Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia.

Introduction: Detailed assessment of the population structure of group B Streptococcus (GBS) among adults is still lacking in Saudi Arabia. Here we characterized a representative collection of isolates from colonized and infected adults. Methods: GBS isolates (n=89) were sequenced by Illumina and screened for virulence and antimicrobial resistance determinants. Genetic diversity was assessed by single nucleotide polymorphisms and core-genome MLST analyses. Results: Genome sequences revealed 28 sequence types (STs) and nine distinct serotypes, including uncommon serotypes VII and VIII. Majority of these STs (n=76) belonged to the human-associated clonal complexes (CCs) CC1 (33.71%), CC19 (25.84%), CC17 (11.24%), CC10/CC12 (7.87%), and CC452 (6.74%). Major CCs exhibited intra-lineage serotype diversity, except for the hypervirulent CC17, which exclusively expressed serotype III. Virulence profiling revealed that nearly all isolates (94.38%) carried at least one of the four alpha family protein genes (i.e., alphaC, alp1, alp2/3, and rib), and 92.13% expressed one of the two serine-rich repeat surface proteins Srr1 or Srr2. In addition, most isolates harbored the pilus island (PI)-2a alone (15.73%) or in combination with PI-1 (62.92%), and those carrying PI-2b alone (10.11%) belonged to CC17. Phylogenetic analysis grouped the sequenced isolates according to CCs and further subdivided them along with their serotypes. Overall, isolates across all CC1 phylogenetic clusters expressed Srr1 and carried the PI-1 and PI-2a loci, but differed in genes encoding the alpha-like proteins. CC19 clusters were dominated by the III/rib/srr1/PI-1+PI-2a (43.48%, 10/23) and V/alp1/srr1/PI-1+PI-2a (34.78%, 8/23) lineages, whereas most CC17 isolates (90%, 9/10) had the same III/rib/srr2/P1-2b genetic background. Interestingly, genes encoding the CC17-specific adhesins HvgA and Srr2 were detected in phylogenetically distant isolates belonging to ST1212, suggesting that other highly virulent strains might be circulating within the species. Resistance to macrolides and/or lincosamides across all major CCs (n=48) was associated with the acquisition of erm(B) (62.5%, 30/48), erm(A) (27.1%, 13/48), lsa(C) (8.3%, 4/48), and mef(A) (2.1%, 1/48) genes, whereas resistance to tetracycline was mainly mediated by presence of tet(M) (64.18%, 43/67) and tet(O) (20.9%, 14/67) alone or in combination (13.43%, 9/67). Discussion: These findings underscore the necessity for more rigorous characterization of GBS isolates causing infections.

Molecular typing and antimicrobial resistance of group B Streptococcus clinical isolates in Saudi Arabia.

OBJECTIVES: Group B Streptococcus (GBS) has emerged as an important cause of severe infections in adults. However, limited data are available regarding the epidemiology of GBS in Saudi Arabia. METHODS: Isolates were collected over a period of eight months from colonized (n = 104) and infected adults (n = 95). Serotypes and virulence determinants were detected by polymerase chain reactions (PCRs). Genetic relatedness was assessed using Multiple Locus Variable Number Tandem Repeat Analysis (MLVA). Antimicrobial susceptibilities were determined by disk diffusion. RESULTS: Serotypes III and V (25% each) were the most prevalent, followed by serotypes II (16.18%), Ia (13.24%), VI (9.31%), and Ib (8.82%), while five isolates remained non-typeable (2.45%). Hypervirulent serotype III/CC17 clone (n = 21) accounted for 41.18% of the serotype III isolates. Most isolates (53.92%) harboured pilus island (PI) 1 and 2a types, while PI-2b was predominantly detected in the hypervirulent clone. Isolates were variably resistant to tetracycline (76.47%), erythromycin (36.76%), clindamycin (25.49%), and levofloxacin (6.37%), but remained susceptible to penicillin. Macrolide resistant isolates exhibited constitutive (55.42%) and inducible macrolide-lincosamide-streptogramin B resistance phenotypes (33.74%), while a few had L (9.64%) or M (1.2%) phenotypes. MLVA patterns of dominant serotypes III and V revealed 40 different types divided into 12 clusters and 28 singletons. Interestingly, macrolide resistance was significantly associated with two major MLVA types. CONCLUSIONS: GBS isolates belonged predominantly to serotypes III and V, but there were no clear associations between serotypes and patient groups. The studied isolates exhibited high levels of resistance to erythromycin and clindamycin that need further surveillance.

The transmutation of Escherichia coli ATCC 25922 to small colony variants (SCVs) E. coli strain as a result of exposure to gentamicin.

