Our findings suggest that Cas- cade binding to the mutated invader DNA, rather than spacer inte- gration, is the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond quickly to invading threats. We conjecture that CRISPR-Cas dynamics and heterogene- ity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.

Background Cefotaxime is frequently used in critically ill children, however pharmacokinetic (PK) studies to support adequate dosing in this patient population are limited. Objectives To characterize cefotaxime PK in critically ill children and evaluate exposures achieved by current and alternative dosing regimens. Methods Children (0–18 years) admitted to the paediatric ICU, receiving intravenous cefotaxime (100–150 mg/kg/day, interval 6–8 h) were included (Clinicaltrials.gov NCT03248349). Total plasma cefotaxime concentrations were measured on multiple study days. Population-PK analysis was performed using nonlinear mixed effects modelling (NONMEM™). Dose evaluations were performed using typical patients across the paediatric age range and target attainment was determined for MICs of 0.5, 2 and 4 mg/L. Results 479 cefotaxime plasma concentrations from 52 children (median age 1.6, range 0.03–17.7 years) were used to describe cefotaxime PK. We describe a two-compartment structural model with interindividual variability, including bodyweight as covariate for volume of distribution and clearance. Model predicted exposure for 150 mg/kg/day (current dose) showed trough concentrations 4 years of age. The maximum cefotaxime doses (200 mg/kg/day, interval 6 h) proved adequate for MICs ≤0.5 mg/L across the whole age range. Similar daily doses with increased frequency (interval 4 h) covered MICs up to 2 mg/L, while a loading dose followed by continuous infusion regimens are needed to adequately treat MICs of 4 mg/L. Conclusions Higher cefotaxime doses are required for adequate exposure for most pathogens in critically ill children. A higher dose frequency or continuous infusion is advisable to improve target attainment for intermediately susceptible pathogens.

The CRISPR-Cas type III-E RNA-targeting effector complex gRAMP/Cas7-11 is associated with a caspase-like protein (TPR-CHAT/Csx29) to form Craspase (CRISPR-guided caspase). Here, we use cryo–electron microscopy snapshots of Craspase to explain its target RNA cleavage and protease activation mechanisms. Target-guide pairing extending into the 5′ region of the guide RNA displaces a gating loop in gRAMP, which triggers an extensive conformational relay that allosterically aligns the protease catalytic dyad and opens an amino acid side-chain–binding pocket. We further define Csx30 as the endogenous protein substrate that is site-specifically proteolyzed by RNA-activated Craspase. This protease activity is switched off by target RNA cleavage by gRAMP and is not activated by RNA targets containing a matching protospacer flanking sequence. We thus conclude that Craspase is a target RNA–activated protease with self-regulatory capacity.