Complete genome screening of clinical MRSA isolates identifies lineage diversity and provides full resolution of transmission and outbreak events

AbstractWhole-genome sequencing (WGS) of Staphylococcus aureus is increasingly used as part of infection prevention practices, but most applications are focused on conserved core genomic regions due to limitations of short-read technologies. In this study we established a long-read technology-based WGS screening program of all first-episode MRSA blood infections at a major urban hospital. A survey of 132 MRSA genomes assembled from long reads revealed widespread gain/loss of accessory mobile genetic elements among established hospital- and community-associated lineages impacting >10% of each genome, and frequent megabase-scale inversions between endogenous prophages. We also characterized an outbreak of a CC5/ST105/USA100 clone among 3 adults and 18 infants in a neonatal intensive care unit (NICU) lasting 7 months. The pattern of changes among complete outbreak genomes provided full spatiotemporal resolution of its origins and progression, which was characterized by multiple sub-transmissions and likely precipitated by equipment sharing. Compared to other hospital strains, the outbreak strain carried distinct mutations and accessory genetic elements that impacted genes with roles in metabolism, resistance and persistence. This included a DNA-recognition domain recombination in the hsdS gene of a Type-I restriction-modification system that altered DNA methylation. RNA-Seq profiling showed that the (epi)genetic changes in the outbreak clone attenuated agr gene expression and upregulated genes involved in stress response and biofilm formation. Overall our findings demonstrate that long-read sequencing substantially improves our ability to characterize accessory genomic elements that impact MRSA virulence and persistence, and provides valuable information for infection control efforts.

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Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1904861116 ◽

2019 ◽

Vol 116 (40) ◽

pp. 20135-20140 ◽

Cited By ~ 17

Author(s):

Romain Guérillot ◽

Xenia Kostoulias ◽

Liam Donovan ◽

Lucy Li ◽

Glen P. Carter ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Genetic Basis ◽

Host Cells ◽

Type I ◽

Modification System ◽

Persistent Infections ◽

Restriction Modification System ◽

Long Read ◽

Small Colony ◽

Restriction Modification

Staphylococcus aureus small-colony variants (SCVs) are associated with unusually chronic and persistent infections despite active antibiotic treatment. The molecular basis for this clinically important phenomenon is poorly understood, hampered by the instability of the SCV phenotype. Here we investigated the genetic basis for an unstable S. aureus SCV that arose spontaneously while studying rifampicin resistance. This SCV showed no nucleotide differences across its genome compared with a normal-colony variant (NCV) revertant, yet the SCV presented the hallmarks of S. aureus linked to persistent infection: down-regulation of virulence genes and reduced hemolysis and neutrophil chemotaxis, while exhibiting increased survival in blood and ability to invade host cells. Further genome analysis revealed chromosome structural variation uniquely associated with the SCV. These variations included an asymmetric inversion across half of the S. aureus chromosome via recombination between type I restriction modification system (T1RMS) genes, and the activation of a conserved prophage harboring the immune evasion cluster (IEC). Phenotypic reversion to the wild-type–like NCV state correlated with reversal of the chromosomal inversion (CI) and with prophage stabilization. Further analysis of 29 complete S. aureus genomes showed strong signatures of recombination between hsdMS genes, suggesting that analogous CI has repeatedly occurred during S. aureus evolution. Using qPCR and long-read amplicon deep sequencing, we detected subpopulations with T1RMS rearrangements causing CIs and prophage activation across major S. aureus lineages. Here, we have discovered a previously unrecognized and widespread mechanism of reversible genomic instability in S. aureus associated with SCV generation and persistent infections.

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A Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak

Journal of Clinical Microbiology ◽

10.1128/jcm.01261-19 ◽

2019 ◽

Vol 57 (12) ◽

Cited By ~ 3

Author(s):

Mitchell J. Sullivan ◽

Deena R. Altman ◽

Kieran I. Chacko ◽

Brianne Ciferri ◽

Elizabeth Webster ◽

...