BACKGROUND: Small colony variants (SCVs) are biotypes of bacteria that have a size of approximately one-tenth or less of the wild types and has distinct characteristics comparing to the wild type strains. Clinical SCVs are usually associated with persistent infection and require a long-term treatment program with antibiotics. In Saudi Arabia, there are few studies about SCVs Escherichia coli for this reason, this study is aimed to investigate the ability of gentamicin to mutate E. coli ATCC 25922 to produce small SCVs and investigate the genotypes and phenotypes changes and stress tolerance comparing to clinical SCVs E. coli and normal clinical E. coli Isolated from blood samples. METHODS: In this investigation, four clinical blood samples were collected ted from patients and the cultivation and isolation were carried out in KFMC between December 2019 and February 2021. The identification of positive blood culture samples was done using phoenix MD. Non-SCV E. coli ATCC25922 were mutated to SCV using exposure to increasing gradual concentrations of gentamicin at 100-generation intervals. Biochemical features and susceptibility to standard antibiotics using automated Phoenix MD 50 and. The survival assays were done using several stresses including heat shock, low pH, high osmotic pressure, and oxidative pressure. Virulence genes screening included the detection of genes that encoded to α-haemolysin, CS12 fimbriae, F17-like fimbrial adhesion, P-related fimbriae, yersiniabactin siderophore system, P-fimbriae, aerobactin, iron-regulated genes using PCR and gel electrophoresis. RESULTS: The data from the mutating E. coli ATCC 25922 small colony test with gentamicin revealed that the first emergence of the multidrug resistance (MDR) SCV E. coli strain occurred at generation number 250, corresponding to a gentamicin concentration of 57 g/ml. Pathogenicity islands detection revealed that all tested E. coli strains have PAI IV 536 genes on their chromosomes furthermore, mutated SCV E. coli ATCC 25922 acquired PAII CFT073 and PAI IV 536. Survival tests showed no significant differences changes in tolerance of mutated SCVs comparing to parental strain. CONCLUSION: The present work concluded that gentamicin sub-MIC concentration gradual exposure can induce mutation responsible for SCV formation and evolving of MDR E. coli strains. The mutated SCVs evolved high-level aminoglycoside resistance for gentamicin and resistance to amikacin, it also developed resistance to 2 cephalosporin antibiotics cefuroxime, and cephalothin and a resistance to aztreonam.

Mapping the intrinsic photocurrent streamlines through micromagnetic heterostructure devices.

Photocurrent in quantum materials is often collected at global contacts far away from the initial photoexcitation. This collection process is highly nonlocal. It involves an intricate spatial pattern of photocurrent flow (streamlines) away from its primary photoexcitation that depends sensitively on the configuration of current collecting contacts as well as the spatial nonuniformity and tensor structure of conductivity. Direct imaging to track photocurrent streamlines is challenging. Here, we demonstrate a microscopy method to image photocurrent streamlines through ultrathin heterostructure devices comprising platinum on yttrium iron garnet (YIG). We accomplish this by combining scanning photovoltage microscopy with a uniform rotating magnetic field. Here, local photocurrent is generated through a photo-Nernst type effect with its direction controlled by the external magnetic field. This enables the mapping of photocurrent streamlines in a variety of geometries that include conventional Hall bar-type devices, but also unconventional wing-shaped devices called electrofoils. In these, we find that photocurrent streamlines display contortion, compression, and expansion behavior depending on the shape and angle of attack of the electrofoil devices, much in the same way as tracers in a wind tunnel map the flow of air around an aerodynamic airfoil. This affords a powerful tool to visualize and characterize charge flow in optoelectronic devices.

Genomic Characterization of Colistin-Resistant Isolates from the King Fahad Medical City, Kingdom of Saudi Arabia.

