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This work was funded by Sidra Internal Research Funding Grant [Project ID: SIRF_200040] to AP-L, and a Qatar University Grant [No. QUUG-BRC-2017-2] to NOE.

Whole-genome sequencing was used to characterize carbapenemase-producing Enterobacterales (CPE) strains recovered from rectal screening swab samples obtained from children at a tertiary-care pediatric hospital in Qatar during a 3-year period. A total of 72 CPE isolates recovered from 61 fecal carriers were characterized. Escherichia coli (47 isolates [65.3%]) and Klebsiella pneumoniae (22 isolates [30.6%]) were the most common species identified. High levels of genetic diversity were observed for both species. These 72 isolates produced 78 carbapenemases, characterized as either NDM-type (41 enzymes [52.6%]) or OXA-48-type (37 enzymes [47.4%]). NDM-5 (24 enzymes [30.8%]), NDM-1 (15 enzymes [19.2%]), and OXA-181 (15 enzymes [19.2%]) were the most common variants detected within each type. Twenty-three NDM producers exhibited difficult-to-treat resistance, compared with only 2 of the OXA-48 producers. Multiple comorbidities were identified in 88.5% of the patients, whereas recent travel history to countries in which CPE are endemic was documented for 57.4% of the patients. All 9 blaOXA-48-type-gene-containing E. coli sequence type 38 (ST38) strains were isolated from patients without international travel history. The mean quarterly incidence of fecal carriage decreased more than 6-fold after the implementation of coronavirus disease 2019 (COVID-19)-related international travel restrictions in Qatar in mid-March 2020. Our data suggest that NDM-type and OXA-48-type carbapenemases expressed by a large diversity of E. coli and K. pneumoniae genotypes are largely dominant in the pediatric population of Qatar. Although our data indicate successful local expansion of E. coli ST38 strains harboring blaOXA-244 genes, at least within health care settings, blaOXA-48-type and blaNDM-type genes appear to have been mainly introduced sporadically by asymptomatic carriers who visited or received health care in some nearby countries in which the genes are endemic. IMPORTANCE To the best of our knowledge, this is the first study addressing the molecular characteristics of CPE in a pediatric population in Qatar using whole-genome sequencing. Since several countries in the Arabian Peninsula share relatively similar demographic patterns and international links, it is plausible that the molecular characteristics of CPE in children, at least in the middle and eastern parts of the region, are similar to those observed in our study.

Lower levels of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) in the nasal epithelium of children may be related to a lower incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, compared to adults. However, no direct evidence is available to support this hypothesis. In this study, we compared the transcript levels of ACE2 and TMPRSS2 in nasopharyngeal swab samples (n = 234) from children and adult family members within SARS-CoV-2-exposed families and assessed the association with SARS-CoV-2 infection status. Transcript levels for ACE2, but not TMPRSS2, were higher in adults than in children (n = 129 adults and 105 children; P

Nanocomposite generators convert mechanical energy into electrical energy and are attractive low-power solutions for self-powered sensors and wearables. Homogeneous dispersion, high concentration, and orientation of the embedded filler strategies have been assumed to maximize the voltage output in nanocomposite generators. This work contrast these assumptions by studying the dominance of the interphase in low filler concentrations (i10%) and random dispersions in a ZnO/PDMS nanocomposite generator with high peak-to-peak voltage generation capabilities ( ≈ 150 V). The interphase in the nanocomposite was studied by the analysis of the random dispersion of the nanocomposite through the estimation of the effective volume fraction ( ϕ a g g ) which allowed us to identify three levels of interaction: individual interphases, interacting interphases, and overlapping between NPs and interphases. The interacting interphase is responsible here for the high generated voltage. In addition, the impact of the interphase was studied by applying lumped element (LE) and interphasial power-law (IPL) models that capture the measured voltages and the electromechanical film properties. The obtained results justify that engineering of interphases could be a design strategy for high voltage generation.

Rhodotorula mucilaginosa is an opportunistic fungal pathogen of public health importance. We present the draft genome sequence of an isolate (Rhodo3571) cultured from an immunocompetent patient. The isolate is similar to other R. mucilaginosa genomes in the NCBI database. Presented here are the genome assembly and its comparison to other reference genomes.