Keyword(s):

Intensive Care Unit ◽

Staphylococcus Aureus ◽

Intensive Care ◽

Neonatal Intensive Care Unit ◽

Neonatal Intensive Care ◽

Screening Program ◽

Type I ◽

Methicillin Resistant ◽

Content Type ◽

Long Read

ABSTRACT Whole-genome sequencing (WGS) of Staphylococcus aureus is increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant Staphylococcus aureus (MRSA) blood infections at a major urban hospital. A survey of 132 MRSA genomes assembled from long reads enabled detailed characterization of an outbreak lasting several months of a CC5/ST105/USA100 clone among 18 infants in a neonatal intensive care unit (NICU). Available hospital-wide genome surveillance data traced the origins of the outbreak to three patients admitted to adult wards during a 4-month period preceding the NICU outbreak. The pattern of changes among complete outbreak genomes provided full spatiotemporal resolution of its progression, which was characterized by multiple subtransmissions and likely precipitated by equipment sharing between adults and infants. Compared to other hospital strains, the outbreak strain carried distinct mutations and accessory genetic elements that impacted genes with roles in metabolism, resistance, and persistence. This included a DNA recognition domain recombination in the hsdS gene of a type I restriction modification system that altered DNA methylation. Transcriptome sequencing (RNA-Seq) profiling showed that the (epi)genetic changes in the outbreak clone attenuated agr gene expression and upregulated genes involved in stress response and biofilm formation. Overall, our findings demonstrate the utility of long-read sequencing for hospital surveillance and for characterizing accessory genomic elements that may impact MRSA virulence and persistence.

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Complete Genome Sequence of Brevibacterium linens SMQ-1335

Genome Announcements ◽

10.1128/genomea.01242-16 ◽

2016 ◽

Vol 4 (6) ◽

Cited By ~ 1

Author(s):

Alessandra G. de Melo ◽

Simon J. Labrie ◽

Jeannot Dumaresq ◽

Richard J. Roberts ◽

Denise M. Tremblay ◽

...

Keyword(s):

Complete Genome Sequence ◽

Open Reading Frames ◽

Type I ◽

Industrial Strain ◽

Modification System ◽

Brevibacterium Linens ◽

Restriction Modification System ◽

New Type ◽

Restriction Modification ◽

Reading Frames

Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.

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DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes

PLoS Pathogens ◽

10.1371/journal.ppat.1007841 ◽

2019 ◽

Vol 15 (6) ◽

pp. e1007841 ◽

Cited By ~ 9

Author(s):

Taylor M. Nye ◽

Kristin M. Jacob ◽

Elena K. Holley ◽

Juan M. Nevarez ◽

Suzanne Dawid ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Streptococcus Pyogenes ◽

Type I ◽

Modification System ◽

Restriction Modification System ◽

Restriction Modification

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The EcoKI Type I Restriction-Modification System in Escherichia coli Affects but Is Not an Absolute Barrier for Conjugation

Journal of Bacteriology ◽

10.1128/jb.02418-14 ◽

2014 ◽

Vol 197 (2) ◽

pp. 337-342 ◽

Cited By ~ 27

Author(s):

Louise Roer ◽

Frank M. Aarestrup ◽

Henrik Hasman

Keyword(s):

Escherichia Coli ◽

Rapid Evolution ◽

Type I ◽

Modification System ◽

Major Barrier ◽

Exogenous Dna ◽

Content Type ◽

Restriction Modification System ◽

K 12 ◽

Restriction Modification

The rapid evolution of bacteria is crucial to their survival and is caused by exchange, transfer, and uptake of DNA, among other things. Conjugation is one of the main mechanisms by which bacteria share their DNA, and it is thought to be controlled by varied bacterial immune systems. Contradictory results about restriction-modification systems based on phenotypic studies have been presented as reasons for a barrier to conjugation with and other means of uptake of exogenous DNA. In this study, we show that inactivation of the R.EcoKI restriction enzyme in strainEscherichia coliK-12 strain MG1655 increases the conjugational transfer of plasmid pOLA52, which carriers two EcoKI recognition sites. Interestingly, the results were not absolute, and uptake of unmethylated pOLA52 was still observed in the wild-type strain (with an intacthsdRgene) but at a reduction of 85% compared to the uptake of the mutant recipient with a disruptedhsdRgene. This leads to the conclusion that EcoKI restriction-modification affects the uptake of DNA by conjugation but is not a major barrier to plasmid transfer.

