Category Archives: Infectious Disease

Moffitt Intern Report Pearls 6.8.17

CONGRATS INTERNS ON YOUR LAST INTERN REPORT!!! And HUGE thank you to Lev for presenting a fascination case of middle aged man s/p prolonged treatment with steroids for EtoH hepatitis who presented with fevers and abdominal pain found to be in decompensated cirrhosis and later found to have semi-invasive pulmonary aspergillosis – wow!

Key Pearls

  1. If the direct bilirubin makes up greater than 20% of total bilirubin this is defined as direct predominance.
  2. Patients likely have impaired cellular immunity when steroid dosing reaches 20 mg for at least 14 days. At this dosing level you should consider starting PCP prophylaxis. More details below…
  3. Classical risk factors for semi-invasive Aspergilosis pulmonary infection:
    • severe or prolonged neutropenia
    • receipt of high dose corticosteroids per above
    • Other drugs or conditions that lead to chronically impaired cellular immune responses (e.g. AIDs, immunosuppressive regimen)

Thank you, Brad Monash, for sharing some more info on PCP prophylaxis in the setting of steroid use:

  1. The evidence for when to start PCP prophylaxis is weak. Some say that PCP ppx should be considered for patients on > 20 mg prednisone for > 2-3 weeks.
  2. Most evidence pertains to patients on steroids + underlying immunosuppressed state. Many experts will not use PCP ppx for steroids alone in the absence of other immunodeficiency.
  3. Here’s a fantastic review of PCP ppx from 2004, and one of the most cited papers on the topic (
  4. The article below cites the lowest dose of steroids on which patients developed PCP as 16 mg daily. (
  5. Interestingly, PCP has been described in Cushing syndrome!
  6. Check out this outstanding review of glucocorticoids and infection from 2008. (




ZSFG AM Report – 6.2.17 – HIV-Associated GI Pathology

Thank you Kenny for presenting a case of a patient with AIDS, abdominal pain, diarrhea, and fevers found to have a partial SBO and inflammation in the terminal ileum.

Top Pearls:

  1. Partial or complete small bowel obstruction in a patient without prior surgery is very unusual and should raise suspicion for tumors, complicated hernias, Crohn’s disease or other inflammatory processes, gallstones, volvulus, or intussusception.
  2. CT Abdomen/Pelvis is better than KUB for identifying the specific site and severity of obstruction (partial vs. complete), as well as potentially determining the etiology.
  3. Infections in HIV can localize to different parts of the bowel with small bowel etiologies including: HIV enteropathy, MAC, protozoan (Giardia and the spordia), and helminths (strongy)


More Information on HIV-Associated GI Pathology by Location in GI Track:
HIV-Associated GI Pathology (By Location):
                -CMV, HSV
                -Kaposi’s Sarcoma
                -Idiopathic ulceration
                -Neoplasia (Kaposi’s sarcoma, lymphoma)
Small Bowel:
                -HIV enteropathy
                -Protozoa (Giardia, Isospora, Cryptosporidia, Microsporidia)
                -Helminths (Stronglyoides)
                -Viral (CMV, HSV)
                -Bacterial (Clostridia, Salmonella, Shigella, Campylobacter)
                -Fungal (Cryptococcus, histoplasmosis)
                -Neoplastic (KS, lymphoma)


For more info on HIV-associated diarrhea, see this Evernote from Rachel Greenblatt:


Bhaijee F, Subramony C, Tang SJ, Pepper DJ. Human immunodeficiency virus-associated gastrointestinal disease: common endoscopic biopsy diagnoses. Patholog Res Int 2011;2011:247923.

Evernote Link:


ZSFG Morning Report: Dactylitis ddx, IGRA’s, and a hint of NTM/TB

Thanks to Lily Kornbluth for presenting the case of a woman from China admitted with a swollen and painful finger which turned out to be mycobacterial dactylitis!

