Comparative Genome Sequencing of an Isogenic Pair of USA800 Clinical Methicillin-Resistant Staphylococcus aureus Isolates Obtained before and after Daptomycin Treatment Failure

ABSTRACTWe describe here a clinical daptomycin treatment failure in a patient with recurrent methicillin-resistantStaphylococcus aureus(MRSA) bacteremia in whom daptomycin was administered after a failed empirical treatment course with vancomycin and piperacillin-tazobactam. We had the opportunity to compare the genome sequences of an isogenic pair of daptomycin-susceptible and -resistant MRSA isolates obtained before and after initiation of daptomycin therapy, respectively. The genotype of both isolates was USA800, ST5, SCCmectype IV,agrtype II. There was no increase in cell wall thickness in the daptomycin-resistant strain despite having decreased susceptibility to both vancomycin and daptomycin. By comparing the genome sequences by pyrosequencing, we identified a polymorphism (S337L) in the tenth transmembrane segment of the multiple peptide resistance factor, MprF, encoding lysyl phosphatidylglycerol transferase. This enzyme has been shown previously to promote repulsion of daptomycin at the cell surface by addition of positively charged lysine to phosphatidylglycerol. Also, thehlbopen reading frame (ORF) encoding the β-toxin was interrupted by a prophage in the daptomycin-susceptible strain; this phage was missing in the daptomycin-resistant isolate and thehlbORF was restored. Loss of the phage in the resistant isolate also resulted in loss of the virulence factor genesclpP,scn, andsak. This is the first study to use pyrosequencing to compare the genomes of a daptomycin-susceptible/resistant MRSA isolate pair obtained during failed daptomycin therapy in humans.

Download Full-text

Commercially Distributed Meat as a Potential Vehicle for Community-Acquired Methicillin-Resistant Staphylococcus aureus

Applied and Environmental Microbiology ◽

10.1128/aem.07470-11 ◽

2012 ◽

Vol 78 (8) ◽

pp. 2797-2802 ◽

Cited By ~ 33

Author(s):

Kikuyo Ogata ◽

Hiroshi Narimatsu ◽

Masahiro Suzuki ◽

Wataru Higuchi ◽

Tatsuo Yamamoto ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Drug Susceptibility ◽

Methicillin Resistant ◽

Content Type ◽

Reading Frame ◽

Type Iv ◽

Mrsa Infection ◽

Stool Samples ◽

Mrsa Strains ◽

Meat Samples

ABSTRACTThe incidence of community-acquired methicillin-resistantStaphylococcus aureus(CA-MRSA) infection has been increasing; however, the sources of infection remain unclear. Therefore, we investigated the involvement of meat as a possible mediator of CA-MRSA infection. We examined the distribution of MRSA strains in commercially distributed raw meat samples (n= 197) and diarrheal stool samples of outpatients (n= 1,287) that were collected in Oita Prefecture, Japan, between 2003 and 2009 for routine legal inspections. Fourteen MRSA strains were isolated from three meat and 11 stool samples. Among these, seven isolates from three meat and four stool samples exhibited the same epidemiological marker profiles [coagulase type III, staphylococcal enterotoxin C, staphylococcal chromosomal cassettemec(SCCmec) type IV, ST8,spatype 606 (t1767), and toxic shock syndrome toxin-1 (TSST-1) producing type]. Furthermore, of the seven strains, three isolates from two meat samples and one stool sample collected in 2007 exhibited completely identical characteristics with respect to phage open reading frame (ORF) typing, pulsed-field gel electrophoresis, and drug susceptibility profiles. The results suggest that commercially distributed meat could play a role in the prevalence of CA-MRSA in the community.

Download Full-text

Complete Genome Sequences of Methicillin-Resistant Staphylococcus aureus Strains 110900 and 128254, Two Representatives of the CRISPR-Cas-Carrying Sequence Type 630/spa Type t4549 Lineage

Microbiology Resource Announcements ◽

10.1128/mra.00891-20 ◽

2020 ◽

Vol 9 (41) ◽

Author(s):

Raphael N. Sieber ◽

Søren Overballe-Petersen ◽

Hülya Kaya ◽

Anders R. Larsen ◽

Andreas Petersen

Keyword(s):

Staphylococcus Aureus ◽

Complete Genome ◽

Methicillin Resistant Staphylococcus Aureus ◽

Nordic Countries ◽

Sequence Type ◽

Genome Sequences ◽

Methicillin Resistant ◽

Content Type ◽

Spa Type

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) sequence type 630 (ST630) and spa type t4549 is an emerging lineage in Nordic countries, and some representatives carry the CRISPR-Cas system. Here, the complete genome sequences of two isolates from this lineage are presented, comprising chromosomes of 2,918,239 and 2,877,083 nucleotides, respectively, and a 2,473-nucleotide plasmid carrying erm(C).

