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Impact of strain typing method on assessing the relationship of paired 3
nares and wound isolates of methicillin-resistant Staphylococcus aureus 4
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Jill E. Clarridge III,1, 2#** A.T. Harrington1, 2** 6
M.C. Roberts3, O. O. Soge3, and K. Maquelin4 7
1 Pathology and Laboratory Medicine Service, Veterans Affairs Puget Sound Health Care System, Seattle, 8 WA, 2 Department of Laboratory Medicine, University of Washington, Seattle, WA, 3Department of 9 Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, 4Center for 10 Optical Diagnostics & Therapy, Department of Dermatology, University of Utrecht, Rotterdam, NL 11
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Corresponding author: Jill E. Clarridge, III 16 Pathology and Laboratory Medicine Service (113), VA PSHCS 17 1660 S. Columbian Way 18 Seattle WA, 98108 19 206-277-4514 office; FAX 206-794-2001 20 [email protected] 21 22
**Contributed equally to this work 23
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Running title: Strain typing MRSA from paired nares and wound cultures 25
1. International Working Group on the Classification of Staphylococcal Cassette Chromosome 310 Elements (IWG-SCC). 2009. Classification of staphylococcal cassette chromosome mec 311 (SCCmec): guidelines for reporting novel SCCmec elements. Antimicrob.Agents Chemother. 312 53:4961-4967. 313
2. Babouee, B., R. Frei, E. Schultheiss, A. F. Widmer, and D. Goldenberger. 2011. Comparison of 314 the DiversiLab Repetitive Element PCR System with spa Typing and Pulsed-Field Gel 315 Electrophoresis for Clonal Characterization of Methicillin-Resistant Staphylococcus aureus. 316 J.Clin.Microbiol. 49:1549-1555. 317
3. Berthelot, P., F. Grattard, C. Cazorla, J. P. Passot, J. P. Fayard, R. Meley, J. Bejuy, F. Farizon, B. 318 Pozzetto, and F. Lucht. 2010. Is nasal carriage of Staphylococcus aureus the main acquisition 319 pathway for surgical-site infection in orthopaedic surgery? Eur.J.Clin.Microbiol.Infect.Dis. 320 29:373-382. 321
4. Caffrey, A. R. and K. L. Laplante. 2012. Changing epidemiology of methicillin-resistant 322 Staphylococcus aureus in the Veterans Affairs Healthcare System, 2002-2009. Infection 40:291-323 297. 324
5. Carrico, J. A., C. Silva-Costa, J. Melo-Cristino, F. R. Pinto, L. H. de, J. S. Almeida, and M. 325 Ramirez. 2006. Illustration of a common framework for relating multiple typing methods by 326 application to macrolide-resistant Streptococcus pyogenes. J.Clin.Microbiol. 44:2524-2532. 327
6. Chen, A. E., J. B. Cantey, K. C. Carroll, T. Ross, S. Speser, and G. K. Siberry. 2009. Discordance 328 between Staphylococcus aureus nasal colonization and skin infections in children. 329 Pediatr.Infect.Dis.J. 28:244-246. 330
7. Church, D. L., B. L. Chow, T. Lloyd, and D. B. Gregson. 2011. Comparison of automated 331 repetitive-sequence-based polymerase chain reaction and spa typing versus pulsed-field gel 332 electrophoresis for molecular typing of methicillin-resistant Staphylococcus aureus. Diagnostic 333 Microbiology and Infectious Disease 69:30-37. 334