You’re probably asking yourself: Wait, aren’t those swollen digits just in psoriatic arthritis??? Do I have a framework or a DDX FOR DACTYLITIS??? Well, NOW YOU DO! Here’s a short list generated in report today with the help of Lisa Winston, Stephanie Cohen, Lily, and the #fabulous ZSFG resident crew!

dactyl 1

Dactylitis DDX:


  • NTM
  • TB
  • Syphilis
  • Leprosy
  • Fungi like Blasto, Cocci, Aspergillus
  • Bacterial tenosynovitis or septic arthritis or osteo w/ Staph, Strep, Gonorrhea, Nocardia, and Vibrio (this patient noted a history of food preparation…;)


  • Psoriatic arthritis
  • Reactive arthritis
  • Gout
  • Sarcoid
  • SLE
  • RA

Malignant: Leukemia

Heme: Sickle Cell dz

As we narrowed in on the dx, a diagnostic test returned: POSITIVE QUANTIFERON GOLD! Lisa Winston reminded us about the power of the QTF-Gold and that it’s more specific than the PPD! Here’s a quick refresher and an elegant representation of the box/test….
quant gold

QuantiFERON Gold or more technically since it just rolls off the tongue: Interferon-gamma release assays (IGRA’s):

  • What are they?
    • Diagnostic tools for latent TB indicating a cellular immune response to M. tuberculosis.
      • IGRAs can’t distinguish between latent and active TB aka don’t use them to dx active TB
      • IGRA’s available around the world: QuantiFERON-TB Gold In-Tube (QFT-GIT) assay, Quantiferon-TB Gold (QFT-G) assay, and the T-SPOT.TB assay

  • How do they work?
    • By capitalizing on the M. tuberculosis–specific antigens: early secreted antigenic target 6 (ESAT-6) and culture filtrate protein 10 (CFP-10)!
      • QFT-GIT assay is an ELISA-based test that uses peptides from three TB antigens (ESAT-6, CFP-10, and TB7.7). A positive test denotes IFN-gamma response to TB antigens that’s above the test cut-off.
      • Of note, ESAT-6 and CFP-10 are encoded by genes in the region of difference 1 (RD1) segment of the M. tuberculosis genome. These antigens are more specific for M. tuberculosis than the PPD because they are not shared with any BCG vaccine strains or most species of NTM.
        • HOWEVER: Two of the NTM that affect humans, Mycobacterium marinum and Mycobacterium kansasii, contain gene sequences that encode for ESAT-6 or CFP-10. So infxn with either of these NTM’s=positive QTF test 😦

  • What are their test characteristics?
    • IGRA’s have specificity >95% for diagnosis of latent TB, especially great as unaffected by BCG vaccination. The sensitivity for the IGRA’s T-SPOT.TB and QFT-GIT are 90 and 80%, respectively. PPD sensitivity as reference is 80%. Of note, IGRA sensitivity decreases in patients with HIV!

Once the deep skin biopsy came back “swimming in AFB’s,” we discussed how to approach mycobacteria based on rapid or slow growth. Here is a simplified algorithm to consider…
mycobact outline


*Lisa Winston, Stephanie Cohen, and ZSFG resident crew
*Pai M et al. Systematic review: T-cell-based assays for the diagnosis of latent tuberculosis infection: an update. Ann Intern Med. 2008 Aug 5;149(3):177-84. Epub 2008 Jun 30. PMID:18593687




ZSFG can’t be MIF’d by penile lesion ddx & indications for sgy in endocarditis

At the General, we give you a little bit of this and a little bit of that in report. And same thing goes for the chiefs’ blog. This is a quick run-through of a few recent legendary reports!


In Neuro Report today, we crushed, I mean discussed, hypercarbic respiratory failure and the role of neuromuscular causes for it. We were joined by neurology guru, Andy Romeo, and here are a few of his pearls:

-Whenever you come across someone reporting dysphagia, make sure to ask about other bulbar sx’s
-In a patient with increased work of breathing in whom you’re considering if diaphragmatic weakness is playing a role, check neck flexor strength to assess if a new neuromuscular weakness is present
MIF & VC are the confrontational tests for the diaphragm. To remind ourselves about those two entities:

