Breakpoint Breakdown

Working bacteriology benches in the clinical microbiology laboratory often comes with its fair share of questions about the susceptibility of patient isolates. In training, we are taught about breakpoints – clinically essential values which determine if an organism is susceptible, resistant, or somewhere in-between for a given drug. These values are readily accessible to us in guidance documents (e.g., CLSI M100, FDA website), and are programmed into instruments to allow for automated interpretation. But, have you ever wondered how these values are derived? Raw microbiological and pharmacological data, patient outcomes, and regulatory considerations must be examined through multiple lenses, and by many different entities, before these values ever make it to the printed page and used clinically. Here, we will highlight some of the “moving parts” of breakpoint determination an effort to demystify this process and gain a better understanding and appreciation of the clinical application of these life-saving measurements. To help, I’ve recruited two of our outstanding infectious disease pharmacists from UT Southwestern Medical Center to enhance this discussion. It’s my hope we will all learn something in the process!

Breakpoint Breakdown – The ABC’s of MICs and ECVs, plus Pharmacology 101!

A breakpoint represents a defined antibiotic concentration or zone of inhibition diameter that serves as a gatekeeper for antimicrobial use. This value categorizes organisms as susceptible, susceptible-dose dependent, intermediate, resistant, or nonsusceptible to various antimicrobials. As such, is an indispensable component of appropriate and effective antimicrobial prescribing.1 Breakpoints are set through a rigorous examination of data by various national and international organizations which we will discuss in a later post. Determining the optimal value at which a breakpoint should be set is multifactorial, requiring a multidisciplinary approach to incorporate data from bench and bedside. Now, if that introduction sounded daunting, don’t panic! We’re going start at the beginning with basic biological measurements of susceptibility that are needed to begin to establish a breakpoint. For those not currently working in microbiology (or if it’s been a while), a basic understanding of susceptibility testing mechanisms is necessary and we will briefly review here. Bacteria will be the focus for this discussion, but many of these concepts are also broadly applicable to fungi as well.

Determination of susceptibility to an antibiotic can be evaluated by examining the response of a bacterial isolate to antimicrobial exposure. In the laboratory, this is usually achieved through dilution, whereby an isolate may grow at some drug concentrations, and growth is inhibited at others. Dilution of the antimicrobial can come either through directly applying the antibiotic at defined concentrations uniformly to growth media (i.e. broth dilution, agar dilution), or utilizing a diffusion gradient through media when an antibiotic is applied at a single source (i.e. disk diffusion) (Image 1). Application of defined antibiotic concentrations to the growth media allows for a minimal inhibitory concentration (MIC) to be determined, while a diffusion gradient allows for a zone of inhibition to be measured (ZOI). An MIC is the lowest concentration of antimicrobial that inhibits organism growth of an isolate. This value is unique to the isolate that is being tested. However, when establishing a broad measurement which will encompass all isolates of that species (or group of species) such as a breakpoint, it’s easy to imagine that significantly more data is needed.

Image 1. Three methods of antimicrobial susceptibility testing. Kirby-Bauer disk diffusion generates a zone of inhibition – the diameter of that zone is measured and correlated with MIC data to establish breakpoints. Broth and agar dilution are two dilution methods which directly generate an MIC as an endpoint; the lowest concentration of antibiotic in which growth is inhibited. In the broth microdilution experiment, isolate 1 has an MIC of 4μg/mL. In the agar dilution experiment, isolate 2 has an MIC of 1μg/mL.

Thus, a first step in setting an optimal breakpoint begins with an antimicrobial’s in vitro activity against an organism. A descriptive summary of the MIC range across a given species helps define the MIC distribution. This analysis usually includes MICs from hundreds of tested isolates! This MIC distribution helps to define epidemiologic cutoff values (ECV or ECOFF). Like a breakpoint, these values separate the MIC distribution into bacterial populations that are either wild-type, and those with resistance. The wild-type MIC distribution aims to exclude outlier MICs that may represent organisms with acquired resistance (either through mutation or acquisition of resistance determinants) reflected by elevated MICs.  An isolate in the population with an MIC above the ECV is likely to have acquired resistance, whereas an isolate with an MIC lower than the ECV likely originates from the wild-type distribution and lacks mechanisms of acquired resistance or reduced susceptibility.2 So great, we have an experimental MIC value which separates wild-type organisms from ones that have acquired resistance, why not just stop there and call it a breakpoint? The answer is the ECV does not account for host responses, clinical outcomes, site of infection, pharmacokinetics/pharmacodynamics, dosing, and a number of other important variables which go into establishing a clinical breakpoint. Thus, using ECVs for clinical decision making is challenging.

Now that we have considered some aspects of the microbiological side of the equation, let’s switch gears and look at the host and other factors not addressed by an ECV. Pharmacokinetic (PK) and pharmacodynamic (PD) parameters are key to assessing the clinical applicability of a breakpoint. PK parameters represent how the body handles the antimicrobial, including absorption, distribution, metabolism and elimination, whereas PD parameters represent the effect between the drug and bug. Taken together, PK/PD parameters represent the relationship between drug concentration (PK) and antimicrobial effect (PD) over time. Different antimicrobials have distinct PK and PD characteristics, thus several PK/PD indices are utilized to determine optimal target concentrations or exposures that improve antibacterial efficacy. Common PK/PD indices are the percent of time the free drug concentration remains above an organism’s MIC (fT > MIC), the ratio of free max drug concentration (or peak) to MIC (fCmax/MIC), and the ratio of free drug exposure (area under the curve, AUC) over a 24-hour period to MIC (fAUC/MIC) (Image 2).3

Image 2. Common PK/PD Indices

For example, β-lactam antimicrobials require 40-60% fT > MIC for maximum antibacterial efficacy; however, the exact fT > MIC (or other exposure) required for optimal efficacy varies between different β-lactam antimicrobials and bacterial species. Importantly, the desired antimicrobial exposure should be obtainable based on the established breakpoint, meaning the β-lactam of interest should achieve 40-60% fT > breakpoint. Various strategies are employed to optimize PK/PD parameters relative to a given breakpoint (more on that to come in Part 2 of this series). These target exposures are calculated from data for each bug-drug combination.

Of note, the antimicrobial exposure in relation to MIC is often based on antimicrobial blood concentrations. However, this is obviously not always the site of infection. The same bug-drug combination can have multiple breakpoints specific to infection site. For example, central nervous system (CNS) infections may have lower established breakpoints compared with non-CNS infections. The use of a lower breakpoint improves PK/PD target attainment in areas where there may be low drug concentrations, such as the CNS. For CNS-specific breakpoints, only organisms with MICs within the lower range of the MIC distribution will be deemed susceptible. With a lower MIC, the PK/PD exposure may be more obtainable given the potential poor drug penetration to the site of infection.

Outcomes from clinical data are often deemed the most important factor used to determine breakpoints. Treatment successes or failures of an antimicrobial against a specific MIC may provide validity to an established breakpoint or support revision. For example, the piperacillin-tazobactam breakpoint for Pseudomonas aeruginosa, was lowered from 64/4 mcg/mL to 16/4 mcg/mL due to an increase in mortality observed in patients who had organisms with MICs 32 or 64 mcg/mL.4 Unfortunately, clinical outcome data is often influenced by other confounders beyond antimicrobial therapy and the organism’s MIC, such as source control and other therapeutic interventions. Furthermore, clinical data for “resistant” organisms may not be available, limiting the assessment of the antimicrobial against organisms with high MICs.

Finally, it is important to remember that breakpoints are not set in stone and change regularly as more data become available. Common reasons for breakpoint revisions include: 1) new PK/PD data suggesting the breakpoint is too low or high based on antimicrobial exposure, 2) identification of novel resistance mechanisms, and 3) new clinical data to suggest poor correlation of clinical response with the established breakpoint. Furthermore, microbiological methods may become more accurate and ultimately affect quantification of the MIC.5

In summary, establishing a breakpoint is not a straightforward process and requires an aggregate of information. We are really only scratching the surface of the very complex process here, but hope that this sheds some light on where these important values originate. Various types of data; microbiological, pharmacological, in vitro, in vivo, they all create the story. However, a complete picture is often not available at the time of breakpoint creation, resulting in the need to constantly review and update breakpoints as more data becomes available.

