Complete genome sequence of community-associated methicillin-resistant Staphylococcus aureus (strain USA400-0051), a prototype of the USA400 clone

Côrtes, Marina Farrel; Costa, Maiana O. C.; Lima, Nicholas CB; Souza, Rangel Celso; Almeida, Luiz Gonzaga Paula de; Guedes, Luciane Prioli Ciapina; Vasconcelos, Ana Tr; Nicolás, Marisa Fabiana; Figueiredo, A.M.S.

doi:10.1590/0074-02760170128

Cited by 9 publications

(9 citation statements)

References 8 publications

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“…This CA-MRSA was isolated from soft tissue outbreaks of skin in USA but USA400 isolates can also be involved in severe infections resulting in deaths 7. DNA isolation was performed by phenol extraction and ethanol precipitation 8. Whole genome sequencing was performed using the Ion Torrent Platform (Ion PGM sequencer; Thermo Fisher Scientific, Waltham, MA, USA) according to the recommended protocol.…”

Section: Methodsmentioning

confidence: 99%

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Community-acquired methicillin-resistant Staphylococcus aureus from ST1 lineage harboring a new SCCmec IV subtype (SCCmec IVm) containing the tetK gene

Côrtes¹,

Botelho²,

Almeida

et al. 2018

IDR

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A pivotal event in the evolutionary path of methicillin-resistant Staphylococcus aureus (MRSA) is the acquisition of the staphylococcal cassette chromosome mec (SCCmec) element carrying the mecA gene, the determinant of methicillin resistance. Community-acquired (CA) MRSA is commonly associated with skin/soft tissue infections, and doxycycline is one of the drug choices for this purpose. Doxycycline resistance is associated with the acquisition of the tetK gene carried by the S. aureus plasmid pT181, which may also be integrated into SCCmec III and V. The aim of this study was to describe a novel SCCmec IV subtype (IVm) carrying tetK and reveal the genetic context of this element. The SCCmec sequence was obtained by whole-genome sequencing of the MRSA strain 2288 (ST1 CA-MRSA) and genomic analysis performed using different bioinformatics tools. A copy of pT181 was found to be integrated in the new SCCmec IVm of the strain 2288. The SCCmec IVm has high nucleotide identity (99%) with SCCmec IVa of the strain MW2, except for the J3 region, where the pT181 – carrying tetK gene – is inserted. Inverted repeats (IRs) flanking pT181 were found in this region, suggesting the occurrence of recombination events. The strain 2288 (spa type t125) shares most of the virulence attributes with MW2 (spa type t128), which is recognized in the past as a cause of severe infections in children in USA. The pattern of branching in the phylogenetic tree depicts a recent common ancestor shared by the 2228 strain and other MRSA from USA, including ERS410852, TCH70, CIG1835, CO-41, MW2, and USA400-0051, but none of them carried pT181. This study also showed that the tetK carried by SCCmec IVm is functional, determining resistance to doxycycline and tetracycline. The potential dissemination of the tetK and mecA genes in the same genetic event by the acquisition of this new SCCmec subtype is of concern for community infections.

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Section: Methodsmentioning

confidence: 99%

“…Contigs derived from the reads were assembled into scaffold sequences using Newbler software (version 2.3; Hoffman-La Roche Ltd.). Gaps within scaffolds were resolved as previously described 8. Automatic and manual genome annotation was performed using the System for Automated Bacterial Integrated Annotation (SABIA) 9.…”

Section: Methodsmentioning

confidence: 99%

Community-acquired methicillin-resistant Staphylococcus aureus from ST1 lineage harboring a new SCCmec IV subtype (SCCmec IVm) containing the tetK gene

Côrtes¹,

Botelho²,

Almeida

et al. 2018

IDR

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“…The two isolates differed each other, as IM-MRSA was assigned to ST9-XII type, while PD-MRSA to ST1-IVa type as was the case in a previous study(Karampatakis et al 2021b). The two t127 MRSA isolates transferred the γ-hemolysin genes hlgA, hlgB, hlgC and aureolysin aur gene, which have been previously described in both ST1-IVa and ST9-XII MRSA(Cortes et al 2017;Yu et al 2021). PD-MRSA carried the enterotoxin seh gene and the gene encoding leukocidin lukED, as previously described in ST1-IVa MRSA isolates(Shukla et al 2010;Cortes et al 2017).…”

mentioning

confidence: 86%

“…The two t127 MRSA isolates transferred the γ-hemolysin genes hlgA, hlgB, hlgC and aureolysin aur gene, which have been previously described in both ST1-IVa and ST9-XII MRSA(Cortes et al 2017;Yu et al 2021). PD-MRSA carried the enterotoxin seh gene and the gene encoding leukocidin lukED, as previously described in ST1-IVa MRSA isolates(Shukla et al 2010;Cortes et al 2017). IM-MRSA lacked leucocidin components, however it carried the enterotoxin sei, sem, seo, seu genes, although enterotoxin genes are usually absent in ST9-XII MRSA isolates(Yu et al 2021).…”

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confidence: 86%

Spa Diversity and Genetic Characterization of t127 Methicillin-resistant Staphylococcus Aureus in a Tertiary Greek Hospital

