An inconspicuous identification: Isolation and identification of a novel Pichia species presenting as fungemia following cardiac surgery

Fungemia is common in critically ill patient populations, and is associated with a high rate of mortality, especially when caused by nonalbicans Candida species. Herein, we describe a fatal case of fungemia following cardiothoracic surgery in which the organism, initially identified as Candida inconspicua, represents a novel species: Pichia alaskaensis.

Epidemiology, Timing, and Secondary Prophylaxis of Recurrent Nocardiosis

Background

Nocardia tends to cause infection in immunocompromised patients or those with chronic pulmonary disease. Nocardia is known to recur, prompting the practice of secondary prophylaxis in patients perceived at high risk. However, few data exist regarding the epidemiology of recurrent nocardiosis or the effectiveness of secondary prophylaxis.

Methods

We performed a multicenter, retrospective cohort study of adults diagnosed with nocardiosis from November 2011 to April 2022, including patients who completed primary treatment and had at least 30 days of posttreatment follow-up. Propensity score matching was used to analyze the effect of secondary prophylaxis on Nocardia recurrence.

Results

Fifteen of 303 (5.0%) patients developed recurrent nocardiosis after primary treatment. Most recurrences were diagnosed either within 60 days (N = 6/15, 40.0%) or between 2 to 3 years (N = 4/15, 26.7%). Patients with primary disseminated infection tended to recur within 1 year, whereas later recurrences were often nondisseminated pulmonary infection. Seventy-eight (25.7%) patients were prescribed secondary prophylaxis, mostly trimethoprim-sulfamethoxazole (N = 67/78). After propensity-matching, secondary prophylaxis was not associated with reduced risk of recurrence (hazard ratio, 0.96; 95% confidence interval, .24-3.83), including in multiple subgroups. Eight (53.3%) patients with recurrent nocardiosis required hospitalization and no patients died from recurrent infection.

Conclusions

Recurrent nocardiosis tends to occur either within months because of the same Nocardia species or after several years with a new species. Although we did not find evidence for the effectiveness of secondary prophylaxis, the confidence intervals were wide. However, outcomes of recurrent nocardiosis are generally favorable and may not justify long-term antibiotic prophylaxis for this indication alone.

Temporal trends in antifungal susceptibility of Cryptococcus neoformans isolates from a reference laboratory in the United States, 2011-2021

BACKGROUND

There are no established clinical breakpoints for antifungal agents against Cryptococcus species; however, epidemiological cut-off values can help distinguish wild-type (WT) isolates without any acquired resistance from non-WT strains, which may harbour resistance mechanisms.

PATIENTS/METHODS

We describe the trends of antifungal MICs and percentages of WT C. neoformans species complex (CNSC) isolates processed in our reference laboratory from November 2011 to June 2021. There were only nine isolates in 2011, thus, we included them in the year 2012 for data analysis. Clinical data is also described when available.

RESULTS

We identified 632 CNSC, the majority collected from blood (n = 301), cerebrospinal fluid (n = 230), and respiratory (n = 71) sources. The overall percentage of WT isolates for amphotericin B (AMB), 5-flucytosine, and fluconazole was 77%, 98%, and 91%, respectively. We noticed a statistically significant change in the percentage of AMB WT isolates over the years, with 98% of isolates being WT in 2012 compared to 79% in 2021 (p < .01). A similar change was not observed for other antifungal agents. Clinical data was available for 36 patients, primarily non-HIV immunocompromised patients with disseminated cryptococcosis. There were no statistically significant differences in the clinical characteristics and outcomes between patients with WT (58.3%) versus non-WT (41.7%) isolates, but we noticed higher mortality in patients infected with an AMB non-WT CNSC isolate.

CONCLUSIONS

We observed an increase in the percentage of AMB non-WT CNSC isolates in the past decade. The clinical implications of this finding warrant further evaluation in larger studies.

A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC

The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

Outcomes of transplant recipients with pretransplant Nocardia colonization or infection

BACKGROUND

Specific pretransplant infections have been associated with poor posttransplant outcomes. However, the impact of pretransplant Nocardia isolation has not been studied.

METHODS

We performed a retrospective study from three centers in Arizona, Florida, and Minnesota of patients with Nocardia infection or colonization who subsequently underwent solid organ or hematopoietic stem cell transplantation from November 2011 through April 2022. Outcomes included posttransplant Nocardia infection and mortality.

RESULTS

Nine patients with pretransplant Nocardia were included. Two patients were deemed colonized with Nocardia, and the remaining seven had nocardiosis. These patients underwent bilateral lung (N = 5), heart (N = 1), heart-kidney (N = 1), liver-kidney (N = 1), and allogeneic stem cell transplantation (N = 1) at a median of 283 (interquartile range [IQR] 152-283) days after Nocardia isolation. Two (22.2%) patients had disseminated infection, and two were receiving active Nocardia treatment at the time of transplantation. One Nocardia isolate was resistant to trimethoprim-sulfamethoxazole (TMP-SMX) and all patients received TMP-SMX prophylaxis posttransplant, often for extended durations. No patients developed posttransplant nocardiosis during a median follow-up of 1.96 (IQR 0.90-6.33) years. Two patients died during follow-up, both without evidence of nocardiosis.

CONCLUSIONS

This study did not identify any episodes of posttransplant nocardiosis among nine patients with pretransplant Nocardia isolation. As patients with the most severe infections may have been denied transplantation, further studies with larger sample sizes are needed to better analyze any impact of pretransplant Nocardia on posttransplant outcomes. However, among patients who receive posttransplant TMP-SMX prophylaxis, these data suggest pretransplant Nocardia isolation may not impart a heightened risk of posttransplant nocardiosis.