The pervasive use of portable electronic devices, powered from rechargeable batteries, represents a significant portion of the electricity consumption in the world. A sustainable and alternative energy source for these devices would require unconventional power sources, such as harvesting kinetic/potential energy from mechanical vibrations, ultrasound waves, and biomechanical motion, to name a few. Piezoelectric materials transform mechanical deformation into electric fields or, conversely, external electric fields into mechanical motion. Therefore, accurate prediction of elastic and piezoelectric properties of materials, from the atomic structure and composition, is essential for studying and optimizing new piezogenerators. Here, we demonstrate the application of harmonic-covalent and reactive force fields (FF), Dreiding and ReaxFF, respectively, coupled to the polarizable charge equilibration (PQEq) model for predicting the elastic moduli and piezoelectric response of crystalline zinc oxide (ZnO) and polyvinylidene difluoride (PVDF). Furthermore, we parametrized the ReaxFF atomic interactions for Zn-F in order to characterize the interfacial effects in hybrid PVDF matrices with embedded ZnO nanoparticles (NPs). We capture the nonlinear piezoelectric behavior of the PVDF-ZnO system at different ZnO concentrations and the enhanced response that was recently observed experimentally, between 5 and 7 wt % ZnO concentrations. From our simulation results, we demonstrate that the origin of this enhancement is due to an increase in the total atomic stress distribution at the interface between the two materials. This result provides valuable insight into the design of new and improved piezoelectric nanogenerators and demonstrates the practical value of these first-principles based modeling methods in materials science.

Antibiotic resistance is a growing public health problem globally, incurring health and cost burdens. The occurrence of antibiotic-resistant bacterial infections has increased significantly over the years. Gram-negative bacteria display the broadest resistance range, with bacterial species expressing extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases. All carbapenem-resistant Enterobacteriaceae (CRE) isolates from pediatric urinary tract infections (UTIs) between October 2015 and November 2019 (n = 30). All isolates underwent antimicrobial resistance phenotypic testing using the Phoenix NMIC/ID-5 panel, and carbapenemase production was confirmed using the NG-Test CARBA 5 assay. Whole-genome sequencing was performed on the CREs. The sequence type was identified using the Achtman multi-locus sequence typing scheme, and antimicrobial resistance markers were identified using ResFinder and the CARD database. The most common pathogens causing CRE UTIs were E. coli (63.3%) and K. pneumoniae (30%). The most common carbapenemases produced were OXA-48-like enzymes (46.6%) and NDM enzymes (40%). Additionally, one E. coli harbored IMP-26, and two K. pneumoniae possessed mutations in ompK37 and/or ompK36. Lastly, one E. coli had a mutation in the marA porin and efflux pump regulator. The findings highlight the difference in CRE epidemiology in the pediatric population compared to Qatar’s adult population, where NDM carbapenemases are more common.

What you need to know A previously healthy and fully vaccinated (including 13-valent pneumococcal conjugate vaccine) 22 month old boy is brought to the emergency department because of a 12 hour history of high fever (up to 40°C). He had had low grade fever, runny nose, cough, and decreased oral intake for the past two days. On examination, he did not look severely ill but was febrile (38.3°C). His respiratory rate was 45 breaths/minute (normal range 25-40 breaths/min at 18-24 months old), heart rate was 140 beats/minute (normal range 98-135 beats/min at 18-24 months), and blood oxygen level was 95%. Although breath sounds were not decreased, some bibasilar crackles were noted on chest auscultation. A chest x ray was interpreted as having bilateral peribronchial infiltrates and haziness in the right lower lobe. To aide their decision whether to initiate antibiotic therapy, clinicians requested blood tests, which revealed a white blood cell count of 22.5×109/L (60.0% neutrophils), a CRP of 30 mg/L (normal

There is accumulating evidence that the lower levels of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) in the nasal epithelium of children may be related to a lower incidence of COVID-19 compared to adults. However, no direct evidence is available to support this hypothesis. In this study, we compared the transcript levels of ACE2 and TMPRSS2 in nasopharyngeal swabs (n=207) from children and adult members within COVID-19-exposed families and assessed their association with SARS-CoV-2 infection status. The expression of both genes was higher in adults compared to the children (n=115 adults and 92 children, p

