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Asset Tag: Bacterial genome

July 7, 2019

Complete genome sequence of Achromobacter spanius type strain DSM 23806T, a pathogen isolated from human blood.

Achromobacter spanius is a newly described, non-fermenting, Gram-negative, coccoid pathogen isolated from human blood. Whole-genome sequencing of the A. spanius type strain was performed to investigate the mechanism of pathogenesis of this strain at a genomic level.The complete genome of A. spanius type strain DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing.The complete genome of DSM 23806T consists of one circular DNA chromosome of 6425783bp with a G+C content of 64.26%. The entire genome contains 5804 predicted coding sequences (CDS) and 55 tRNAs. Genomic island (GI) analysis showed that this strain encodes several important pathogenesis- and resistance-related genes.These results strongly suggest that GIs provide some fitness advantages in A. spanius type strain DSM 23806T. This report provides an extensive understanding of A. spanius at a genomic level as well as an understanding of the evolution of A. spanius. Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

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July 7, 2019

Complete genome sequence of Lactobacillus paracasei EG9, a strain accelerating free amino acid production during cheese ripening.

Lactobacillus paracasei EG9 is a strain isolated from well-ripened cheese and accelerates free amino acid production during cheese ripening. Its complete genome sequence was determined using the PacBio RS II platform, revealing a single circular chromosome of 2,927,257 bp, a G+C content of 46.59%, and three plasmids. Copyright © 2018 Asahina et al.

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July 7, 2019

Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic Rhizobia.

Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants, species from the Rhizobiales order define a core lineage of the plant microbiota, suggesting additional functional interactions with plant hosts. In this work, genome analyses of 1,314 Rhizobiales isolates along with amplicon studies of the root microbiota reveal the evolutionary history of nitrogen-fixing symbiosis in this bacterial order. Key symbiosis genes were acquired multiple times, and the most recent common ancestor could colonize roots of a broad host range. In addition, root growth promotion is a characteristic trait of Rhizobiales in Arabidopsis thaliana, whereas interference with plant immunity constitutes a separate, strain-specific phenotype of root commensal Alphaproteobacteria. Additional studies with a tripartite gnotobiotic plant system reveal that these traits operate in a modular fashion and thus might be relevant to microbial homeostasis in healthy roots. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

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July 7, 2019

Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.

Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions. Copyright © 2018. Published by Elsevier B.V.

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July 7, 2019

First description of novel arginine catabolic mobile elements (ACMEs) types IV and V harboring a kdp operon in Staphylococcus epidermidis characterized by whole genome sequencing.

The arginine catabolic mobile element (ACME) was first described in the methicillin-resistant Staphylococcus aureus strain USA300 and is thought to facilitate survival on skin. To date three distinct ACME types have been characterized comprehensively in S. aureus and/or Staphylococcus epidermidis. Type I harbors the arc and opp3 operons encoding an arginine deaminase pathway and an oligopeptide permease ABC transporter, respectively, type II harbors the arc operon only, and type III harbors the opp3 operon only. To investigate the diversity and detailed genetic organization of ACME, whole genome sequencing (WGS) was performed on 32 ACME-harboring oro-nasal S. epidermidis isolates using MiSeq- and PacBio-based WGS platforms. In nine isolates the ACMEs lacked the opp3 operon, but harbored a complete kdp operon (kdpE/D/A/B/C) located a maximum of 2.8?kb upstream of the arc operon. The kdp operon exhibited 63% DNA sequence identity to the native S. aureus kdp operon. These findings identified a novel, previously undescribed ACME type (designated ACME IV), which could be subtyped (IVa and IVb) based on distinct 5′ flanking direct repeat sequences (DRs). Multilocus sequence typing (MLST) sequences extracted from the WGS data identified the sequence types (STs) of the isolates investigated. Four of the nine ACME IV isolates belonged to ST153, and one to ST17, a single locus variant of ST153. A tenth isolate, identified as ST5, harbored another novel ACME type (designated ACME V) containing the kdp, arc and opp3 operons and flanked by DR_F, and DR_B but lacked any internal DRs. ACME V was colocated with a staphylococcal chromosome cassette mec (SCCmec) IV element and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) in a 116.9?kb composite island. The extensive genetic diversity of ACME in S. epidermidis has been further elucidated by WGS, revealing two novel ACME types IV and V for the first time. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Acinetobacter radioresistens strain LH6, a multidrug-resistant bacteriophage-propagating strain.

Antimicrobial resistance is a major problem worldwide. Understanding the interplay between drug-resistant pathogens, such as Acinetobacter baumannii and related species, potentially acting as environmental reservoirs is critical for preventing the spread of resistance determinants. Here we report the complete genome sequence of a multidrug-resistant bacteriophage-propagating strain of Acinetobacter radioresistens.

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July 7, 2019

Complete genome sequences of Canadian epidemic methicillin-resistant Staphylococcus aureus strains CMRSA3 and CMRSA6.

Methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 8 (CC8) sequence type 239 (ST239) represents a predominant hospital-associated MRSA sublineage present worldwide. The Canadian epidemic MRSA strains CMRSA3 and CMRSA6 are moderately virulent members of this group but are closely related to the highly virulent strain TW20. Whole-genome sequencing of CMRSA3 and CMRSA6 was conducted to identify genetic determinants associated with their virulence.

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July 7, 2019

Complete genome sequence of Aeromonas rivipollensis KN-Mc-11N1, isolated from a wild nutria (Myocastor coypus) in South Korea.

We report here the complete genome sequence of Aeromonas rivipollensis KN-Mc-11N1, which was isolated from a wild nutria (Myocastor coypus) in South Korea. Genomic analysis indicated that A. rivipollensis may have zoonotic potential similar to that of other aeromonads, and nutria could be one of the sources of transmission of zoonotic pathogens to humans.

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