Validation of the PyloPlus Urea Breath Test System in pediatric patients.

IMPORTANCE: For the diagnosis and post-treatment monitoring of H. pylori infection, non-invasive testing methodologies improve patient comfort, particularly for children. Previously, only the BreathTek UBT had FDA approval for use in pediatric patients and required an adjustment calculation based on age, height, and weight of the patient. The purpose of this study was to evaluate the performance of the PyloPlus UBT assay in a pediatric population.

Short Signature rpoB Gene Sequence to Differentiate Species in Mycobacterium abscessus Group.

Mycobacterium abscessus group (MAG) are rapidly growing acid-fast bacteria that consist of three closely related species: M. abscessus (Ma), M. bolletii (Mb), and M. massiliense (Mm). Differentiation of these species can be difficult but is increasingly requested owing to recent infectious outbreaks and their differential drug resistance. We developed a novel and rapid pyrosequencing method using short signature sequences (35 to 45 bp) at a hypervariable site in the rpoB gene to differentiate the three MAG species, along with M. chelonae (Mc), and M. immunogenum (Mi). This method was evaluated using 111 M. chelonae-abscessus complex (MCAC) isolates, including six reference strains. All isolates were successfully differentiated to the species level (69 Ma, four Mb, six Mm, 23 Mc, and nine Mi). The species identifications by this method had 100% agreement with Sanger sequencing as well as an in-silico rpoB typing method. This short signature sequencing (SSS) method is rapid (6 to 7 h), accurately differentiates MAG species, and is useful for informing antimicrobial therapy decision. IMPORTANCE Mycobacterium abscessus group (MAG) are rapidly growing acid-fast bacteria that include three species: M. abscessus, M. massiliense, and M. bolletii. These species are among the leading causes of nontuberculosis mycobacteria infections in humans but difficult to differentiate using commonly used methods. The differences of drug resistance among the species shape the treatment regimens and make it significant for them to be differentiated accurately and quickly. We developed and evaluated a novel short signature sequencing (SSS) method utilizing a gene called rpoB to differentiate the three MAG species, as well as other two species (M. chelonae and M. immunogenum). The identification results had 100% agreement with both the reference method of Sanger sequencing and rpoB typing method via a computer-simulated analysis. This SSS method was accurate and quick (6 to 7 h) for species differentiation, which will benefit patient care. The technology used for this method is affordable and easy to operate.

Elevated Rates of Indeterminate Results on QuantiFERON-TB Gold Plus in COVID-19 Patients.

Interferon gamma release assays are used to screen various patient populations for latent tuberculosis infection. In this issue of the Journal of Clinical Microbiology, J. D. Ward, C. Cornaby, and J. L. Schmitz (J Clin Microbiol 59:e00811-21, 2021, https://doi.org/10.1128/JCM.00811-21) investigated an increased indeterminate rate in the QuantiFERON-TB Gold Plus assay among COVID-19 patients that was independent of immunosuppressive agents and lymphopenia. In their study, COVID-19 patients with indeterminate QuantiFERON-TB Gold Plus results trended toward decreased survival as well as increased serum interleukin-6 (IL-6) and IL-10 levels, although the differences were not statistically significant. They suggest that this pattern of cytokine expression supports an impairment of Th1, specifically interferon gamma production, in critically ill COVID-19 patients, as indicated by indeterminate QuantiFERON-TB Gold Plus results. Clinicians should be aware of the increased rate of indeterminate QuantiFERON-TB Gold Plus results in critically ill COVID-19 patients.

Recovery and Its Dynamics of Filamentous Fungi from Clinical Specimen Cultures: An Extensive Study.

The culture method remains vital in diagnosing fungal infections, but extensive data-based evaluation of the method, especially for filamentous fungi (molds), is minimal. The purpose of this study was to characterize mold recoveries from fungal cultures and the impact of media and incubation duration. Clinical specimens for fungal cultures were submitted primarily from the eastern and central United States, and mold isolation data were prospectively collected and analyzed. A total of 1,821 molds in 59 genera were isolated from 1,687 positive specimens, accounting for approximately 5.6% of our cohort of 30,000 fungal cultures. Within 2 weeks, nearly 90% of molds and 97.3% of Aspergillus fumigatus complex were recovered (>95% confidence interval [CI]). All Mucorales fungi were recovered within 11 days of incubation. The recovery peak time was day 3 for Mucorales fungi, day 4 for hyaline molds, day 5 for dematiaceous molds, and day 7 for Onygenales fungi. The recovery of Histoplasma capsulatum and Trichophyton species in the fourth week of incubation reveals that a 3-week incubation time is insufficient. Inhibitory mold agar was the best medium for recovering all mold types among all tested specimen types, yielding nearly 78% of mold growth overall, indicating the necessity of selective medium for fungal cultures. IMPORTANCE Fungal culture is the gold standard method of diagnosing fungal infections, but important information, such as the impact of media and incubation times on fungal recovery, is not well documented. This study addressed these gaps using extensive data-based evaluation focused on molds. We identified the best medium types and incubation times for better fungal culture practice. We analyzed 1,821 molds from 1,687 positive specimens in our cohort of approximately 30,000 fungal cultures. Mold recovery peaked between 3 and 7 days of incubation, dependent upon the type of mold. Some well-defined fungal pathogens, such as Histoplasma capsulatum and Trichophyton species, were isolated in the fourth week of incubation. Inhibitory mold agar was identified as the best medium for recovering all mold types among all tested specimen sources. As we are aware, this is the largest study of fungal culture methods and supports 4 weeks of incubation for optimal mold recovery.

Current significance of the Mycobacterium chelonae-abscessus group.

