Draft genome sequence of Staphylococcus agnetis 3682, the producing strain of the broad-spectrum lantibiotic agneticin 3682.

Here we report the draft genome sequence of Staphylococcus agnetis 3682, a strain producing agneticin 3682, a broad-spectrum lantibiotic with potential medical applications. The inhibitory activity of S. agnetis 3682 against multidrug-resistant methicillin-resistant Staphylococcus aureus (MRSA) isolates involved in human infections was also investigated. A sequencing library was constructed using a Nextera XT DNA Library Preparation Kit. An Illumina MiSeq system was used to perform whole-genome shotgun sequencing. De novo genome assembly was performed using the A5-miseq pipeline. Staphylococcus agnetis 3628 genome annotation was performed by the RAST server, and BAGEL4 and antiSMASH v.4.0 platforms were used for mining bacteriocin gene clusters. The inhibitory activity of S. agnetis 3682 against 20 multidrug-resistant MRSA strains involved in human infections in two Brazilian hospitals was determined by the deferred antagonism assay on brain-heart infusion (BHI) agar plates. The total scaffold size was determined to be 2 502 817bp with a G+C content of 35.6%. Genome analyses revealed 2437 coding sequences, 76 RNA genes, 27 genes involved in drug resistance and 2 bacteriocinogenic gene clusters (for agneticin 3682 and hyicin 4244). Staphylococcus agnetis 3682 inhibited 80% of the MRSA isolates tested. This study describes the main features of the draft genome of S. agnetis 3682, a strain producing the first bacteriocin (agneticin 3682) reported in this species. A second gene cluster encoding a sactipeptide was also found in the bacterial chromosome. Agneticin 3682 shows a new potential application against clinical MRSA isolates.

Fagundes PC ，Francisco MS ，Sousa Santos IN ，Marques-Bastos SLS ，Paz JAS ，Albano RM ，do Carmo de Freire Bastos M ... -  《-》

Draft genome sequence of Staphylococcus agnetis 4244, a strain with gene clusters encoding distinct post-translationally modified antimicrobial peptides.

Here we report the draft genome sequence of Staphylococcus agnetis 4244, a strain involved in bovine mastitis, and its ability to inhibit different species of antibiotic-resistant Gram-positive bacteria owing to bacteriocin production. An Illumina MiSeq platform was used for genome sequencing. De novo genome assembly was done using the A5-miseq pipeline. Genome annotation was performed by the RAST server, and mining of bacteriocinogenic gene clusters was done using the BAGEL4 and antiSMASH v.5.0 platforms. Investigation of the spectrum of activity of S. agnetis 4244 was performed on BHI agar by deferred antagonism assay. The total scaffold size was determined to be 2 511 708 bp featuring a G+C content of 35.6%. The genome contains 2431 protein-coding sequences and 80 RNA sequences. Genome analyses revealed three prophage sequences inserted in the genome as well as several genes involved in drug resistance and two bacteriocin gene clusters (encoding a thiopeptide and a sactipeptide) encoded on the bacterial chromosome. Staphylococcus agnetis 4244 was able to inhibit all 44 strains of antibiotic-resistant Gram-positive bacteria tested in this study, including vancomycin-resistant enterococci (VRE), methicillin-resistant Staphylococcus aureus (MRSA) and other antibiotic-resistant staphylococcal strains. This study emphasises the potential biotechnological application of this strain for production of bacteriocins that could be used in the food industry as biopreservatives and/or in medicine as alternative therapeutic options against VRE, MRSA, vancomycin-intermediate S. aureus and other antibiotic-resistant Gram-positive bacteria, including biofilm-forming isolates. It also provides some genetic features of the draft genome of S. agnetis 4244.

Francisco MS ，Coelho MLV ，Duarte AFS ，Towle KM ，Chiorean S ，Almeida GS ，van Belkum MJ ，Nes IF ，Vederas JC ，Bastos MDCF ... -  《-》

Draft genome sequence of the producer strain of aureocin 4181, an antimicrobial peptide with antagonistic activity against multidrug-resistant staphylococci.