8. Cookson, B. D., D. A. Robinson, A. B. Monk, S. Murchan, A. Deplano, R. R. de, M. J. Struelens, 335 C. Scheel, V. Fussing, S. Salmenlinna, J. Vuopio-Varkila, C. Cuny, W. Witte, P. T. Tassios, N. J. 336 Legakis, L. W. van, B. A. van, A. Vindel, J. Garaizar, S. Haeggman, B. Olsson-Liljequist, U. 337 Ransjo, M. Muller-Premru, W. Hryniewicz, A. Rossney, B. O'Connell, B. D. Short, J. Thomas, S. 338 O'Hanlon, and M. C. Enright. 2007. Evaluation of molecular typing methods in characterizing a 339 European collection of epidemic methicillin-resistant Staphylococcus aureus strains: the 340 HARMONY collection. J.Clin.Microbiol. 45:1830-1837. 341
9. Deplano, A., A. Schuermans, E. J. Van, W. Witte, H. Meugnier, J. Etienne, H. Grundmann, D. 342 Jonas, G. T. Noordhoek, J. Dijkstra, B. A. van, L. W. van, P. T. Tassios, N. J. Legakis, A. van der 343 Zee, A. Bergmans, D. S. Blanc, F. C. Tenover, B. C. Cookson, G. O'Neil, and M. J. Struelens. 344 2000. Multicenter evaluation of epidemiological typing of methicillin-resistant Staphylococcus 345
aureus strains by repetitive-element PCR analysis. The European Study Group on 346 Epidemiological Markers of the ESCMID. J.Clin.Microbiol. 38:3527-3533. 347
10. Enright, M. C., N. P. Day, C. E. Davies, S. J. Peacock, and B. G. Spratt. 2000. Multilocus sequence 348 typing for characterization of methicillin-resistant and methicillin-susceptible clones of 349 Staphylococcus aureus. J.Clin.Microbiol. 38:1008-1015. 350
11. Frazee, B. W., J. Lynn, E. D. Charlebois, L. Lambert, D. Lowery, and F. Perdreau-Remington. 351 2005. High prevalence of methicillin-resistant Staphylococcus aureus in emergency department 352 skin and soft tissue infections. Ann.Emerg.Med. 45:311-320. 353
12. Gurieva, T., M. C. Bootsma, and M. J. Bonten. 2012. Successful Veterans Affairs initiative to 354 prevent methicillin-resistant Staphylococcus aureus infections revisited. Clin.Infect.Dis. 54:1618-355 1620. 356
13. Harrington, A. T., S. D. Mahlen, and J. E. Clarridge, III. 2010. Significantly larger numbers of 357 methicillin-resistant Staphylococcus aureus bacteria are recovered from polymicrobial 358 respiratory and wound sites by use of chromogenic primary media than by use of conventional 359 culture. J.Clin.Microbiol. 48:1350-1353. 360
14. Jain, R., S. M. Kralovic, M. E. Evans, M. Ambrose, L. A. Simbartl, D. S. Obrosky, M. L. Render, R. 361 W. Freyberg, J. A. Jernigan, R. R. Muder, L. J. Miller, and G. A. Roselle. 2011. Veterans Affairs 362 initiative to prevent methicillin-resistant Staphylococcus aureus infections. N.Engl.J.Med. 363 364:1419-1430. 364
15. Kazakova, S. V., J. C. Hageman, M. Matava, A. Srinivasan, L. Phelan, B. Garfinkel, T. Boo, S. 365 McAllister, J. Anderson, B. Jensen, D. Dodson, D. Lonsway, L. K. McDougal, M. Arduino, V. J. 366 Fraser, G. Killgore, F. C. Tenover, S. Cody, and D. B. Jernigan. 2005. A clone of methicillin-367 resistant Staphylococcus aureus among professional football players. N.Engl.J.Med. 352:468-368 475. 369
16. Lindstedt, B. A. 2005. Multiple-locus variable number tandem repeats analysis for genetic 370 fingerprinting of pathogenic bacteria. Electrophoresis 26:2567-2582. 371