Organisms of the Mycobacterium chelonae-abscessus group can be significant pathogens in humans. They produce a number of diseases including acute, invasive and chronic infections, which may be difficult to diagnose correctly. Identification among members of this group is complicated by differentiating at least eleven (11) known species and subspecies and complexity of identification methodologies. Treatment of their infections may be problematic due to their correct species identification, antibiotic resistance, their differential susceptibility to the limited number of drugs available, and scarcity of susceptibility testing.

Acid-fast bacterium detection and identification from paraffin-embedded tissues using a PCR-pyrosequencing method.

AIMS: Acid-fast bacterium (AFB) identification from formalin-fixed paraffin-embedded (FFPE) tissues is challenging and may not be readily available to the clinical laboratory. A method to detect and identify AFB from FFPE tissues using PCR and pyrosequencing (PCR-Seq) was developed and evaluated. METHODS: The method was validated using spiked cell-clotted paraffin blocks before use with patients' specimens. DNA was extracted from tissue sections, and a 16S rRNA gene fragment was amplified and a signature sequence was produced on a PyroMark ID system. Sequences were aligned to established databases for AFB identification. Additional tissue sections were stained and examined for AFB. RESULTS: Both sensitivity and specificity were 100% on spiked cell-clotted blocks without cross-reactivity with non-AFB. Of 302 FFPE tissues from patients, 116 (38%) were AFB-stain positive; 83 (72%) of these had AFB identified. The 21 AFB identified included Mycobacterium tuberculosis complex (14 cases), Mycobacterium leprae (3), Mycobacterium genavense (2), Mycobacterium marinum-ulcerans group (3) and 17 other AFB (61). Thirteen cases were AFB-stain indeterminate and 4 were positive by the PCR-Seq method. Of the AFB stain-negative cases, 167 were negative and 6 were positive by PCR-Seq. CONCLUSIONS: The PCR-Seq method provided specific identification of various AFB species or complexes from FFPE tissues.

Determining a clinical framework for use of cefepime and ß-lactam/ß-lactamase inhibitors in the treatment of infections caused by extended-spectrum-ß-lactamase-producing Enterobacteriaceae.

Traditionally, physicians have not used cefepime (a fourth-generation cephalosporin with greater stability against ß-lactamases) or ß-lactam/ß-lactamase inhibitors (BLBLIs) for infections caused by bacteria (generally Escherichia coli and Klebsiella species) that produce an extended-spectrum ß-lactamase (ESBL). Many microbiology laboratories have historically labelled these ESBL-producing organisms as resistant to all cephalosporins regardless of their MIC. The recommendation to eliminate ESBL identification started with EUCAST in 2009, followed by CLSI in 2010. As a consequence, many ESBL-producing organisms that were previously labelled as resistant to all cephalosporins may be reclassified as susceptible to some (particularly cefepime), depending on their MICs. Because there are limited treatment options against ESBL-producing organisms, there is growing interest in using cefepime and BLBLIs. In this review, we examine the clinical outcomes of therapy directed against ESBL-producing Enterobacteriaceae and the pharmacokinetics/pharmacodynamics of cefepime and BLBLIs to construct a clinical framework for how physicians can best employ these carbapenem-sparing alternatives for the treatment of infections caused by ESBL-producing Enterobacteriaceae. We conclude that standard-dose cefepime is a reasonable option for the definitive therapy of invasive infections resulting from ESBL-producing E. coli and Klebsiella species when the MIC for the organism is ≤ 2 mg/L (CLSI) or ≤ 1 mg/L (EUCAST), although higher doses may be considered for MICs in the 4-8 mg/L range. Piperacillin/tazobactam is also a reasonable option when the MIC is ≤ 16 mg/L.

In vitro C3 deposition on Cryptococcus capsule occurs via multiple complement activation pathways.

Complement can be activated via three pathways: classical, alternative, and lectin. Cryptococcus gattii and Cryptococcus neoformans are closely related fungal pathogens possessing a polysaccharide capsule composed mainly of glucuronoxylomannan (GXM), which serves as a site for complement activation and deposition of complement components. We determined C3 deposition on Cryptococcus spp. by flow cytometry and confocal microscopy after incubation with serum from C57BL/6J mice as well as mice deficient in complement components C4, C3, factor B, and mannose binding lectin (MBL). C. gattii and C. neoformans activate complement in EGTA-treated serum indicating that they can activate the alternative pathway. However, complement activation was seen with factor B(-/-) serum suggesting activation could also take place in the absence of a functional alternative pathway. Furthermore, we uncovered a role for C4 in the alternative pathway activation by Cryptococcus spp. We also identified an unexpected and complex role for MBL in complement activation by Cryptococcus spp. No complement activation occurred in the absence of MBL-A and -C proteins although activation took place when the lectin binding activity of MBL was disrupted by calcium chelation. In addition, alternative pathway activation by C. neoformans required both MBL-A and -C, while either MBL-A or -C was sufficient for alternative pathway activation by C. gattii. Thus, complement activation by Cryptococcus spp. can take place through multiple pathways and complement activation via the alternative pathway requires the presence of C4 and MBL proteins.

Aureobasidium pullulans var. melanigenum fungemia in a pediatric patient.

This report describes a chronically ill child who presented with high fever and was diagnosed with catheter-related sepsis. Aureobasidium pullulans variety melanigenum, a dematiaceous fungus that rarely causes opportunistic infections, was recovered from multiple blood cultures. Antifungal susceptibilities were performed and the minimum inhibitory concentration (MIC) for fluconazole was 64 mg/l, suggestive of fluconazole resistance. The patient made a full recovery after removal of the catheter line and treatment with liposomal amphotericin B. This is the first case report of an elevated in vitro fluconazole MIC of an A. pullulans isolate and only the third case of successful treatment of A. pullulans fungemia.