  • For Vital capacity (VC) and Mean inspiratory force (MIF), there is the 20-30 rule
  • VC: deep breath and exhalation maximally into spirometer; goal is at least 20cc/kg
  • MIF: inhalation against a closed valve with negative force recorded; goal is “more negative” than -30 cmH20. -60cmH20 is expected or what is associated with weak cough in NL person


In a recent ID report, we discussed the well-known penile lesion ddx and added in a lesser known branch point of the *PRURITIC* penile lesion. The following is a non-exhaustive (and likely with much overlap) summary of what we came up with:

PAINFUL penile lesion

  • Chancroid/H. ducreyi
  • SJS/TEN drug lesion
  • SCC
  • Traumatic lesion/entrapment injury
  • Ulcers in s/o foley
  • HSV
  • Paraphimosis

 PAINLESS penile lesion

  • Syphilis
  • LGV (Of note, the lymphadenopathy *IS* painful in Lymphogranuloma venereum; LGV caused by L1, L2, L3 serovars of Chlamydia trachomatis)
  • Granuloma Inguinale (uncommon infection caused by K. granulomatis)
  • HIV
  • HPV
  • Pearly penile papule

*PRURITIC* penile lesion

  • Fixed drug reaction, DRESS/DHR
  • Yeast
  • Infestation-scabies/pubic lice
  • HSV
  • Behcet’s

 So how do we diagnosis LGV? Does our usual urine test work??????
Lisa Winston teaches us:

Turns out the usual Chalmydia culture or the more commonly ordered/sensitive NAAT test will be positive in LGV as the serovars will be picked up—it just won’t specify that it detected the L1-3 serovars. Usually when the sx’s are classic, empiric tx (longer course) is initiated. If you want a definitive dx, you can talk to colleagues at communicable dz and public health to see if need to send serology or special PCR to the SF public health lab (and then potentially to state’s public health lab or CDC).


Lastly, Mike and Carine presented a patient in intern report with MV endocarditis 2/2 MSSA where we discussed the role of early surgical intervention in infective endocarditis.

There is a fantastic 2013 NEJM Infective Endocarditis review article by Hoen and Duval that breaks down the indications for surgery into three big categories: heart failure, uncontrolled infection, and prevention of embolic events. Or in image form:

indications for sgy

For those of you who want more…

Punag, one of the cardiology fellows, passes on the following for the ACC/AHA class indications for surgical intervention:

Early surgery is recommended for patients with complicated infective endocarditis (IE), but data from randomized trials are scarce. The following are points to remember about the timing of surgery among patients with IE:

  1. The main indications for early surgery in IE are heart failure, uncontrolled infection, and prevention of embolization. The reduction in mortality with surgery is greatest among patients with IE and moderate to severe heart failure.
  2. Heart failure. The European Society of Cardiology (ESC) guideline (2009) recommends emergent surgery for heart failure with refractory pulmonary edema or cardiogenic shock (Class I), or urgent surgery for persistent heart failure with signs of poor hemodynamic tolerance (Class IIa). The American Heart Association (AHA)/American College of Cardiology (ACC) guideline (2014) recommends early surgery for valve dysfunction causing heart failure (Class I).
  3. Uncontrolled infection. The ESC guideline recommends urgent surgery (Class I) for evidence of uncontrolled infection defined as either abscess, fistula, or pseudoaneurysm; or for an enlarging vegetation, persistent fever, or positive blood cultures after 7-10 days of appropriate therapy. The AHA/ACC guideline recommends early surgery (Class I) for evidence of persistent infection, heart block or abscess, or a resistant organism ( aureus, fungi).
  4. Prevention of embolization. The ESC guideline recommends urgent surgery for a vegetation >10 mm with previous embolization or other surgical indication (Class I), or for isolated vegetation >15 mm and feasible valve repair (Class IIb). The AHA/ACC guideline recommends early surgery for recurrent emboli and persistent vegetations despite appropriate antibiotic therapy (Class IIa); or a large mobile vegetation on a native valve (Class IIb).
  5. Neurological complications. Patients with a neurological complication may have other indications for early surgery. However, early surgery may pose a significant risk for perioperative neurological deterioration (related to anticoagulation potentiating the risk of intracerebral bleeding, and to hypotension during cardiopulmonary bypass aggravating neurological ischemia and edema).
  6. Prosthetic valve IE. Prosthetic valve endocarditis is the most serious form of IE, and more difficult to treat using antibiotics alone. In general, current guidelines support consideration of a surgical strategy for high-risk subgroups with prosthetic valve IE, including patients with heart failure, abscess, or persistent fever.
  7. Definitions of early surgery. There is no consensus as to the optimal timing of early surgery. The ESC guideline classifies surgical indications in IE as emergent (within 24 hours), urgent (within a few days), and elective (after 1-2 weeks of antibiotic therapy). The AHA/ACC guideline defines early surgery as occurring during the initial hospitalization and before completion of a full therapeutic course of antibiotics.