17. Luo, L., Y. Xie, C. He, F. Qiao, H. Zhuang, L. Guo, W. Yin, M. Kang, and L. Wang. 2012. Molecular 372 Epidemiological Analysis of Methicillin-Resistant Staphylococcus aureus Isolates From a Medical 373 Intensive Care Unit: A Comparison Of Nasal and Clinical Isolates. Am.J.Med.Sci. 374
18. McDougal, L. K., C. D. Steward, G. E. Killgore, J. M. Chaitram, S. K. McAllister, and F. C. 375 Tenover. 2003. Pulsed-field gel electrophoresis typing of oxacillin-resistant Staphylococcus 376 aureus isolates from the United States: establishing a national database. J.Clin.Microbiol. 377 41:5113-5120. 378
19. Melles, D. C., L. Schouls, P. Francois, S. Herzig, H. A. Verbrugh, B. A. van, and J. Schrenzel. 379 2009. High-throughput typing of Staphylococcus aureus by amplified fragment length 380 polymorphism (AFLP) or multi-locus variable number of tandem repeat analysis (MLVA) reveals 381 consistent strain relatedness. Eur.J.Clin.Microbiol.Infect.Dis. 28:39-45. 382
20. O'Sullivan, M. V., F. Zhou, V. Sintchenko, and G. L. Gilbert. 2012. Prospective genotyping of 383 hospital-acquired MRSA using a novel, highly discriminatory binary typing system. 384 J.Clin.Microbiol. 385
21. Pinto, F. R., J. Melo-Cristino, and M. Ramirez. 2008. A confidence interval for the wallace 386 coefficient of concordance and its application to microbial typing methods. PLoS.One. 3:e3696. 387
22. Reighard, A., D. Diekema, L. Wibbenmeyer, M. Ward, and L. Herwaldt. 2009. Staphylococcus 388 aureus nasal colonization and colonization or infection at other body sites in patients on a burn 389 trauma unit. Infect.Control Hosp.Epidemiol. 30:721-726. 390
23. Roberts, M. C., O. O. Soge, D. No, N. K. Beck, and J. S. Meschke. 2011. Isolation and 391 characterization of methicillin-resistant Staphylococcus aureus from fire stations in two 392 northwest fire districts. Am.J.Infect.Control 39:382-389. 393
24. Ross, T. L., W. G. Merz, M. Farkosh, and K. C. Carroll. 2005. Comparison of an automated 394 repetitive sequence-based PCR microbial typing system to pulsed-field gel electrophoresis for 395 analysis of outbreaks of methicillin-resistant Staphylococcus aureus. J.Clin.Microbiol. 43:5642-396 5647. 397
25. Shopsin, B. and B. N. Kreiswirth. 2001. Molecular epidemiology of methicillin-resistant 398 Staphylococcus aureus. Emerg.Infect.Dis. 7:323-326. 399
26. Tenover, F. C., E. A. Gay, S. Frye, S. J. Eells, M. Healy, and J. E. McGowan, Jr. 2009. Comparison 400 of typing results obtained for methicillin-resistant Staphylococcus aureus isolates with the 401 DiversiLab system and pulsed-field gel electrophoresis. J.Clin.Microbiol. 47:2452-2457. 402
27. Tenover, F. C., I. A. Tickler, R. V. Goering, B. N. Kreiswirth, J. R. Mediavilla, and D. H. Persing. 403 2012. Characterization of nasal and blood culture isolates of methicillin-resistant Staphylococcus 404 aureus from patients in United States Hospitals. Antimicrob.Agents Chemother. 56:1324-1330. 405
28. Tracy, L. A., J. P. Furuno, A. D. Harris, M. Singer, P. Langenberg, and M. C. Roghmann. 2011. 406 Staphylococcus aureus infections in US veterans, Maryland, USA, 1999-2008. Emerg.Infect.Dis. 407 17:441-448. 408
