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Challenging Cases in Clinical Microbiology

Challenging Cases in Clinical Microbiology. Kamaljit Singh, MD, D(ABMM) May 7, 2013. Objectives. 1. Interpreting and Reporting interesting Cultures and Gram-stains  2. Some unusual enteric Gram-negative rods encountered organisms in the Microbiology Laboratory 

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Challenging Cases in Clinical Microbiology

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  1. Challenging Cases in Clinical Microbiology Kamaljit Singh, MD, D(ABMM) May 7, 2013

  2. Objectives • 1. Interpreting and Reporting interesting Cultures and Gram-stains  • 2. Some unusual enteric Gram-negative rods encountered organisms in the Microbiology Laboratory  • 3. Challenges in Interpreting Susceptibility Results for Enterococci

  3. Case 1: 36 yo with Failure to thrive • A 36 year-old male with NK cell lymphoma and concomitant hemophagocyticlymphohistiocytosis (completed 8 cycles of EPOCH chemotherapy two months prior to admission) and recent treatment with pulse dexamethasone for disease relapse was admitted to the hospital with failure to thrive. • His wife also reported that over the last 24 hours, he had been very drowsy and unable to recognize her. • Finally, she noted that he had an intermittent cough and appeared more short of breath

  4. Physical examination • On admission, the patient appeared cachectic and sleepy but arousable and appeared to resist neck flexion • He was afebrile (97.2°F) but tachycardic (126 bpm) and tachypneic (44 rpm). • The remainder of his examination was only significant for a faint petechial rash over the abdomen. • His laboratory findings were significant for a normal WBC (4.29/L), chronic anemia (HgB: 8.4g/dl) but with new thrombocytopenia (plt: 84,000/ul), worsening transaminitis, AST: 154 U/L, ALT: 190 U/L and hypoalbuminemia (1.4 g/dl).

  5. CXR on presentation

  6. Hospital course • Within 24 hours of admission, the patient developed worsening confusion, mumbling to himself, with increased oxygen requirement (SaO2: 95% on 6L/min O2) and hypotension requiring 6L IV fluid boluses. • He underwent a brain CT which was unremarkable. • His repeat CXR revealed worsening diffuse bilateral parenchymalgroundglass opacities in both lungs. • He was transferred to the MICU and started on empiric antibiotics with Doripenem, Levofloxacin, Caspofungin, Vancomycin, Oseltamivir and Trimethoprim-Sulfamethoxazole.

  7. Repeat CXR

  8. MICU Course • Because of his rapid deterioration and concern for atypical pneumonia an urgent bronchoscopy was performed which revealed diffuse alveolar hemorrhage. • The patient became more hypoxic post-bronchoscopy and was intubated. • The petechiae which were especially prominent over his abdomen (some scattered petechiae over both upper extremities, palms and soles) became more purpuric on day 2 and were biopsied.

  9. Diagnosis is made: • Two sets of blood cultures on admission were positive for S. epidermidis. • The result of Bronchoalveolar lavage fluid culture is shown:

  10. BAL culture

  11. Skin biopsy

  12. Hospital course • Ivermectin 200mcg/kg is started via NGT on Day 3 and steroids tapered rapidly • Unfortunately he developed progressive worsening pulmonary hemorrhage and family decided on comfort measures. He expired on hospital Day 4.

  13. Case 2: Why are my patient’s cultures Negative • This is a 75y/o African American female with a history of Diabetes and Kidney transplant in 1997 (Cr: 1.3) on Azathioprine and Cyclosporine • Recurrent UTIs on Fosfomycin prophylaxis q10 days • She presented with acute onset of nausea and vomiting followed by chills and increased urinary frequency and dysuria for 2 days. • In the ED, she was given a diagnosis of urosepsis based on abnormal urinalysis with >200WBC

  14. Results of Urinalysis

  15. Medicine Resident’s Note: • Admitted with fever, dysuria and UA consistent with UTI. Patient has also been having productive cough for the past 2 days • BloodCultures x 2 with NGTD and UC negative • CXR without any acute process. Will obtain CXR PA/Lat today given productive cough and abnormal auscultation • S/p ertapenem 500 mg IV in ED. Continuing 500 mg Q 24h • - On fosfomycin (monurol) 3 g PO Q 10 days at home - Currently on hold • - Acetaminophen 650 mg Q 6h PRN • - Will continue to monitor for today

  16. Other strange MD notes!! • 1)  She has no rigors or shaking chills, but her husband states she was hot in bed last night. • 2) The patient has been depressed since she began seeing me in 1993.

  17. Patient has persistent fevers because: • 1. Patient’s fevers are due to some other diagnosis and urinalysis was inaccurate • 2. The patient has an Anaerobic UTI • 3. The Fosfomycin antibiotic suppressed growth of bacteria to undetectable levels • 4. The patient’s pyuria is possibly due to a fastidious organism eg. H. influenzae or TB • 5. The patient’s abnormal urinalysis is due to a STD

  18. Repeat Urine Culture using 0.01ml Loop

  19. Other weird MD notes! • 1) While in ER, she was examined, X-rated and sent home. • 2) The lab test indicated abnormal lover function.

