Impact of Strain Typing Methods on Assessment of Relationship between Paired Nares and Wound Isolates of Methicillin-Resistant Staphylococcus aureus

Abstract

The anterior nares are the site of choice for the Veterans Administration methicillin-resistant Staphylococcus aureus (MRSA) surveillance program; however, a correlation between nares colonization and concomitant wound infections has not been well established. The purpose of this study was 3-fold: to determine the relatedness of MRSA isolates from 40 paired wound and nares specimens by four different strain typing methods, to determine concordance of typing methods, and to establish a baseline of MRSA types at this medical center. Isolates were typed by repetitive PCR (rep-PCR) (DiversiLab System; DL) and SpectraCell Raman analysis (SCRA) (commercially available methods that can be performed within a clinical lab), pulsed-field gel electrophoresis (PFGE), and an antibiotic susceptibility profile (AB). Whole-genome optical mapping (WGM) (OpGen, Inc.) was performed on selected isolates. All methods agreed that 26 pairs were indistinguishable and four pairs were different. Discrepant results were as follows: 4 where only SCRA was discordant, 3 where only AB was discordant, 2 where both DL and AB were discordant, and 1 where both DL and SCRA were discordant. All WGM agreed with PFGE. After discrepancy resolution, 80% of the pairs were indistinguishable and 20% were different. A total of 56% of nares results were nonpredictive if negative nares and positive wound cultures are included. Methods agreed 85 to 93% of the time; however, congruence of isolates to a clade was lower. Baseline analysis of types showed that 15 pairs were unique to single patients (30 strains, 38%; 47% of the matching pairs). Twenty-five strains (30%) represented a single clade identical by PFGE, SCRA, and DL, decreasing specificity. Typing method and institutional type frequency are important in assessing MRSA strain relatedness.

Comparison of Pulsed-Gel Electrophoresis and a Commercial Repetitive-Element PCR Method for Assessment of Methicillin-Resistant Staphylococcus aureus Clustering in Different Health Care Facilities

“…In this study, global congruence between rep-PCR and PFGE as determined by the adjusted Rand coefficient was only 0.08. Global congruence between rep-PCR and PFGE was higher (adjusted Rand, 0.56) in a recent study performed using MRSA isolates recovered from patients receiving care at a Veterans Administration (VA) medical center (33). Patients in this study submitted paired nasal and wound isolates, which may explain discrepancies with our findings.…”

In Vitro Activity of Retapamulin and Antimicrobial Susceptibility Patterns in a Longitudinal Collection of Methicillin-Resistant Staphylococcus aureus Isolates from a Veterans Affairs Medical Center

“…Although the number of patient isolates evaluated was small, the postmupirocin strain was different from the premupirocin strain for the isolates from nares cultures that demonstrated MIC changes after mupirocin therapy. Previously reported data confirmed that patients may be colonized with more than one strain of MRSA at different anatomical sites and that surveillance of the nares alone may not be the best predictor of subsequent wound infection (12,13). Colonization by multiple strain types and variations in colonization at different anatomical sites have the potential to affect the decolonization process (22).…”

“…Given that the worldwide rates of linezolid resistance and elevated MICs for MRSA are low (Ͻ0.8% in 2002 to 2010) (20), our findings were unexpected. These isolates were not tested for the presence of the cfr gene but, after reviewing the strain typing analysis, we found that the majority of these isolates were segregated into two larger clonal groups (12). Based on the rarity of MRSA isolates with elevated MICs and the clonality of the isolates in this study, the data suggest the possibility that these organisms were nosocomially acquired.…”

“…Of the 153 isolates that underwent Rep-PCR strain typing analysis, 93 (61%) were classified as USA300 (composed of two Rep-PCR types) and 54 (35%) were classified as USA100 (composed of two Rep-PCR types) (12). The remaining isolates in unique Rep-PCR types were classified as USA400 (1 isolate), USA800 (4 isolates), and USA1000 (1 isolate).…”

High Throughput Sequencing Advances and Future Challenges

“…WGM utilize singlemolecule restriction examination to acquire results concerning the magnitude of the control splinter and their substantial positions beside the DNA strand [45]. Whole genome has been exploit in a number of functions, which comprised of phylogenetic analyses and genotyping of associated with microbial isolates [46,47], discovery of outsized genomic structural rearrangements or variations [48,49], and quality control or verification for genome sequences which were assembled [50,51]. Physical genome maps based a restriction also having the potential to be used as a model for the exact arrangement of NGS contigs and to assist concluding the spaces between mapped contig.…”