An Iconoclastic View of Isolates from Acute, Chronic, and Anaerobic Lesions

1. 2013 ISM May 7, 2013 An Iconoclastic View ofIsolates from Acute, Chronic, and Anaerobic Lesions Larry D Gray, PhD, ABMM Bethesda Hospital and Good Samaritan Hospital University of Cincinnati College of Medicine Clinical Microbiology Laboratory Consultants, LLC Cincinnati, Ohio

2. Disclosures • financial, professional, and ethical conflicts of interest • relevant commercial relationships NONE

3. i·con·o·clast / ahy-kon-uh-klast / noun one who attacks and seeks to overthrow traditional or popular ideas or institutions i·con·o·clas·tic / ahy-kon-uh-klas-tik / adjective attacking or ignoring cherished beliefs and long-held traditions, etc., as being based on error, superstition, or lack of creativity

4. Clinical microbiologists fret too much. -- L. Gray, 1988

5. Objectives • present the differences between acute and chronic lesions • describe cost-effective approaches to the identification and susceptibility testing of clinically relevantisolates from acute, chronic, and anaerobic lesions.

6. “ABDOMEN”

7. PRELIMINARY • AEROBIC CULTURE RESULTS • 1. GPC #1 • 2. GPC #2 • 3. GNR • 4. GPR

8. FINAL AEROBIC CULTURE RESULTS SPECIMEN DESCRIPTION:ABDOMEN CULTURE RESULTS:1. E. coli + AST 2. S. aureus + AST 3.diphtheroids REPORT STATUS:FINAL REPORT 10/28/2010 2 days / ~$225

9. PRELIMINARY • ANAEROBIC CULTURE RESULTS • lg β-heme GPC #1 • lg β-heme GPC #2 • lg grey-white GPC • med grey-white GPC • med trans GNR • tiny GPC • small grey GPC • Mixed Culture (7 Isolates)

10. FINAL ANAEROBIC CULTURE RESULTS SPECIMEN DESCRIPTION:ABDOMEN CULTURE RESULTS:Mixed Culture (>5 Isolates). Strongly Suggests Polymicrobial Infection or Contamination with Normal Mucosal Bacteria. Consult with Director of Clinical Microbiology If Identification Is Clinically Warranted. REPORT STATUS:FINAL REPORT 11/31/2010 5 days / ~$200

12. CLINICALLY IRRELEVANT FINAL ANAEROBIC CULTURE RESULTS • S. aureus (2 types) + 2 AST • CNS(2 types) + 2 AST • Propionibacterium spp. (2 types) • Ana GNR Unable to ID – 1 type 12 days / >$1,200

13. Question: How far should you go to ID / AST isolates from AW, CW, and ANA cultures? Answer: In my opinion…

14. Three New CM Commandments 1. Say “No” as often as possible. 2. 1 procedure = 1 table 3. Base all procedures on the following statement…

15. Base All of Your Procedures on This Statement …specimens that contain the largest number of microbial species incur the greatest amount of lab cost, yet are less likely to provide useful guidelines for diagnosis and treatment than are specimens that yield fewer types of organisms. -- Dr. Raymond Bartlett, 1982

16. An Infectious Diseases and Clinical Microbiology Pearl >4 3 2 1 Number of Isolates in a Culture Low High Lab Costs ( ) Clinical Utility of Results ( )

17. In a healthy patient, could you touch the source of the specimen with your finger? YES NO • Was the source contiguous • with or did it touch • skin, • mucus membrane, • intestinal tract, or • oral, nasal, or N/P cavities? NOT NORMALLY STERILE LESION procedure NO YES >4 isolates <3 isolates:NORMALLYSTERILE procedure NORMALLY STERILE

18. Acute Lesions / Wounds

19. What is an Acute Wound? • result from surgery, trauma, lacerations, • abrasions, penetrations, bites, and burns • Infections are usually are polymicrobial. • normally proceed through an orderly • and timely reparative process that results • in sustained restoration of anatomic and • functional integrity • Sharpe, Bowler, & Church. 2010. CMPH, 3rd ed. 3.13. ASM.

21. Specimens Considered to Be from Lesions lesion burn decubitis pus gastric contents wound abrasion incision abscess catheter exit ulcer drainage empyema hematoma peritoneal dialysis fluid G tube placenta fistula trauma site appendix cyst skin burn peritoneal dialysate wound lesion etc……….. peritoneal, ascites, or pleural fluid on a swab exudate or drainage on swabs fluid received in a Culturette tube any specimen which likely touched skin, mucosa, or bowel

22. Acute Lesions: Deciding What to Identify Table 1

23. Acute Lesions: Deciding How Far to Go Table 2 a If >3 potential pathogens, report only quant and Gram morph of each. b pure culture: Q I S a

24. Chronic Lesions / Ulcers / Wounds

26. What is a Chronic Wound? • >4 weeks duration and only 20-40% of area healed • pressure ulcers • diabetic foot ulcers • venous ulcers • critical factors • insufficient CT and skin to enhance healing • reduced vascularization • delayed re-epithelization • formation of biofilm • annual US cost/year: $10 billion