  20. 30%–50% of patients with acute urethral syndrome will have colony counts of <105 cfu/mL

  21. Case 3: How do you report this? Urine Culture: Enterococcus spp. > 105 cfu/mL

  22. Susceptibility Result: • Penicillin: 2 S • Levofloxacin: 2 S • Trimeth/Sulfa: ≤0.5/9.5 • Daptomycin: ≤0.5 S • Linezolid: 2 S • Nitrofurantoin: ≤32 S • Vancomycin: 8 I Note: Vancomycin E-test: 8

  23. Question • How do you report the Vancomycin susceptibility for Infection Control? • Resistant? • Susceptible?

  24. Further testing • Motility: Positive • Final identification by Microscan: E. casseliflavus • Intrinsic Vancomycin resistance (Van C) in E. casseliflavus & E. gallinarum See: CLSI M100-S22. Table 2D, Supplemental Table 1

  25. Case 4: A Blood culture with the same bug • This is a 59 yo female with chronic sinusitis who presented with a 4 week history of R-sided periorbital edema treated with multiple antibiotics and eventually underwent biopsy of the R-lateral nasal wall and hard palate on 3/14/2013 and found to have NK-cell lymphoma. • Patient completed her 1st cycle of chemotherapy in Apr 2013 and presents with 7 days of fevers and positive blood cultures

  26. Blood cultures: E. casseliflavus Penicillin: 2 S Ampicillin: : ≤2 S Daptomycin: ≤0.5 S Linezolid: 2 S Synercid: 2 I Vancomycin: 4 S Gent Synergy : ≤500 S Strep Synergy: : ≤1000 S

  27. How do we report Vancomycin?

  28. Mucoid E. faecalis

  29. Case 5: ESBL What? • 60 female yo with HTN, Chronic Hepatitis C and Kidney transplant (Cr: 2.2) on Tacrolimus, Prednisone and Bactrim. • Patient has urinary incontinence with recurrent UTIs • most recent 2013: C. freundii, E. coli and Enterococcus spp.

  30. Urine Cx: 104 -105 cfu/mL ESBL Positive EGNR Non-lactose fermenter ONPG: Pos Ornithine: Pos Indole: Pos Citrate: Neg Urease: Neg VP: Negative

  31. Genus Escherichia Koneman’s Color Atlas & Textbook of Diagnostic Microbiology , 6th Edition

  32. Yellow pigmented EGNR • Enterobacter sakazakii • Enterobacter cowanii (66%) • Escherichia hermanii • Escherichia vulneris (50%) • Leclerchia adecarboxylata (37%) • Pantoea agglomerans (75%) • Photorhabdus (50%) • Xenorhabdus (60%) Koneman’s Color Atlas & Textbook of Diagnostic Microbiology , 6th Edition

  33. Case 6: Another Weird Bug? • This is a 77 yo Cambodian female with HTN, DM, who was transferred to Rush in Feb 2013 with fever to 102.3F and R-hip mass increasing in size for last 2 months. • On exam, she had a R-hip mass measuring at least 15 cm that was very hard to palpation

  34. She was put on NSAIDs and her fevers resolved • The patient subsequently had an IR guided biopsy that revealed high grade sarcoma • She was started on chemotherapy and returned to Rush after the 2nd cycle on 4/16/2013 with a 3 day history of fevers and blood cultures turned positive for EGNR

  35. Blood culture results

  36. Microscan: Genus Enterobacter • ONPG: Positive • Ornithine: Positive • Citrate: Negative • VP: Negative • Urease: Negative • Indole: Negative • Non-motile

  37. Non-motile EGNR • SKY organisms • Shigella spp • Klebsiella spp (&Raoultella) • Yersinia spp. • Enterobacter asburiae • Enterobacter dissolvens • Enterobacter nimipressuralis • Escherichia albertii • Escherichia blattae • Citrobacter rodentium • Rahnella aquatilis Koneman’s Color Atlas & Textbook of Diagnostic Microbiology , 6th Edition

  38. Oh Great! – Another decubitus ulcer • This is a 41 year old male with quadriplegia due to spinal cord injury, multiple decubiti, including a non-healing R-hip decubitus ulcer • Recently treated with antibiotics for polymicrobial wound infection with MRSA, Group G streptococcus, P. aeruginosa, Morganella and Peptostreptococcus complicated by C diff colitis • Now admitted for fever and low blood pressure.

  39. Wound G-stain and Culture R-hip Many WBCs Many Gram-Positive Rods Moderate Gram-Positive Cocci in pairs Few Gram-Positive Cocci in chains Few Gram-Negative Rods • Moderate growth VRE • Moderate growth of Group G B-hemolytic Streptococci • Light growth of P. mirabilis • Moderate growth of Gram-positive Rods

  40. Gram-positive rods on CNA plate • Gram-stain: Diphteroid appearing • B-hemolytic • Catalase Negative • H2S Negative

  41. Diagnosis • Commonly causes pharyngitis in young adults • Also cause of wound infections • Penicillin tolerant • Drug of choice: Erthromycin S. aureus

  42. Case 8: MRN: 5675888 • This is a 58 yo Hispanic male who presents with several months of worsening headaches and 1 week of progressive bilateral upper extremity weakness, lower extremity pain, and urinary retention • He had no fevers, chills, sweats, weight loss • MRI Brain & Spine: Diffuse and nodular leptomeningeal enhancement throughout the spinal cord with involvement of the roots of the cauda equina…Superior extension into the intracranial cavity with leptomeningeal enhancement along the superior cerebellar folia, tectum, ventral aspect surface of mid brain, pons and medulla.

  43. MRI Brain, Spinal Cord and CT Chest 9mm Cavitary nodule Leptomeningeal Enhancement

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