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Automated repetitive PCR (rep-PCR; DiversiLab) was compared to PCR ribotyping of the 16S-23S RNA intergenic spacer of Clostridium difficile (CD) as the "gold standard" method for CD typing. PCR products were separated on DiversiLab LabChips (bioMérieux, St. Laurent, Quebec, Canada) utilizing a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) operating the DiversiLab v1.4 assay. Bioanalyzer data were exported to a secure DiversiLab website and analyzed with DiversiLab v3.4 software. Replicability of each method was verified by confirming that the 5 CD reference strains (RS) formed distinct clusters (CD4, CD6, VL0047, VL0013 [ribotype 027], VL0018 [ribotype 001]) by both typing methods. Ninety randomly selected clinical isolates (CS) were analyzed by both methods: 49 from community-acquired and 41 from hospital-acquired cases. A similarity index (SI) of ≥90% was used to define clusters when comparing the known RS cluster to the PCR ribotyping and rep-PCR patterns of CS. Fourteen different PCR-ribotype clusters were identified, but most CS formed 4 major clusters (i.e., CD4 [15/90; 17%], CD6 [17%], 027 [12%], and 001 [9%]). A total of 7 rep-PCR types were identified, but most CS formed 2 major rep-PCR clusters (i.e., CD4 [29/90; 32%] and CD6 [23%]); several PCR ribotypes occurred within a single rep-PCR cluster. Rep-PCR did not distinguish 027 or 001 isolates; i) 027 RS strain did not cluster, ii) eleven 027 CS strains clustered as CD4, iii) no 027 CS strains clustered with the 027 RS, and iv) only 2 001 CS clustered with the RS. Agreement between the PCR-ribotype and rep-PCR clusters only occurred for 35/90 (39%) of the CS using a rep-PCR SI of ≥90%. Rep-PCR time to results was similar, but the annual costs of routinely using this method are 32% higher than PCR ribotyping. Routine use of rep-PCR for CD typing is limited by its lack of definitive separation of the hypertoxigenic 027 or 001 outbreak CD strains., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Automated repetitive polymerase chain reaction (PCR) (DiversiLab, bioMérieux, St. Laurent, Quebec, Canada) and single locus sequence typing of the Staphylococcus protein A (spa) gene with spa-type assignment by StaphType RIDOM software were compared to pulsed-field gel electrophoresis (PFGE) as the "gold standard" method for methicillin-resistant Staphylococcus aureus (MRSA) typing. Fifty-four MRSA isolates were typed by all methods: 10 of known PFGE CMRSA type and 44 clinical isolates. Correct assignment of CMRSA type or cluster occurred for 47 of 54 (87%) of the isolates when using a rep-PCR similarity index (SI) of ≥95%. Rep-PCR gave 7 discordant results [CMRSA1 (3), CMRSA2 (1), CMRSA4 (1), and CMRSA10 (2)], and some CMRSA clusters were not distinguished (CMRSA10/5/9, CMRSA 7/8, and CMRSA3/6). Several spa types occurred within a single PFGE or repetitive PCR types among the 19 different spa types found. spa type t037 was shared by CMRSA3 and CMRSA6 strains, and CMRSA9 and most CMRSA10 strains shared spa type t008. Time to results for PFGE, repetitive PCR, and spa typing was 3-4 days, 24 h, and 48 h, respectively. The annual costs of using spa or repetitive PCR were 2.4× and 1.9× higher, respectively, than PFGE but routine use of spa typing would lower annual labor costs by 0.10 full-time equivalents compared to PFGE. Repetitive PCR is a good method for rapid outbreak screening, but MRSA isolates that share the same repetitive PCR or PFGE patterns can be distinguished by spa typing., (Copyright © 2011 Elsevier Inc. All rights reserved.)