Ten Clinical Pearls in Microbiology: How Effective Collaboration Optimizes Patient Care.

Medical microbiology laboratories play an essential role in patient care - appertaining to infectious diseases diagnostics and treatment, infection prevention, and antimicrobial stewardship. Collaboration between clinicians and the microbiology laboratory can promote and enhance the safety, quality, and efficiency of patient care. We review practical, evidence-informed core concepts to explicate how effective partnership between clinicians and the microbiology laboratory improves patient outcomes.

An unusual case of Brodie's abscess in the humerus of an adult female.

Brodie's abscess is a manifestation of subacute to chronic osteomyelitis, characterized as intraosseous abscess formation, usually on the metaphysis of the long tubular bones in the lower extremities of male pediatric patients. Clinically, Brodie's abscess presents with atraumatic bone pain of an insidious onset, with absence of systemic findings. Delay in diagnosis is common, as diagnostic imaging, followed by biopsy for culture and histologic examination are generally required to secure a diagnosis of Brodie's abscess. Treatment of Brodie's abscess is non-standardized, and usually consists of surgical debridement and antibacterial therapy. Despite the variability in therapeutic approaches, outcomes of Brodie's abscess treated with surgery and antibiotics are favourable. Herein we report a case of a delayed diagnosis of Brodie's abscess in the upper extremity of an adult female. While she improved with treatment of Brodie's abscess, the case serves to remind clinicians to consider this entity in adult individuals who present with atraumatic bone pain.

Polymerase chain reaction negative cryptococcal meningitis.

A 61-year-old male with subacute headache was found to have cryptococcal meningitis despite a negative BioFire FilmArray meningitis/encephalitis panel. This case underscores the importance of liberal cryptococcal antigen testing, and that a negative FilmArray panel is inadequate in excluding cryptococcal meningitis, particularly in a HIV-negative host.

Recurrent amebic liver abscesses despite metronidazole treatment: A rare case report.

Amebic liver abscesses should be considered in adult males with a liver abscess and a history of travel to endemic areas. Effective treatment includes metronidazole, followed by paromomycin.

Ten common misconceptions about antibiotic use in the hospital.

Antimicrobials are one of the most administered medications in hospitals. Thoughtful and rational antibiotic prescribing by clinicians are important in reducing the adverse effects to both the host that takes the antibiotic and also the individuals in the host's community. Principles informing antibiotic prescribing in the hospital are commonly rooted in misconceptions. We review 10 common myths associated with antibacterial usage in hospitalized patients and share contemporary evidence in hopes of enhancing evidence-informed practice in this patient care setting.

Management of Pyogenic Liver Abscesses: Contemporary Strategies and Challenges.

Pyogenic liver abscesses (PLAs) are a suppurative infection of the hepatic parenchyma responsible for significant morbidity and mortality. PLAs are categorized into a variety of mechanisms: (1) via the portal vein, (2) through the biliary tract, (3) via the hepatic artery, (4) from trauma, (5) contiguously via direct extension, and (6) cryptogenically. The pathogenesis of PLA, which informs treatment, can often be discerned based on host factors, clinical presentation, and causative microorganisms. The Streptococcus anginosus group, hypervirulent Klebsiella pneumoniae , and multidrug-resistant gram-negative pathogens have emerged as microbiologically challenging organisms to treat. The identification of hypervirulent K. pneumoniae should prompt for assessment for metastatic spread and consideration of prolonged antimicrobial treatment. Abdominal imaging is indispensable in characterizing PLAs and facilitating source control interventions. Source control remains the most critical aspect of PLA management, followed by antimicrobial therapy. Empiric antibiotics for PLAs are informed by the suspected etiology of PLA formation. Duration of antimicrobial therapy is individualized and dependent on multiple components, including the success of achieving source control, host factors, mechanism of PLA development, and the illness course of the individual-factoring in clinical, biochemical, and radiographic parameters.

Incidence, susceptibility and outcomes of candidemia in adults living in Calgary, Alberta, Canada (2010-2018).