Antifungal Susceptibility Pattern of Candida glabrata from a Referral Center and Reference Laboratory: 2012-2022

The prevalence of invasive candidiasis caused by non-Candida albicans has rapidly increased. Candida glabrata (Nakaseomyces glabrata) is an important pathogen associated with substantial mortality. Our study examined the antifungal temporal susceptibility of C. glabrata and cross-resistance/non-wild-type patterns with other azoles and echinocandins. Laboratory data of all adult patients with C. glabrata isolated from clinical specimens at the Mayo Clinic, Rochester, from 2012 to 2022 were collected. Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints were used. We obtained 1046 C. glabrata isolates from 877 patients. Using CLSI and EUCAST breakpoints, 187 (17.9%) isolates and 256 (24.5%) isolates were fluconazole-resistant, respectively. Focusing on C. glabrata bloodstream infections, fluconazole-resistance ranged from 16 to 22%. Among those 187 fluconazole-resistant isolates, 187 (100%) and 184 (98.4%) isolates were also voriconazole and posaconazole non-wild-type, respectively, with 97 (51.9%) isolates deemed non-wild type for itraconazole. The fluconazole susceptibility pattern has not changed over the past decade. The proportion of fluconazole-resistant C. glabrata is relatively high, which could be due to the complexity of patients and fluconazole exposure. Itraconazole appears to be a compelling step-down therapy for fluconazole-resistant C. glabrata, given the high proportion of wild-type isolates. Further research to examine clinical outcomes is warranted.

Mortality After Nocardiosis: Risk Factors and Evaluation of Disseminated Infection

Background

Nocardia primarily infects patients who are immunocompromised or those with chronic lung disease. Although disseminated infection is widely recognized as an important prognostic factor, studies have been mixed on its impact on outcomes of nocardiosis.

Methods

We performed a retrospective cohort study of adults with culture-confirmed nocardiosis. Advanced infection was defined as disseminated infection, cavitary pulmonary infection, or pleural infection. The primary outcome was 1-year mortality, as analyzed by multivariable Cox regression.

Results

Of 511 patients with culture growth of Nocardia, 374 (73.2%) who had clinical infection were included. The most common infection sites were pulmonary (82.6%), skin (17.9%), and central nervous system (14.2%). In total, 117 (31.3%) patients had advanced infection, including 74 (19.8%) with disseminated infection, 50 (13.4%) with cavitary infection, and 18 (4.8%) with pleural infection. Fifty-nine (15.8%) patients died within 1 year. In multivariable models, disseminated infection was not associated with mortality (hazard ratio, 1.16; 95% CI, .62-2.16; P = .650) while advanced infection was (hazard ratio, 2.48; 95% CI, 1.37-4.49; P = .003). N. farcinica, higher Charlson Comorbidity Index, and culture-confirmed pleural infection were also associated with mortality. Immunocompromised status and combination therapy were not associated with mortality.

Conclusions

Advanced infection, rather than dissemination alone, predicted worse 1-year mortality after nocardiosis. N. farcinica was associated with mortality, even after adjusting for extent of infection. While patients who were immunocompromised had high rates of disseminated and advanced infection, immunocompromised status did not predict mortality after adjustment. Future studies should account for high-risk characteristics and specific infection sites rather than dissemination alone.

Emergence of Inducible Macrolide Resistance in Mycobacterium chelonae Due to Broad-Host-Range Plasmid and Chromosomal Variants of the Novel 23S rRNA Methylase Gene, erm(55)

Macrolides are a mainstay of therapy for infections due to nontuberculous mycobacteria (NTM). Among rapidly growing mycobacteria (RGM), inducible macrolide resistance is associated with four chromosomal 23S rRNA methylase (erm) genes. Beginning in 2018, we detected high-level inducible clarithromycin resistance (MICs of ≥16μg/mL) in clinical isolates of Mycobacterium chelonae, an RGM species not previously known to contain erm genes. Using whole-genome sequencing, we identified a novel plasmid-mediated erm gene. This gene, designated erm(55)P, exhibits <65% amino acid identity to previously described RGM erm genes. Two additional chromosomal erm(55) alleles, with sequence identities of 81% to 86% to erm(55)P, were also identified and designated erm(55)C and erm(55)T. The erm(55)T is part of a transposon. The erm(55)P allele variant is located on a putative 137-kb conjugative plasmid, pMchErm55. Evaluation of 133 consecutive isolates from 2020 to 2022 revealed 5 (3.8%) with erm(55). The erm(55)P gene was also identified in public data sets of two emerging pathogenic pigmented RGM species: Mycobacterium iranicum and Mycobacterium obuense, dating back to 2008. In both species, the gene appeared to be present on plasmids homologous to pMchErm55. Plasmid-mediated macrolide resistance, not described previously for any NTM species, appears to have spread to multiple RGM species. This has important implications for antimicrobial susceptibility guidelines and treatment of RGM infections. Further spread could present serious consequences for treatment of other macrolide-susceptible RGM. Additional studies are needed to determine the transmissibility of pMchErm55 and the distribution of erm(55) among other RGM species.

Clinical Characteristics of Central Nervous System Phaeohyphomycosis: A Brief Report of 20 years' Experience

Central nervous system (CNS) phaeohyphomycosis is a rare and often fatal fungal infection. Our study reported a case series of eight CNS phaeohyphomycosis cases at our institution over the past 20 years. We did not observe common pattern of risk factors, abscess location, or number of abscesses among them. Most patients were immunocompetent without classic risk factors for fungal infection. Early diagnosis and aggressive management with surgical intervention and prolonged antifungal therapy can lead to a favorable outcome. The study highlights the need for further research to better understand the pathogenesis and optimal management of this challenging rare infection.

