Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.

BACKGROUND: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS). RESULTS: We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently. CONCLUSION: Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.

Description of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov.

We present polyphasic taxonomic data to demonstrate that strain 125703-2019T, a human blood isolate, represents a novel species within the genus Pseudoclavibacter, and to reclassify the illegitimate Zimmermannella alba Lin et al., 2004 as Pseudoclavibacter albus comb. nov. Upon primary isolation, strain 125703-2019T could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that it belonged to the genus Pseudoclavibacter. Average nucleotide identity and digital DNA-DNA hybridisation analyses confirmed that it represented a novel species within this genus. A detailed physiological characterisation yielded differential tests between the novel species and its nearest neighbor taxa, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify this strain into the novel species Pseudoclavibacter triregionum sp. nov., with strain 125703-2019T (= R-76471T, LMG 31777T, CCUG 74796T) as the type strain. The whole-genome assembly of strain 125703-2019T has a size of 2.4 Mb and a G + C content of 72.74%. A Pseudoclavibacter pangenome analysis revealed that 667 gene clusters were exclusively present in strain 125703-2019T. While these gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that explained the occurrence of this species in human infection. Finally, several phylogenetic and phylogenomic analyses demonstrated that the genus Pseudoclavibacter is polyphyletic with Pseudoclavibacter soli and Pseudoclavibacter caeni representing a unique and deeply branching line of descent within the family Microbacteriaceae. We therefore also propose to reclassify both species into the novel genus Caespitibacter gen. nov. as Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov., respectively, and with C. soli comb. nov. as the type species.

Use of Cefiderocol in the Management of Children With Infection or Colonization With Multi-drug Resistant Gram-negative Bacteria: A Retrospective, Single-center Case Series.

Cefiderocol, a novel siderophore cephalosporin, represents a treatment option for infections with multidrug-resistant Gram-negative bacteria, of which rates are rising worldwide. Clinical data on its use in children is limited. In our pediatric case series, the largest reported to date, cefiderocol seems safe and well tolerated, with more favorable clinical outcomes when compared to the literature reviewing adult cases.

Home visits to identify the roles lifestyle and stress play in families of children with obesity.

One-sixth of Swiss children are affected by overweight, and despite the implementation of an evidence-based multiprofessional approach, there has only been moderate therapeutic success. An unfavourable home environment and psychosocial stresses on the family may impede lifestyle changes. This longitudinal observational study included children with obesity (body mass index [BMI] ≥97th percentile [P.]) or overweight (BMI ≥ 90th P.) with a comorbidity, and who were participating in a regional 12-month multiprofessional group programme (MGP). Two health professionals routinely visited the family home at baseline (T0) to identify obesogenic environmental factors and psychosocial stress using an observation and question checklist and the Heidelberger stress scale (HSS). At T0 and after an 8-month intensive intervention phase (T1), the BMI standard deviation score (BMI-SDS) and its associations with the environmental and psychosocial factors were assessed. Twenty-eight children (17 male) met the criteria for participation in the MGP. At T0, age was 11.2 ± 1.71 years, BMI 28.1 ± 4.7 kg/m2 and BMI-SDS 2.9 ± 0.8, means ±SD. By T1, the mean BMI-SDS had decreased significantly, by -0.11 (p < .05). The stress scores (30.46 ± 17.8) were elevated and the subcategories of financial and social stress showed a trend towards predicting BMI or BMI-SDS at T0 and T1, but none of the other supposed obesogenic risk factors significantly predicted weight status. Conducting home visits allowed health professionals to identify obesity-promoting home conditions and, more importantly, otherwise undisclosed high psychosocial stress and resource limitations in families that impacted the children's obesity before and after the MGP intervention.

Association between perioperative prophylaxis with cefuroxime plus metronidazole or amoxicillin/clavulanic acid and surgical site infections in paediatric uncomplicated appendectomy: a Swiss retrospective cohort study.

OBJECTIVE: We aimed to evaluate the association between post-appendectomy SSI rates and the two most commonly used regimens for perioperative antimicrobial prophylaxis in Swiss children. METHODS: We conducted a retrospective cohort study, analysing data from the Swiss national SSI surveillance database with a study period from 2014 to 2018. All hospitals undertaking paediatric appendectomies in Switzerland participate in the surveillance. We compared the cumulative incidence and odds of post-appendectomy SSI within 30 days of surgery in children ≤ 16 years of age undergoing appendectomy for uncomplicated appendicitis and receiving perioperative antimicrobial prophylaxis with cefuroxime plus metronidazole or with amoxicillin/clavulanic acid using multivariable adjusted logistic regression and propensity-score matching. RESULTS: A total of 6207 cases were recorded in the study time frame. Overall SSI cumulative incidence was 1.9% (n = 119). 4256 children (54.9% male, median (IQR) age 12 [10, 14] years) received either cefuroxime plus metronidazole (n = 2348, 53.8% male) or amoxicillin/clavulanic acid (n = 1491, 57.0% male). SSI cumulative incidence was 1.1% (25/2348) among children receiving cefuroxime plus metronidazole and 2.8% (42/1491, p < 0.001) when receiving amoxicillin/clavulanic acid. The administration of cefuroxime plus metronidazole was associated with statistically significantly lower SSI odds compared to amoxicillin/clavulanic acid (aOR 0.35, 95%CI [0.20, 0.61], p < 0.001), and this was confirmed upon propensity-score matching. CONCLUSION: We found lower odds of post-appendectomy SSI in children receiving cefuroxime plus metronidazole compared to amoxicillin/clavulanic acid. Treating amoxicillin/clavulanic acid as the baseline, only 55 children need to receive cefuroxime plus metronidazole perioperative prophylaxis to avert one SSI. Existing guidelines recommending amoxicillin/clavulanic acid may need to be revised. Trial registration ISRCTN47727811, registered retrospectively.