BACKGROUND: Candidemia is increasing in frequency and is associated with high mortality. We sought to determine the burden of illness, the population it affects and its resistance profile in our region. METHODS: The Calgary Zone (CZ) provides all care for residents of Calgary and surrounding communities (~ 1.69 million) via five tertiary hospitals each served by a common single laboratory for acute care microbiology. All adult patients in the CZ with at least one Candida spp.-positive blood culture between January 1, 2010, and December 31, 2018, were identified using microbiological data from Calgary Lab Services, the laboratory that processes > 95% of all blood culture samples in the CZ, were reviewed for the study. RESULTS: The overall annual incidence of candidemia among individuals living in the CZ was 3.8 per 100,000 persons (Median age 61 years (IQR 48-72) and 221/455 (47.4%) were female). C. albicans was the most common species (50.6%), followed by C. glabrata, (24.0%). No other species accounted for more than 7% of cases. Overall mortality at 30, 90, and 365 days was 32.2, 40.1, and 48.1% respectively. Mortality rate did not differ by Candida species. Of individuals who developed candidemia, more than 50% died within the next year. No new resistance pattern has emerged in the most common Candida species in Calgary, Alberta. CONCLUSIONS: In Calgary, Alberta, the incidence of candidemia has not increased in the last decade. C. albicans was the most common species and it remains susceptible to fluconazole.

How I manage bacterial prostatitis.

BACKGROUND: Bacterial prostatitis is a highly prevalent infection responsible for significant morbidity among men. The diagnosis and treatment for bacterial prostatitis remains complicated. The difficulty in diagnosis is in part owing to the paucity of high-quality evidence that guides a clinician's interpretation of patients' history, physical examination, and laboratory findings. Treatment is challenging because of the few antimicrobials capable of prostate penetration, growing antimicrobial resistance limiting effective treatment options, and the high risk of recurrence. OBJECTIVES: We aimed to provide a useful resource for clinicians in effectively diagnosing and managing acute bacterial prostatitis (ABP) and chronic bacterial prostatitis (CBP). SOURCES: A PubMed literature search on prostatitis was performed with no restrictions on publication date. CONTENT: The epidemiology, pathophysiology, diagnosis, and treatment for ABP and CBP are explored using a clinical vignette as relevant context. IMPLICATIONS: Bacterial prostatitis can be diagnosed through a focused history and microbiological investigations. The Meares-Stamey 4-glass test or modified 2-glass test can help confirm the diagnosis if uncertainty exists. Typical uropathogens are common contributors to bacterial prostatitis but there is growing interest in exploring the role atypical and traditional non-pathogenic organisms may have. Fluoroquinolones remain first-line therapy, followed by trimethoprim-sulfamethoxazole (TMP-SMX) or doxycycline if the pathogen is susceptible. Fosfomycin has emerged as a repurposed and useful agent because of the increasing incidence of multidrug-resistant pathogens. Selection of appropriate antimicrobial regimens can be challenging and is dependent on the host, chronicity of symptoms, uropathogens' susceptibilities, antimicrobials' side effect profile, and the presence of prostatic abscesses or calcifications. ABP can typically be treated similar to other complicated urinary tract infections. However, CBP requires prolonged therapy, with a minimum of 4 weeks and up to 12 weeks of therapy.

The Golden Grapes of Wrath - Staphylococcus aureus Bacteremia: A Clinical Review.

Staphylococcus aureus bacteremia is common and associated with fatality rates approximating 25%. We provide a brief overview of S. aureus bacteremia from a clinical and microbiological lens and review the relevant evidence and literature gaps in its management. Using a case-based approach, evidence and clinical judgement are meshed to highlight and justify the 5 core interventions that ought to be performed for all cases of S. aureus bacteremia: 1) appropriate anti-staphylococcal therapy, 2) screening echocardiography, 3) assessment for metastatic phenomena and source control, 4) decision on duration of antimicrobial therapy, and 5) Infectious Diseases consultation.

Disseminated nocardiosis in an immunocompetent host with occupational exposure.

Nocardia is a genus of Gram-positive, partially acid-fast bacteria consisting of over 120 species, of which 50 are recognized as human pathogens. Nocardia spp. are common colonizers in the environment, particularly in soil and water. Nocardia spp. typically cause opportunistic infections in the immunocompetent host, although cases of nocardiosis have been described in those with a normal immune system. Nocardiosis can be localized, most often in the skin or lung, or be disseminated, with involvement of the brain, bone, and visceral organs. Treatment of nocardiosis is complex, as multiple culture-directed antibacterials with appropriate tissue penetration may need to be used for a prolonged duration. To our knowledge, we describe the first successfully treated case of disseminated Nocardia beijingensis infection in an immunocompetent host with doxycycline and trimethoprim-sulfamethoxazole and hypothesize that his occupational exposure to ubiquitous saprophytes may have led to his infection.