The present study reports the draft genome sequence of Staphylococcus aureus 4181, a strain involved in bovine mastitis that produces aureocin 4181, a broad-spectrum antimicrobial peptide (AMP). Inhibition of multidrug-resistant (MDR) staphylococci involved in human infections by S. aureus 4181 was also investigated. A sequencing library was constructed using a Nextera XT DNA Library Preparation Kit (Illumina). Whole-genome shotgun sequencing was performed using an Illumina MiSeq System. The A5-miseq pipeline was employed for de novo genome assembly. Genome annotation was performed by the RAST server. The online automated tools BAGEL4 and antiSMASH v.5.0 were used for mining gene clusters encoding AMP production. The virulence potential of the strain was investigated employing online tools. Its inhibitory activity toward MDR staphylococcal isolates associated with human infections was tested by the deferred antagonism assay on brain-heart infusion agar medium. The total scaffold size was determined to be 2 719 949 bp, with a G + C content of 32.7%. Genome analyses revealed 2504 protein-coding sequences and 74 RNA-coding sequences as well as several genes encoding drug resistance and a single AMP gene cluster coding for aureocin 4181. Staphylococcus aureus 4181 exhibited a pathogenic potential and inhibited all MDR staphylococcal isolates tested as a target. This study describes the main features of the draft genome of S. aureus 4181, a strain that produces the third four-component bacteriocin described in the literature, namely aureocin 4181. This bacteriocin is a potential alternative drug to control MDR staphylococcal isolates involved in human infections.

Marques-Bastos SLS ，Coelho MLV ，de Sousa Santos IN ，Farias FM ，Silva Francisco M ，Albano RM ，Sales Alviano C ，de Freire Bastos MDC ... -  《-》

Draft genome sequence of Enterococcus faecium E86, a strain producing broad-spectrum antimicrobial peptides: Description of a novel bacteriocin immunity protein and a novel sequence type.

The aim of this study was to report the draft genome sequence of the bacteriocinogenic strain Enterococcus faecium E86. Bacteriocins are prokaryotic peptides or proteins with antimicrobial activity. The genome information may contribute to the identification of enterocins produced by this strain that exhibit inhibitory activity against the foodborne pathogen Listeria monocytogenes and vancomycin-resistant enterococci (VRE) involved in human infections, among other bacterial genera and species. An Illumina MiSeq platform was used for genome sequencing. De novo assembly of 5 735 838 paired-end reads was done using the A5-miseq pipeline, yielding >300-fold average genome coverage. Genome annotation was performed by the RAST server, and mining of the bacteriocinogenic gene clusters was done using the BAGEL3 and antiSMASH v.4 platforms. The total scaffold size was determined to be 2 689 107 bp, approximately 2.7 Mbp, featuring a G + C content of 38.1%. The genome contains 2858 coding sequences and 74 RNA genes. Genome analyses revealed the presence of: 30 genes involved in drug resistance; 2 bacteriocinogenic gene clusters (for enterocin P and enterocin TW21); EntiTW21, a novel bacteriocin immunity protein and a novel multilocus sequence type (ST1500). This work highlights the potential biotechnological application of this strain for the production of enterocin P, a bacteriocin that can be employed in the food industry as a biopreservative against L. monocytogenes and as an alternative to classical antibiotics against VRE.

Miceli de Farias F ，Silva Francisco M ，Nascimento de Sousa Santos I ，Salustiano Marques-Bastos SL ，Lemos Miguel MA ，Mattos Albano R ，de Freire Bastos MDC ... -  《-》

Whole-genome sequencing of Staphylococcus aureus L401, a mecA-negative community-associated methicillin-resistant strain isolated from a healthy carrier.

Methicillin-resistant Staphylococcus aureus (MRSA) is a human pathogen of great concern owing to its antimicrobial resistance and virulence properties. Here we report the first draft genome sequence of a mecA-negative community-associated MRSA strain isolated from a healthy young Mexican paediatric carrier in order to reveal the genomic structure underlying the multidrug-resistant phenotype and to discover the virulence properties of this strain. The draft genome sequence of S. aureus L401 was obtained using an Ion Torrent™ PGM platform. De novo assembled contigs were annotated, and antimicrobial resistance genes and virulence factors were identified using ResFinder and VirulenceFinder, respectively. In addition, a mutational survey of native pbp, gdpP and yjbH genes was performed. In silico multilocus sequence typing (MLST) and spa typing were also performed. S. aureus L401 has a genome size of 2 831 587 bp with 2799 protein-coding sequences. Various antimicrobial resistance genes conferring resistance to aminoglycosides, β-lactams, fluoroquinolones and macrolide-lincosamide-streptogramin B antimicrobials were found. Although both mecA and staphylococcal cassette chromosome mec (SCCmec) elements were absent, a missense mutation in PBP3 was identified. Moreover, genes encoding exfoliative toxin A, γ- and β-haemolysin, and several enterotoxins were also identified. S. aureus L401 belongs to ST109 and spa type t209. The availability of this genome will allow an insight into S. aureus resistance and virulence determinants as well as its epidemiology, lineage, evolution and genomic features involved in the paediatric commensal carriage.

Magaña-Lizárraga JA ，Parra-Unda JR ，Ahumada-Santos YP ，de J Uribe-Beltrán M ，Gómez-Gil B ，Vega-López IF ，Prieto-Alvarado R ，Báez-Flores ME ... -  《-》