NIH Funds Antimicrobial Resistance Diagnostics Projects

As I mentioned in a previous post, diagnostic uncertainty drives antibiotic use, so getting answers to clinicians faster is an important piece of the antimicrobial stewardship pie. NIH is stepping up and funding several efforts around the country. From the press release:

“The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, has awarded more than $11 million in first-year funding for nine research projects supporting enhanced diagnostics to rapidly detect antimicrobial-resistant bacteria.”

The funded researchers include a mix of companies and academic centers including BioFire Diagnostics, LLC and Brigham Young University in Provo, Utah.

Read the full press release here.

 

Swails

Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

 

 

Microbiology Case Study–Pleural Thickening in Lung Transplant Patient

Case history:

A 71-year-old man with a past medical history of idiopathic pulmonary fibrosis and asbestosis status post recent single lung transplant presented with worsening dyspnea. He had a right pleural catheter since the time of his lung transplant surgery five months ago. A chest CT scan was performed and revealed a right pleural effusion with pleural thickening. A sample of the pleural fluid was sent to the microbiology laboratory with the following gram stain and colony morphology:

Gram stain showing gram positive bacilli with subtle palisading arrangements and formations that resemble Chinese letters.
Gram stain showing gram positive bacilli with subtle palisading arrangements and formations that resemble Chinese letters.
Blood agar plate with gray-white, moist, smooth, non-hemolytic bacterial colonies.
Blood agar plate with gray-white, moist, smooth, non-hemolytic bacterial colonies.

 

Laboratory Identification:

The pleural fluid grew bacterial colonies on blood agar plates as shown above. No growth was present on MacConkey agar (selective for gram negative bacteria). The colony morphology and gram stain was suggestive of Corynebacterium species. Mass spectrometry confirmed the bacteria as Corynebacterium striatum.

Discussion:

Corynebacterium striatum are gram-positive bacilli that are normal skin and mucosal membrane flora. C. striatum is commonly regarded as a contaminant but may be an opportunistic pathogen in immunocompromised patients such as the patient presented in the above case. Transmission of C. striatum most likely occurs when the patient’s endogenous strain gains access to a normally sterile site of the body. C. striatum has also been documented to spread nosocomially in patients with severe chronic obstructive pulmonary disease. C. striatum is associated with a spectrum of diseases including infectious endocarditis, bacteremia, pneumonia, lung abscess, arthritis, chorioamnionitis and foreign medical device infections. Patients with C. striatum infections are empirically treated with vancomycin because the susceptibility to other antibiotics is variable. Additionally, removal of foreign medical device should be performed if indicated.

 

Jill Miller, MD is a 2nd year anatomic and clinical pathology resident at the University of Vermont Medical Center.

Wojewoda-small

-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Assistant Professor at the University of Vermont.

Microbiology Case Study–Infection at Wisdom Tooth Extraction Site

Clinical

56 year old male with stage IV chronic kidney disease, hypertension, and gout who underwent a left lower wisdom tooth extraction presented two days post-op with throbbing pain on left side of his face and neck, dysphagia and dyspnea. He was sent to an outside ED by his dentist. He was given 900 mg of clindamycin, a dose of steroids and pain management and was sent to our institution. Surgical site was intact, but there was massive swelling of the floor of the mouth, submandibular gland, and neck. Symptoms worsened despite being given IV clindamycin. Infectious disease was consulted he was started on meropenem and blood cultures were drawn.

Microbiology

Two anaerobic blood culture bottles became positive at 48 and 61 hours.

Gram stain:

Gram stain of organism 1
Gram stain of organism 1

 

Gram stain of organism 2
Gram stain of organism 2

 

Plates:

Anaerobic blood agar plate showing predominately two colony types
Anaerobic blood agar plate showing predominately two colony types

 

Isolate of organism 1 on anaerobic blood agar showing dry, white colonies.
Isolate of organism 1 on anaerobic blood agar showing dry, white colonies.
Isolate of organism 2 on anaerobic blood agar showing small, white colonies with no hemolysis
Isolate of organism 2 on anaerobic blood agar showing small, white colonies with no hemolysis

Discussion:

Two organisms were identified.

