Large scale expansion of mobile elements in specific hotspot regions of the German outbreak _Escherichia coli_ O104:H4

The outbreak strain of _E. coli_ O104:H4 has been sequenced by several groups and made available publicly for CrowdSourcing purposes. Genome comparisons of the complete finished sequence of TY2482 (BGI), have been made with the draft assemblies of c22711 (PacBio) and an historical outbreak strain from 2001 (U. Münster & Life Technologies). A plasmid, pTY2, carrying the _agg_ operon specifying the genes for aggregative adherence fimbriae reveals a frameshift in a gene, _aggB_, that may result in altered binding _in vivo_ compared to the unframeshifted state. Comparisons additionally reveal the presence of genomic islands specific to the outbreak strain relative to other sequenced _E. coli_ strains. These regions, and islands shared with the closest previously sequenced relative _E. coli_ 55989 have been analyzed for insertion sequences and transposable elements. Several islands found in the above strains that are not present in other sequenced _E. coli_ are found to harbor a large-scale expansion of mobile elements that are by and large confined to these hotspot or permissive areas of the chromosome. The implication is that these regions are in genomic flux and may represent specific areas of future concern due to the possibility of mobilisation of the associated genomic features likely responsible for the pathogenic features and antibiotic resistance seen in these strains

The mucin-degradation strategy of Ruminococcus gnavus:The importance of intramolecular trans-sialidases

We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit

The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract

Background Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown. Results To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity. Conclusions This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations

Identification and characterisation of enteroaggregative Escherichia coli subtypes associated with human disease

Enteroaggregative E. coli (EAEC) are a major cause of diarrhoea worldwide. Due to their heterogeneity and carriage in healthy individuals, identification of diagnostic virulence markers for pathogenic strains has been difficult. In this study, we have determined phenotypic and genotypic differences between EAEC strains of sequence types (STs) epidemiologically associated with asymptomatic carriage (ST31) and diarrhoeal disease (ST40). ST40 strains demonstrated significantly enhanced intestinal adherence, biofilm formation, and pro-inflammatory interleukin-8 secretion compared with ST31 isolates. This was independent of whether strains were derived from diarrhoea patients or healthy controls. Whole genome sequencing revealed differences in putative virulence genes encoding aggregative adherence fimbriae, E. coli common pilus, flagellin and EAEC heat-stable enterotoxin 1. Our results indicate that ST40 strains have a higher intrinsic potential of human pathogenesis due to a specific combination of virulence-related factors which promote host cell colonization and inflammation. These findings may contribute to the development of genotypic and/or phenotypic markers for EAEC strains of high virulence

Genomic and physiological variability within Group II (non-proteolytic) Clostridium botulinum

BACKGROUND: Clostridium botulinum is a group of four physiologically and phylogenetically distinct bacteria that produce botulinum neurotoxin. While studies have characterised variability between strains of Group I (proteolytic) C. botulinum, the genetic and physiological variability and relationships between strains within Group II (non-proteolytic) C. botulinum are not well understood. In this study the genome of Group II strain C. botulinum Eklund 17B (NRP) was sequenced and used to construct a whole genome DNA microarray. This was used in a comparative genomic indexing study to compare the relatedness of 43 strains of Group II C. botulinum (14 type B, 24 type E and 5 type F). These results were compared with characteristics determined from physiological tests. RESULTS: Whole genome indexing showed that strains of Group II C. botulinum isolated from a wide variety of environments over more than 75 years clustered together indicating the genetic background of Group II C. botulinum is stable. Further analysis showed that strains forming type B or type F toxin are closely related with only toxin cluster genes targets being unique to either type. Strains producing type E toxin formed a separate subset. Carbohydrate fermentation tests supported the observation that type B and F strains form a separate subset to type E strains. All the type F strains and most of type B strains produced acid from amylopectin, amylose and glycogen whereas type E strains did not. However, these two subsets did not differ strongly in minimum growth temperature or maximum NaCl concentration for growth. No relationship was found between tellurite resistance and toxin type despite all the tested type B and type F strains carrying tehB, while the sequence was absent or diverged in all type E strains. CONCLUSIONS: Although Group II C. botulinum form a tight genetic group, genomic and physiological analysis indicates there are two distinct subsets within this group. All type B strains and type F strains are in one subset and all type E strains in the other

Bacterial antimicrobial metal ion resistance

Metals such as mercury, arsenic, copper and silver have been used in various forms as antimicrobials for thousands of years with until recently, little understanding of their mode of action. The discovery of antibiotics and new organic antimicrobial compounds during the twentieth century saw a general decline in the clinical use of antimicrobial metal compounds, with the exception of the rediscovery of the use of silver for burns treatments and niche uses for other metal compounds. Antibiotics and new antimicrobials were regarded as being safer for the patient and more effective than the metal-based compounds they supplanted. Bacterial metal ion resistances were first discovered in the second half of the twentieth century. The detailed mechanisms of resistance have now been characterized in a wide range of bacteria. As the use of antimicrobial metals is limited, it is legitimate to ask: are antimicrobial metal resistances in pathogenic and commensal bacteria important now? This review details the new, rediscovered and 'never went away' uses of antimicrobial metals; examines the prevalence and linkage of antimicrobial metal resistance genes to other antimicrobial resistance genes; and examines the evidence for horizontal transfer of these genes between bacteria. Finally, we discuss the possible implications of the widespread dissemination of these resistances on re-emergent uses of antimicrobial metals and how this could impact upon the antibiotic resistance problem

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

The complete Stenotrophomonas maltophilia genome sequence suggests that it can act as a reservoir of antibiotic resistance determinants

Deep Recurrent Neural Networks for the Generation of Synthetic Coronavirus Spike Protein Sequences

With the advent of deep learning techniques for text generation, comes the possibility of generating fully simulated or synthetic genomes. For this study, the dataset of interest is that of coronaviruses. Coronaviridae are a family of positive-sense RNA viruses capable of infecting humans and animals. These viruses usually cause mild to moderate upper respiratory tract infection; however, they can also cause more severe symptoms, gastrointestinal and central nervous system diseases. The viruses are capable of flexibly adapting to new environments, hence health threats from coronavirus are constant and long-term. Immunogenic spike proteins are glycoproteins found on the surface of Coronaviridae particles that mediate entry to host cells. The aim of this study was to train deep learning neural networks to produce simulated spike protein sequences, which may be able to aid in knowledge and/or vaccine design by creating alternative possible spike sequences that could arise from zoonotic sources in future. Deep learning recurrent neural networks (RNN) were trained to provide computer-simulated coronavirus spike protein sequences in the style of previously known sequences and examine their characteristics. The deep generative model was created as a recurrent neural network employing text embedding and gated recurrent unit layers in TensorFlow Keras. Training used a dataset of alpha, beta, gamma, and delta coronavirus spike sequences. In a set of 100 simulated sequences, all 100 had most significant BLAST matches to Spike proteins in searches against NCBI non-redundant dataset (NR) and possessed the expected Pfam domain matches. Simulated sequences from the neural network may be able to guide us with future prospective targets for vaccine discovery in advance of a potential novel zoonosis