Next post we will discuss how breakpoints are used at the bedside.

References

  1. Clinical and Laboratory Standards Institute. Development of In Vitro Susceptibility Testing Criteria and Quality Control Parameters, 5th Edition (M23).
  2. Turnidge J, Paterson DL. Setting and revising antibacterial susceptibility breakpoints. Clin Microbiol Rev. 2007 Jul;20(3):391-408.
  3. Craig WA. Pharmacokinetic/pharmacodynamic parameters: rationale for antibacterial dosing of mice and men. Clin Infect Dis. 1998 Jan;26(1):1-10; quiz 11-2. doi: 10.1086/516284.
  4. Tam V, et al. Outcomes of bacteremia due to Pseudomonas aeruginosa with reduced susceptibility to piperacillin-tazobactam: implications on the appropriateness of the resistance breakpoint. Clin Infect Dis. 2008 Mar 15;46(6):862-7.
  5. Humphries RM, Abbott A, Hindler JA. Understanding and Addressing CLSI Breakpoint Revisions: a Primer for Clinical Laboratories. J Clin Microbiol. 2019 May 24;57(6):e00203-19.

-Marguerite Monogue, PharmD is an infectious diseases pharmacy specialist and assistant professor at the University of Texas Southwestern Medical Center in Dallas, Texas. She is interested in antimicrobial pharmacokinetics/pharmacodynamics and multi-drug resistant Gram-negative bacteria.

-James Sanders, PharmD, PhD, is an infectious diseases pharmacy specialist and assistant professor at the University of Texas Southwestern Medical Center in Dallas, Texas. His academic and research interests are focused on multi-drug resistant Gram-negative bacteria, surgical site infections and HIV pharmacotherapy.

-Andrew Clark, PhD, D(ABMM) is an Assistant Professor at UT Southwestern Medical Center in the Department of Pathology, and Associate Director of the Clements University Hospital microbiology laboratory. He completed a CPEP-accredited postdoctoral fellowship in Medical and Public Health Microbiology at National Institutes of Health, and is interested in antimicrobial susceptibility and anaerobe pathophysiology.

Microbiology Case Study: 83 Year Old Male with Bladder Cancer

Case History An 83 year old male with bladder cancer was treated with Mycobacterium bovis Bacillus Calmette-Guérin (BCG), his last treatment occurring 1.5 months prior to presentation. He has a past medical history of chronic obstructive pulmonary disease, hypertension, obstructive sleep apnea, obesity, and diabetes. The patient has been hospitalized four times over the last two months and his symptoms include generalized weakness, malaise, shortness of breath and recurrent fever. He was found to have patchy lung infiltrates and he was diagnosed with pneumonia, COPD exacerbation and symptoms of heart filature. He was treated previously with antibiotics, steroids and fluid management which would temporarily relieve his symptoms. He presents to the hospital again, four days after his last hospital discharge, with generalized weakness, malaise, shortness of breath and recurrent fever. On initial evaluation he was found to be pancytopenic.  

Laboratory Identification

Blood cultures were negative. A bone marrow biopsy was performed for fever of unknown origin and pancytopenia. The biopsy showed non-caseating granulomas which were negative for acid-fast bacilli (AFB) by Ziehl-Neelsen stain and fungal elements by Gomori Methenamine Silver Stain (GMS). A laboratory-develped PCR test for Mycobacterium tuberculosis complex (MTBC) was performed on the bone marrow and was negative. AFB culture of bone marrow was positive for after 30 days of incubation and the organism was confirmed to be acid-fast bacilli by auramine-rhodamine fluorescent dye and Kinyoun stain. A second laboratory-developed test that uses heat shock protein (HSP) 2 and HSP3 to determine species level identification of Mycobacteria identified the organism as M. tuberculosis complex. Due to the patient’s history, further identification was performed at a reference lab using specific oligonucleotides targeting the gyrb DNA sequence polymorphisms which is able to separate different members of the MTBC. The patient’s isolate contained a RD1 deletion which is specific for Mycobacterium bovis bacillus Calmette-Guérin (BCG).

Discussion

Mycobacterium bovis is a slow growing mycobacterium which produces rough, dry colonies on growth solid media. It is one of the species in the MTBC with a natural host of domestic and wild animals. Routine molecular tests will not accurately differentiate between members of the MTBC. For definitive identification of M. bovis, 16S rRNA and gyrB gene sequencing is necessary. Safe handling procedures should be followed prior to molecular testing of MTBC.

Mycobacterium bovis BCG is a live, attenuated strain of Mycobacterium bovis that was created for vaccine and is used in the treatment of superficial bladder cancer. The treatment may cause localized symptoms including hematuria, fever, nausea, and dysuria which are marker of anti-tumor effect. Serious complications occur in <5% of patients with complications including sepsis, pneumonitis, hepatitis, lymphocytic meningitis, bone marrow involvement, and mycotic aneurysms. The cardinal sign of BCG infection is a relapsing fever with drenching night sweats persisting beyond 48 hours. Disseminated infection can occur days to years after the therapy. Clinical suspicion should be high for M. bovis BCG dissemination if there are symptoms and a high grade fever ≥72 hours. Treatment includes a regiment of isoniazid, rifampin and ethambutol. Most isolates of M. bovis are resistant to pyrazinamide.

References

  1. Lamm DL. Efficacy and safety of bacille Calmette-Guérin immunotherapy in superficial bladder cancer. Clin Infect Dis 2000; 31 Suppl 3:S86.
  2. Shelley MD, Court JB, Kynaston H, et al. Intravesical Bacillus Calmette-Guerin in Ta and T1 Bladder Cancer. Cochrane Database Syst Rev 2000; :CD001986.
  3. Richter E, Weizenegger M, Rusch-Gerdes S, Niemann S. Evaluation of Genotype MTBC Assay for Differentiation of Clinical Mycobacterium tuberculosis Complex Isolates. Journal of Clinical Microbiology 2003; 41(6): 2672-2675
  4. UpToDate

-Crystal Bockoven, MD is a 4th year anatomic pathology resident at University of Chicago (NorthShore). Crystal has an interest in and will be doing a fellowship in pediatric and perinatal pathology. In her spare time, she enjoys reading, hiking and biking. 

-Erin McElvania, PhD, D(ABMM), is the Director of Clinical Microbiology NorthShore University Health System in Evanston, Illinois. Follow Dr. McElvania on twitter @E-McElvania. 

Microbiology Case Study: 35 Year Old Male with Chest Pain

Case History

A 35 year old man presented to the Emergency Department (ED) with intermittent chest pain for 3-4 days, abdominal pain, fatigue, and lightheadedness over the same time period. Additionally, his family reported symptoms of progressive malaise for about a month, worse over the last week. In the ED, he was found to have ST elevations in the inferior leads of the electrocardiogram, which can be indicative of a heart attack. He was given 325 mg of aspirin and was emergently taken to the catheterization lab. He was found to have multiple complete occlusions in the distal left anterior descending artery (LAD), posterior descending artery (PDA), and posterior left ventricular artery (PLV). He underwent aspiration thrombectomy and the resulting clots were thought to be emboli; segments were sent to pathology for histopathologic evaluation and to microbiology for culture. There was no evidence of underlying plaque. He was admitted for management of ST-elevation myocardial infarction (STEMI). While in the ED, he was found to have white blood cell count of 23,000 and tachycardia to 110 beats per minute. A transthoracic echocardiogram demonstrated thickened aortic valve leaflets with evidence of leaflet destruction, severe aortic insufficiency, and right coronary cusp perforation which are consistent with endocarditis. Blood cultures were obtained and he was started on broad spectrum antibiotics (Vancomycin and Cefepime).