Evernote link:


Hoen B, Duval X. Infective Endocarditis. N Engl J Med 2013; 368:1425-1433April 11, 2013DOI: 10.1056/NEJMcp1206782

ZSFG ID Report Pearls: Epididymitis, GU TB, and Crypto meningitis in HIV-neg

We’ve had really exciting cases at ID report this month! Will highlight a few points about Cryptococcal meningitis in non-HIV patients and the infamous entity of epididymitis, with which our story begins…

Acute epididymitis:

Hx: <6 wks of (unilateral) pain, swelling, and inflammation of the epididymis (most patients won’t say that their epididymis hurts, but scrotal/testicular pain may be mentioned).

  • Occasionally involving the testis (epididymo-orchitis, like in 12% of patients w/ Behcets dz) or accompanied by urethritis which is usually asymptomatic

Frequent offenders:

  • Among sexually active men aged <35 years, C. trachomatis or N. gonorrhoeae.
  • If pt is insertive partner in anal sex, consider sexually transmitted enteric organisms (e.g., Escherichia coli and Pseudomonas spp.)
  • If >35 years of age, don’t forget CT/GC though bacteriuria is usually 2/2 obstructive urinary disease, urinary tract instrumentation or surgery, systemic disease, and immunosuppression.

Ddx: R/o STI, torsion, abscess, hydrocele, hernia, testicular cancer, drug reaction (AMIODARONE-induced epididymitis, self-limited situation w/ onset 4-71 months after introduction of amio, whoknew?!)



  • Suspect epididymitis by physical exam, tenderness around posterior testicle/epididymis
  • Diagnostics:
    • Use (urine) NAATs for the detection of N. gonorrhoeae and C. trachomatis
    • Gram stain & culture of urethral secretions
      • ≥5 WBC/oil immersion field is highly sensitive & specific urethritis; can see intracellular Gram-negative diplococci on Gram stain to dx gonococcal infxn


    • Positive leukocyte esterase test on first-void urine or urine w/ ≥10 WBC/hpf
    • Other STI’s: RPR, HIV
    • Sono—do this to r/o torsion as the ultrasound findings in epididymitis are of minimal utility in dx/tx and include epididymal hyperemia and swelling

Tx: CTX 250mg IM x1 + Doxy 100mg BID x10d OR if considering enteric organisms, Levofloxacin 500mg daily x10d.

  • For sexual partners: refer all sexual partners (within 60d prior to sx onset) for eval and tx; avoid sex until pt and all sexual partners have completed tx
  • Adjunct therapy:
    • Bed rest, ice, scrotal elevation (scrotal sling, perhaps)
    • Re-examine in 72hr to reassess dx and abx selection. FAILURE TO IMPROVE WARRANTS RE-EVAL OF DX/TX
    • If swelling and pain persists (like in the patient presented this morning), do a comprehensive eval for tumor, abscess, TB**, infarction, fungal infxn


Chronic epididymitis:

Dx by hx: ≥6 wks of discomfort and/or pain in the scrotum, testicle, or epididymis. The CDC recommends we divide this entity into inflammatory chronic epididymitis, obstructive chronic epididymitis, and chronic epididymalgia, but let’s not get crazy.

Frequent offenders:

  • Consider entities w/ granulomatous reaction, specifically Mycobacterium tuberculosis (TB) is the most common granulomatous disease affecting the epididymis

The case today ended up being GU TB, which brings up that in culture negative recurrent epididymitis (or really culture-negative anything), consider TB!