Clinical manifestations, treatment and outcomes of patients infected with Mycobacterium haemophilum with a focus on immune reconstitution inflammatory syndrome: a retrospective multi-site study

BACKGROUND

Mycobacterium haemophilum is a nontuberculous mycobacterium with fastidious in vitro growth requirements and an increasingly reported cause of extrapulmonary disease. Timely diagnosis and management of M. haemophilum infections and the immune reconstitution inflammatory syndromes (IRIS) observed in a subset of patients during treatment remain challenging.

METHODS

We conducted a retrospective chart review between January 1, 2010, and January 1, 2022 and identified 26 patients diagnosed with M. haemophilum infection at our institution. We describe their clinical presentation, diagnostic results, management, and outcomes.

RESULTS

The majority of patients in our cohort had upper and/or lower extremity skin involvement, were immunosuppressed, and had generally favourable treatment outcomes. All tested M. haemophilum isolates were susceptible in vitro to clarithromycin and trimethoprim-sulfamethoxazole. Moreover, high rates of susceptibility were noted for ciprofloxacin (95%), linezolid (90%), and rifampin (85%). IRIS was identified in 31% of cases and should be considered in patients who develop worsening skin lesions or systemic symptoms following the initiation of effective antimicrobial therapy. Visualisation of acid-fast bacilli on initial tissue stains, a positive mycobacterial blood culture, and rapid de-escalation of tumour necrosis factor-α inhibitors and/or corticosteroids were more frequently encountered among patients in our cohort who developed IRIS.

CONCLUSION

M. haemophilum infection should be considered among patients receiving immunomodulatory therapy who develop discoloured or nodular skin lesions involving the extremities, worsening focal arthritis, tenosynovitis, or isolated adenopathy. A heightened awareness of this pathogen's clinical and laboratory characteristics can lead to a timely diagnosis and favourable outcome.

Toto, we're not in Kansas anymore: First reported case of M. persicum septic arthritis

In this report, we describe a case of septic arthritis caused by the newly described Mycobacterium persicum (formerly Mycobacterium kansasii complex). The patient's only significant exposure was home gardening. To our knowledge, this represents the first documented case of M. persicum infection in the United States and first septic arthritis.

Cardiovascular device infections due to rapidly growing Mycobacteria: A review of cases at a tertiary care hospital

Cardiovascular device infection due to rapidly growing mycobacteria (RGM) is rarely encountered in clinical practice. Due to the increasing number of indications and use of cardiovascular devices in an aging population, optimized management of these infections is of great importance. We report seven cases of RGM cardiovascular device infection. Three patients had left-ventricular assist device (LVAD) infections; two patients had cardiovascular implantable device (CIED) infections; and one had an aortic vascular stent infection. Specific cardiac valvular infection was not detected among any of the patients. All patients had a high number of comorbidities which limited some patients from receiving optimal combination antimicrobial therapy. The prognosis of cardiovascular device infections with RGM is guarded with only four patients still alive; however, the treatment approach for each patient varied considerably and often based on concurrent medical conditions, overall adjustments to goals of care, and specific patient preferences. Further analysis of cardiovascular device infections with RGM is warranted to establish a more systematic approach in successful management.

Fungal and mycobacterial cultures should not be routinely obtained for diagnostic work-up of patients with suspected periprosthetic joint infections

AIMS

Fungal and mycobacterial periprosthetic joint infections (PJI) are rare events. Clinicians are wary of missing these diagnoses, often leading to the routine ordering of fungal and mycobacterial cultures on periprosthetic specimens. Our goal was to examine the utility of these cultures and explore a modern bacterial culture technique using bacterial blood culture bottles (BCBs) as an alternative.

METHODS

We performed a retrospective review of patients diagnosed with hip or knee PJI between 1 January 2010 and 31 December 2019, at the Mayo Clinic in Rochester, Minnesota, USA. We included patients aged 18 years or older who had fungal, mycobacterial, or both cultures performed together with bacterial cultures. Cases with positive fungal or mycobacterial cultures were reviewed using the electronic medical record to classify the microbiological findings as representing true infection or not.

RESULTS

There were 2,067 episodes of PJI diagnosed within the study period. A total of 3,629 fungal cultures and 2,923 mycobacterial cultures were performed, with at least one of these performed in 56% of episodes (n = 1,157). Test positivity rates of fungal and mycobacterial cultures were 5% (n = 179) and 1.2% (n = 34), respectively. After a comprehensive review, there were 40 true fungal and eight true mycobacterial PJIs. BCB were 90% sensitive in diagnosing true fungal PJI and 100% sensitive in detecting rapidly growing mycobacteria (RGM). Fungal stains were performed in 27 true fungal PJI but were only positive in four episodes (14.8% sensitivity). None of the mycobacterial stains was positive.

CONCLUSION

Routine fungal and mycobacterial stains and cultures should not be performed as they have little clinical utility in the diagnosis of PJI and are associated with significant costs. Candida species and RGM are readily recovered using BCB. More research is needed to predict rare non-Candida fungal and slowly growing mycobacterial PJI that warrant specialized cultures. Cite this article: Bone Joint J 2022;104-B(1):53-58.

