Draft genome sequences of three newly identified species in the genus Cronobacter, C. helveticus LMG23732T, C. pulveris LMG24059, and C. zurichensis LMG23730T

Cronobacter helveticus, Cronobacter pulveris, and Cronobacter zurichensis are newly described species in the Cronobacter genus, which is associated with serious infections of neonates. This is the first report of draft genome sequences for these species

Draft genome sequence of the earliest Cronobacter sakazakii sequence type 4 strain, NCIMB 8272

The Cronobacter sakazakii clonal lineage defined as sequence type 4 (ST4) is associated with severe cases of neonatal meningitis and persistence in powdered infant formula. For genome sequencing of the earliest deposited culture collection strain of Cronobacter sakazakii ST4, we used the strain NCIMB 8272, originally isolated from milk powder in 1950

Increased human pathogenic potential of Escherichia coli from polymicrobial urinary tract infections in comparison to isolates from monomicrobial culture samples

The current diagnostic standard procedure outlined by the Health Protection Agency for urinary tract infections (UTIs) in clinical laboratories does not report bacteria isolated from samples containing three or more different bacterial species. As a result many UTIs go unreported and untreated, particularly in elderly patients, where polymicrobial UTI samples are especially prevalent. This study reports the presence of the major uropathogenic species in mixed culture urine samples from elderly patients, and of resistance to front-line antibiotics, with potentially increased levels of resistance to ciprofloxacin and trimethoprim. Most importantly, the study highlights that Escherichia coli present in polymicrobial UTI samples are statistically more invasive (P<0.001) in in vitro epithelial cell infection assays than those isolated from monomicrobial culture samples. In summary, the results of this study suggest that the current diagnostic standard procedure for polymicrobial UTI samples needs to be reassessed, and that E. coli present in polymicrobial UTI samples may pose an increased risk to human health

Genomic dissection of the 1994 Cronobacter sakazakii outbreak in a French neonatal intensive care unit

Background: Cronobacter sakazakii is a member of the genus Cronobacter that has frequently been isolated from powdered infant formula (PIF) and linked with rare but fatal neonatal infections such as meningitis and necrotising enterocolitis. The Cronobacter MLST scheme has reported over 400 sequence types and 42 clonal complexes; however C. sakazakii clonal complex 4 (CC4) has been linked strongly with neonatal infections, especially meningitis. There have been a number of reported Cronobacter outbreaks over the last three decades. The largest outbreak of C. sakazakii was in a neonatal intensive care unit (NICU) in France (1994) that lasted over 3 months and claimed the lives of three neonates. The present study used whole genome sequencing data of 26 isolates obtained from this outbreak to reveal their relatedness. This study is first of its kind to use whole genome sequencing data to analyse a Cronobacter outbreak. Methods: Whole genome sequencing data was generated for 26 C. sakazakii isolates on the Illumina MiSeq platform. The whole genome phylogeny was determined using Mugsy and RaxML. SNP calls were determined using SMALT and SAMtools, and filtered using VCFtools. Results: The whole genome phylogeny suggested 3 distant clusters of C. sakazakii isolates were associated with the outbreak. SNP typing and phylogeny indicate the source of the C. sakazakii could have been from extrinsic contamination of reconstituted infant formula from the NICU environment and personnel. This pool of strains would have contributed to the prolonged duration of the outbreak, which was up to 3 months. Furthermore 3 neonates were co-infected with C. sakazakii from two different genotype clusters. Conclusion: The genomic investigation revealed the outbreak consisted of an heterogeneous population of C. sakazakii isolates. The source of the outbreak was not identified, but probably was due to environmental and personnel reservoirs resulting in extrinsic contamination of the neonatal feeds. It also indicated that C. sakazakii isolates from different genotype clusters have the ability to co-infect neonates

Draft genome sequence of a meningitic isolate of Cronobacter sakazakii clonal complex 4, strain 8399

The Cronobacter sakazakii clonal lineage defined as clonal complex 4 (CC4), composed of nine sequence types, is associated with severe cases of neonatal meningitis. To date, only closely related C. sakazakii sequence type 4 (ST4) strains have been sequenced. C. sakazakii strain 8399, isolated from a case of neonatal meningitis, was sequenced as the first non-ST4 C. sakazakii strain

Draft genome sequence of "Candidatus Cronobacter colletis" NCTC 14934T, a new species in the genus Cronobacter

Members of the Cronobacter genus are associated with serious infections in neonates. This is the first report of the draft genome sequence for the newly proposed species Cronobacter colletis

Directional gene flow and ecological separation in Yersinia enterocolitica

Yersinia enterocolitica is a common cause of food-borne gastroenteritis worldwide. Recent work defining the phylogeny of the genus Yersinia subdivided Y. enterocolitica into six distinct phylogroups. Here, we provide detailed analyses of the evolutionary processes leading to the emergence of these phylogroups. The dominant phylogroups isolated from human infections, PG3–5, show very little diversity at the sequence level, but do present marked patterns of gain and loss of functions, including those involved in pathogenicity and metabolism, including the acquisition of phylogroup-specific O-antigen loci. We tracked gene flow across the species in the core and accessory genome, and show that the non-pathogenic PG1 strains act as a reservoir for diversity, frequently acting as donors in recombination events. Analysis of the core and accessory genome also suggested that the different Y. enterocolitica phylogroups may be ecologically separated, in contrast to the long-held belief of common shared ecological niches across the Y. enterocolitica species

Temperature Fluctuations driven by Magnetorotational Instability in Protoplanetary Disks

The magnetorotational instability (MRI) drives magnetized turbulence in sufficiently ionized regions of protoplanetary disks, leading to mass accretion. The dissipation of the potential energy associated with this accretion determines the thermal structure of accreting regions. Until recently, the heating from the turbulence has only been treated in an azimuthally averaged sense, neglecting local fluctuations. However, magnetized turbulence dissipates its energy intermittently in current sheet structures. We study this intermittent energy dissipation using high resolution numerical models including a treatment of radiative thermal diffusion in an optically thick regime. Our models predict that these turbulent current sheets drive order unity temperature variations even where the MRI is damped strongly by Ohmic resistivity. This implies that the current sheet structures where energy dissipation occurs must be well resolved to correctly capture the flow structure in numerical models. Higher resolutions are required to resolve energy dissipation than to resolve the magnetic field strength or accretion stresses. The temperature variations are large enough to have major consequences for mineral formation in disks, including melting chondrules, remelting calcium-aluminum rich inclusions, and annealing silicates; and may drive hysteresis: current sheets in MRI active regions could be significantly more conductive than the remainder of the disk.Comment: 16 pages, 13 figures, ApJ In Press, updated to match proof

'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution

In the study of molecular microbiology and bacterial genetics, pathogenic species of the Yersinia genus have been pillars for research aimed at understanding how bacteria evolve into mammalian pathogens. The advent of large-scale population genomic studies has hugely accelerated progress in this field, and the pathogenic Yersinia species have re-emerged as model organisms to help shape our understanding of the evolutionary processes involved in pathogenesis. In this review, we highlight how microbial genomic studies of the yersiniae have revealed distinct features marking the evolutionary path towards pathogenesis, which are changing our understanding of pathogen evolution. As these features are also found in the genomes of other members of the Enterobacteriaceae, they provide a blueprint for the evolution of enteropathogenic bacteria