Neonates with SARS-CoV-2 infection: spectrum of disease from a prospective nationwide observational cohort study.

BACKGROUND: Coronavirus disease 2019 (COVID-19) can be more severe in infants than in older children. To date, only a few case series have reported data on neonates with COVID-19, including mostly asymptomatic neonates who were tested because of exposure to maternal SARS-CoV-2 infection. This study summarises nationwide epidemiological data, clinical characteristics, treatment and outcomes of neonates presenting with symptomatic SARS-CoV-2 infection. METHODS: Data were prospectively collected through the Swiss Paediatric Surveillance Unit from hospitalised neonates with laboratory-confirmed SARS-CoV-2 infection (positive polymerase chain reaction on a respiratory sample) from 1 March 2020 to 31 September 2021. All 29 paediatric hospitals in Switzerland reported cases. RESULTS: In total, 73 neonates were included; 7 (10%) were preterm. The median age at presentation was 17 days (interquartile range [IQR] 11-23); 40 (55%) were female. The majority of neonates (64, 88%) were admitted from home. Nine (12%) had a pre-existing medical condition. Overall, the most common symptom recorded was fever in 52 (71%), followed by rhinorrhoea or nasal congestion in 32 (44%) and respiratory distress in 19 (26%). Twenty (27%) neonates presented with fever without a source. Seven (10%) neonates were admitted to an intensive care unit (5 for respiratory failure and 2 for monitoring). One (1%) neonate required inotropic support. The median length of hospital stay in term neonates was 4 days (IQR 3-5). Two (3%) were treated with corticosteroids and 1 (1%) with remdesivir. In total, 60 (82%) neonates had contact with a known or suspected SARS-CoV-2 index case. All of the 71 neonates for whom data were available were discharged to their homes without symptoms. CONCLUSION: In neonates, COVID-19 mainly presents with fever, and symptoms of upper and lower respiratory tract infection. The clinical course is mostly mild, requiring a short period of hospitalisation. COVID-19 needs to be added as a differential diagnosis in neonates who present with fever without a source. However, the presence of SARS-CoV-2 should not deter from the search for a serious bacterial infection. Further data from surveillance studies are needed to better understand COVID-19 in neonates, guide therapy and to evaluate whether the clinical spectrum is changing with new SARS-CoV-2 variants.

Impact of compulsory admission on treatment and outcome: A propensity score matched analysis.

BACKGROUND: Despite multiple ethical issues and little evidence of their efficacy, compulsory admission and treatment are still common psychiatric practice. Therefore, we aimed to assess potential differences in treatment and outcome between voluntarily and compulsorily admitted patients. METHODS: We extracted clinical data from inpatients treated in an academic hospital in Zurich, Switzerland between January 1, 2013 and December 31, 2019. Observation time started upon the first admission and ended after a one-year follow-up after the last discharge. Several sociodemographic and clinical characteristics, including Health of the Nation Outcome Scales (HoNOS) scores, were retrospectively obtained. We then identified risk factors of compulsory admission using logistic regression in order to perform a widely balanced propensity score matching. Altogether, we compared 4,570 compulsorily and 4,570 voluntarily admitted propensity score-matched patients. Multiple differences between these groups concerning received treatment, coercive measures, clinical parameters, and service use outcomes were detected. RESULTS: Upon discharge, compulsorily admitted patients reached a similar HoNOS sum score in a significantly shorter duration of treatment. They were more often admitted for crisis interventions, were prescribed less pharmacologic treatment, and received fewer therapies. During the follow-up, voluntarily admitted patients were readmitted more often, while the time to readmission did not differ. CONCLUSIONS: Under narrowly set circumstances, compulsory admissions might be helpful to avert and relieve exacerbations of severe psychiatric disorders.

Utility and validity of the Brief Psychiatric Rating Scale (BPRS) as a transdiagnostic scale.

The Brief Psychiatric Rating Scale (BPRS) was originally conceived to assess psychopathology in several psychiatric disorders, making it an appropriate candidate to be used as a transdiagnostic instrument. We analyzed the utility and validity of the BPRS in a diagnostically heterogeneous sample of 600 psychiatric inpatients. As a comparator, we chose the mini-ICF-APP, a scale used to measure functioning and impairment across the diagnostic spectrum. Both scales had good internal consistency. The BPRS and the mini-ICF-APP showed a moderate correlation, with good levels of agreement. We were able to identify general symptoms present across the diagnostic spectrum, influencing severity and a cluster of symptoms specific for each diagnosis. Our results show the utility and validity of the BPRS as a transdiagnostic assessment tool that could easily be introduced in routine clinical work.