Diagnostic Methods and Risk Factors for Severe Disease and Mortality in Blastomycosis: A Retrospective Cohort Study

Background: Blastomycosis can cause severe disease with progressive respiratory failure and dissemination even in immunocompetent individuals. We sought to evaluate risk factors for severe disease and mortality using clinical and laboratory data within a large health system in an endemic area. Methods: We performed a retrospective cohort study of patients diagnosed with blastomycosis at all Mayo Clinic sites from 1 January 2004 through 31 March 2020. Diagnosis was established by culture, histopathology/cytopathology, serology, antigen testing, or PCR. Disease was categorized as mild for patients treated in the outpatient setting, moderate for hospitalized patients who did not require intensive care, and severe for patients admitted to the intensive care unit. Logistic regression was used to evaluate risk factors for severe disease. A Cox proportional hazards model was constructed to evaluate mortality. Findings: We identified 210 patients diagnosed with blastomycosis. Mean age was 51 years (range, 6–84). Most subjects were male (71.0%). Extrapulmonary disease was confirmed in 24.8%. In this cohort, 40.5% of patients had mild disease, 37.6% had moderate disease, and 21.9% had severe disease. Independent risk factors for severe disease were neutrophilia (odds ratio (OR) 3.35 (95% CI 1.53–7.35), p = 0.002) and lymphopenia (OR 3.34 (95% CI 1.59–7.03), p = 0.001). Mortality at 90 days was 11.9%. Median time from diagnosis to death was 23 days (interquartile range 8–31 days). Independent risk factors for mortality were age (OR 1.04 (95% CI 1.01–1.08), p = 0.009), neutrophilia (OR 2.84 (95% CI 1.04–7.76), p = 0.041), and lymphopenia (OR 4.50 (95% CI 1.67–12.11), p = 0.003). Blastomyces immunodiffusion had an overall sensitivity of 39.6% (95% CI 30.1–49.8). Sensitivity was higher among those who were tested 4 weeks or longer after the onset of symptoms. Urine Blastomyces antigen had a significantly higher sensitivity of 80.8% (95% CI 68.1–89.2) compared to serology. There was a trend towards higher antigen concentration in patients with severe disease. The sensitivity of PCR from respiratory specimens was 67.6% (95% CI 50.1–85.5). Conclusion: In this cohort, we did not find an association between pharmacologic immunosuppression and disease severity. Lymphopenia at diagnosis was an independent risk factor for mortality. This simple marker may aid clinicians in determining disease prognosis.

Misidentification of Mycobacterium smegmatis as Mycobacterium fortuitum by DNA line probe assay

Optimal management of infection with mycobacterial species requires accurate identification down to complex/species level due to variations in outcomes. Over the last few decades, there have been significant advances in laboratory diagnostics with development of newer and rapid molecular methods. Here we describe a case of Mycobacterium smegmatis that was misidentified as Mycobacterium fortuitum by DNA line probe assay.

Utility of Mycobacterium tuberculosis PCR in ruling out active disease and impact on isolation requirements in a low prevalence setting

OBJECTIVE

To analyze and interpret clinical microbiology data for specimens tested with the fluorochrome stain (AFB stain), mycobacterial culture and a laboratory-developed Mycobacterium tuberculosis (MTB) PCR in order to understand the performance of each test and to demonstrate the utility of MTB PCR to assist with decisions regarding discontinuation of airborne isolation.

METHODS

Retrospective cohort analysis of 2798 respiratory specimens from 2006 patients in the period between November 1st, 2011 and January 1st, 2018.

RESULTS

53.7% were males, median age was 61 years, and 43 patients were HIV positive. Results demonstrated positive mycobacterial cultures for MTB in 52 specimens (1.9%) and for nontuberculous mycobacteria (NTM) or aerobic actinomycetes (eg., Nocardia spp.) in 435 specimens (16%). Using mycobacterial culture as the gold standard, AFB smear had a sensitivity of 48.1% while MTB PCR had a sensitivity of 96.0% in AFB smear positive specimens and an overall sensitivity of 57.7% with PPV of 94% and a NPV of 99%.

CONCLUSIONS

The combination of a positive AFB smear with a negative MTB PCR offers a rapid result to rule out active pulmonary MTB in a low prevalence setting. In this study, that combination reliably excluded active tuberculosis (NPV of 99.2%). The combination of a positive AFB smear with a negative MTB PCR indicated pulmonary NTM infection with the results available within 1 day. There was little benefit to pursuing collection and testing of more than 2 respiratory specimens in a low prevalence setting for both long term diagnostic or rapid isolation discontinuation purposes.

Non-Aspergillus Hyaline Molds: Emerging Causes of Sino-Pulmonary Fungal Infections and Other Invasive Mycoses

Hyaline molds, widely distributed in nature, are an important and increasing cause of invasive fungal infections in humans, likely due to an expanding population of immunosuppressed hosts, increases in antifungal resistance, and improvements in laboratory diagnostics. Sinopulmonary disease and disseminated infection are common manifestations in neutropenic patients and transplant recipients, whereas, catheter-related and localized soft tissue infections predominate in immunocompetent hosts. These organisms are not reliably differentiated based on their morphology in tissue; rather, efforts should be made to establish a microbiologic diagnosis via culture or molecular-based methods to guide antifungal management and inform prognosis. Herein, we review the epidemiology, clinical manifestations, diagnosis, and management of these opportunistic pathogens known to cause hyalohyphomycoses: Scedosporium spp., Lomentospora prolificans, Fusarium spp., Scopulariopsis spp., Arthrographis kalrae, Trichoderma spp., Acremonium spp., Paecilomyces variotii, Purpureocillium lilacinum, and Penicillium species.

Multicenter Study Demonstrates Standardization Requirements for Mold Identification by MALDI-TOF MS

Objectives

Rapid and accurate mold identification is critical for guiding therapy for mold infections. MALDI-TOF MS has been widely adopted for bacterial and yeast identification; however, few clinical laboratories have applied this technology for routine mold identification due to limited database availability and lack of standardized processes. Here, we evaluated the versatility of the NIH Mold Database in a multicenter evaluation.

