Novel insights in bacterial vaginosis etiology through genomic approaches.

Bacterial vaginosis (BV) has been considered as dysbiosis state whose etiology is not fully understood. This condition affects a large number of women of reproductive age and its study has been highly relevant due to the growing association of BV with and gynecological and obstetric complications and diseases, in addition to a greater susceptibility to sexually transmitted diseases, including HIV. The vaginal microbiota composition presents high variability among different ethnic groups of women, although, generally, the prevalence of lactobacilli species has been reported. Several studies suggest they may play a protective role, especially Lactobacillus crispatus whose population is typically present in low proportions in women with BV. This review article describes the contributions and limitations of genomic approaches in elucidating protective characteristics and mechanisms associated with colonization and persistence of lactobacilli strains. Although some genetic features were associated with resilience of L. crispatus during BV, furher studies are required to uncover their functions.

Characterization of a new multidrug-resistant Brazilian K. pneumoniae isolate and 172 Klebsiella spp. sequenced strains: Genomic island, multilocus sequence typing and capsule locus dataset.

The genus Klebsiella comprises species that cause nosocomial and community-acquired infections. A dataset was created to compile the sequence type (ST) and capsule type (K-locus) information predicted for 172 worldwide isolates of Klebsiella spp. whose complete genomes could be retrieved from the GenBank (NCBI) repository. The dataset also includes information related to one multidrug-resistant strain (B31) isolated from a patient who was admitted to an intensive care unit in the Northeast region of Brazil. This strain was phenotypically characterized and submitted to whole-genome sequencing and comparative genomics analysis as we recently reported [1]. The dataset also compiles information on Pathogenicity Islands (PIs), Resistance Islands (RIs) and Miscellaneous Islands (MIS) present in the genome of strain B31. The information provided here may support outbreak prevention policies and future epidemiological studies involving Klebsiella spp.

Comparative genomics with a multidrug-resistant Klebsiella pneumoniae isolate reveals the panorama of unexplored diversity in Northeast Brazil.

The emergence of community acquired infections increases the public health concern on K. pneumoniae and closely related bacteria among which antimicrobial resistance spreads. We report a multidrug-resistant K. pneumoniae isolate, B31, of a patient infected in the community and admitted to an intensive care unit in Northeast Brazil. Antimicrobial susceptibility and genome information were thoroughly investigated to characterize B31 in front of 172 sequenced strains of different countries. Assigned to the Sequence Type 15, which is globally spread, B31 presented extended spectrum beta-lactamase, tigecycline and ciprofloxacin resistance. Genome sequencing revealed most resistance genes being carried by plasmids with high dissemination potential. The absence of main virulence factors, like yersiniabactin and colibactin, apparently suggests a mild pathogenic strain which, on the contrary, persisted and caused severe infection in a previously healthy patient. The present study contributes to unveil the unclear genomic scenario of virulent and multidrug-resistant K. pneumoniae in Brazil.

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico.

Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software. The automatic genome annotation was done using the software RAST and in-house scripts for transference, followed by manual curation using Artemis software and BLAST against NCBI and UniProt databases. The six genomes are publicly available in NCBI database. The analysis of nucleotide sequence similarity and the generated phylogenetic tree led to the observation that the Mexican strains are more similar between strains from the same host, but the genetic structure is probably more influenced by transportation of animals between farms than host preference. Also, a putative drug target was predicted and in silico analysis of 46 strains showed two gene clusters capable of differentiating the biovars equi and ovis: Restriction Modification system and CRISPR-Cas cluster.

Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.

Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as "pigeon fever" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two distinct clades, one formed by nitrate non-reducing species (biovar ovis) and another formed by nitrate-reducing species (biovar equi). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar equi of C. pseudotuberculosis. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of C. pseudotuberculosis were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer.

Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 03-8664 Isolated from a Human Throat.

Corynebacterium ulcerans is an emergent pathogen infecting wild and domesticated animals worldwide that may serve as reservoirs for zoonotic infections. In this study, we present the draft genome of C. ulcerans strain 03-8664. The draft genome has 2,428,683 bp, 2,262 coding sequences, and 12 rRNA genes.

Draft Genome Sequence of Corynebacterium ulcerans Strain 04-3911, Isolated from Humans.

Corynebacterium ulceransis a pathogenic bacterium infecting wild and domesticated animals; some infection cases in humans have increased throughout the world. The current study describes the draft genome of strain 04-3911, isolated from humans. The draft genome has 2,492,680 bp, 2,143 coding sequences, 12 rRNA genes, and 50 tRNA genes.

Draft Genome Sequence of Toxigenic Corynebacterium ulcerans Strain 04-7514, Isolated from a Dog in France.

Here, we present the draft genome of toxigenicCorynebacterium ulceransstrain 04-7514. The draft genome has 2,497,845 bp, 2,059 coding sequences, 12 rRNA genes, 46 tRNA genes, 150 pseudogenes, 1 clustered regularly interspaced short palindromic repeat (CRISPR) array, and a G+C content of 53.50%.

Genome Sequence of Corynebacterium pseudotuberculosis MB20 bv. equi Isolated from a Pectoral Abscess of an Oldenburg Horse in California.

The genome of Corynebacterium pseudotuberculosis MB20 bv. equi was sequenced using the Ion Personal Genome Machine (PGM) platform, and showed a size of 2,363,089 bp, with 2,365 coding sequences and a GC content of 52.1%. These results will serve as a basis for further studies on the pathogenicity of C. pseudotuberculosis bv. equi.