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Plasmid R16 ArdA Protein Preferentially Targets Restriction Activity of the Type I Restriction-Modification System EcoKI

Journal of Bacteriology ◽

10.1128/jb.185.6.2022-2025.2003 ◽

2003 ◽

Vol 185 (6) ◽

pp. 2022-2025 ◽

Cited By ~ 17

Author(s):

Angela T. Thomas ◽

William J. Brammar ◽

Brian M. Wilkins

Keyword(s):

Type I ◽

Bacterial Conjugation ◽

Modification System ◽

Restriction Modification System ◽

Modification Activity ◽

Restriction Modification

ABSTRACT The ArdA antirestriction protein of the IncB plasmid R16 selectively inhibited the restriction activity of EcoKI, leaving significant levels of modification activity under conditions in which restriction was almost completely prevented. The results are consistent with the hypothesis that ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification.

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Improved transformation efficiency of group A Streptococcus by inactivation of a type I restriction modification system

PLoS ONE ◽

10.1371/journal.pone.0248201 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0248201

Author(s):

Meredith B. Finn ◽

Kathryn M. Ramsey ◽

Hunter J. Tolliver ◽

Simon L. Dove ◽

Michael R. Wessels

Keyword(s):

Genetic Transformation ◽

Parent Strain ◽

Transformation Efficiency ◽

Genetic Manipulation ◽

Spontaneous Mutation ◽

Type I ◽

Modification System ◽

Restriction Modification System ◽

Group A ◽

Restriction Modification

Streptococcus pyogenes or group A Streptococcus (GAS) is a leading cause of bacterial pharyngitis, skin and soft tissue infections, life-threatening invasive infections, and the post-infectious autoimmune syndromes of acute rheumatic fever and post-streptococcal glomerulonephritis. Genetic manipulation of this important pathogen is complicated by resistance of the organism to genetic transformation. Very low transformation efficiency is attributed to recognition and degradation of introduced foreign DNA by a type I restriction-modification system encoded by the hsdRSM locus. DNA sequence analysis of this locus in ten GAS strains that had been previously transformed with an unrelated plasmid revealed that six of the ten harbored a spontaneous mutation in hsdR, S, or M. The mutations were all different, and at least five of the six were predicted to result in loss of function of the respective hsd gene product. The unexpected occurrence of such mutations in previously transformed isolates suggested that the process of transformation selects for spontaneous inactivating mutations in the Hsd system. We investigated the possibility of exploiting the increased transformability of hsd mutants by constructing a deletion mutation in hsdM in GAS strain 854, a clinical isolate representative of the globally dominant M1T1 clonal group. Mutant strain 854ΔhsdM exhibited a 5-fold increase in electrotransformation efficiency compared to the wild type parent strain and no obvious change in growth or off-target gene expression. We conclude that genetic transformation of GAS selects for spontaneous mutants in the hsdRSM restriction modification system. We propose that use of a defined hsdM mutant as a parent strain for genetic manipulation of GAS will enhance transformation efficiency and reduce the likelihood of selecting spontaneous hsd mutants with uncharacterized genotypes.

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Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci

mSphere ◽

10.1128/msphere.00799-21 ◽

2021 ◽

Author(s):

Sruti DebRoy ◽

William C. Shropshire ◽

Chau Nguyen Tran ◽

Haiping Hao ◽

Marc Gohel ◽

...

Keyword(s):

Dna Methylation ◽

Epigenetic Modification ◽

Type I ◽

Whole Genome ◽

Group A Streptococci ◽

Modification System ◽

Restriction Modification System ◽

Group A ◽

Restriction Modification

The advent of whole-genome approaches capable of detecting DNA methylation has markedly expanded appreciation of the diverse roles of epigenetic modification in prokaryotic physiology. For example, recent studies have suggested that DNA methylation impacts gene expression in some streptococci.

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