Methods

The NIH Mold Database was evaluated by eight US academic centers using a solid media extraction method and a challenge set of 80 clinical mold isolates. Multiple instrument parameters important for spectra optimization were evaluated, leading to the development of two specialized acquisition programs (NIH method and the Alternate-B method).

Results

A wide range in performance (33–77%) was initially observed across the eight centers when routine spectral acquisition parameters were applied. Use of the NIH or the Alternate-B specialized acquisition programs, which are different than those used routinely for bacterial and yeast spectral acquisition (MBT_AutoX), in combination with optimized instrument maintenance, improved performance, illustrating that acquisition parameters may be one of the key limiting variable in achieving successful performance.

Conclusion

Successful mold identification using the NIH Database for MALDI-TOF MS on Biotyper systems was demonstrated across multiple institutions for the first time following identification of critical program parameters combined with instrument optimization. This significantly advances our potential to implement MALDI-TOF MS for mold identification across many institutions. Because instrument variability is inevitable, development of an instrument performance standard specific for mold spectral acquisition is suggested to improve reproducibility across instruments.

Fungal Diagnostic Stewardship in Bronchoscopy Specimens for Immunocompetent Patients in the Intensive Care Unit

OBJECTIVE

To evaluate the diagnostic yield of fungal smears and cultures from bronchial lavage and wash specimens obtained from immunocompetent patients in the intensive care unit (ICU) because respiratory tract samples from patients in the ICU often undergo extensive microbiological testing.

PATIENTS AND METHODS

In total, we enrolled 112 immunocompetent adult patients treated in the medical and surgical ICU between July 1, 2016, and June 30, 2017. We evaluated whether the results of fungal smears and cultures of specimens obtained from bronchoscopy and bronchoalveolar lavage changed patient care.

RESULTS

In total, 131 bronchoscopic specimens and 31 bronchoalveolar lavage specimens were tested for fungi. Cultures were held for an estimated 4680 culture-days. Two results changed patient therapy. In both cases, other routine tests provided the same information as fungal culture before these results were returned.

CONCLUSION

In immunocompetent, critically ill patients, fungal culture of respiratory tract specimens does not add diagnostic value. Routine fungal culture of respiratory tract specimens should be discouraged in this population.

Microbiological Laboratory Testing in the Diagnosis of Fungal Infections in Pulmonary and Critical Care Practice. An Official American Thoracic Society Clinical Practice Guideline

Background: Fungal infections are of increasing incidence and importance in immunocompromised and immunocompetent patients. Timely diagnosis relies on appropriate use of laboratory testing in susceptible patients.Methods: The relevant literature related to diagnosis of invasive pulmonary aspergillosis, invasive candidiasis, and the common endemic mycoses was systematically reviewed. Meta-analysis was performed when appropriate. Recommendations were developed using the Grading of Recommendations Assessment, Development, and Evaluation approach.Results: This guideline includes specific recommendations on the use of galactomannan testing in serum and BAL and for the diagnosis of invasive pulmonary aspergillosis, the role of PCR in the diagnosis of invasive pulmonary aspergillosis, the role of β-d-glucan assays in the diagnosis of invasive candidiasis, and the application of serology and antigen testing in the diagnosis of the endemic mycoses.Conclusions: Rapid, accurate diagnosis of fungal infections relies on appropriate application of laboratory testing, including antigen testing, serological testing, and PCR-based assays.

Mycobacterium scrofulaceum disease: experience from a tertiary medical centre and review of the literature

Introduction: Mycobacterium scrofulaceum infection has been identified in cases of paediatric cervical lymphadenitis but is less well defined in adults. To further characterize manifestations of M. scrofulaceum disease and treatment approaches, we reviewed our medical centre's experience and other published reports. Methods: We performed a retrospective chart review of patients at our medical centre with a positive M. scrofulaceum culture over a 15-year period. We compare our findings with those published in the literature to identify commonalities in disease presentations and treatment outcomes. Results: We identified 17 patients in our centre with positive M. scrofulaceum cultures, 10 of whom were diagnosed with clinical infection. The types of disease encountered included pulmonary and pleural infection (4), bone and joint infections with a foreign body (2), skin and soft tissue infection (2), brain abscess (1) and paediatric cervical adenitis (1). Structural lung disease was a common finding in cases of pulmonary infection. All adult patients except those with bone and joint infections had some type of immunomodulatory condition and/or structural lung disease. In seven patients, M. scrofulaceum was isolated in urinary or respiratory cultures without signs of clinical disease. Conclusion: M. scrofulaceum is a rare cause of non-tuberculosis mycobacterial infection in humans but can infect any tissue. Adults with pulmonary disease often have underlying structural lung disease, and those with extrapulmonary disease commonly have immunosuppressive conditions or foreign body-associated infections. Treatment outcomes are generally favourable; however, in patients with pulmonary M. scrofulaceum disease prognosis is more guarded.

Eumycetoma caused by Cladophialophora bantiana in the United States

A female presented in the sixth decade of life with a history of undifferentiated small cell carcinoma of the right breast in clinical remission, status-post chemotherapy and resection 6 years previously, presented with a chronic anterior knee skin nodule that grew in size over the prior 5–6 weeks. She had no history of opportunistic infections or recent immunosuppression. As it grew, the nodule became tender to touch. Examination revealed a 4–6 mm superficial purple-red nodule. Also, a similar lesion was present on the dorsum of her left foot for the past year, which also recently grew and became tender. The patient did report frequently kneeling on soil when gardening in Florida. She reported no other symptoms. Due to a concern for cutaneous metastasis of the patient’s previously diagnosed small cell carcinoma of the breast, the anterior knee lesion was biopsied. Histology revealed histocyte-rich inflammation with foci of acute inflammation as well as pigmented fungal forms. Subsequent fungal culture of excised tissue grew Cladophialophora bantiana, identified by ribosomal gene DNA sequencing.