Background Multisystem Inflammatory Syndrome in Children (MIS-C) is a severe complication of coronavirus disease 2019 (COVID-19) in children, which is increasingly being reported worldwide. Here we report the first case series of 7 children diagnosed with MIS-C in Qatar. Methods Clinical features and outcomes of COVID-19 positive patients admitted to Sidra Medicine, Qatar from June to October 2020, who met the WHO case definition for MIS-C were reviewed. Results The mean age in our case series was 5.6 years, of which 71.4% were males. All patients were previously healthy but had a history of COVID-19 infection. Fever, rash, vomiting and abdominal pain were the most common symptoms (70–100%). The average hospitalization was 12.9 days with no case fatalities. Laboratory findings included lymphopenia and thrombocytopenia in most patients, as well as evidence of coagulopathy and elevated inflammatory markers such as C-reactive protein, ferritin and procalcitonin. Many patients (71.4%) required inotropic support in intensive care, while only one required respiratory support. Although all patients had elevated cardiac biomarkers, cardiovascular involvement was observed in 42.9% of patients with one patient developing a giant coronary aneurysm. All patients received intravenous immunoglobulin (IVIG) and 86% of patients received corticosteroids, with two patients requiring treatment with IL-1 inhibitors. Conclusions Our report is one of the first reports on MIS-C from Asia. Although clinical features and outcomes are not significantly different from those reported elsewhere, lack of case fatalities in our cohort may indicate that early recognition and prompt medical attention is necessary for a favorable outcome in MIS-C.

Peritoneal dialysis (PD)–associated peritonitis constitutes a major complication associated with the procedure. PD-associated peritonitis caused by nontuberculous mycobacteria, usually as a result of an infection related to the PD catheter, has been reported in adults and is associated with significant complications and poor outcome. The management of PD-associated peritonitis caused by Mycobacterium abscessus is particularly challenging because this species is resistant to many antimicrobials commonly used to treat mycobacterial species. We present here the second reported case of PD-associated peritonitis caused by M. abscessus in children. Our patient was a 9-year-old boy with end-stage renal disease (ESRD) who presented with suspected peritonitis, and his PD fluid cultures eventually grew M. abscessus. The patient received a 3-week course of triple therapy with clarithromycin, amikacin, and meropenem in addition to PD catheter removal. The infection completely resolved even though a susceptibility report at the end of treatment revealed that the isolate was resistant to clarithromycin and had decreased susceptibility to carbapenems. Our observations suggest that PD catheter removal is important in PD-associated peritonitis caused by M. abscessus in children and that more studies are needed to define the optimal length of treatment.

Introduction: Although extended-spectrum β-lactamase (ESBL)-producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited. Aim: To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar. Methods: Whole-genome sequencing (WGS) was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018. Results: A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae. Non-susceptibility rates to non-beta-lactam antibiotics for both species were: 18.1% and 30.1% for gentamicin, 0.8% and 4.1% for amikacin, 41.3% and 41.1% for ciprofloxacin, and 65.8% and 76.1% for co-trimoxazole. The most common sequence types (ST) were ST131 (16.9%), ST38 and ST10 (8.2 % each) in E. coli and ST307 (9.7%), ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBL were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other beta lactamases, TEM-1B and OXA-1 were co-produced in 41% and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes co-carried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only 2 of 57 isolates harboring aac(6’)-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae. Conclusions: Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited given the frequent co-production of OXA-1 and TEM-1B enzymes and co-resistance to antibiotic classes other than β-lactams.

To circumvent the limited availability of RNA extraction reagents, we aimed to develop a protocol for direct RT-qPCR to detect SARS-CoV-2 in nasopharyngeal swabs without RNA extraction. Nasopharyngeal specimens positive for SARS-CoV-2 and other coronaviruses collected in universal viral transport (UVT) medium were pre-processed by several commercial and laboratory-developed methods and tested by RT-qPCR assays without RNA extraction using different RT-qPCR master mixes. The results were compared to that of standard approach that involves RNA extraction. Incubation of specimens at 65°C for 10 minutes along with the use of TaqPath™ 1-Step RT-qPCR Master Mix provides higher analytical sensitivity for detection of SARS-CoV-2 RNA than many other conditions tested. The optimized direct RT-qPCR approach demonstrated a limit of detection of 6.6x103 copy/ml and high reproducibility (co-efficient of variation = 1.2%). In 132 nasopharyngeal specimens submitted for SARS-CoV-2 testing, the sensitivity, specificity and accuracy of our optimized approach were 95%, 99% and 98.5%, respectively, with reference to the standard approach. Also, the RT-qPCR CT values obtained by the two methods were positively correlated (Pearson correlation coefficient r = 0.6971, p = 0.0013). The rate of PCR inhibition by the direct approach was 8% compared to 9% by the standard approach. Our simple approach to detect SARS-CoV-2 RNA by direct RT-qPCR may help laboratories continue testing for the virus despite reagent shortages or expand their testing capacity in resource limited settings.