29. Udo, E. E., N. Y. Aly, E. Sarkhoo, R. Al-Sawan, and A. S. Al-Asar. 2011. Detection and 409 characterization of an ST97-SCCmec-V community-associated meticillin-resistant Staphylococcus 410 aureus clone in a neonatal intensive care unit and special care baby unit. J.Med.Microbiol. 411 60:600-604. 412
30. van Belkum, A. 2007. Tracing isolates of bacterial species by multilocus variable number of 413 tandem repeat analysis (MLVA). FEMS Immunol.Med.Microbiol. 49:22-27. 414
31. van Belkum, A., P. T. Tassios, L. Dijkshoorn, S. Haeggman, B. Cookson, N. K. Fry, V. Fussing, J. 415 Green, E. Feil, P. Gerner-Smidt, S. Brisse, and M. Struelens. 2007. Guidelines for the validation 416 and application of typing methods for use in bacterial epidemiology. Clin.Microbiol.Infect. 13 417 Suppl 3:1-46. 418
32. van Leeuwen, W. B., S. Snoeijers, C. Werken-Libregts, A. Tuip, A. van der Zee, D. Egberink, P. 419 M. de, E. Bik, B. Lunter, J. Kluytmans, E. Gits, D. van, I, M. Heck, K. van der Zwaluw, W. 420 Wannet, G. T. Noordhoek, S. Mulder, N. Renders, M. Boers, S. Zaat, D. van der Riet, M. 421 Kooistra, A. Talens, L. Dijkshoorn, T. van der Reyden, D. Veenendaal, N. Bakker, B. Cookson, A. 422 Lynch, W. Witte, C. Cuny, D. Blanc, I. Vernez, W. Hryniewicz, J. Fiett, M. Struelens, A. Deplano, 423 J. Landegent, H. A. Verbrugh, and B. A. van. 2002. Intercenter reproducibility of binary typing 424 for Staphylococcus aureus. J.Microbiol.Methods 51:19-28. 425
33. von Eiff, C., K. Becker, K. Machka, H. Stammer, and G. Peters. 2001. Nasal carriage as a source 426 of Staphylococcus aureus bacteremia. Study Group. N.Engl.J.Med. 344:11-16. 427
34. Willemse-Erix, D. F., M. J. Scholtes-Timmerman, J. W. Jachtenberg, W. B. van Leeuwen, D. 428 Horst-Kreft, T. C. Bakker Schut, R. H. Deurenberg, G. J. Puppels, B. A. van, M. C. Vos, and K. 429 Maquelin. 2009. Optical fingerprinting in bacterial epidemiology: Raman spectroscopy as a real-430 time typing method. J.Clin.Microbiol. 47:652-659. 431
453 Table 2. Discrepant Analysis. For each method we indicate whether the pair was the same (S) or 454 different (D) by each measure 455 456 Patient #: Discrepant
PFGE SCRA DL Antibiotic Profile
OpGen FinalAssessment
1 S D S S S 7 S D S S S S 10 D D S S D D 14 S S S Da S 18 D S S D D D 22 D D S S D D 26 S S S Db S 29 S D S S S 30 D S D D D 35 S S S Dc S Patient #: Controls
27 S S S S S S 36 S S S S S S 457 aOnly mupirocin different 458
Table 3. Congruence of strain typing results as indicated by adjusted Rand coefficients (95%CI)* 468 469
Adjusted Rand and jackknife pseudo-values 95% CI
PFGE SCRA DLPFGE
SCRA 0.241
(0.099-0.389)
DL 0.562 0.377
(0.396-0.739) (0.221-0.542)
AB 0.154 0.166 0.251
(0.058-0.253) (0.040-0.295) (0.121-0.379)
p-values between Adjusted Rands 470 * Data were generated using the Comparing Partitions website 471 (http://darwin.phyloviz.net/ComparingPartitions/index.php?link=Tool). CI, confidence interval. 472 473 Although PFGE and DL agreed 93% in their assessment of the patient pairs, the congruence value of 474
0.563, while highest amongst our testing methods is not high. This is because PFGE is more 475
discriminatory as shown in Figure 2 and in the contingency table (Table 5). The congruence of AB typing 476