Download Full-text

Complete Genome Sequences of Eight Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients in Japan

Microbiology Resource Announcements ◽

10.1128/mra.01212-19 ◽

2019 ◽

Vol 8 (47) ◽

Cited By ~ 2

Author(s):

Miyako Hikichi ◽

Miki Nagao ◽

Kazunori Murase ◽

Chihiro Aikawa ◽

Takashi Nozawa ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Soft Tissue ◽

Complete Genome ◽

Methicillin Resistant Staphylococcus Aureus ◽

Clinical Manifestations ◽

Invasive Disease ◽

Genome Sequences ◽

Methicillin Resistant ◽

Content Type ◽

Mrsa Strains

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing nosocomial infections, and the clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to soft tissue infection to fulminant invasive disease. Here, we report the complete genome sequences of eight MRSA strains isolated from patients in Japan.

Download Full-text

Nasal Methicillin-Resistant Staphylococcus aureus (MRSA) PCR Testing Reduces the Duration of MRSA-Targeted Therapy in Patients with Suspected MRSA Pneumonia

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02432-16 ◽

2017 ◽

Vol 61 (4) ◽

Cited By ~ 19

Author(s):

Nidhu Baby ◽

Andrew C. Faust ◽

Terri Smith ◽

Lyndsay A. Sheperd ◽

Laura Knoll ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Targeted Therapy ◽

Length Of Hospital Stay ◽

Serum Levels ◽

Methicillin Resistant ◽

Content Type ◽

Before And After ◽

Health Care Associated Pneumonia ◽

The Impact ◽

Suspected Pneumonia

ABSTRACT The objective of this study was to evaluate the impact of pharmacist-ordered methicillin-resistant Staphylococcus aureus (MRSA) PCR testing on the duration of empirical MRSA-targeted antibiotic therapy in patients with suspected pneumonia. This is a retrospective analysis of patients who received vancomycin or linezolid for suspected pneumonia before and after the implementation of a pharmacist-driven protocol for nasal MRSA PCR testing. Patients were included if they were adults of >18 years of age and initiated on vancomycin or linezolid for suspected MRSA pneumonia. The primary endpoint was the duration of vancomycin or linezolid therapy. After screening 368 patients, 57 patients met inclusion criteria (27 pre-PCR and 30 post-PCR). Baseline characteristics were similar between the two groups, with the majority of patients classified as having health care-associated pneumonia (68.4%). The use of the nasal MRSA PCR test reduced the mean duration of MRSA-targeted therapy by 46.6 h (74.0 ± 48.9 h versus 27.4 ± 18.7 h; 95% confidence interval [CI], 27.3 to 65.8 h; P < 0.0001). Fewer patients in the post-PCR group required vancomycin serum levels and dose adjustment (48.1% versus 16.7%; P = 0.02). There were no significant differences between the pre- and post-PCR groups regarding days to clinical improvement (1.78 ± 2.52 versus 2.27 ± 3.34; P = 0.54), length of hospital stay (11.04 ± 9.5 versus 8.2 ± 7.8; P = 0.22), or hospital mortality (14.8% versus 6.7%; P = 0.41). The use of nasal MRSA PCR testing in patients with suspected MRSA pneumonia reduced the duration of empirical MRSA-targeted therapy by approximately 2 days without increasing adverse clinical outcomes.

Download Full-text

Draft Genome Sequences of 14 Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolates from Swine Farms in the United States

Genome Announcements ◽

10.1128/genomea.01082-17 ◽

2017 ◽

Vol 5 (44) ◽

Author(s):

Samantha J. Hau ◽

Darrell O. Bayles ◽

David P. Alt ◽

Timothy S. Frana ◽

Tracy L. Nicholson

Keyword(s):

United States ◽

Staphylococcus Aureus ◽

Methicillin Resistant Staphylococcus Aureus ◽

Draft Genome ◽

The United States ◽

Sequence Type ◽

Genome Sequences ◽

Methicillin Resistant ◽

Content Type ◽

Mrsa St398

ABSTRACT Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is a bacterium carried by or obtained from swine and other livestock. The initial and predominant swine-associated LA-MRSA sequence type (ST) identified is ST398. Here, we present 14 draft genome sequences from LA-MRSA ST398 isolates found in the United States.

