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      Complete Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Strain SQL1/USA300, Used for Testing the Antimicrobial Properties of Clay Phyllosilicates and Customized Aluminosilicates

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      Author(s): a , , b , c ,
      Editor(s):
      Publication date (Electronic, pub):
      Publication date (Electronic, collection):
      Journal: Microbiology Resource Announcements
      Publisher: American Society for Microbiology

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          ABSTRACT

          Methicillin-resistant Staphylococcus aureus (MRSA) is a Gram-positive bacterium that causes community-acquired and health care-acquired infections. We previously demonstrated that clay phyllosilicates and customized aluminosilicates display antimicrobial activity against the MRSA strain SQL1. The SQL1 annotated genome reveals a USA300 lineage and contributes critical knowledge of the MRSA virulence factors associated with tissue infection.

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          Minimap2: pairwise alignment for nucleotide sequences

          Heng Li (2018)
          Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
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            RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

            Wenjun Li, Kathleen O’Neill, Daniel H. Haft … (2020)
            The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP) since 2018 have resulted in a substantial reduction in spurious annotation. The hierarchical collection of protein family models (PFMs) used by PGAP as evidence for structural and functional annotation was expanded to over 35 000 protein profile hidden Markov models (HMMs), 12 300 BlastRules and 36 000 curated CDD architectures. As a result, >122 million or 79% of RefSeq proteins are now named based on a match to a curated PFM. Gene symbols, Enzyme Commission numbers or supporting publication attributes are available on over 40% of the PFMs and are inherited by the proteins and features they name, facilitating multi-genome analyses and connections to the literature. In adherence with the principles of FAIR (findable, accessible, interoperable, reusable), the PFMs are available in the Protein Family Models Entrez database to any user. Finally, the reference and representative genome set, a taxonomically diverse subset of RefSeq prokaryotic genomes, is now recalculated regularly and available for download and homology searches with BLAST. RefSeq is found at  https://www.ncbi.nlm.nih.gov/refseq/ .
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              Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study

              Laura García-Álvarez, Matthew TG Holden, Heather Lindsay … (2011)
              Summary Background Animals can act as a reservoir and source for the emergence of novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human beings. Here, we report the discovery of a strain of S aureus (LGA251) isolated from bulk milk that was phenotypically resistant to meticillin but tested negative for the mecA gene and a preliminary investigation of the extent to which such strains are present in bovine and human populations. Methods Isolates of bovine MRSA were obtained from the Veterinary Laboratories Agency in the UK, and isolates of human MRSA were obtained from diagnostic or reference laboratories (two in the UK and one in Denmark). From these collections, we searched for mecA PCR-negative bovine and human S aureus isolates showing phenotypic meticillin resistance. We used whole-genome sequencing to establish the genetic basis for the observed antibiotic resistance. Findings A divergent mecA homologue (mecA LGA251) was discovered in the LGA251 genome located in a novel staphylococcal cassette chromosome mec element, designated type-XI SCCmec. The mecA LGA251 was 70% identical to S aureus mecA homologues and was initially detected in 15 S aureus isolates from dairy cattle in England. These isolates were from three different multilocus sequence type lineages (CC130, CC705, and ST425); spa type t843 (associated with CC130) was identified in 60% of bovine isolates. When human mecA-negative MRSA isolates were tested, the mecA LGA251 homologue was identified in 12 of 16 isolates from Scotland, 15 of 26 from England, and 24 of 32 from Denmark. As in cows, t843 was the most common spa type detected in human beings. Interpretation Although routine culture and antimicrobial susceptibility testing will identify S aureus isolates with this novel mecA homologue as meticillin resistant, present confirmatory methods will not identify them as MRSA. New diagnostic guidelines for the detection of MRSA should consider the inclusion of tests for mecA LGA251. Funding Department for Environment, Food and Rural Affairs, Higher Education Funding Council for England, Isaac Newton Trust (University of Cambridge), and the Wellcome Trust.
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                Author and article information

                Contributors
                Enrique G. Medrano:
                ORCID: https://orcid.org/0000-0002-6079-0302
                Shelley E. Haydel
                Steven R. Gill: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (publisher-id): mra
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic, pub): 11 November 2021
                Publication date (Electronic, collection): November 2021
                Publication date PMC-release: 11 November 2021
                Volume: 10
                Issue: 45
                Electronic Location Identifier: e00861-21
                Affiliations
                [a ] Insect Control and Cotton Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, College Station, Texas, USA
                [b ] School of Life Sciences, Arizona State University, Tempe, Arizona, USA
                [c ] Biodesign Institute Center for Bioelectronics and Biosensors, Arizona State University, Tempe, Arizona, USA
                University of Rochester School of Medicine and Dentistry
                Author information
                https://orcid.org/0000-0002-6079-0302
                Article
                Publisher ID: MRA00861-21 Publisher ID: mra.00861-21
                DOI: 10.1128/MRA.00861-21
                PMC ID: 8582308
                PubMed ID: 34761956
                SO-VID: 31f5b3d2-8d44-4b6c-810b-057d09b302fd
                Copyright © Copyright © 2021 Medrano and Haydel.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 30 August 2021
                Date accepted : 23 October 2021
                Page count
                Figures: 1, Tables: 0, Equations: 0, References: 16, Pages: 3, Words: 1509
                Funding
                Funded by: HHS | NIH | OSC | Common Fund (NIH Common Fund), FundRef https://doi.org/10.13039/100015326;
                Award ID: AT004690
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Compound subject: bacteriology, Bacteriology
                Custom metadata
                cover-date November 2021

                Data availability:

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