28. A STUDY • Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota • Price L B et al. 2009. PLoS ONE July, 4(7):e6462. • 24 patients / 32 chronic wounds • + / - antimiccobial agents • pyrosequencing (+ rarefaction & Shannon-Weaver • index plots, diversity value plots, NMDS, MRPP, • and BCR)

29. Results detected 44 bacterial families 6 to 25 families / CW; average = 10 fam/CW probably 100s of species culture only Staph, Strep, Entero, Enterococcus,Pseudo, Peptostrepto, Bact, Coryne, & Prevo could not culture 35 families Conclusions complex bacterial communities Abx Rx alters communities: reduces some and selects for others (Pseudo increased with Rx)

30. A REVIEW • A Review of the Microbiology, Antibiotic Usage and Resistance in Chronic Skin Wounds • Howell-Jones RS et al. 2005. J Antimicrob Chemother 55(2):143-149. • The presence of microbes per se is not indicative • of wound infection. • … microorganisms are identified in deep tissue of • all CW, yet the role they play and the impact of • specific species on wound longevity are unclear. • …insufficient evidence…for the use [of systemic • antibiotics] in wound healing… • …inadequate data to address effectiveness of abx • regimens for serious diabetic foot infections and • superficial or deep ulcers.

31. Four Types of Chronic Wounds # 4 INFECTED • organism conc >105 CFU/gram tissue • typical of decubitus, pressure, and diabetic foot ulcers • important organisms assoc with poor healing P. aeruginosa S. aureus β-heme Streptococcus(gp A and B) • >4 organisms associated with poor healing P. Gilligan, 2011; Price et al PLoS ONE 2009 4:e6462; Martin J Inv Derm 2010 130:38-48; Howell-Jones et al 2005 J Antimicrob Chemo 55:143-149.

32. Current Status of Workup of Isolates from Chronic Wounds There are no widely published guidelines except what seems to be the right thing to do according to… • physicians • clinical microbiologists • literature • Dr. No

33. IDSA Clinical Practice Guidelines for the Diagnosis and Treatment of Diabetic Foot Ulcers no recommendations re: extent of ID/AST of isolates from DFU Clin Infect Dis 2012 54:1679-1684

34. What are the top 8 ways to approach chronic wounds?

35. Chronic Wounds: Deciding How Far to Go a If >3 potential pathogens, report only quant and Gram morph of each. b pure culture: Q I S a

36. Chronic Wounds Be sure to look for • S. aureus • Pseudomonas spp. • β-heme Streptococcus (gp A) • + / - MDRO (VRE, CRE, Acinetobacter, etc.)

37. Dr. XXX: As I promised, here are the rationale and support for limited ID/AST of isolates from CW. I feel sure if we work together and you understand the details of our current protocols for NSBS and lesions (wounds) the protocols can serve you and your fellow physicians well. Our ID physicians find the protocols work well and have always supported limited ID/AST of CW. We are not reimbursed for extensive ID/AST of isolates from any specimen from any source. So, we try to support TriHealth’s mission by providing clinically relevant and cost-effective results. Regards,

38. Survey of 21 Medical Centers, Hospitals, and Consultants Nov-Dec, 2011 • Labs need to agree with ASM, IDSA, and ID/CM organizations. • ID, derms, & surgs: CW should be cultured and worked up as AW. • CW are processed according to ASM pubs and guidelines for AW. • Quant culs have been D/C. • Phy’s could not provide literature to support full ID and AST of CW. • >1,000 CW cultures/year -- no special protocol for CW. • AST of isolates from CW has not proven beneficial (reserv osteo) • several: No special protocol for CW. ID/AST like protocols for AW. • several: CW are cultured and worked up as AW.

39. Rationale and Support for Limited ID/AST of Isolates from Chronic Wounds abridged version

40. Anaerobic Cultures

41. …the interpretation of [anaerobic] cultures with multiple species is often little more than guesswork…a report indicating…a mixture of B. bivius, F. necrophorum, P. magnus, and P. acnes is of no greater clinical value than one indicating “mixed anaerobic flora”… Physicians who want specific identification of each anaerobe in such cultures should be prepared to justify their request. -- a respected clinical microbiologist, 1990

42. Deciding How Many (if Any) Anaerobes to Identify Table 1 a “Mixed Culture (>5 Isolates) Strongly Suggests Polymicrobial Infection or Contamination with Normal Mucosal Bacteria. Consult with Director of Clinical Microbiology If Identification Is Clinically Warranted.” b “Mixed Anaerobes (3 or 4) Types”

43. Deciding Extent of Identification of Anaerobes Table 2

44. AST of Anaerobes • Perform only beta-lactamase testing. • Test all • GNR which are either fully identified • or are identified only by Gram stain • Clostridium spp. except C. perfringens.

45. Bacteroidesfragilis gp. Appendix D (CLSI 2013 M100-S23)

46. Other than Bacteroidesfragilis gp. Appendix E (CLSI 2013 M100-S23)

47. Antibiogram of Anaerobic Bacteria from MCM, 10th andCLSI M100-S22 (2012)