BACKGROUND: Whole-genome sequencing is one of the best ways to investigate resistance mechanisms of clinical isolates as well as to detect and identify circulating multi-drug-resistant (MDR) clones or sub-clones in a given hospital setting. METHODS: Here, we sequenced 37 isolates of Acinetobacter baumannii, 10 Klebsiella pneumoniae, and 5 Pseudomonas aeruginosa collected from the biobank of the hospital setting of the King Fahad Medical City. Complete phenotypic analyses were performed, including MALDI-TOF identification and antibiotic susceptibility testing. After the genome assembly of raw data, exhaustive genomic analysis was conducted including full resistome determination, genomic SNP (gSNP) analysis, and comparative genomics. RESULTS: Almost all isolates were highly resistant to all tested antibiotics, including carbapenems and colistin. Resistome analysis revealed many antibiotic resistance genes, including those with resistance to ß-lactams, aminoglycosides, macrolides, tetracyclines, sulfamids, quinolones, and phenicols. In A. baumannii isolates, the endemic carbapenemase blaOXA-23 gene was detected in 36 of the 37 isolates. Non-synonymous mutations in pmrB were detected in almost all of the isolates and likely mediated colistin resistance. Interestingly, while classical analyses, such as MLST, revealed the predominance of an ST2 clone in A. baumannii isolates, the genomic analysis revealed the presence of five circulating sub-clones and identified several isolate transmissions between patients. In the 10 K. pneumoniae isolates, several resistance genes were identified, and the observed carbapenem resistance was likely mediated by overexpression of the detected extended-spectrum-ß-lactamase (ESBL) genes associated with low membrane permeability as few carbapenemase genes were detected with just blaOXA-48 in three isolates. Colistin resistance was mediated either by non-synonymous mutations in the MgrB regulator, PmrA, PmrB, and PhoQ proteins or the presence of the MCR-1 protein. Here, gSNP analysis also revealed the existence of bacterial clones and cases of isolate transmissions between patients. The five analyzed P. aeruginosa isolates were highly resistant to all tested antibiotics, including carbapenems mediated by loss or truncated OprD porin, and colistin resistance was associated with mutations in the genes encoding the PmrA, PmrB, or PhoQ proteins. CONCLUSION: We demonstrate here the usefulness of whole-genome sequencing to exhaustively investigate the dissemination of MDR isolates at the sub-clone level. Thus, we suggest implementing such an approach to monitor the emergence and spread of new clones or sub-clones, which classical molecular analyses cannot detect. Moreover, we recommend increasing the surveillance of the endemic and problematic colistin resistance mcr-1 gene to avoid extensive dissemination.

Role of Magnon-Magnon Scattering in Magnon Polaron Spin Seebeck Effect.

The spin Seebeck effect (SSE) signal of magnon polarons in bulk-Y_{3}Fe_{5}O_{12} (YIG)/Pt heterostructures is found to drastically change as a function of temperature. It appears as a dip in the total SSE signal at low temperatures, but as the temperature increases, the dip gradually decreases before turning to a peak. We attribute the observed dip-to-peak transition to the rapid rise of the four-magnon scattering rate. Our analysis provides important insights into the microscopic origin of the hybridized excitations and the overall temperature dependence of the SSE anomalies.

Spin current from sub-terahertz-generated antiferromagnetic magnons.

Spin dynamics in antiferromagnets has much shorter timescales than in ferromagnets, offering attractive properties for potential applications in ultrafast devices1-3. However, spin-current generation via antiferromagnetic resonance and simultaneous electrical detection by the inverse spin Hall effect in heavy metals have not yet been explicitly demonstrated4-6. Here we report sub-terahertz spin pumping in heterostructures of a uniaxial antiferromagnetic Cr2O3 crystal and a heavy metal (Pt or Ta in its ß phase). At 0.240 terahertz, the antiferromagnetic resonance in Cr2O3 occurs at about 2.7 tesla, which excites only right-handed magnons. In the spin-canting state, another resonance occurs at 10.5 tesla from the precession of induced magnetic moments. Both resonances generate pure spin currents in the heterostructures, which are detected by the heavy metal as peaks or dips in the open-circuit voltage. The pure-spin-current nature of the electrically detected signals is unambiguously confirmed by the reversal of the voltage polarity observed under two conditions: when switching the detector metal from Pt to Ta, reversing the sign of the spin Hall angle7-9, and when flipping the magnetic-field direction, reversing the magnon chirality4,5. The temperature dependence of the electrical signals at both resonances suggests that the spin current contains both coherent and incoherent magnon contributions, which is further confirmed by measurements of the spin Seebeck effect and is well described by a phenomenological theory. These findings reveal the unique characteristics of magnon excitations in antiferromagnets and their distinctive roles in spin-charge conversion in the high-frequency regime.

Spin Seebeck Effect from Antiferromagnetic Magnons and Critical Spin Fluctuations in Epitaxial FeF_{2} Films.

We report a longitudinal spin Seebeck effect (SSE) study in epitaxially grown FeF_{2}(110) antiferromagnetic (AFM) thin films with strong uniaxial anisotropy over the temperature range of 3.8-250 K. Both the magnetic-field and temperature-dependent SSE signals below the Néel temperature (T_{N}=70 K) of the FeF_{2} films are consistent with a theoretical model based on the excitations of AFM magnons without any net induced static magnetic moment. In addition to the characteristic low-temperature SSE peak associated with the AFM magnons, there is another SSE peak at T_{N} which extends well into the paramagnetic phase. All the SSE data taken at different magnetic fields up to 12 T near and above the critical point T_{N} follow the critical scaling law very well with the critical exponents for magnetic susceptibility of 3D Ising systems, which suggests that the AFM spin correlation is responsible for the observed SSE near T_{N}.

Highly Efficient Spin-Orbit Torque and Switching of Layered Ferromagnet Fe3GeTe2.