He has a past medical history significant for previous shoulder abscess with Methicillin-resistant Staphylococcus aureus (MRSA) and intravenous drug use (IVDU) (heroin, last use ~6 days prior to admission).

Computed tomography (CT) of his abdomen and pelvis revealed multiple renal infarctions and a splenic infarction (Image 1). In addition, the CT of the brain showed: “Multifocal scattered supratentorial and infratentorial subarachnoid hemorrhages and findings suggestive of evolving ischemic infarct involving the right inferior frontal gyrus, without evidence of hemorrhagic transformation currently. No midline shift or other complication identified.”

Image 1. Computed tomography of the abdomen demonstrating multiple renal infarctions (left, circled) and a splenic infarction (right, circled).

On hospital day 1 (HD1), both sets of initial blood cultures turned positive with gram positive cocci (GPC) in clusters and thrombectomy cultures were also growing GPC in clusters (Image 2). On HD2, the GPC in the thrombectomy culture was identified as Rothia mucilaginosa. GPC growing in the blood cultures were also Rothia mucilaginosa (Image 2). The patient was continued on Vancomycin. Repeat blood cultures were obtained after catheterization on HD0, and HD2, which were negative. On HD2, the pathology of the initial clots showed “fibrinopurulent debris and fibrin plaques with innumerable cocci in clusters” (Image 3).

Image 2. Microscopic and culture morphology of Rothia mucilaginosa. Left: Gram stain from a blood culture demonstrating groups of Gram-positive cocci in small clusters (1000x magfication, oil immersion). Right: Blood agar plate with mucoid light pink-gray colonies.
Image 3. Hematoxylin and eosin stained slide of formalin fixed paraffin embedded tissue of the thrombus removed during the initial emergent catheterization procedure. Sections demonstrate fibrinous material with entrapped white cells and innumerable cocci. Top: 100x magnification; Bottom: 400x magnification.

On HD3, the patient developed 10/10 chest pain with troponin elevation and T-wave inversion. He was taken back to the catheterization lab for another procedure where he was found to have recurrent, complete occlusion of the PDA with unsuccessful recanalization due to the dense thrombus. On HD6, he developed tamponade physiology due to a large pericardial effusion that was drained. Cultures of the pericardial fluid were negative. Given the recurrent embolization events, the patient was transferred to another hospital to undergo aortic valve replacement surgery and coronary artery bypass graft surgery. Cultures taken at the time of the valve replacement surgery were negative and the valve tissue was not sent for pathologic evaluation.  

Discussion

We present an uncommon case of extensive Rothia mucilaginosa sepsis with septic emboli and endocarditis. Rothia mucilaginosa has experienced the scientific name-change game over the last several decades. It was first identified as Micrococcus mucilaginosus, then became Stomatococcus mucilaginosus, was also known as Staphylococcus salivarius before finally arriving to today’s name of Rothia mucilaginosa.1,2 R. mucilaginosa is a normal inhabitant of the oropharynx and is often associated with dental caries.3 R. mucilaginosa can cause invasive infections, typically in patients with compromised immune systems, disrupted mucosal barriers or injection drug use.4

R. mucilaginosa is a facultatively anaerobic, gram positive, non-fastidious coccus that is coagulase negative but with variable catalase positivity. Colony morphology is usually white to gray nonhemolytic colonies with a mucoid appearance. Although the variable catalase reaction may point toward a Streptococcus spp., the Gram stain morphology of clusters helps to rule it out. Although not all strains are mucoid, the classic colony morphology is wet and is due to polysaccharide capsule.

The organism is generally susceptible to antibiotics designed to target gram positive bacteria including, penicillin, ampicillin, cefotaxime, rifampin and vancomycin.4 It is important to note that R. mucilaginosa is not predictably susceptible to clindamycin, trimethoprim-sulfamethoxazole or ciprofloxacin.5 The patient presented in this case received intravenous vancomycin in part due to the extensive disease on presentation, but also because he was at risk for methicillin-resistant Staphylococcus aureus (MRSA) sepsis and had a previously documented abscess from MRSA.

References

  1. Bergan T, Kocur M. 1982. Stomatococcus mucilaginosus gen. nov., sp.nov., ep. Rev., a member of the family Micrococcaceae. Int. J. Syst. Bacteriol. 32:374-377
  2. Collins MD, Hutson RA, Baverud V, Falsen E. 2000. Characterization of a Rothia-like organism from a mouse: description of Rothia nasimurium sp.nov. and reclassification of Stomatococcus mucilaginosus as Rothia mucilaginosa comb.nov. Int. J. Syst. Evol. Microbiol. 3:1247-1251.
  3. Trivedi MN, Malhotra P. Rothia prosthetic knee joint infection. 2015. J. Microbiol. Immunol. Infect. 48(4):453-455.
  4. Bruminhent J, Tokarczyk MJ, Jungkind D, DeSimone JA. Rothia mucilaginosa Prosthetic Device Infections: A Case of Prosthetic Valve Endocarditis. J. Clin. Microbiol. 5;15:1629-1632.
  5. Kaasch AJ, Saxler G, Seifert H. 2011. Septic arthritis due to Rothia mucilaginosa. Infection. 39:81-82.

-Doreen Palsgrove, MD is a board certified Anatomic and Clinical Pathologist who joined the faculty at UT Southwestern as an Assistant Professor in 2019. She specializes in head and neck and genitourinary pathology. 

Dominick Cavuoti, DO is a professor of AP and CP at UT Southwestern, specializing in infectious disease pathology, cytology and medical microbiology.

-Clare McCormick-Baw, MD, PhD is an Assistant Professor of Clinical Microbiology at UT Southwestern in Dallas, Texas. She has a passion for teaching about laboratory medicine in general and the best uses of the microbiology lab in particular.

Microbiology Case Study: An 80 Year Old Man with Dyspnea, Fatigue, and Weight Loss

Case History

An 80 year old male was seen by his cardiologist for approximately one month of dyspnea, fatigue, and weight loss. Past medical history was significant for aortic stenosis requiring placement of a bioprosthetic valve and multivessel coronary artery disease 13 years prior. He underwent cardiac catheterization and echocardiography that revealed severe bioprosthetic valve stenosis. The patient was in the process of evaluation for a prosthetic valve replacement when he presented to the emergency room for rapid decline of the previously noted symptoms. Exam upon hospital admission was notable for cardiac murmur, lower extremity edema, mild leukocytosis, and anemia. He had normal dentition and no skin lesions. A pre-operative TEE confirmed severe aortic prosthetic valve stenosis, restricted leaflet motion, thrombus on all three leaflets, and thickening of the periannular aortic root and ascending aorta. Subsequent cardiac CT was concerning for either pseudoaneurysm or paravalvular leak suggestive of an infectious or inflammatory process.

Due to the persistent, mild leukocytosis, blood cultures were obtained on the second day of admission. On hospital day 3, one set of blood cultures flagged positive with Gram-variable rods in the aerobic bottle (Image 1). The patient was empirically started on vancomycin and piperacillin/tazobactam. Repeat blood cultures were obtained on hospital days 4 and 7, both again positive for Gram-variable rods within 2 days of collection. The infectious diseases consult team suspected subacute bacterial endocarditis and changed therapy to ceftriaxone.On hospital day 9, the patient underwent a redo sternotomy for aortic valve replacement and aortic root repair. Intraoperative findings included a large amount of phlegmon on the aortic leaflets, near circumferential aortic annulus tissue destruction and abscess cavity. Culture of the intraoperative specimens was negative for bacterial growth. The anatomic pathology findings revealed fibrinoid vegetations and acute inflammation and reparative changes. The patient was subsequently discharged home in stable condition 20 days after his admission. Interval outpatient clinic visits demonstrate that he is recovering well, including a return to baseline levels of endurance and function.

