b Laboratory-based in vitro antimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidal Salmonella and correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred forty Salmonella of 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n ‫؍‬ 59) in the 104 human isolates than in the 536 retail meat isolates (n ‫؍‬ 36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum ␤-lactamases (ESBLs) (bla CTX-M1 and bla SHV2a ) in retail meat isolates of Salmonella in the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidal Salmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.

WGS can provide comprehensive resistance genotypes and is capable of accurately predicting resistance phenotypes, making it a valuable tool for surveillance. Moreover, the data presented here showing the ability to accurately predict resistance suggest that WGS may be used as a screening tool in selecting anti-infective therapy, especially as costs drop and methods improve.

BackgroundPandemic Vibrio parahaemolyticus has undergone rapid changes in both K- and O-antigens, making detection of outbreaks more difficult. In order to understand these rapid changes, the genetic regions encoding these antigens must be examined. In Vibrio cholerae and Vibrio vulnificus, both O-antigen and capsular polysaccharides are encoded in a single region on the large chromosome; a similar arrangement in pandemic V. parahaemolyticus would help explain the rapid serotype changes. However, previous reports on "capsule" genes are controversial. Therefore, we set out to clarify and characterize these regions in pandemic V. parahaemolyticus O3:K6 by gene deletion using a chitin based transformation strategy.ResultsWe generated different deletion mutants of putative polysaccharide genes and examined the mutants by immuno-blots with O and K specific antisera. Our results showed that O- and K-antigen genes are separated in V. parahaemolyticus O3:K6; the region encoding both O-antigen and capsule biosynthesis in other vibrios, i.e. genes between gmhD and rjg, determines the K6-antigen but not the O3-antigen in V. parahaemolyticus. The previously identified "capsule genes" on the smaller chromosome were related to exopolysaccharide synthesis, not K-antigen.ConclusionUnderstanding of the genetic basis of O- and K-antigens is critical to understanding the rapid changes in these polysaccharides seen in pandemic V. parahaemolyticus. This report confirms the genetic location of K-antigen synthesis in V. parahaemolyticus O3:K6 allowing us to focus future studies of the evolution of serotypes to this region.

Controlling electronic processes in low-dimension electron systems is centrally important for both fundamental and applied researches. While most of the previous works focused on SrTiO 3 -based two-dimensional electron gases (2DEGs), here we report on a comprehensive investigation in this regard for amorphous-LaAlO 3 / KTaO 3 2DEGs with the Fermi energy ranging from ∼13 meV to ∼488 meV. The most important observation is the dramatic variation of the Rashba spin−orbit coupling (SOC) as Fermi energy sweeps through 313 meV: The SOC effective field first jumps and then drops, leading to a cusp of ∼2.6 T. Above 313 meV, an additional species of mobile electrons emerges, with a 50-fold enhanced Hall mobility. A relationship between spin relaxation distance and the degree of band filling has been established in a wide range. It indicates that the maximal spin precession length is ∼70.1 nm and the maximal Rashba spin splitting energy is ∼30 meV. Both values are much larger than the previously reported ones. As evidenced by density functional theory calculation, these unusual phenomena are closely related to the distinct band structure of the 2DEGs composed of 5d electrons. The present work further deepens our understanding of perovskite conducting interfaces, particularly those composed of 5d transition-metal oxides.