Organism 1: Fusobacterium nucleatum – anaerobic gram-negative, non-spore-forming rods. They are pale-staining, long, slender, spindle-shaped rods with sharply pointed or tapered ends; occasionally the cells occur in pairs end to end. Sometimes there are spherical swellings. Cells are usually 5-10 µm long, but can be shorter. They grow well on anaerobic blood agar plates under anaerobic conditions and are killed readily by exposure to ambient air. Colonies on anaerobic blood agar are 1-2 mm in diameter, slightly convex with slightly irregular margins and have a characteristic internal flecking referred to as “crystalline internal structures”. They can have three morphologies: bread crumblike (white), speckled, or smooth (gray to gray-white). There is greening of the agar on exposure to air, they are usually nonhemolytic and fluoresce chartreuse under UV light.

The Fusobacterium species are normally found in the upper respiratory, gastrointestinal, and genitourinary tracts of humans. They are common causes of serious infections in multiple body sites. They are associated with infections of the mouth, bite wounds, and respiratory tract. F. nucleatum are the most frequently involved in anaerobic pleuropulmonary infections (aspiration pneumonia, lung abscess, necrotizing pneumonia, thoracic empyema). They are also fairly common pathogens in brain abscesses, chronic sinusitis, metastatic osteomyelitis, septic arthritis, liver abscess, and other intraabdominal infections. Fusobacterium nucleatum is the species most commonly found in clinical materials. It can cause severe systemic infection in patients with neutropenia and mucositis following chemotherapy.

They can be differentiated from similar species of Bacterioides, Prevotella, Porphyromanas, and Leptotrichia by their production of butyric acid but not isobutyric or isovaleric acid. Bacterioides and Porphyromanas species produce all three acids.

Organism 2: Parvomonas micra – formerly called Peptostreptococcus micros or Micromonas micros, are anaerobic, gram-positive cocci, <0.7 µm in diameter; occur in packets and short chains. Grow on anaerobic blood agar. Colonies are tiny, white, opaque, nonhemolytic. This is a periodontal pathogen that contributes to periodontitis.

 

Kirsten J. Threlkeld, MD is a 4th year anatomic and clinical pathology resident at the University of Vermont Medical Center.

Wojewoda-small

-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Assistant Professor at the University of Vermont.

 

Illinois Summit on Antibiotic Stewardship

Last week, I attended the Illinois Summit on Antimicrobial Stewardship at Northwestern Memorial Hospital. While the target audience was physicians, nurses, pharmacists, and administrators, as a clinical laboratory scientist I found the presentations (with a few caveats, which I’ll get to in a moment) quite informative.

The morning sessions covered the relationship between antibiotic use and resistance patterns; interpretations and implementation of the national guideless for stewardship; and using behavioral science to increase compliance with stewardship programs. Participants spent part of the afternoon in small groups to discuss designing and implementing a stewardship program.

A few notes:

-50% of antibiotics for upper respiratory infections aren’t needed; 50% of antibiotics for inpatients aren’t needed, either

-antibiotics are the only drug where use in one person impacts it effectiveness in another

-based on the literature, antibiotic stewardship programs have at least a transient effect on antibiotic effectiveness—eventually, resistance numbers begin to climb again

-hospital antibiograms are the most widely available measure of resistant organisms, but we aren’t using them as effectively as we could. For example, we typically report that, say, “62.5% of E. coli isolates are resistant to ciprofloxacin,” but we don’t say where those isolates come from. Are they urinary tract infections or upper respiratory infections? What’s the rate of resistance for infected wounds?

-a weighted antibiogram might make empirical treatments for effective. For example, “what % of urinary tract infections are resistant to ciprofloxacin?”

-it’s important to note that the IT department, hospital information systems, and laboratory information systems play a huge role in stewardship programs

-stewardship programs depend on the “5 D’s” Diagnosis, drug selection, dose, duration, and de-escalation of use

-diagnostic uncertainty—driven by lack of early organism identification—drives a significant amount of antibiotic use

-when combined with stewardship, rapid bacterial identification methods such as MALDI-ToF platforms decrease parameters such as length of patient say, time to treatment, etc.

-we can use peer pressure to drive improvements. No one wants to perform worse than the doctor next door

-our efforts might be moot, anyway; other countries take a much laxer stance on antibiotic use

While the laboratory in general and clinical microbiology departments specifically were mentioned during the presentations, I must say they were only mentioned in the context of how little perceived impact we have on stewardship. (“Well, we know the laboratory isn’t going to give us any useful information for another three days…”) It wasn’t until I participated in the small group sessions in the afternoon that attendees at my table admitted that the laboratory is an important piece of the stewardship puzzle. We have mountains of data we can assimilate (antibiogram creation, anyone?). We can bring in new technologies to make identifications faster. We can work closely with the infectious disease doctors to help guide treatment. That brings up a good point—if microbiology labs aren’t in-house, then creating an antibiotic stewardship program becomes that much harder because results can be delayed.