Download Full-text

Characterization of Methicillin-Resistant Staphylococcus aureus Isolates from Food and Food Products of Poultry Origin in Germany

Applied and Environmental Microbiology ◽

10.1128/aem.00561-11 ◽

2011 ◽

Vol 77 (20) ◽

pp. 7151-7157 ◽

Cited By ~ 134

Author(s):

Andrea T. Feßler ◽

Kristina Kadlec ◽

Melanie Hassel ◽

Tomasz Hauschild ◽

Christopher Eidam ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Meat Products ◽

Poultry Meat ◽

The Novel ◽

Methicillin Resistant ◽

Content Type ◽

Turkey Meat ◽

Poultry Products ◽

Type Iv ◽

Toxic Shock Syndrome Toxin

ABSTRACTDuring a survey of fresh chicken and turkey meat as well as chicken and turkey meat products for the presence of methicillin-resistantStaphylococcus aureus(MRSA) isolates in Germany, 32 (37.2%) of 86 samples were MRSA positive. Twenty-eight of these MRSA isolates belonged to clonal complex 398 (CC398), which is widespread among food-producing animals. These CC398 isolates carried SCCmecelements of type IV or V and exhibitedspatype t011, t034, t899, t2346 or t6574 and either the knowndrutypes dt2b, dt6j, dt10a, dt10q, dt11a, dt11v, and dt11ab or the noveldrutypes dt6m, dt10as, and dt10at. In addition, two MRSA sequence type 9 (ST9) isolates with a type IV SCCmeccassette,spatype t1430, anddrutype dt10a as well as single MRSA ST5 and ST1791 isolates with a type III SCCmeccassette,spatype t002, anddrutype dt9v were identified. All but two isolates were classified as multiresistant. A wide variety of resistance phenotypes and genotypes were detected. All isolates were negative for the major virulence factors, such as Panton-Valentine leukocidin, toxic shock syndrome toxin 1, or exfoliative toxins. In contrast to the MRSA CC398 isolates, the four ST9, ST5, or ST1791 isolates harbored theegcgene cluster for enterotoxin G, I, M, N, O, and U genes. Although the relevance of contamination of fresh poultry meat or poultry products with MRSA is currently unclear, the presence of multiresistant and, in part, enterotoxigenic MRSA emphasizes the need for further studies to elucidate possible health hazards for consumers.

Download Full-text

Draft Genome Sequences of One Methicillin-Sensitive and Seven Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained in California

Genome Announcements ◽

10.1128/genomea.01084-17 ◽

2017 ◽

Vol 5 (42) ◽

Cited By ~ 3

Author(s):

Samantha J. Hau ◽

Darrell O. Bayles ◽

David P. Alt ◽

Tracy L. Nicholson

Keyword(s):

Staphylococcus Aureus ◽

Genome Sequence ◽

Methicillin Resistant Staphylococcus Aureus ◽

Draft Genome ◽

Mobile Genetic Elements ◽

Sequence Type ◽

Commensal Bacterium ◽

Genome Sequences ◽

Methicillin Resistant ◽

Content Type

ABSTRACT Staphylococcus aureus is a commensal bacterium of humans that can cause a spectrum of diseases. An isolate’s capacity to cause disease is partially attributed to the acquisition of novel mobile genetic elements. This report provides the draft genome sequence of one methicillin-susceptible and seven methicillin-resistant clinical human S. aureus isolates.

Download Full-text

agrDysfunction Affects Staphylococcal Cassette ChromosomemecType-Dependent Clinical Outcomes in Methicillin-Resistant Staphylococcus aureus Bacteremia

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.04962-14 ◽

2015 ◽

Vol 59 (6) ◽

pp. 3125-3132 ◽

Cited By ~ 15

Author(s):

Chang Kyung Kang ◽

Jeong Eun Cho ◽

Yoon Jeong Choi ◽

Younghee Jung ◽

Nak-Hyun Kim ◽

...

Keyword(s):