  • Up to 25% of patients w/ TB epididymitis have bilateral disease
  • Ultrasound shows enlarged hyperemic epididymis with multiple cysts and calcifications
  • Consider **Tuberculous epididymitis in pt’s w/ exposure to (this pt lived in India for 30yrs, left 5yrs ago) or h/o TB infxn or in pt’s who worsen clinically despite approp abx


At a separate, equally exciting ID report, we discussed the (Short) Ddx for high protein level in CSF:
-Epidural abscess
We also spent some time discussing Cryptococcal Meningitis in non-HIV patients:

-The patient presented had a negative serum CrAg, though a positive CSF CrAg. This is a rare, but observed entity…

-There is a group of patients who are non-HIV, non-transplant who get cryptococcal infections. Usually, they are more likely to get pulmonary crypto as the sole manifestation, though meningoencephalitis is also common. A few diagnostic pearls in this scenario:

  • Serum CrAg titers in immunocompromised hosts tend to be higher than titers in immunocompetent patients
  • Immunocompetent patients have higher mean CSF leukocyte counts, higher CSF protein, and lower CSF glucose
  • Immunocompetent patients are less likely to be India ink-positive
  • Higher 90-day and 1-year mortality for immunocompromised patients
  • CrAg test characteristics are pretty great (see table below) in HIV-patients, and there’ve been recent studies suggesting the sensitivity of the lateral flow assay (LFA) is just as good in non-HIV patients (PMCID: PMC4733170)


The false negative serum CrAg pearls below come from our 2003 UCSF Chief foremothers and forefathers!

*Causes of a false negative serum cryptococcal antigen test*: tests for antigen against crypto surface polysaccharide

  • The serum CrAg is often negative in non-HIV patients
  • Low titers of cryptococcus
  • Early infection
  • Presence of immune complexes
  • Poorly encapsulated strains with low production of polysaccharide
  • Prozone phenomenon of high titers




Sadek I, Biron P, Kus T: Amiodarone-induced epididymitis: report of a new case and literature review of 12 cases. Can J Cardiol 9:833, 1993 [PMID:8281484]
Pappas PG. Cryptococcal Infections in Non-Hiv-Infected Patients. Transactions of the American Clinical and Climatological Association. 2013;124:61-79.
Jitmuang A, Panackal AA, Williamson PR, Bennett JE, Dekker JP, Zelazny AM. Performance of the Cryptococcal Antigen Lateral Flow Assay in Non-HIV-Related Cryptococcosis. Diekema DJ, ed. Journal of Clinical Microbiology. 2016;54(2):460-463. doi:10.1128/JCM.02223-15.

MOFFITT CARDIOLOGY REPORT PEARLS 4/11/17: Endocarditis and Septic Emboli!

Wow, thanks to Salman for presenting an amazing case this morning of a young woman with right-sided endocarditis and septic emboli who was critically ill and underwent high risk cardiac surgery. Thankfully she is doing well after surgery. Loved that Salman actually went in on the OR case, but a little concerned that he may switch from medicine to surgery… Pearls below!


Top Pearls:

  1. Patients with tricuspid endocarditis often do not have a detectable heart murmur.
  2. Heart failure is unusual in tricuspid endocarditis.
  3. Data do NOT support antithrombotic therapy for septic emboli.


For those who want more info:

Pathogenesis of endocarditis in IV drug use: Injection of particulate matter (e.g. talc) causes endothelial damage to heart valves and increases endocarditis risk. Bacteria or fungi from skin, drug, or diluents/filters may also be directly injected.

*Pearl: Remember that saliva contact with needles (e.g. licking needle to “clean” it before injection) increases risk of endocarditis from oropharyngeal flora such as Haemophilus parainfluenzae, Eikenella corodens, and Streptococcus milleri.

Staph aureus accounts for more than half of endocarditis cases in injection drug users.

*Pearl: Patients with tricuspid endocarditis often do not have a detectable heart murmur!

*Pearl: Heart failure is unusual in tricuspid endocarditis but common in aortic endocarditis.