—Reverberation time is an important room acoustic parameter, useful for many acoustic signal processing applications. Most of the existing work on blind reverberation time estimation focuses on the single-channel case. However, the recent developments and interest on immersive audio have brought to the market a number of spherical microphone arrays, together with the usage of ambisonics as a standard spatial audio convention. This work presents a novel blind reverberation time estimation method, which specifically targets ambisonic recordings, a field that remained unexplored to the best of our knowledge. Experimental validation on a synthetic reverberant dataset shows that the proposed algorithm outperforms state-of-he-art methods under most evaluation criteria in low noise conditions.

Introduction Although extended-spectrum β-lactamase (ESBL)–producing Enterobacterales are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited. Aim To determine the molecular characteristics of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the pediatric population of Qatar. Methods Whole-genome sequencing was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018. Results A total of 327 ESBL producers were sequenced: 254 E. coli and 73 K. pneumoniae. Non-susceptibility rates to non-β-lactam antibiotics for both species were 18.1 and 30.1% for gentamicin, 0.8 and 4.1% for amikacin, 41.3 and 41.1% for ciprofloxacin, and 65.8 and 76.1% for cotrimoxazole. The most common sequence types (STs) were ST131 (16.9%), ST38 and ST10 (8.2% each) in E. coli and ST307 (9.7%), and ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBLs were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Among other β-lactamases, TEM-1B and OXA-1 were coproduced in 41 and 19.6% of isolates. The most common plasmid-mediated quinolone resistance genes cocarried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harbored genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only two of 57 isolates harboring aac(6′)-Ib-cr were non-susceptible to amikacin. Chromosomal mutations in genes encoding DNA gyrase and topoisomerase IV enzymes were detected in 96.2% fluoroquinolone-non-susceptible E. coli and 26.7% fluoroquinolone-non-susceptible K. pneumoniae. Conclusion Our data show that CTX-M enzymes are largely the most prevalent ESBLs in children in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited, given the frequent coproduction of OXA-1 and TEM-1B enzymes and coresistance to antibiotic classes other than β-lactams.

The etiology of central nervous system (CNS) infections such as meningitis and encephalitis remains unknown in a large proportion of cases partly because the diversity of pathogens that may cause CNS infections greatly outnumber available test methods. We developed a metagenomic next generation sequencing (mNGS)-based approach for broad-range detection of pathogens associated with CNS infections suitable for application in the acute care hospital setting. The analytical sensitivity of mNGS performed on an Illumina MiSeq was assessed using simulated cerebrospinal fluid (CSF) specimens (n = 9). mNGS data were then used as a training dataset to optimize a bioinformatics workflow based on the IDseq pipeline. For clinical validation, residual CSF specimens (n = 74) from patients with suspected CNS infections previously tested by culture and/or PCR, were analyzed by mNGS. In simulated specimens, the NGS reads aligned to pathogen genomes in IDseq were correlated to qPCR CT values for the respective pathogens (R = 0.96; p

Klebsiella oxytoca is an opportunistic human pathogen causing nosocomial infection. We report the draft genome of an extended-spectrum β-lactamase-producing K. oxytoca isolate harboring an mcr-9 gene, a recently discovered colistin resistance analog, from Qatar. The genome statistics, along with the sequence type and resistance mechanisms, are predicted for the assembled genome.

Background: Although extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are a public health problem in the Arabian Peninsula, data on the molecular characteristic of their antimicrobial resistance determinants in children is limited.Methods: Whole-genome sequencing (WGS) was performed on ESBL-producing E. coli and K. pneumoniae isolates recovered from screening and clinical specimens from pediatric patients at Sidra Medicine in Doha from January to December 2018.Results: WGS was performed on 327 ESBL producers: 255 E. coli and 72 K. pneumoniae. The most common sequence types (ST) were ST131 (16.5%), ST38 and ST10 (8.2 each%) in E. coli and ST307 (9.7%), ST45 and ST268 (6.9% each) in K. pneumoniae. CTX-M type ESBL were found in all but one isolate, with CTX-M-15 accounting for 87.8%. Co-carriage of OXA-1 alone or in combination with TEM-1B was associated with reduced susceptibility toamoxicillin/clavulanate (P=0.002 and PP=0.02 and P=0.004). The most common plasmid-mediated quinolone resistance genes co-carried were qnr A/B/E/S (45.3%). Ninety percent of gentamicin non-susceptible isolates harboured genes encoding AAC(3) enzymes, mainly aac(3)-IIa. Only 2 of 57 isolates harbouring aac(6’)-Ib-cr were non-susceptible to amikacin. Eighty-five percent of isolates carried IncF plasmids. Conclusions: Our data show that CTX-M is largely the most prevalent ESBL type in the pediatric population in Qatar with a predominance of CTX-M-15. Carbapenem-sparing options to treat ESBL infections are limited given the frequent co-production of OXA-1 and TEM-1B enzymes and co-resistance to antibiotic classes other than β-lactams.