Eighty Years of Mycopathologia: A Retrospective Analysis of Progress Made in Understanding Human and Animal Fungal Pathogens

Mycopathologia was founded in 1938 to 'diffuse the understanding of fungal diseases in man and animals among mycologists.' This was an important mission considering that pathogenic fungi for humans and animals represent a tiny minority of the estimated 1.5-5 million fungal inhabitants on Earth. These pathogens have diverged from the usual saprotrophic lifestyles of most fungi to colonize and infect humans and animals. Medical and veterinary mycology is the subdiscipline of microbiology that dwells into the mysteries of parasitic, fungal lifestyles. Among the oldest continuing scientific publications on the subject, Mycopathologia had its share of 'classic papers' since the first issue was published in 1938. An analysis of the eight decades of notable contributions reveals many facets of host-pathogen interactions among 183 volumes comprising about 6885 articles. We have analyzed the impact and relevance of this body of work using a combination of citation tools (Google Scholar and Scopus) since no single citation metric gives an inclusive perspective. Among the highly cited Mycopathologia publications, those on experimental mycology accounted for the major part of the articles (36%), followed by diagnostic mycology (16%), ecology and epidemiology (15%), clinical mycology (14%), taxonomy and classification (10%), and veterinary mycology (9%). The first classic publication, collecting nearly 200 citations, appeared in 1957, while two articles published in 2010 received nearly 150 citations each, which is notable for a journal covering a highly specialized field of study. An empirical analysis of the publication trends suggests continuing interests in novel diagnostics, fungal pathogenesis, review of clinical diseases especially with relevance to the laboratory scientists, taxonomy and classification of fungal pathogens, fungal infections and carriage in pets and wildlife, and changing ecology and epidemiology of fungal diseases around the globe. We anticipate that emerging and re-emerging fungal pathogens will continue to cause significant health burden in the coming decades. It remains vital that scientists and physicians continue to collaborate by learning each other's language for the study of fungal diseases, and Mycopathologia will strive to be their partner in this increasingly important endeavor to its 100th anniversary in 2038 and beyond.

2424. Review of Antimicrobial Susceptibility Profile of Different Nocardia Species, a Tertiary Center Experience

Background

Nocardia spp. are ubiquitous Gram-positive weakly acid-fast environmental microorganisms. Although considered an opportunistic infection, approximately 1/3 of the reported infections are in immunocompetent patients. Treatment is usually challenging, prolonged and involves multiple agents depending on the site of infection, clinical syndrome and the immune status of the patient.

Methods

We conducted a retrospective review of clinical samples with positive cultures for Nocardia spp. from 2011 to 2017. Specimens were cultured in MGIT broth or on Middlebrook agar biplates and isolated colony growth was then identified using MALDI-TOF MS or 16S rDNA gene sequencing. Antimicrobial susceptibility testing was performed using the TREK Sensititre Rapid Growing Mycobacteria Plate.

Results

We reviewed total of 1,840 samples positive for Nocardia spp. Most commonly isolated species included N. cyriacigeorgica (16.9%), N. nova complex (15.7%), N. farcinica complex (14.8%), N. brasiliensis (11.5%) and N. abscessus complex (8.2%). Susceptibilities of the more common Nocardia species are shown in the graph. Source of the positive cultures was variable with majority (>60%) from pulmonary source (sputum, BAL and lung tissue), blood in 5.7% and brain in 3.6%. Most common Nocardia species isolated from brain specimens were N. farcinica complex (24/59) followed by N. abscessus complex (17/59). Most common Nocardia species isolated from blood were N. farcinica complex (38/99) followed by N. nova complex (22/99) and N. cyriacigeorgica (15/99).

Conclusion

The antimicrobials that continue to show high activity against most Nocardia species (>95%) are: amikacin, linezolid and TMP/SMX. N. pseudobrasiliensis was noted to have high rates of resistance to TMP/SMX (87%). N. farcinia, N. brasiliensis and N. transvalensis/wallacei complex were >90% susceptible to amoxicillin/clavulanate. Clarithromycin had >99% activity against N. nova complex while both ceftriaxone and doxycycline had> 90% activity against N. abscessus complex. It is crucial to identify Nocardia species and obtain susceptibilities to help better choose the regimen with the best clinical outcome.

Disclosures

All authors: No reported disclosures.

Mycobacterium decipiens sp. nov., a new species closely related to the Mycobacterium tuberculosis complex

Two mycobacterial strains with close similarity to the Mycobacterium tuberculosis complex (MTBC) were isolated from cutaneous lesions of patients in the USA and Italy. At the phenotypic level, similarities to the MTBC included slow growth rate, rough morphotype of the unpigmented colonies and nearly identical high-performance liquid chromatography profiles of mycolic acids. In contrast to the MTBC, the strains were niacin- and nitrate-negative, and catalase-positive both at 68 °C and in semi-quantitative tests. The clinical isolates were more closely related to M. tuberculosis than to any other known mycobacterium and scored positive with commercial DNA probes (Hologic AccuProbe M. tuberculosis). Both average nucleotide identity and genome-to-genome distance suggested the strains are different from the MTBC. Therefore, given the distinguishing phenotypic and genomic-scale differences, we submit that the strains belong to a new species we have named Mycobacteriumdecipiens with type strain TBL 1200985^T (=ATCC TSD-117^T=DSM 105360^T).