Principles of empiric antimicrobial usage and dosing: Lessons learned.

A lack of clinical response to empiric antimicrobials behooves the clinician to reflect further on diagnostic considerations. When prescribing antibiotics, determining the correct dose, most optimal route of administration, and considering the pharmacokinetic properties of the drug with respect to clinical and patient factors are crucial.

Epidemiology and risk factors for pyogenic liver abscess in the Calgary Health Zone revisited: a population-based study.

BACKGROUND: Pyogenic liver abscess (PLA), although uncommon in North America, is associated with significant morbidity and mortality. We sought to re-examine the epidemiology, risk factors, and outcomes of PLA in a large, diverse Canadian health zone. METHODS: All Calgary Health Zone (CHZ) residents aged ≥20 with PLA between 2015 and 2017 were identified. Incidence and mortality rates were calculated using census data. Risk factors for PLA were identified using a multivariate analysis. Data was compared to 1999-2003 data, also collected in the CHZ. RESULTS: There were 136 patients diagnosed with PLA between 2015 and 2017. Incidence rate during this period increased significantly relative to 1999-2003 (3.7 vs 2.3 cases/100,000 population, p < 0.01), however, mortality rates remained similar. The microbiological composition of PLA did not change over this 15-year time period but the number of antimicrobial resistant isolates did increase (8% vs 1%, p = 0.04). The greatest risk factors for PLA relative to general populations included current malignancy, liver-transplant, end-stage renal disease, and cirrhosis. Thirty-day mortality was 7.4% and independent risk factors included polymicrobial bacteremia, absence of abscess drainage, congestive-heart failure, a history of liver disease, and admission bilirubin. CONCLUSIONS: Pyogenic liver abscess is a health concern with rising incidence rate. The increasing prevalence of comorbidities in our population and factors that are associated with risk of PLA suggests this will continue to be an emerging diagnosis of concern. Increasing prevalence of antibiotic resistant organisms compounding unclear optimal treatment regimens is an issue that requires urgent study.

Forgoing transesophageal echocardiogram in selected patients with complicated Staphylococcus aureus bacteremia.

Infective endocarditis (IE) has been increasingly recognized as an important complication of Staphylococcus aureus bacteremia (SAB), leading to a low threshold for echocardiography and extended treatment with anti-staphylococcal agents. However, outside of IE, many indications for prolonged anti-staphylococcal therapy courses are present. We sought to determine the frequency in which findings from a transesophageal echocardiogram (TEE) changed clinical SAB management in a large Canadian health region. Residents (> 18 years) with SAB from 2012 to 2014 who underwent transthoracic echocardiogram (TTE) and TEE were assessed. Patients potentially benefiting from an extended course of anti-staphylococcal agents were defined a priori. Patient demographics, treatment (including surgical), and clinical outcomes were extracted and evaluated. Of the 705 episodes of SAB that underwent a screening echocardiogram, 203 episodes underwent both a TTE and TEE, of which 92.1% (187/203) contained an a priori indication for extended anti-staphylococcal therapy. Regardless of TEE results, actual duration of therapy did not differ in SAB episodes that had ≥ 1 extended anti-staphylococcal therapy criteria (36.7 days, IQR 23.4-48.6 vs. 43.8 days, IQR 33.3-49.5, p = 0.17). Additionally, there were no cases in which TEE was utilized as the sole reason to shorten duration of therapy or proceed to surgery for those with SAB. Routine performance of TEE may be unnecessary in all SAB as many patients have pre-existing indications for extended anti-staphylococcal therapy independent of TEE findings. An algorithm to selectively identify cases of SAB that would benefit from TEE can reduce resource and equipment expenditure and patient risks associated with TEE.

A case of tick-borne relapsing fever in pregnancy.

Tick-borne relapsing fever (TBRF) is an infection caused by Borrelia spirochetes. In North America, Borrelia hermsii is the most common cause for TBRF. This vector-borne disease is transmitted by Ornithodoros hermsi, a soft-bodied tick found in high altitudes in northwestern United States and southwestern Canada. Once bitten by the tick and infected by B. hermsii, episodes of fever alternating with afebrile periods can occur. A case of TBRF in a pregnant host was complicated by Jarisch-Herxheimer reaction requiring critical care. This case emphasizes the importance of maintaining a high index of suspicion in TBRF. Clinician recognition, diagnosis and treatment of TBRF as well as public awareness of strategies to prevent tick bites should be strengthened.