BackgroundVibrio parahaemolyticus is a common cause of foodborne disease. Beginning in 1996, a more virulent strain having serotype O3:K6 caused major outbreaks in India and other parts of the world, resulting in the emergence of a pandemic. Other serovariants of this strain emerged during its dissemination and together with the original O3:K6 were termed strains of the pandemic clone. Two genomes, one of this virulent strain and one pre-pandemic strain have been sequenced. We sequenced four additional genomes of V. parahaemolyticus in this study that were isolated from different geographical regions and time points. Comparative genomic analyses of six strains of V. parahaemolyticus isolated from Asia and Peru were performed in order to advance knowledge concerning the evolution of V. parahaemolyticus; specifically, the genetic changes contributing to serotype conversion and virulence. Two pre-pandemic strains and three pandemic strains, isolated from different geographical regions, were serotype O3:K6 and either toxin profiles (tdh+, trh-) or (tdh-, trh+). The sixth pandemic strain sequenced in this study was serotype O4:K68.ResultsGenomic analyses revealed that the trh+ and tdh+ strains had different types of pathogenicity islands and mobile elements as well as major structural differences between the tdh pathogenicity islands of the pre-pandemic and pandemic strains. In addition, the results of single nucleotide polymorphism (SNP) analysis showed that 94% of the SNPs between O3:K6 and O4:K68 pandemic isolates were within a 141 kb region surrounding the O- and K-antigen-encoding gene clusters. The "core" genes of V. parahaemolyticus were also compared to those of V. cholerae and V. vulnificus, in order to delineate differences between these three pathogenic species. Approximately one-half (49-59%) of each species' core genes were conserved in all three species, and 14-24% of the core genes were species-specific and in different functional categories.ConclusionsOur data support the idea that the pandemic strains are closely related and that recent South American outbreaks of foodborne disease caused by V. parahaemolyticus are closely linked to outbreaks in India. Serotype conversion from O3:K6 to O4:K68 was likely due to a recombination event involving a region much larger than the O-antigen- and K-antigen-encoding gene clusters. Major differences between pathogenicity islands and mobile elements are also likely driving the evolution of V. parahaemolyticus. In addition, our analyses categorized genes that may be useful in differentiating pathogenic Vibrios at the species level.

Two-dimensional electron gas (2DEG) at the perovskite oxide interface exhibits a lot of exotic properties, presenting a promising platform for the exploration of emergent phenomena. While most of the previous works focused on SrTiO-based 2DEG, here we report on the fabrication of high-quality 2DEGs by growing an amorphous LaAlO layer on a (001)-orientated KTaO substrate, which is a 5d metal oxide with a polar surface, at a high temperature that is usually adopted for crystalline LaAlO. Metallic 2DEGs with a Hall mobility as high as ∼2150 cm/(V s) and a sheet carrier density as low as 2 × 10 cm are obtained. For the first time, the gating effect on the transport process is studied, and its influence on spin relaxation and inelastic and elastic scattering is determined. Remarkably, the spin relaxation time can be strongly tuned by a back gate. It is reduced by a factor of ∼69 while the gate voltage is swept from -25 to +100 V. The mechanism that dominates the spin relaxation is elucidated.

Altered El Tor Vibrio cholerae O1, with classical cholera toxin B gene, was isolated from 16 patients with severe diarrhea at St. Mark’s Hospital, Arbonite, Haiti, <3 weeks after onset of the current cholera epidemic. Variable-number tandem-repeat typing of 187 isolates showed minimal diversity, consistent with a point source for the epidemic.

The recent discovery of van der Waals magnetic materials has attracted great attention in materials science and spintronics. The preparation of ultrathin magnetic layers down to atomic thickness is challenging and is mostly by mechanical exfoliation. Here, we report vapor deposition of magnetic van der Waals NiI2 crystals. Two-dimensional (2D) NiI2 flakes are grown on SiO2/Si substrates with a thickness of 5–40 nm and on hexagonal boron nitride (h-BN) down to monolayer thickness. Temperature-dependent Raman spectroscopy reveals robust magnetic phase transitions in the as-grown 2D NiI2 crystals down to trilayer. Electrical measurements show a semiconducting transport behavior with a high on/off ratio of 106 for the NiI2 flakes. Lastly, density functional theory calculation shows an intralayer ferromagnetic and interlayer antiferromagnetic ordering in 2D NiI2. This work provides a feasible approach to epitaxy 2D magnetic transition metal halides and also offers atomically thin materials for spintronic devices.