MacConkey agar is one of the earliest and most common bacteriological media used in clinical microbiology for the isolation and identification of Gram-negative bacteria ([1][1][–][2][3][3]). The medium has been listed as an aerobic medium for use with a wide range of clinical specimens ([4][4])

Several applications in spatial audio signal processing benefit from the knowledge of the diffuseness of the sound field. In this paper, several experiments are performed to determine the response of a tetrahedral microphone array under a spherically isotropic sound field. The data were gathered with numerical simulations and real recordings using a spherical loudspeaker array. The signal analysis, performed in the microphone signal and spherical harmonic domains, reveals the characteristic coherence curves of spherical isotropic noise as a function of the frequency.

This work describes and discusses an algorithm submitted to the Sound Event Localization and Detection Task of DCASE2019 Challenge. The proposed methodology relies on parametric spatial audio analysis for source localization and detection, combined with a deep learning-based monophonic event classifier. The evaluation of the proposed algorithm yields overall results comparable to the baseline system. The main highlight is a reduction of the localization error on the evaluation dataset by a factor of 2.6, compared with the baseline performance., 5 pages, 5 figures, submitted to DCASE2019 Workshop

Invasive pneumococcal infections are a major cause of morbidity and mortality in the pediatric population. We report the draft genomes of two clinical Streptococcus pneumoniae isolates associated with severe infections in children in Qatar., Invasive pneumococcal infections are a major cause of morbidity and mortality in the pediatric population. We report the draft genomes of two clinical Streptococcus pneumoniae isolates associated with severe infections in children in Qatar. The genome statistics are described, along with the strain types and serotypes predicted from the assembled genomes.

Pulsed laser ablation in liquids (PLAL) synthesis of Nanoparticles (NPs) is a bottom-up process with the advantage of the absence of chemical reagents in the solutions. In this process, NPs shape and diameter distributions on PLAL experimental parameters. We research the hydrodynamic diameter of the ZnO Nps correlation to media, wavelength, fluence, and irradiation time. Nine solutions, five in methanol and four in ultra-pure water were processed with fluences ranged from 4 to 15 J cm−2, target irradiation times from 8 to 15 min, and for wavelength of 532 nm and 1064 nm. We characterized the morphology and diameter distribution using Scanning Electron Microscopy (SEM) and Dynamic Light Scattering (DLS). Results showed that prolonging the irradiation time, reduces the diameter of the ZnO NPs by 41.4 % in methanol and increases it by 19.8 % in ultra-pure water. Change of medium from ultra-pure water to methanol revealed a maximum decrease of 84.2 % in NPs diameter while lowering the fluence resulted in a 62.6 % diameter reduction. The experimental results indicate that the medium and fluence were the most relevant parameters to obtain small NPs in methanol media with 80 nm diameter at 5 J cm−2, a wavelength of 1064 nm, and 20 min irradiation time and the diameter was less dependent on wavelength. Understanding the synthesis parameters and their effect on Nps diameter dispersion is critical for the scaling-up production to meet the PLAL’s promise of several grams per hour.

The spatial nature of Ambisonics audio recordings makes them specially interesting for source localization and source separation tasks. Although existing proposals have already shown promising results, there is a lack of annotated databases, required for algorithm design, training and evaluation in this particular scenario. In this paper we present AmbiScaper, a tool for the automatic generation and annotation of reverberant Ambisonics sound scenes, published under an Open Source license to facilitate research reproducibility. As a use case, a database of annotated audio scenes has been created and published, along with an analysis with state-of-the-art sound localization algorithms.

The Bigram Notation is an alternative approach to musical notation, based on the chromatic nature of Western music. As observed historically with alternative notation systems, their spread and consolidation is based on the existence of complementary and supportive tools, as ideosyncratic instruments and specific written material. Accordingly, we present the binary keyboards and the Bigram Editor, a graphical bigram score editor with automatic transcription and reproduction capabilities