Among van der Waals (vdW) layered ferromagnets, Fe3GeTe2 (FGT) is an excellent candidate material to form FGT/heavy metal heterostructures for studying the effect of spin-orbit torques (SOT). Its metallicity, strong perpendicular magnetic anisotropy built in the single atomic layers, relatively high Curie temperature (Tc ∼ 225 K), and electrostatic gate tunability offer a tantalizing possibility of achieving the ultimate high SOT limit in monolayer all-vdW nanodevices. In this study, we fabricate heterostructures of FGT/Pt with 5 nm of Pt sputtered onto the atomically flat surface of ∼15-23 nm exfoliated FGT flakes. The spin current generated in Pt exerts a damping-like SOT on FGT magnetization. At ∼2.5 × 1011 A/m2 current density, SOT causes the FGT magnetization to switch, which is detected by the anomalous Hall effect of FGT. To quantify the SOT effect, we measure the second harmonic Hall responses as the applied magnetic field rotates the FGT magnetization in the plane. Our analysis shows that the SOT efficiency is comparable with that of the best heterostructures containing three-dimensional (3D) ferromagnetic metals and much larger than that of heterostructures containing 3D ferrimagnetic insulators. Such large efficiency is attributed to the atomically flat FGT/Pt interface, which demonstrates the great potential of exploiting vdW heterostructures for highly efficient spintronic nanodevices.

Probing Magnetism in Insulating Cr2Ge2Te6 by Induced Anomalous Hall Effect in Pt.

Two-dimensional ferromagnet Cr2Ge2Te6 (CGT) is so resistive below its Curie temperature that probing its magnetism by electrical transport becomes extremely difficult. By forming heterostructures with Pt, however, we observe clear anomalous Hall effect (AHE) in 5 nm thick Pt deposited on thin (<50 nm) exfoliated flakes of CGT. The AHE hysteresis loops persist to ∼60 K, which matches well to the Curie temperature of CGT obtained from the bulk magnetization measurements. The slanted AHE loops with a narrow opening indicate magnetic domain formation, which is confirmed by low-temperature magnetic force microscopy (MFM) imaging. These results clearly demonstrate that CGT imprints its magnetization in the AHE signal of the Pt layer. Density functional theory calculations of CGT/Pt heterostructures suggest that the induced ferromagnetism in Pt may be primarily responsible for the observed AHE. Our results establish a powerful way of investigating magnetism in 2D insulating ferromagnets, which can potentially work for monolayer devices.

Spin Hall-induced auto-oscillations in ultrathin YIG grown on Pt.

We experimentally study nanowire-shaped spin-Hall nano-oscillators based on nanometer-thick epitaxial films of Yttrium Iron Garnet grown on top of a layer of Pt. We show that, although these films are characterized by significantly larger magnetic damping in comparison with the films grown directly on Gadolinium Gallium Garnet, they allow one to achieve spin current-driven auto-oscillations at comparable current densities, which can be an indication of the better transparency of the interface to the spin current. These observations suggest a route for improvement of the flexibility of insulator-based spintronic devices and their compatibility with semiconductor technology.

Observation of magnon-mediated current drag in Pt/yttrium iron garnet/Pt(Ta) trilayers.

Pure spin current, a flow of spin angular momentum without flow of any accompanying net charge, is generated in two common ways. One makes use of the spin Hall effect in normal metals (NM) with strong spin-orbit coupling, such as Pt or Ta. The other utilizes the collective motion of magnetic moments or spin waves with the quasi-particle excitations called magnons. A popular material for the latter is yttrium iron garnet, a magnetic insulator (MI). Here we demonstrate in NM/MI/NM trilayers that these two types of spin currents are interconvertible across the interfaces, predicated as the magnon-mediated current drag phenomenon. The transmitted signal scales linearly with the driving current without a threshold and follows the power-law T(n) with n ranging from 1.5 to 2.5. Our results indicate that the NM/MI/NM trilayer structure can serve as a scalable pure spin current valve device which is an essential ingredient in spintronics.

Child homicide in Cairo from 2006 to 2010: characteristics and trends.

BACKGROUND: Crimes towards children have drawn public attention over the decades. Several studies have been conducted to determine the risk factors of victimizing children. Conducting studies of this crime in Cairo, the capital city of Egypt, would help in understanding the motives behind it in such a densely populated area. RESEARCH DESIGN AND METHODOLOGY: A review of death charts was conducted in Zeinhom morgue in the years of 2006-2010 to study the trends and characteristics of child homicide in Cairo. The cut-off for a child age was at 18 years. Data related to the victim and offender was collected. RESULTS: Child homicides represented 7.97% of total child deaths in the studied period. Most of them (25%) fall in the age group of 1-6 years. Females were the majority in the age group of 12-18 years (89%). The offender was the father in 28% of cases and the cause of death was mainly trauma to the head (42%). CONCLUSION: Further studies should be conducted to discern the risk factors of this crime in Cairo with special considerations to the motives behind murdering females in teen ages.