Staphylococcus Aureus ◽

South Korea ◽

Clinical Outcomes ◽

Tertiary Care ◽

High Rate ◽

Care Hospital ◽

Virulence Determinants ◽

Methicillin Resistant ◽

Content Type ◽

Type Iv

ABSTRACTStaphylococcal cassette chromosomemecelement (SCCmec) type-dependent clinical outcomes may vary due to geographical variation in the presence of virulence determinants. We compared the microbiological factors and mortality attributed to methicillin-resistantStaphylococcus aureus(MRSA) bacteremia between SCCmectypes II/III and type IV. All episodes of MRSA bacteremia in a tertiary-care hospital (South Korea) over a 4.5-year period were reviewed. We studied the microbiological factors associated with all blood MRSA isolates, includingspatype,agrtype,agrdysfunction, and the genes for Panton-Valentine leukocidin (PVL) and phenol-soluble modulin (PSM)-mec, in addition to SCCmectype. Of 195 cases, 137 involved SCCmectypes II/III, and 58 involved type IV. The mortality attributed to MRSA bacteremia was less frequent among the SCCmectype IV (5/58) than that among types II/III (39/137,P= 0.002). This difference remained significant when adjusted for clinical factors (adjusted odds ratio [aOR], 0.14; 95% confidence interval [CI], 0.04 to 0.49;P= 0.002). Of the microbiological factors tested,agrdysfunction was the only significant factor that showed different positivity between the SCCmectypes, and it was independently associated with MRSA bacteremia-attributed mortality (aOR, 4.71; 95% CI, 1.72 to 12.92;P= 0.003). SCCmectype IV is associated with lower MRSA bacteremia-attributed mortality than are types II/III, which might be explained by the high rate ofagrdysfunction in SCCmectypes II/III in South Korea.

Download Full-text

Complete Genome Sequences of Two USA300-Related Community-Associated Methicillin-Resistant Staphylococcus aureus Clinical Isolates

Microbiology Resource Announcements ◽

10.1128/mra.00404-19 ◽

2019 ◽

Vol 8 (18) ◽

Cited By ~ 1

Author(s):

Jo-Ann McClure ◽

Kunyan Zhang

Keyword(s):

Staphylococcus Aureus ◽

North America ◽

Complete Genome ◽

Methicillin Resistant Staphylococcus Aureus ◽

Evolutionary Relationships ◽

Significant Morbidity ◽

Genome Sequences ◽

Methicillin Resistant ◽

Content Type ◽

Strain Type

USA300 is a predominant community-associated methicillin-resistant Staphylococcus aureus strain causing significant morbidity and mortality in North America. We present the full annotated genome sequences of two methicillin-resistant Staphylococcus aureus isolates related to the USA300 pulsotype with the goal of studying the evolutionary relationships of this highly successful strain type.

Download Full-text

First Report ofcfr-Carrying Plasmids in the Pandemic Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Staphylococcal Cassette ChromosomemecType IV Clone

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02949-15 ◽

2016 ◽

Vol 60 (5) ◽

pp. 3007-3015 ◽

Cited By ~ 21

Author(s):

Anna C. Shore ◽

Alexandros Lazaris ◽

Peter M. Kinnevey ◽

Orla M. Brennan ◽

Gráinne I. Brennan ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Ribosomal Proteins ◽

Resistance Mechanisms ◽

Sequence Type ◽

23S Rrna ◽

Methicillin Resistant ◽

Content Type ◽

First Report ◽

Type Iv ◽

Linezolid Resistance

ABSTRACTLinezolid is often the drug of last resort for serious methicillin-resistantStaphylococcus aureus(MRSA) infections. Linezolid resistance is mediated by mutations in 23S rRNA and genes for ribosomal proteins;cfr, encoding phenicol, lincosamide, oxazolidinone, pleuromutilin, and streptogramin A (PhLOPSA) resistance; its homologuecfr(B); oroptrA, conferring oxazolidinone and phenicol resistance. Linezolid resistance is rare inS. aureus, andcfris even rarer. This study investigated the clonality and linezolid resistance mechanisms of two MRSA isolates from patients in separate Irish hospitals. Isolates were subjected tocfrPCR, PhLOPSAsusceptibility testing, 23S rRNA PCR and sequencing, DNA microarray profiling,spatyping, pulsed-field gel electrophoresis (PFGE), plasmid curing, and conjugative transfer. Whole-genome sequencing was used for single-nucleotide variant (SNV) analysis, multilocus sequence typing, L protein mutation identification,cfrplasmid sequence analysis, andoptrAandcfr(B) detection. Isolates M12/0145 and M13/0401 exhibited linezolid MICs of 64 and 16 mg/liter, respectively, and harbored identical 23S rRNA and L22 mutations, but M12/0145 exhibited the mutation in 2/6 23S rRNA alleles, compared to 1/5 in M13/0401. Both isolates were sequence type 22 MRSA staphylococcal cassette chromosomemectype IV (ST22-MRSA-IV)/spatype t032 isolates, harboredcfr, exhibited the PhLOPSAphenotype, and lackedoptrAandcfr(B). They differed by five PFGE bands and 603 SNVs. Isolate M12/0145 harboredcfrandfexAon a 41-kb conjugative pSCFS3-type plasmid, whereas M13/0401 harboredcfrandlsa(B) on a novel 27-kb plasmid. This is the first report ofcfrin the pandemic ST22-MRSA-IV clone. Differentcfrplasmids and mutations associated with linezolid resistance in genotypically distinct ST22-MRSA-IV isolates highlight that prudent management of linezolid use is essential.

Download Full-text