Bartonella quintana infective endocarditis in northern Alberta: A case report.

We present a case of Bartonella quintana infective endocarditis requiring valvular surgery in an Indigenous patient from northern Alberta that was identified months after initial presentation to hospital with undifferentiated laboratory abnormalities. Syndromes caused by B. quintana are often challenging to diagnose due to their non-specific presentation and the difficulty in detecting this organism using traditional culture methods. Additionally, risk factors for B. quintana include marginal housing and alcohol use disorder, which often impede access to health care. Indigenous patients in northern Canada often face worse health outcomes compared with other regions owing to poor economic conditions, substandard housing, and limited access to health care resources. Given that risk factors for B. quintana are prevalent throughout northern Canada and that this infection is difficult to diagnose, we surmise that the prevalence of B. quintana infection is underestimated in northern Canada.

Les auteurs présentent un cas d'endocardite infectieuse à Bartonella quintana exigeant une chirurgie valvulaire chez un patient autochtone du nord de l'Alberta, dépisté des mois après la première consultation à l'hôpital, alors que les anomalies de laboratoires étaient indifférenciées. Les syndromes causés par le Bartonella quintana sont souvent difficiles à diagnostiquer à cause de leur présentation non spécifique et de la difficulté à déceler cet organisme au moyen des méthodes de culture classiques. De plus, les facteurs de risque de Bartonella quintana incluent des logements inférieurs aux normes et des troubles de l'usage de l'alcool, qui nuisent souvent à l'accès aux soins. Les patients autochtones du nord du Canada présentent souvent des résultats cliniques pires que ceux d'autres régions à cause des mauvaises conditions économiques, des logements inférieurs aux normes et de l'accès limité aux ressources de santé. Puisque les facteurs de risque de Bartonella quintana prévalent dans tout le nord du Canada et que cette infection est difficile à diagnostiquer, les auteurs postulent que la prévalence d'infection à Bartonella quintana est sous-estimée dans cette région.

Epidemiology and Outcome Determinants of Staphylococcus aureus Bacteremia Revisited: A Population-Based Study.

PURPOSE: Staphylococcus aureus bacteremia (SAB) is associated with significant morbidity and mortality. We sought to re-define the burden, epidemiology and mortality-associated risk factors of SAB in a large Canadian health region. METHODS: Residents (> 18 years) experiencing SAB from 2012 to 2014 were assessed. Incidence rates were calculated using civic census results. Factors associated with 30-day mortality were determined through multivariate logistic regression. Incidence and risk factors for SAB were compared to 2000-2006 data. RESULTS: 780 residents experienced 840 episodes of SAB (MRSA; 20%). Incidence rates increased from 23.5 to 32.0 cases/100,000 from 2012 to 2014; [IRR 1.15 (95% CI 1.07-1.23); p < 0.001]. Compared to a decade ago, incidence of SAB has increased [IRR 1.28 (95% CI 1.21-1.36); p < 0.001] despite minimal change in nosocomial SAB. MRSA proportion did not change through the study (p = 0.3), but did increase relative to a decade ago (20.0% vs 11.0%, p < 0.001). Thirty-day mortality rates were 30.6% and 21.3% for MRSA and MSSA, respectively (p = 0.01), similar to rates from 2000 to 2006. Several clinical, demographic, and biochemical factors were independently associated with SAB mortality. CONCLUSIONS: SAB is common within our population resulting in significant mortality. Incidence rates of SAB are increasing in our health region; however, 30-day mortality rates remain stable.

Case Report: Bartonella quintana Endocarditis Outside of the Europe-African Gradient: Comprehensive Review of Cases within North America.

Clinical syndromes associated with Bartonella quintana infection can be insidious and difficult to diagnose for multiple reasons. Clinically, B. quintana can manifest as asymptomatic bacteremia or with subtle subacute constitutional symptoms. Second, it is a fastidious organism that is difficult to identify using traditional culture methods. Last, the body lice vector of B. quintana transmission is likely not uncommon in most patients affected, who are homeless and of low socioeconomic status. Therefore, barriers in seeking medical care and financial constraints for medications are important considerations. The mainstay of literature surrounding B. quintana endocarditis is from Europe and the developing nations. Herein, we describe a case of native valve endocarditis secondary to B. quintana in a homeless male with preexisting valvular disease and undertake a comprehensive literature review of documented B. quintana endocarditis in North America.