Laboratory Identification

Gram stain of the positive blood cultures revealed pleomorphic gram variable rods which were arranged in clusters, pairs, short chains, and characteristic rosette patterns (Image 1 and inset). Pinpoint, opaque colonies were visible on blood and chocolate agars after 48-72 hours of incubation at 35°C in CO2 (Image 2). No growth was observed on MacConkey agar. The colonies were catalase-negative, and oxidase- and indole-positive. The recovered organism was definitively identified by MALDI-TOF MS as Cardiobacterium hominis.

Image 1. Gram stain from the positive aerobic blood culture bottles exhibiting gram variable rods (1000X magnification, oil immersion). Organisms were visualized in characteristic “rosette” patterns. Image inset is a magnified view of the rosette arrangement from another field.
Image 2. Growth on blood agar following 48 hours incubation at 35°C in 5% CO2. Small, white, pinpoint colonies were observed on blood and chocolate agars.

Discussion

In 1962, four cases of infective endocarditis (IE) due to a Pasteurella-like organism belonging to CDC Group-IID were reported. Two years later, this group of organisms was reclassified as Cardiobacterium in recognition of their ability to cause endocarditis. Two species, Cardiobacterium hominis and Cardiobacterium valvarum, have been reported to cause IE, with the former being the etiological agent in a vast majority of cases.1 There is a strong association between C. hominis bacteremia and IE, as the organism is rarely recovered from blood cultures outside of this setting. Most cases of C. hominis endocarditis involve the aortic valve, particularly in the presence of pre-existing abnormalities or when a prosthetic valve is in place.2 C. hominis is a member of the normal flora of the nose and throat of ~70% of individuals (1), and endocarditis can be caused by periodontitis or dental procedures without prophylaxis.3

C. hominis is a member of the HACEK group of organisms which also include Haemophilus spp., Aggregatibacter spp., Eikenella corrodens, and Kingella kingae. HACEK organisms exhibit similar manifestations of disease, prognosis, and epidemiology. While over 80% of cases of IE are caused by Gram-positive bacteria (notably staphylococci and oral streptococci), Gram-negative IE is far less frequent, with a majority of cases caused by HACEK organisms (1-3% of all IE cases).4 In general, IE caused by HACEK organisms has an excellent prognosis, but delays in diagnosis and associated complications can lead to poorer outcomes.2 Susceptibility testing of C. hominis is difficult to perform due to its nutritional requirements. Most strains are susceptible to fluoroquinolones, rifampin, tetracycline, and beta-lactams. As beta-lactamase producing isolates have been reported, the current American Heart Association Guidelines recommend the use of a 4-6 week course of ceftriaxone for treatment of HACEK IE; fluoroquinolones may be used in cases where patients cannot tolerate cephalosporin therapy.5

Historically, prolonged blood culture incubation for the recovery of HACEK group organisms has been recommended due to their fastidious nature and slow growth rate. However, modern automated blood culture systems utilize enriched media which readily support their growth and facilitate recovery within a standard 5-day incubation period (average of 3.4 days incubation).6 Additional studies have demonstrated that prolonged incubation times do not significantly enhance the recovery of HACEK organisms and are of little clinical value.7 This case demonstrates many hallmarks of a characteristic description of a HACEK bacterial endocarditis: 1) the patient had a prosthetic valve as a pre-existing risk factor, 2) the subacute presentation caused a delay in recognition of an infectious etiology as contributing to his clinical decline, 3) C. hominis grew in less than 5 days in our automated blood culture system without prolonged incubation, 4) blood culture Gram stain findings were consistent with the MALDI identification of a HACEK group member, and 5) the patient was treated with ceftriaxone and with surgical intervention and has recovered successfully.

References

  1. Malani AN, Aronoff DM, Bradley SF, Kauffman CA.2006. Cardiobacterium hominis endocarditis: two cases and a review of the literature. European Journal of Clinical Microbiology and Infectious Diseases 25:587-595.
  2. Sharara SL, Tayyar R, Kanafani ZA, Kanj SS.2016. HACEK endocarditis: a review. Expert Review of Anti-infective Therapy 14:539-545.
  3. Steinberg JP, Burd EM. 2015. 238 – Other Gram-Negative and Gram-Variable Bacilli, p 2667-2683.e4. In Bennett JE, Dolin R, Blaser MJ (ed), Mandell, Douglas, and Bennett’s Principles and Practice of Infectious Diseases (Eighth Edition) doi:https://doi.org/10.1016/B978-1-4557-4801-3.00238-1. Elsevier, Philadelphia, PA.
  4. Revest M, Egmann G, Cattoir V, Tattevin P.2016. HACEK endocarditis: state-of-the-art. Expert Review of Anti-infective Therapy 14:523-530.
  5. Baddour Larry M, Wilson Walter R, Bayer Arnold S, Fowler Vance G, Tleyjeh Imad M, Rybak Michael J, Barsic B, Lockhart Peter B, Gewitz Michael H, Levison Matthew E, Bolger Ann F, Steckelberg James M, Baltimore Robert S, Fink Anne M, O’Gara P, Taubert Kathryn A.2015. Infective Endocarditis in Adults: Diagnosis, Antimicrobial Therapy, and Management of Complications. Circulation 132:1435-1486.
  6. Petti CA, Bhally HS, Weinstein MP, Joho K, Wakefield T, Reller LB, Carroll KC.2006. Utility of extended blood culture incubation for isolation of Haemophilus, Actinobacillus, Cardiobacterium, Eikenella, and Kingella organisms: a retrospective multicenter evaluation. Journal of clinical microbiology 44:257-259.
  7. Weinstein MP.2005. Emerging Data Indicating that Extended Incubation of Blood Cultures Has Little Clinical Value. Clinical Infectious Diseases 41:1681-1682.

-Francesca Lee, MD, is an associate professor in the Departments of Pathology and Internal Medicine (Infectious Diseases) at UT Southwestern Medical Center. She serves as Medical Director of the microbiology laboratory and pre-analytical services at Clements University Hospital.

-Julia Sweetnam, MLS(ASCP)CM has worked for six years as medical technologist in the microbiology laboratory at Clements University Hospital. She is interested in antimicrobial susceptibility testing and diagnostic bacteriology.

-Andrew Clark, PhD, D(ABMM) is an Assistant Professor at UT Southwestern Medical Center in the Department of Pathology, and Associate Director of the Clements University Hospital microbiology laboratory. He completed a CPEP-accredited postdoctoral fellowship in Medical and Public Health Microbiology at National Institutes of Health, and is interested in antimicrobial susceptibility and anaerobe pathophysiology.

Microbiology Case Study: 40 Year Old Male with A Diabetic Foot Ulcer

Clinical Presentation and History

The patient is a 40 year old male with a past medical history of type 2 diabetes mellitus with significant neuropathy and hypertension with a past surgical history of right metatarsal osteomyelitis. He presents to hospital with fever, right ear pain, headache, two episodes of diarrhea and redness and blistering to the right 3rd metatarsal. Upon examination he was noted to have a 1 cm ulceration on the right 3rd toe on the dorsal aspect associated with redness and edema. He was therefore assessed as having diabetic foot ulcer with possible osteomyelitis for which blood cultures were performed.

Laboratory Identification

Gram stains performed on the positive blood culture broth showed gram negative rods (Image 1). In our institution initial positive blood cultures are tested by the Verigene System (Luminex Corp., Austin, TX), which allows for rapid identification of common bacterial pathogens causing blood stream infections (Escherichia coli, Klebsiella oxytoca, Klebsiella pneumonia, Pseudomonas aeruginosa, Acinetobacter spp., Citrobacter spp., Enterobacter spp., and Proteus spp.) along with detection of several resistance genes (CTX-M, IMP, KPC, NDM, OXA, VIM) within ~ 3 hours. In this case, no targets on the Verigene panel were detected. Simultaneously, the specimen was plated onto blood, chocolate and MacConkey agars where the organism grew robustly on all three plates (Image 2). The MacConkey agar showed the organism to be a non-lactose fermenter. Once the organism adequately grew on these agar plates, final species identification was performed on the automated MALDI-TOF instrument which showed Salmonella species. To appropriately type the organism, Salmonella latex agglutination testing was performed which identified Salmonella species Group B (Non-typhoidal). Of note, multiple blood cultures from this patient were positive for Salmonella species, Group B.