Tsergouli

Κarampatakis

Κοντοπούλου

et al. 2021

Preprint

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Introduction: Methicillin-resistant Staphylococcus aureus (MRSA) causes severe community and hospital acquired infections. Identification of staphylococcal cassette chromosome mec (SCCmec), multilocus-sequence typing, and sequencing of S. aureus protein A (spa) gene are used for MRSA typing. The aim was to investigate the spa types of MRSA isolates in a tertiary hospital in Greece and analyse the whole genome sequences of two t127 MRSA isolates. Methods: Totally, 39 MRSA isolates collected during July 2019 to June 2020 in “Georgios Gennimatas” General Hospital of Thessaloniki, Greece, were included in the study. Identification and antimicrobial susceptibility testing were performed using VITEK II automated system, and spa typing was performed. A minimum spanning tree was used to display the spa type frequencies and the genetic distances among them. Two t127-MRSA isolates (IM-MRSA and PD-MRSA) were selected for WGS.Results: Twenty-two different spa types were detected, with t002, t003, and t422 being the most frequent (5/39, 12.8% each), followed by t1994 (4/39, 10.3%). The isolates presented high genetic diversity and, taking into account the time between hospital admission and sampling, intrahospital spread did not occur. Even the two t127 isolates were assigned to different sequence types, ST9-XII-t127 and ST1-IVa-t127. Plasmids and genes conferring antimicrobial resistance and virulence were also identified.Conclusions: Various spa types were identified and together with the information about the time between hospital admission and sampling supports polyclonal MRSA spread in the hospital excluding a nosocomial infection. WGS provides a more detailed analysis distinguishing even the isolates belonging to the same spa type.

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“…High-throughput whole-genome sequencing (WGS) – a powerful tool based on next-generation sequencing – offers new opportunities for studying pathogenic bacteria and is now used widely to investigate pathogenesis and drug resistance mechanisms in a wide range of pathogens. 8 – 10 Supplementary to WGS, is whole-genome resequencing (WGRS) – a technique whereby a genome is sequenced and compared with the genome of a previously sequenced reference strain to identify sequence polymorphisms between the two sequences, such as single-nucleotide polymorphisms (SNPs), gene acquisition, recombination, loss as well as insertions and deletions (indels), that are potentially important in epidemiological analyses, drug resistance detection, and phylogenetic investigations. 11 Although there are several pneumococcal genomes in the public domain, WGRS is rarely used for investigation of drug resistance of S. pneumonia isolated in China.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of multidrug-resistant Streptococcus pneumoniae isolates

Pan

Zhang

Dong

et al. 2018

IDR

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IntroductionMultidrug resistance in Streptococcus pneumoniae has emerged as a serious problem to public health. A further understanding of the genetic diversity in antibiotic-resistant S. pneumoniae isolates is needed.MethodsWe conducted whole-genome resequencing for 25 pneumococcal strains isolated from children with different antimicrobial resistance profiles. Comparative analysis focus on detection of single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) was conducted. Moreover, phylogenetic analysis was applied to investigate the genetic relationship among these strains.ResultsThe genome size of the isolates was ~2.1 Mbp, covering >90% of the total estimated size of the reference genome. The overall G+C% content was ~39.5%, and there were 2,200–2,400 open reading frames. All isolates with different drug resistance profiles harbored many indels (range 131–171) and SNPs (range 16,103–28,128). Genetic diversity analysis showed that the variation of different genes were associated with specific antibiotic resistance. Known antibiotic resistance genes (pbps, murMN, ciaH, rplD, sulA, and dpr) were identified, and new genes (regR, argH, trkH, and PTS-EII) closely related with antibiotic resistance were found, although these genes were primarily annotated with functions in virulence as well as carbohydrate and amino acid transport and metabolism. Phylogenetic analysis unambiguously indicated that isolates with different antibiotic resistance profiles harbored similar genetic backgrounds. One isolate, 14-LC.ER1025, showed a much weaker phylogenetic relationship with the other isolates, possibly caused by genomic variation.ConclusionIn this study, although pneumococcal isolates had similar genetic backgrounds, strains were diverse at the genomic level. These strains exhibited distinct variations in their indel and SNP compositions associated with drug resistance.

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Complete genome sequence of community-associated methicillin-resistant Staphylococcus aureus (strain USA400-0051), a prototype of the USA400 clone

Cited by 9 publications

References 8 publications

Community-acquired methicillin-resistant <em>Staphylococcus aureus</em> from ST1 lineage harboring a new SCC<em>mec</em> IV subtype (SCC<em>mec</em> IVm) containing the <em>tetK</em> gene

Community-acquired methicillin-resistant <em>Staphylococcus aureus</em> from ST1 lineage harboring a new SCC<em>mec</em> IV subtype (SCC<em>mec</em> IVm) containing the <em>tetK</em> gene

Spa Diversity and Genetic Characterization of t127 Methicillin-resistant Staphylococcus Aureus in a Tertiary Greek Hospital

Comparative genomic analysis of multidrug-resistant <em>Streptococcus pneumoniae</em> isolates

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