Endocarditis surgical indications: Generally the same in right- and left-sided endocarditis.

  • Symptomatic valve dysfunction or signs of heart failure
  • Paravalvular extension of infection
  • Fungal or MDR organisms
  • Persistent infection after 7 days of appropriate therapy
  • >1 cm vegetation (left-sided lesions)


Tyler asked some great questions about how vegetations form and whether we should anticoagulate septic emboli.

The following steps lead to vegetation formation:

  • Endocardial injury
  • Focal adherence of platelets and fibrin
  • Platelet-fibrin nidus secondarily infected from circulating microorganisms
    • From distant focal infectious source or transient bacteremia from mucosa/skin
  • Microbial growth further activates coagulation cascade forming macroscopic vegetation

*Pearl: Staph aureus is so virulent that it can directly infect undamaged heart valves!


Should we anticoagulate septic emboli?

Up to 80% of patients with left-sided endocarditis have evidence of stroke on imaging! The risk of embolism markedly declines after initiation of antibiotic therapy.

The limited data we have do not support antithrombotic therapy (anticoag or aspirin) in endocarditis since it does not reduce embolism risk. Additionally, septic emboli are at high risk of hemorrhage!

This is particularly relevant if the patient has a surgical indication, because bypass required for the surgery also requires systemic anticoagulation. Consult CT surgery early in these cases!

What if they’re already on anticoagulation for another reason?? Case by case risk/benefit analysis. A great cardiology consult question if they’re not already on the cardiology service. 🙂




Have a great day everyone!


MOFFITT PULMONARY REPORT PEARLS 4/10/17: Aspergillosis and Rhinovirus!

Hey everyone! Thanks to Ashley for presenting the case of an elderly man with a history of malignancy and invasive fungal disease who developed cough and a new pulmonary nodule. Workup was still pending, but RVP returned with rhinovirus. Pearls below!


Top Pearls:

  1. Aspergillosis can affect the GI tract! (the patient this morning also had GI symptoms)
  2. Rhinovirus is associated with CAP (direct causation controversial in immunocompetent adults)
  3. Rhinovirus can be deadly in immunocompromised and critically ill patients.


For those who want more info:

Aspergillosis can manifest in MANY different ways.


  • Pulmonary aspergillosis
    • Bronchopneumonia
    • Angioinvasive aspergillosis
    • Tracheobronchitis
    • Subacute invasive aspergillosis (aka chronic necrotizing)
    • Chronic (>3 months): aspergilloma, nodules, chronic cavitation, chronic fibrosis
    • ABPA (asthma and CF patients)
  • Rhinosinusitis
  • Disseminated infection: skin, brain, eyes, liver, kidneys, endocarditis
  • GI: enterocolitis, appendicitis, colonic ulcers, abdominal pain, GI bleeding


Some info on Rhinovirus!

  • Most common “cold” virus but can also infect lower respiratory tract!
  • Causes greater morbidity than previously thought
  • Frequent cause of asthma exacerbations
  • Children are the major reservoir J
  • About half of rhinovirus infections in immunocompetent adults are asymptomatic
  • Typical illness is nasal discharge, cough, sore throat. Fever is rare in immunocompetent adults.
  • Controversial whether rhinovirus directly contributes to CAP since most specimens in which it is identified are from the upper airway. What is clear is that rhinovirus is strongly associated with CAP. The direct association is stronger in transplant patients (see below).
  • *Pearl: Rhinovirus is dangerous in immunocompromised and critically ill patients.
    • Recent studies show comparable rhinovirus morbidity and mortality in hospitalized elderly and immunocompromised patients to that of influenza (Hung Int J Mol Sci 2017, Kraft J Clin Microbiol 2012)
    • Particularly high mortality when rhinovirus infects the lower resp tract of bone marrow transplant patients (Seo Haematologica 2017, Jacobs Transpl Infect Dis 2013)
    • Our pulmonary experts taught us that rhinovirus is a cause of lung transplant rejection!
  • Treatment: None currently, but there is a drug in the pipeline, vapendavir, that binds to rhinovirus capsid protein and prevents viral RNA release.




Have a great day everyone!