Image 1. Gram stain of blood culture broth containing gram negative rods.
Image 2. Growth of the organism on chocolate, 5% sheep blood, and MacConkey agars.

Discussion

Salmonella is a gram negative, flagellated facultative anaerobic, non-lactose fermenting bacilli. The taxonomy and nomenclature of salmonella organisms are quite complex however the most widely used classification scheme is the Kauffman-White which is updated yearly by the WHO. Currently, members of the 7 Salmonella subspecies can be serotyped into one of more than 2500 serotypes (serovars) according to antigenically diverse surface structures: somatic O antigens (the carbohydrate component of lipopolysaccharide [LPS]) and flagellar (H) antigens.

Nontyphoidal salmonellae are a major cause of diarrhea worldwide. In the United States, non-typhoidal salmonellosis is one of the leading causes of foodborne disease. Salmonella enteritidis and Salmonella typhimurium are among the most frequently isolated organisms. Salmonella is most commonly associated with ingestion of contaminated poultry, eggs, and milk products. Salmonella gastroenteritis typically occur within 8 to 72 hours following exposure, however lower bacterial doses can prolong the incubation period. Although Salmonella typically causes diarrheal diseases including gastroenteritis and enteric fever, however there are rare instances where hematogenous involvement leads to bacteremia, osteomyelitis or endovascular infections.

In this case the source of Salmonella-related bacteremia is still a mystery. The presumed source was osteomyelitis, but the patient’s subsequent toe amputation revealed minimal osteomyelitis and rare fungal organisms.

References

  1. Procop, Gary W. et al (2017). Koneman’s Color Atlas and Textbook of Diagnostic Microbiology. 7th edition. Philadelphia, PA.
  2. Hohmann, Elizabeth L. (2018). Nontyphoidal salmonella: Gastrointestinal infection and carriage. Uptodate.com. Retrieved on November 14, 2019. https://www-uptodate.com/contents/nontyphoidal-salmonella-gastrointestinal-infection-and-carriage

-Anna-Lee Clarke-Brodber, MD is a 3rd year AP/CP resident at University of Chicago (NorthShore). Academically, Anna-Lee has a particular interest in Cytopathology. In her spare time she enjoys hanging out with her family.

-Erin McElvania, PhD, D(ABMM), is the Director of Clinical Microbiology NorthShore University Health System in Evanston, Illinois. Follow Dr. McElvania on twitter @E-McElvania. 

Microbiology Case Study: A 24 year old with Sore Throat and Difficulty Breathing

Case History

A 24 year old male with a past medical history of recurrent streptococcal pharyngitis presents to the emergency department with a sore throat and dyspnea. His symptoms began three days prior and included left-sided upper neck and lower jaw pain and odynophagia. The patient’s evaluation demonstrated tachycardia, cervical lymphadenopathy, and a small left tonsillar abscess. Labs were significant for an elevated WBC count but blood cultures, Group A streptococcal and mononucleosis screens were negative. The patient was admitted for pain management and treated with a combination of IV ampicillin/sulbactam (amp/sulb) and steroids. He improved with treatment and was discharged the following day on oral amoxicillin/clavulanic acid (amox/clav). Nine days later, the patient re-presented with similar complaints. The tonsillar abscess had increased in size to 2cm. Labs were significant for leukocytosis and a now positive Group A streptococcal screen. 2mL of pus was aspirated from the lesion but no cultures were ordered. The patient’s status again improved, and he was discharged home again on oral amox/clav. The patient returned the following day and was placed on IV amp/sulb and admitted for imaging and symptom management. A neck CT with contrast revealed a now 3cm tonsillar abscess with reactive cervical lymphadenopathy (Image 1). A throat culture was collected; however, no beta-hemolytic streptococci were recovered after 48 hours of incubation. Incision and drainage of the abscess was performed at bedside, recovering an additional 10 mL of purulence that was sent to the microbiology laboratory for aerobic and anaerobic culture. The patient improved on IV amp/sulb and was switched to high dose amox/clav on day 15.  

Laboratory Identification

Gram stain of the aspirated purulence revealed many WBCs and a mixture of gram positive rods and cocci (Image 2). The aerobic culture grew a heavy amount of tiny, weakly beta-hemolytic colonies on blood agar. Smears of these colonies revealed Gram-positive coryneform rods. Biochemical testing determined the growth to be catalase-negative and MALDI-TOF MS definitively identified the organism as Arcanobacterium haemolyticum. The anaerobic culture grew oral flora.

Image 1. Computed tomography of the neck in a 24 year old male who presents with difficulty breathing. Area of large tonsillar abscess (yellow circle).
Image 2. Gram stain demonstrating small, pleomorphic gram positive rods in a background of neutrophils and Gram-positive cocci in pairs or short chains. (1000x magnification, oil immersion)
Image 3. A. haemolyticum isolate after 48 hours of incubation. The weak beta-hemolysis was not readily apparent using room (reflected) light. Placing the plate on a lightbox revealed beta-hemolysis.
Image 4. Streptococcus agalactiae exhibiting synergetic hemolysis with a beta-lysin producing strain of S. aureus (CAMP reaction, top). A. haemolyticum inhibits hemolysis by S. aureus in a CAMP-test set up (CAMP inhibition, middle). A. haemolyticum exhibits synergistic hemolysis with S. agalactiae. (Reverse CAMP, bottom).

Discussion

A. haemolyticum is an infrequently isolated  gram positive rod which is an etiologic agent of non-streptococcal pharyngitis diagnosed predominantly in adolescents or young adults. The diagnosis of A. haemolyticum can be challenging because itis often clinically indistinguishable from cases caused by beta-hemolytic streptococci. Most patients exhibit some degree of cervical lymphadenopathy, and a scarlatiniform rash can be present in up to 50% of cases. From a laboratory perspective, A. haemolyticum is slowly growing and weakly beta hemolytic after 24-48 hours on media containing sheep blood (including SBA and Strep Selective agars routinely used for screening throat cultures). The beta-hemolytic activity of A. haemoltyicum is attributed to expression of arcanolysin, a cholesterol-dependent cytolysin. Interestingly, arcanolysin more robustly binds to rabbit and human erythrocytes than those from sheep,1 which may explain the organism’s weak beta hemolysis on routine media.  In this setting, the organism can be missed or dismissed as commensal flora without careful observation. Conversely, if beta-hemolysis is observed, the colony morphology and catalase non-reactivity can lead to misidentification as beta-hemolytic streptococci in the absence of a Gram stain or other determinative methods (i.e. MALDI-TOF MS).

The beta hemolysis of this patient’s A. haemolyticum isolate is difficult to appreciate in reflected (room) light, and was best observed after 48 hours using transduced light from a light box (Image 3). A. haemolyticum displays CAMP inhibition due to the production of phospholipase D which inhibits the hemolytic activity of beta-lysin produced by S. aureus (Image 4) and is reverse-CAMP positive when perpendicular to Group B streptococci which can aid in identification.2

Erythromycin is the drug of choice for treatment of A. haemolyticum, further highlighting the need for definitive identification of this organism in settings of pharyngitis. The use of penicillin for treatment of A. haemolyticum pharyngitis can result in treatment failure, possibly due to invasion of host cells, thus establishing a reservoir,3 or due to a penicillin-tolerant phenotype.4 It is unclear in this case if source control or decreased susceptibility necessitated the multiple courses of antibiotics utilized. Fortunately, the patient’s symptoms resolved on high dose amoxicillin/clavulanic acid following thorough incision and drainage. He subsequently returned for an outpatient tonsillectomy.