Posttreatment Lyme Disease Syndrome-What It Might Be and What It Is Not.

Lyme disease is a multisystem disease caused by Borrelia burgdorferi infection and accounts for well-defined manifestations, appearing either at an early or late stage. Appropriate antibiotic therapy generally leads to a favorable outcome. Still, unspecific persisting symptoms such as fatigue, myalgia, arthralgia or cognitive dysfunction are reported by several patients months to years after adequate treatment. Their underlying pathophysiologic mechanism is unclear. However, there is no evidence for microbiological persistence in these cases and attempts to resolve the symptoms by repeated or prolonged antibiotic treatment have not been convincingly successful, but they may rather be harmful. To narrow down the controversially handled entity of posttreatment Lyme disease syndrome (PTLDS) and to avoid overdiagnosis and overtreatment, case definitions have been proposed, acknowledging PTLDS as a complex of nonspecific, subjective symptoms, which are neither caused by ongoing infection nor by any other identifiable disease. PTLDS is mainly a diagnosis of exclusion and requires careful evaluation of differential diagnosis followed by counseling about optimal management in light of missing specific therapeutic options.

MIS-C-Implications for the Pediatric Surgeon: An Algorithm for Differential Diagnostic Considerations.

BACKGROUND: multisystem inflammatory syndrome in children (MIS-C) is a new disease associated with a recent infection with severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Affected children can present predominantly with abdominal symptoms, fever and high inflammatory parameters that might lead to a consult by the pediatric surgeon and an indication for surgery. METHODS: clinical data of three patients with MIS-C that underwent surgery were collected. Histopathological analysis of the appendix was performed. RESULTS: we present the clinical course of three children with fever, abdominal pain and vomiting for several days. Clinical examination and highly elevated inflammation markers led to indication for laparoscopy; appendectomy was performed in two patients. Because of intraoperative findings or due to lack of postoperative improvement, all patients were reevaluated and tested positive for MIS-C associated laboratory parameters and were subsequently treated with corticosteroids, intravenous immunoglobulins, acetyl salicylic acid and/or light molecular weight heparin. CONCLUSIONS: we discuss the implications of MIS-C as a new differential diagnosis and stress the importance of assessing the previous medical history, identifying patterns of symptoms and critically surveilling the clinical course. We implemented an algorithm for pediatric surgeons to consider MIS-C as a differential diagnosis for acute abdomen that can be integrated into the surgical workflow.

X-Linked Lymphoproliferative Disease Mimicking Multisystem Inflammatory Syndrome in Children-A Case Report.

Most children with a SARS-CoV-2 infection are asymptomatic or exhibit mild symptoms. However, a small number of children develop features of substantial inflammation temporarily related to the COVID-19 also called multisystem inflammatory syndrome in children (MIS-C) or pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS), clinically similar to Kawasaki disease, toxic shock syndrome and hemophagocytic lymphohistiocytosis (HLH). It is well-known that genetic pre-disposition plays an important role in virally-triggered diseases such as Epstein-Barr virus (EBV)-associated HLH, while this has not yet been established for patients with MIS-C. Here we describe a male patient fulfilling the diagnostic criteria of MIS-C, who was initially treated according to current consensus guidelines. Presence of hypofibrinogenemia, normal lymphocyte counts and C-reactive protein, but substantial hyperferritinemia distinguish this patient from others with MIS-C. The clinical course following initial presentation with acute respiratory distress syndrome was marked by fatal liver failure in the context of EBV-associated HLH despite treatment with steroids, intravenous immunoglobulins, interleukin (IL)-1 receptor blockade and eventually HLH-directed treatment. X-linked lymphoproliferative disease type 1 (XLP1), a subtype of primary HLH was diagnosed in this patient post-mortem. This case report highlights the importance of including HLH in the differential diagnosis in MIS-C with severe disease course to allow specific, risk-adapted treatment and genetic counseling.

Sleep recalibrates homeostatic and associative synaptic plasticity in the human cortex.

Sleep is ubiquitous in animals and humans, but its function remains to be further determined. The synaptic homeostasis hypothesis of sleep-wake regulation proposes a homeostatic increase in net synaptic strength and cortical excitability along with decreased inducibility of associative synaptic long-term potentiation (LTP) due to saturation after sleep deprivation. Here we use electrophysiological, behavioural and molecular indices to non-invasively study net synaptic strength and LTP-like plasticity in humans after sleep and sleep deprivation. We demonstrate indices of increased net synaptic strength (TMS intensity to elicit a predefined amplitude of motor-evoked potential and EEG theta activity) and decreased LTP-like plasticity (paired associative stimulation induced change in motor-evoked potential and memory formation) after sleep deprivation. Changes in plasma BDNF are identified as a potential mechanism. Our study indicates that sleep recalibrates homeostatic and associative synaptic plasticity, believed to be the neural basis for adaptive behaviour, in humans.