If you’d like to see the powerpoints from the presentations, you can do so by clicking the “downloadable content” tab at Northwestern Memorial Hospital’s antibiotic stewardship page.

Swails

Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.

Microbiology Case Study–Diabetic Foot Ulcer

A 68 year old woman with a past medical history of type 2 diabetes mellitus presented with a foot wound clinically consistent with a diabetic foot ulcer. Imaging of the patient’s foot demonstrated a large abscess of the plantar aspect of her foot with extension to the surrounding soft tissues. The patient was taken to the operating room and incision and drainage was performed. Fluid from the wound was submitted to the microbiology laboratory and was planted aerobically and anaerobically. Growth was observed on the anaerobic blood plate with the below gram stain and colony morphology:

Gram stain showing Gram positive bacilli with minimal branching.
Gram stain showing Gram positive bacilli with minimal branching.
actino2
Anaerobic blood plate with small white bacterial colonies.

 

Laboratory Identification:

The fluid received from the patient’s wound was cultured on aerobic and anaerobic grow plates. The bacteria only grew on anaerobic plates. Additionally, the gram stain revealed pleomorphic gram positive bacilli. These findings were suggestive of Actinomyces. Actinomyces species was confirmed by mass spectrometry.

Discussion:

Actinomyces are anaerobic gram positive bacteria that are normal flora of the oral cavity and throat. Actinomyces have variable gram stain and colony morphology. Our case, as shown above, demonstrates the pleomorphic nature of Actinomyces and does not exhibit the classic textbook morphology. The typical gram stain morphology of Actinomyces is branching, filamentous, beaded bacilli. This morphology overlaps with Nocardia. Actinomyces can be distinguished from Norcardia based on its anaerobic growth pattern and lack of partial acid fast staining (Nocardia are strict aerobes that stain partially acid fast). The bacterial colonies of Actinomyces are non-hemolytic, non-pigmented and are classically described as white and nodular (molar tooth shaped). Actinomyces forms “sulfur granules” in patient specimens which are hard yellow granules composed of bacterial filaments solidified with exudative material.

Actinomyces has the potential to cause opportunistic infections when transferred from an endogenous site to a sterile site of the body. Actinomyces is involved in a spectrum of human disease including actinomycosis, wound infections, abscesses, oral infections, genital tract infections, and urinary tract infections. Of these diseases, actinomycosis is the most infamous and is characterized by abscess formation, draining sinus tracts with sulfur granules, and tissue fibrosis. Actinomycosis is most commonly cervicofacial, but may also be thoracic, abdominal, pelvic or involve the central nervous system.

Treatment of Actinomyces includes surgical debridement if indicated and prolonged antibiotics for 3-6 months depending on antibiotic sensitivity. Antibiotic sensitivity ranges from penicillin, amoxicillin, tetracycline, erythromycin, and clindamycin.

 

Jill Miller, MD is a 2nd year anatomic and clinical pathology resident at the University of Vermont Medical Center.

Wojewoda-small

-Christi Wojewoda, MD, is the Director of Clinical Microbiology at the University of Vermont Medical Center and an Assistant Professor at the University of Vermont.

A Potential Paradigm Shift for Strep Cultures?

In a study published a few days ago in the Annals of Internal Medicine, researchers discuss the prevalence of Fusobacterium necrophorum in students with pharyngitis. Typically, severe sore throats are attributed to Streptococcus Group A, C, or G; however, sometimes patients can be symptomatic but negative for these three pathogens. The study authors found F. necrophorum in 20.5% of their symptomatic population (312 students aged 15 to 30 years).

This study does raise an interesting question: should micro labs inoculate a CDC plate as well as a blood plate for strep cultures? This organism is susceptible to penicillin, so the treatment course is the same as for typical strep throat, which would indicate the CDC isn’t really needed. However, as this Healthday article indicates, F. necrophorum infections can lead to Lemierre’s syndrome, a rare but serious complication. Knowing the causative agent of a sore throat would be beneficial.

Swails

Kelly Swails, MT(ASCP), is a laboratory professional, recovering microbiologist, and web editor for Lab Medicine.