References

  1. Jost BH, Lucas EA, Billington SJ, Ratner AJ, McGee DJ. 2011. Arcanolysin is a cholesterol-dependent cytolysin of the human pathogen Arcanobacterium haemolyticum. BMC Microbiology 11:239.
  2. Kang H, Park G, Kim H, Chang K. 2016. Haemolytic differential identification of Arcanobacterium haemolyticum isolated from a patient with diabetic foot ulcers. JMM Case Reports.
  3. Österlund A. 1995. Are Penicillin Treatment Failures in Arcanobacterium haemolyticum Pharyngotonsillitis Caused by Intracellularly Residing Bacteria? Scandinavian Journal of Infectious Diseases 27:131-134.
  4. Nyman M, Danek G, Thore M. 1990. Penicillin Tolerance in Arcanobacterium haemolyticum. The Journal of Infectious Diseases 161:261-265.

-Andrew Clark, PhD, D(ABMM) is an Assistant Professor at UT Southwestern in the Department of Pathology and Associate Director of the Clements University Hospital microbiology laboratory. He completed a CPEP-accredited postdoctoral fellowship in Medical and Public Health Microbiology at National Institutes of Health, and is interested in antimicrobial susceptibility and anaerobe pathophysiology.

-Clare McCormick-Baw, MD, PhD is an Assistant Professor of Clinical Microbiology at UT Southwestern in Dallas, Texas. She has a passion for teaching about laboratory medicine in general and the best uses of the microbiology lab in particular.

Microbiology Case Study: Skin and Soft Tissue Infection Caused by an Unusual Bacterium

Case History

A 20 year old female with no significant past medical history presented with a painful pruritic rash on the bilateral inner thighs that had been persistent for one month. Prior to presentation, she had been treated with oral and topical antihistamines, topical steroids, valacyclovir, and partial courses of doxycycline and cephalexin without improvement. Physical examination was notable for diffuse erythema and dermal edema of the bilateral medial thighs with superimposed exophytic papules with dark, necrotic cores, the largest of which measured 1 cm in diameter (Image 1). Punch biopsy of the lesions was taken and sent for histology. A sample from necrotic tissue was sent to microbiology laboratory for gram stain and cultures.

Laboratory diagnosis

Gram stain showed gram positive cocci in clusters. After 32 hours of incubation, tissue cultures grew white, β-hemolytic colonies which were catalase positive, coagulase negative, and pyrrolidonylarylamidase (PYR) positive. The organism was identified as Staphylococcus lugdunensis by MALDI-TOFmass spectrometry. Histology revealed eosinophilic inclusions consistent with molluscum bodies as well as inflammatory infiltrate (Image 2). Brown and Hopps stain on tissue showed Gram-positive cocci is small clusters (Image 3). A diagnosis of molluscum contagiosum superinfected with Staphylococcus lugdunensis was made based on laboratory and histologic findings.

Image 1. Lesions on left medial thigh (left) and right medial thigh (right).
Image 2. Molluscum bodies
Image 3. Brown and Hopps stain on tissue showing gram positive cocci

Discussion

S. lugdunensis is a coagulase-negative staphylococcus first isolated in 1988 that was initially thought to be a commensal skin organism but has been shown to cause skin and soft tissue infections (SSTIs), bacteremia, endocarditis, prosthetic joint infections, and osteomyelitis,2 with a virulence more similar to S. aureus than to that of other coagulase-negative staphylococci. SSTIs are one of the more common manifestations of S. lugdunensis infection; one analysis of 229 S. lugdunensis clinical isolates demonstrated that 55.4% were associated with SSTIs.3 The spectrum of S. lugdunensis-related SSTIs includes folliculitis, pustulosis, cellulitis, abscesses, and rarer secondary infection of molluscum contagiosum and hidradenitis suppurativa.5 Molluscum superinfection itself is a rare phenomenon, and when it occurs, the superinfecting agent is most often S. aureus.1 Our case suggests that S. lugdunensis should also be considered as a potential causative agent of molluscum superinfection. There is growing recognition that S. lugdunensis is a virulent pathogen that should not be disregarded as a contaminant if found on culture. Importantly, when compared with S. aureus, S. lugdunensis has a more limited resistance profile; methicillin resistance is still uncommon, and 74.6% of isolates in one recent study were penicillin susceptible.4 Awareness of this more favorable resistance profile can facilitate selection of narrower-spectrum antibiotic therapies for S. lugdunensis infections.

In our case, patient received one dose of vancomycin and metronidazole in the emergency department and was then started on cefazolin for cellulitis. After wound culture identified S. lugdunensis, the patient was discharged on cefadroxil 1g twice daily for 10 days. On follow up, the rash had resolved.

References

  1. Berger EM, Orlow SJ, Patel RR, Schaffer JV. Experience With Molluscum Contagiosum and Associated Inflammatory Reactions in a Pediatric Dermatology Practice: The Bump That Rashes. Arch Dermatol. 2012;148(11):1257–1264. doi:10.1001/archdermatol.2012.2414
  2. Douiri N, Hansmann Y, Lefebvre N, Riegel P, Martin M, Baldeyrou M, Christmann D, Prevost G, Argemi X. Staphylococcus lugdunensis: a virulent pathogen causing bone and joint infections. Clinical Microbiology and Infection, 2016;22(8):747-748. doi:10.1016/j.cmi.2016.05.031
  3. Herchline TE, Ayers LW. Occurrence of Staphylococcus lugdunensis in consecutive clinical cultures and relationship of isolation to infection. J Clin Microbiol. 1991;29(3):419–421.
  4. Taha L, Stegger M, Söderquist B. Staphylococcus lugdunensis: antimicrobial susceptibility and optimal treatment options. Eur J Clin Microbiol Infect Dis. 2019;38(8):1449–1455. doi:10.1007/s10096-019-03571-6
  5. Zaaroura H, Geffen Y, Bergman R, Avitan‐Hersh E. Clinical and microbiological properties of Staphylococcus lugdunensis skin infections. J Dermatol, 2018;45: 994-999. doi:10.1111/1346-8138.14496

-Ansa Mehreen, MD. 1st year AP/CP resident at University of Chicago hospital program based at Evanston Hospital. Her academic interests include gastrointestinal pathology.

-Erin McElvania, PhD, D(ABMM), is the Director of Clinical Microbiology NorthShore University Health System in Evanston, Illinois. Follow Dr. McElvania on twitter @E-McElvania. 

Microbiology Case Study: A 27 Year Old Man with Lumbar Pain

Clinical History

A 27 year old male with past medical history of mixed connective tissue disease was transferred from an outside hospital where he had initially presented for 6 days of progressively worsening lumbar pain preceded by 1 day of fevers up to 104 F, as well as chills and rigors. Also noted was pain and swelling in his left thumb and a mild rash present on the hands and feet. It is notable that the patient has multiple pets, including a rat.

Workup at the outside hospital included and MRI showing facet arthrosis and effusions at L4-L5 with mass effect on the S1 nerve root. Neurosurgery recommended biopsy of the lumbar spine by Interventional Radiology.

Laboratory Findings

Two sets of blood cultures at the outside hospital showed no growth at 5 days. Two sets of blood cultures obtained at our institution were positive at 15 and 29 hours, with a smear showing gram negative bacilli. The blood culture media was tested by nucleic acid hybridization and no targets were detected. When subcultured, there was only significant growth on the blood plate, with very small gray-green colonies that were not well appreciated

Image 1. Gram stain showing gram negative bacilli.
Image 2. Blood agar plate showing difficult to discern growth of very small grayish colonies.

A sample was sent to a reference lab for testing, which identified Streptobacillus moniliformis.