Automated broth-based systems versus the MYCOTB plate for antimicrobial susceptibility testing of the Mycobacterium tuberculosis complex: challenges in interpretation

We examined categorical agreement between automated mycobacterial susceptibility testing methods (Mycobacterial Growth Indicator Tube [MGIT] 960 System and the VersaTREK Mycobacteria Detection and Susceptibility System) which are based on single critical concentration (CC) "breakpoints" and a commercial microbroth dilution method (Sensititre Mycobacterium tuberculosis MIC Plate [MYCOTB]) which provides an MIC value. Mycobacterium tuberculosis isolates (n=355) were tested against three first-line antimycobacterial agents (ethambutol [EMB], isoniazid [INH], rifampin [RIF]) using the MYCOTB plate and either the MGIT 960 (site 1, n=142) or VersaTREK (site 2, n=213) systems. Overall categorical agreement was 96.8%. When stratified by drug and CC-defined susceptible and resistant isolates, concordance ranged from 75% to 100%. Interpretation of MIC-based results versus established CC-based results was challenging for drugs whose CC was not represented by an exactly equivalent concentration in the manufacturer-defined dilutions on the MYCOTB plate (EMB, INH). We propose interpretations of MYCOTB plate MICs using the currently available plate configuration.

Laboratory Diagnostics for Fungal Infections: A Review of Current and Future Diagnostic Assays

This article reviews the current diagnostic approaches, both serologic and molecular, for the detection of fungi associated with pulmonary disease. Classic serologic techniques, including immunodiffusion and complement fixation, both of which remain a cornerstone for fungal diagnostic testing, are reviewed and their performance characteristics presented. More recent advances in this field, including novel lateral-flow assays for fungal antigen detection, are also described. Molecular techniques for fungal identification both from culture and directly from patient specimens, including nucleic acid probes, mass spectrometry-based methods, nucleic acid amplification testing, and traditional and broad-range sequencing, are discussed and their performance evaluated.

Disseminated Mycobacterium chimaera Infection After Cardiothoracic Surgery

Ten case reports of disseminated Mycobacterium chimaera infections associated with cardiovascular surgery were published from Europe. We report 3 cases of disseminated M chimaera infections with histories of aortic graft and/or valvular surgery within the United States. Two of 3 patients demonstrated ocular involvement, a potentially important clinical finding.

Diagnosis of active tuberculosis disease: From microscopy to molecular techniques

Methods used for the laboratory diagnosis of tuberculosis are continually evolving in order to achieve more rapid, less expensive, and accurate results. Acid-fast staining and culture for mycobacteria remain at the core of any diagnostic algorithm. Following growth in culture, molecular technologies such as nucleic acid hybridization probes, MALDI-TOF MS, and DNA sequencing may be used for definitive species identification. Nucleic acid amplification methods allow for the direct detection of Mycobacterium tuberculosis complex within respiratory specimens without relying on culture growth, leading to more rapid diagnoses and appropriate patient care.

A Cluster ofMycobacterium wolinskyiSurgical Site Infections at an Academic Medical Center

Objective

To study a cluster ofMycobacterium wolinskyisurgical site infections (SSIs).

Design

Observational and case-control study.

Setting

Academic hospital.

Patients.

Subjects who developed SSIs withM. wolinskyifollowing cardiothoracic surgery.

Methods

Electronic surveillance was performed for case finding as well as electronic medical record review of infected cases. Surgical procedures were observed. Medical chart review was conducted to identify risk factors. A case-control study was performed to identify risk factors for infection; Fisher exact or Kruskal-Wallis tests were used for comparisons of proportions and medians, respectively. Patient isolates were studied using pulsed-field gel electrophoresis (PFGE). Environmental microbiologic sampling was performed in operating rooms, including high-volume water sampling.

Results

Six definite cases ofM. wolinskyiSSI following cardiothoracic surgery were identified during the outbreak period (October 1, 2008–September 30, 2011). Having cardiac surgery in operating room A was significantly associated with infection (odds ratio, 40;P= .0027). Observational investigation revealed a cold-air blaster exclusive to operating room A as well a microbially contaminated, self-contained water source used in heart-lung machines. The isolates were indistinguishable or closely related by PFGE. No environmental samples were positive forM. wolinskyi.

Conclusions

No single point source was established, but 2 potential sources, including a cold-air blaster and a microbially contaminated, self-contained water system used in heart-lung machines for cardiothoracic operations, were identified. Both of these potential sources were removed, and subsequent active surveillance did not reveal any further cases ofM. wolinskyiSSI.

Infect Control Hosp Epidemiol2014;35(9):1169-1175

Pulmonary necrotizing granulomas of unknown cause: clinical and pathologic analysis of 131 patients with completely resected nodules

BACKGROUND

The cause of pulmonary necrotizing granulomas is often unclear, even after histologic examination. Our aim was to determine the clinical significance of histologically unexplained necrotizing granulomas.

METHODS

Pulmonary necrotizing granulomas surgically resected at the Mayo Clinic (1994-2004) were retrieved and reviewed retrospectively. Cases in which a cause was evident at the time of initial histologic examination were excluded. The analysis cohort comprised 131 completely resected histologically unexplained pulmonary necrotizing granulomas. Clinical and laboratory information was abstracted from medical records, chest CT scans were reviewed, histologic slides were reexamined, and additional ancillary studies were performed in selected cases.