Discussion

In the United States, Streptobacillus moniliformis is the most common causative agent of rat bite fever, a relatively rare infectious systemic illness. This syndrome is also caused by infection with Spirillum minus, primarily seen in Asia, and rarely by Streptobacillus notomytis.1,2

S. moniliformis is a fastidious pleomorphic gram negative rod which grows slowly; in cases where there is clinical suspicion for rat bite fever, cultures can be held up to seven days. It is part of the normal nasal and oropharyngeal flora of rodents, with carriage rates of up to 100% in some rat populations. It can be found in oral, nasal, and conjunctival secretions, as well as urine, and can be transmitted to humans via bites, scratches, or oral contact. This includes kissing a pet rat or ingesting food or water that is contaminated with rat secretions.1,2

S. minus is a gram negative spirochete. It cannot be cultured on synthetic media, but may be visualized by Giemsa or Wright stain, or by using dark-field microscopy. Transmission of S. minus is similar to that of Steptobacillus spp., but has not been documented to be associated with contaminated food or water. (1, 2)

The clinical presentation of rat bite fever ranges from a mild case with only a flu-like illness to cases of severe sepsis. In untreated cases, the mortality rate is approximately 10 to 13 percent. Initial symptoms typically begin within 7 days of exposure for S. moniliformis and in 1 to 3 weeks for S. minus. These initial symptoms can include fever, myalgias, vomiting, pharyngitis, headache, and migratory arthralgias. If exposure was through a wound, it is typically resolved by the time symptoms develop, although it may reappear with ulceration, edema, and regional adenopathy in cases caused by S. minus. Cases associated with ingestion may have more severe vomiting and increased likelihood of developing pharyngitis.1,2

Symptoms may further develop to include a maculopapular rash on the extremities, and asymmetric polyarthralgias. The rash is seen most commonly on the extensor surfaces but can involve the palms and soles. Spontaneous remission may occur, but without treatment the fever can show a relapsing course, and the arthritis may last for several years. Possible complications include bacteremia, endocarditis, myocarditis, pneumonia, abscesses, septic arthritis, osteomyelitis, multiorgan failure, fulminant sepsis and death.1,2

Rat bite fever is usually diagnosed empirically based on consistent symptoms and history of rat exposure, because it is difficult or impossible to culture the causative organisms in the lab and there is no serologic test available. 16S rRNA sequencing can be used for definitive diagnosis, but only for certain sample types, and it is not always available.1,2

The empiric treatment of choice is penicillin, with the dose and duration being dependent on the clinical presentation. Ceftriaxone is also commonly used due to better ease of use in the outpatient setting, and tetracyclines are used in patients with beta-lactam allergies. For uncomplicated cases, most patients are treated for a total of 14 days; initially with IV antibiotics, and then transitioned to oral agents after 5 to 7 days if there is sufficient clinical improvement.1,2

Also remarkable in the patient’s history was a note indicating that they had been known to share drinks with his pets and instances of the pet rat licking the patient’s face. Initial treatment was vancomycin and cefepime, with vancomycin discontinued after the gram stain results. The patient was discharged before a definitive identification of the organism was made, with a plan for 6 weeks of outpatient treatment with ceftriaxone via infusion.

References

1.  King, Katherine Yudeh, MD, PhD “Rat Bite Fever.” UpToDate, Wolters Kluwer, 1 Jun. 2020. https://www.cdc.gov/rat-bite-fever/index.html

2.  “Rat-bite Fever (RBF).” Centers for Disease Control and Prevention, 1 Jun. 2020. https://www.uptodate.com/contents/rat-bite-fever?search=rat%20bite%20fever&source=search_result&selectedTitle=1~17&usage_type=default&display_rank=1

-Tom Koster, DO is a 1st year anatomic and clinical pathology resident at the University of Vermont Medical Center.

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

A Resident’s Perspective of SARS-CoV-2 Testing Using the Double Diamond Model of Design Process

During the 2019-2020 residency interview season, I “courted” – no better way to describe those interactions over lunch–several potential co-residents, who were eager to know why I came to University of Chicago (NorthShore) for my residency. My answers and those of my fellow residents would help the candidates determine how high they should rank our program, so I enthusiastically recalled things I liked when I interviewed at NorthShore about a year earlier. I had also recently completed my first microbiology rotation in residency and I had enjoyed seeing all of those factors work synergistically to improve patient health outcomes through improved testing. So passionately, I shared how I fell in love with the physical structure of the department which has almost all the labs and offices one floor, the automation of the labs-especially the core and microbiology labs, the capability and regular expansion of its molecular laboratory, the people and of course, “the feel” about NorthShore.

With these experiences, I looked forward to my second microbiology in March 2020, where I would learn more about the diagnostics of various microorganisms–E. coli: Gram negative short stubby/broad shouldered rods vs. Pseudomonas aeruginosa, Gram negative long slender rods, etc. (Un)fortunately, March came, but the novel coronavirus (SARS-CoV-2) had other plans for my learning. Cases of Coronavirus disease 19 (COVID-19), caused SARS-CoV-2[1] were increasing rapidly in the US, so laboratories, including ours had rapidly implement testing. Rather than have morning rounds and other educational activities where the differential diagnoses of several clinically relevant microorganisms were discussed, we had virtual and in-person meetings discussing what to do about one virus. These continued and by the middle of March, we had become the only non-government lab in Illinois and second in the Midwest that had developed a clinical PCR test for SARS-CoV-2. I was excited to be part of that success, but more so, about learning how we achieved that as a team.

Our approach could be summarized using the Double diamond or 4D model of design process which consists of four phases: Discover, Define, Develop and Deliver (Figure 1).

Figure 1. Double diamond or 4D model of design process which consists of four phases: Discover, Define, Develop and Deliver. Plan Do Study Act (PDSA) is an iterative model of quality improvement embedded in the 4D design process.
  1. In the discover phase, a phase of divergent thought [2] and exploration, we identified from events in China and other parts of the world as well as some other states in the US that the community we care for could potentially be affected by the COVID-19 outbreak.
  2. The next phase- define- is a convergent phase where the problem to be solved, as well as the resources available and resources needed to solve it are delineated [2]. As we transitioned from the discovery to define phases-and recalling the 2009 H1N1 influenza outbreak about 10 years ago- it became evident that an epidemic of a relatively fatal respiratory virus which we knew very little about was heading our way. As clinical laboratory professionals, our objective was to help identify members of the community who had been infected through testing so appropriate steps could be taken to sequester and care for them. Among our available resources was our molecular laboratory, but like most laboratories outside the Centers for Disease Control and Prevention, CDC we lacked the reagents, primers and authorization to run the test.
  3. Develop is the next phase in the process and this is a divergent phase where the team explores and refines potential solution to the issues and selects one[2]. This is often followed by the convergent deliver phase where one of the solutions from the develop phase is implemented. Feedbacks which are used for projects are also received during this phase[2]. But, the outbreak continued to evolve rapidly [3] with briskly increasing positivity rates[4] and some of the solutions we considered would require some time to be implemented and/or have long turnaround times. For instance, since we had a roust molecular laboratory, one option was to develop our assays and test in-house, while another was to send the samples to outside labs where they could be run. Running the tests in-house would have a shorter turnaround time and would be more efficient, which is extremely important considering the severity of COVID-19.
  4. Deliver is the last phase of the process.  We decided to develop a SARS-CoV-2 RT-PCR test at our institution, but we also knew we needed to put logistics and protocols in-place to deliver our solution.  For example, COVID-19 presents with flu-like symptoms but flu is common between December and March[5-7] so it would be impractical to expect to test all patients with flu-like symptoms – at least with the limited resources we had. In any case, it was clear that we would not have an ideal amount of time or information to develop and implement the perfect solution. As such, the revolving and fluid nature of the develop and deliver phases of our response is best depicted using the Plan Do Study Act (PDSA), an iterative model of quality improvement. As shown in Fig. 1, we developed and validated our assay, as well as developed an initial protocol for screening patients and logistics for patient-centered delivery in the “Do” step. Importantly, we also reviewed the effectiveness of these operations, and made necessary changes corresponding in the “Study” and “Act” steps respectively.

The prompt decision to implement in-house COVID-19 testing at NorthShore has proven to be the right one. To date we have tested 75,000 specimens and nearly 20,000 tests have been positive. Success which was possible because of the factors which made me come to NorthShore, amongst others. The LEAN, bright and capacious design of the department limits the innate barriers of hierarchical organizational structure; encouraging seamless horizontal and vertical intradepartmental consultation and collaboration as COVID-19 led us into uncharted territory. Also, having a molecular lab that regularly expands its capability made the decision to test in-house relatively easy. In addition, having an automated microbiology lab made it easier for staff to be flexible and deal with the various demands of testing for a new bug in a pandemic. And of course, the people at NorthShore who are ready to volunteer, take up new roles or change shifts to accommodate the demands of a rapidly evolving pandemic, stay in constant communications and provide feedback, and who make everything else at NorthShore work!

References

  1. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200130-sitrep-10-ncov.pdf?sfvrsn=d0b2e480_2
  2. Council, Design. “Eleven lessons: Managing design in eleven global companies-desk research report.” Design Council (2007).
  3. https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/summary.html
  4. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200324-sitrep-64-covid-19.pdf?sfvrsn=723b221e_2
  5. https://www.who.int/news-room/q-a-detail/q-a-coronaviruses#:~:text=symptoms
  6. https://www.cdc.gov/flu/symptoms/symptoms.htm
  7. https://www.cdc.gov/flu/about/season/flu-season.htm
  8. Christoff, Patricia. “Running PDSA cycles.” Current problems in pediatric and adolescent health care 48.8 (2018): 198-201.

Adesola Akinyemi, M.D., MPH, is a first year anatomic and clinical pathology resident at University of Chicago (NorthShore). He is interested in most areas of pathology including surgical pathology, cytopathology and neuropathology -and is enjoying it all. He is also passionate about health outcomes improvement through systems thinking and design, and other aspects of healthcare management. Twitter: @AkinyemiDesola

-Erin McElvania, PhD, D(ABMM), is the Director of Clinical Microbiology NorthShore University Health System in Evanston, Illinois. Follow Dr. McElvania on twitter @E-McElvania. 

Microbiology Case Study: Elderly woman with Ear Pain

An elderly woman with a past medical history significant for end-stage renal disease status post deceased donor kidney transplant in 2018 (on immunosuppression), type 2 diabetes mellitus, and recurrent urinary tract infections presented to nephrology clinic with right ear pain and rash of three weeks. She was otherwise in her usual state of health. On physical exam, there were exophytic itchy papules with hemorrhagic crust and ulcerations on the ear (Image 1) and arm. A few of these papules showed central umbilication (Image 2). Erosions were also present on the upper back, face, neck, and forearms. Patient was referred to dermatology with concern for disseminated infection versus neoplasia. Complete blood count showed mildly elevated white cells. Serologies, cultures, imaging, lumbar puncture, and biopsy were performed.

Blood studies revealed a Cryptococcus antigen titer of 1:4096 along with a CSF antigen titer of 1:2048. Additionally, the CSF gram stain demonstrated yeast and cultures grew Cryptococcus neoformans. Opening pressure was normal and protein was slightly elevated to 53 mg/mL with 36 nucleated cells with a differential including 64% lymphocytes. Biopsy culture of the left cheek was positive for C. neoformans and a left forearm biopsy showed nodular aggregates of encapsulated yeasts, surrounded by relatively sparse lymphohistiocytic inflammation (Images 3-4). A CT of the chest showed innumerable pulmonary nodules concerning for infection.

Image 1. Erythematous and crusted pink plaque with ulceration on the pinna of the ear.
Image 2. Pink, domed papule on the arm with central umbilication and crust.
Image 3. Hematoxylin and eosin stain of the arm biopsy with Cryptococcus, low magnification. Note the loss of epidermis (left-hand side) and underlying foamy stroma with numerous yeasts within the dermis.
Image 4. Hematoxylin and eosin stain of Cryptococcus, high magnification. The yeasts show variable size and some demonstrate a halo of pale staining capsule. There is no significant inflammation in the background parenchyma.

Discussion

Cryptococcus is an encapsulated basidiomycetous fungus typically found in soil and pigeon droppings.1 Two species comprise the majority of Cryptococcus infections: C. neoformans and C. gatti. C. neoformans is most commonly seen in immunosuppressed patients, particularly in the setting of AIDS.2 C. gatti infections may be seen in more immunocompetent patients and appears to be more geographically restricted to the tropics and Pacific Northwest.3 C. neoformans infections can present as lung disease associated with symptoms of fever, shortness of breath, or cough and characteristically may spread to the central nervous system to cause meningitis.4 Lumbar puncture may show significantly elevated opening pressures.5 Other features of disseminated Cryptococcus infections include rash, endocarditis, ocular lesions, or multiorgan failure.6

This case is a somewhat unusual presentation of disseminated Cryptococcus infection characterized only by skin findings without clinical features of pulmonary or CNS infection. Approximately 15% of patients with disseminated infection may show cutaneous findings but primary cutaneous cryptococcosis is rare.7 Cryptococcal skin findings are quite varied, but may present similar to molluscum contagiosum, as dome shaped papules with central umbilication.7,8 On microscopy, small variably sized round yeasts without hyphae are characteristic. These yeasts may show a clear or pale staining halo representing the capsule and are highlighted well on Grocott’s Methenamine Silver or Periodic Acid-Schiff stains. Histology may demonstrate innumerable extracellular yeasts accompanied by foamy stroma and minimal inflammation or more granulomatous tissue reaction with necrosis, ulceration, and mixed inflammation. In conclusion, disseminated Cryptococcus must be considered in the context of new skin findings in an immunocompromised patient even if typical pulmonary or CNS findings are not identified.

References

  1. Sorrell TC, Ellis DH. Ecology of Cryptococcus neoformans. Rev Iberoam Micol. 1997 Jun;14(2):42-3.
  2. Bratton EW, El Husseini N, Chastain CA, Lee MS, Poole C, Sturmer T, et al. Comparison and temporal trends of three groups with cryptococcosis: HIV-infected, solid organ transplant, and HIV-negative/non-transplant. PloS One. 2012;7(8):e43582
  3. MacDougall L, Fyfe M, Romney M, Starr M, Galanis E. Risk factors for Cryptococcus gattii infection, British Columbia, Canada. Emerg Infect Dis. 2011 Feb;17(2):193-9.
  4. Sabiiti W, May RC. Mechanisms of infection by the human fungal pathogen Cryptococcus neoformans. Future microbiol. 2012 Nov;7(11):1297-313.
  5. Abassi M, Boulware DR, Rhein J. Cryptococcal Meningitis: Diagnosis and Management Update. Curr Trop Med Rep. 2015;2(2):90–99. doi:10.1007/s40475-015-0046-y
  6. Clark RA, Greer D, Atkinson W, Valainis GT, Hyslop N. Spectrum of Cryptococcus neoformans infection in 68 patients infected with human immunodeficiency virus. Rev Infect Dis. 1990 Sep-Oct;12(5):768-77.
  7. Srivastava GN, Tilak R, Yadav J, Bansal M. Cutaneous Cryptococcus: marker for disseminated infection. BMJ Case Rep. 2015;2015:bcr2015210898. Published 2015 Jul 21. doi:10.1136/bcr-2015-210898
  8. Akram SM, Koirala J. Cutaneous Cryptococcus (Cryptococcosis) [Updated 2019 Aug 4]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2019 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK448148/

-Dr. Stanton Miller is a second year AP/CP resident at UT Southwestern Medical Center who is interested in Dermatopathology.

-Dr. IJ Frame is a board-certified Clinical Pathologist who is completing his Medical Microbiology fellowship at UT Southwestern Medical Center.

-Dr. Dominick Cavuoti is a professor of AP and CP at UT Southwestern, specializing in infectious disease pathology, cytology and medical microbiology.

-Clare McCormick-Baw, MD, PhD is an Assistant Professor of Clinical Microbiology at UT Southwestern in Dallas, Texas. She has a passion for teaching about laboratory medicine in general and the best uses of the microbiology lab in particular.