RESULTS

A cause was determined on review in more than one-half of the histologically unexplained necrotizing granulomas (79 of 131, 60%) by reexamining histologic slides (47), incorporating the results of cultures (26), fungal serologies (14), and other laboratory studies (eight), and correlating histologic findings with clinical and radiologic information (13). Infections accounted for the majority (64 of 79), the most common being histoplasmosis (37) and nontuberculous mycobacterial infections (18). Noninfectious diagnoses (15 of 79) were rheumatoid nodule (five), granulomatosis with polyangiitis (Wegener) (five), sarcoidosis (four), and chronic granulomatous disease (one). Many cases remained unexplained even after extensive review (52 of 131, 40%). Most of these patients received no medical therapy and did not progress clinically or develop new nodules (median follow-up, 84 months).

CONCLUSIONS

A cause, the most common being infection, can be established in many surgically resected pulmonary necrotizing granulomas that appear unexplained at the time of initial histologic diagnosis. Patients whose granulomas remain unexplained after a rigorous review have a favorable outcome. Most do not develop new nodules or progress clinically, even without medical therapy.

Genotypic characteristics of Mycobacterium tuberculosis isolated from household contacts of tuberculosis patients in the Philippines

BACKGROUND

The Philippines has an extremely high rate of tuberculosis but little is known about M. tuberculosis genotypes and transmission dynamics in this country. The aim of this study was to determine the proportion of household contacts who develop active TB due to direct transmission from an index case in that household.

METHODS

Mycobacterium tuberculosis isolates from household contacts of tuberculosis patients in the Philippines were characterized using restriction-fragment-length polymorphism analysis, spoligotyping, and mycobacterial interspersed repetitive units - variable number tandem repeats typing (12-loci) to determine their utility in elucidating transmission in an area of high tuberculosis prevalence. Drug susceptibility patterns for these isolates were also determined.

RESULTS

Spoligotyping and MIRU-VNTR typing results matched in 10 (62.5%) of 16 index patient-household contact pairs while IS6110 fingerprints matched in only six (37.5%) pairs. Only 3/16 (18.8%) index patient-household contact pairs had identical drug susceptibility results.

CONCLUSIONS

Strain typing of M. tuberculosis isolates from household contacts in the Philippines indicates that transmission of strains does not necessarily occur directly from the index patient living in close proximity in the same household but rather that community-based transmission also frequently occurs. Accurate susceptibility testing of all isolates is necessary to insure optimal care of both the index patients and any culture-positive household contacts.

Increased incidence of cutaneous nontuberculous mycobacterial infection, 1980 to 2009: a population-based study

OBJECTIVES

To determine the incidence and clinical characteristics of cutaneous nontuberculous mycobacterial (NTM) infection during the past 30 years and whether the predominant species have changed.

PATIENTS AND METHODS

Using Rochester Epidemiology Project data, we identified Olmsted County, Minnesota, residents with cutaneous NTM infections between January 1, 1980, and December 31, 2009, examining the incidence of infection, patient demographic and clinical features, the mycobacterium species, and therapy.

RESULTS

Forty patients (median age, 47 years; 58% female [23 of 40]) had positive NTM cultures plus 1 or more clinical signs. The overall age- and sex-adjusted incidence of cutaneous NTM infection was 1.3 per 100,000 person-years (95% CI, 0.9-1.7 per 100,000 person-years). The incidence increased with age at diagnosis (P=.003) and was higher in 2000 to 2009 (2.0 per 100,000 person-years; 95% CI, 1.3-2.8 per 100,000 person-years) than in 1980 to 1999 (0.7 per 100,000 person-years; 95% CI, 0.3-1.1 per 100,000 person-years) (P=.002). The distal extremities were the most common sites of infection (27 of 39 patients [69%]). No patient had human immunodeficiency virus infection, but 23% (9 of 39) were immunosuppressed. Of the identifiable causes, traumatic injuries were the most frequent (22 of 29 patients [76%]). The most common species were Mycobacterium marinum (17 of 38 patients [45%]) and Mycobacterium chelonae/Mycobacterium abscessus (12 of 38 patients [32%]). In the past decade (2000-2009), 15 of 24 species (63%) were rapidly growing mycobacteria compared with only 4 of 14 species (29%) earlier (1980-1999) (P=.04).

CONCLUSION

The incidence of cutaneous NTM infection increased nearly 3-fold during the study period. Rapidly growing mycobacteria were predominant during the past decade.

Multisite reproducibility of the broth microdilution method for susceptibility testing of Nocardia species

Antimicrobial susceptibility testing (AST) of clinical isolates of Nocardia is recommended to detect resistance to commonly used antimicrobial agents; such testing is complicated by difficulties in inoculum preparation and test interpretation. In this study, six laboratories performed repetitive broth microdilution testing on single strains of Nocardia brasiliensis, Nocardia cyriacigeorgica, Nocardia farcinica, Nocardia nova, and Nocardia wallacei. For each isolate, a total of 30 microdilution panels from three different lots were tested at most sites. The goal of the study was to determine the inter- and intralaboratory reproducibility of susceptibility testing of this group of isolates. Acceptable agreement (>90% agreement at ±1 dilution of the MIC mode) was found for amikacin, ciprofloxacin, clarithromycin, and moxifloxacin. After eliminating MIC values from single laboratories whose results showed the greatest deviation from those of the remaining laboratories, acceptable agreement was also found for amoxicillin-clavulanic acid, linezolid, minocycline, and tobramycin. Results showed unsatisfactory reproducibility of broth microdilution testing of ceftriaxone with N. cyriacigeorgica and N. wallacei, tigecycline with N. brasiliensis and N. cyriacigeorgica, and sulfonamides with N. farcinica and N. wallacei. N. nova ATCC BAA-2227 is proposed as a quality control organism for AST of Nocardia sp., and the use of a disk diffusion test for sulfisoxazole is proposed as a check of the adequacy of the inoculum and to confirm sulfonamide MIC results.