Traditionally, physicians have not used cefepime (a fourth-generation cephalosporin with greater stability against β-lactamases) or β-lactam/β-lactamase inhibitors (BLBLIs) for infections caused by bacteria (generally Escherichia coli and Klebsiella species) that produce an extended-spectrum β-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.

T he newly emerging multidrug-resistant yeast Candida auris can cause serious infections and may be underrepresented, as it can be misidentified as other species (e.g., Candida haemulonii, Candida duobushaemulonii, or Saccharomyces cerevisiae) by some biochemical-based testing systems (1-4). Candida auris can be identified using research use only (RUO) libraries on matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) platforms, such as the Biotyper platform (Bruker, Billerica, MA), but may need labor-intensive full-tube extraction procedures (3-5). Our laboratory uses the Biotyper equipped with both FDA-approved and RUO libraries. The RUO library contains three C. auris entries, but the identification of C. auris remains a challenge, and some isolates are never identified by the system. To improve the identification, a novel database, "CMdb," was developed and evaluated on our two Biotyper systems. The CMdb was created using internationally collected yeasts from the CDC (6) and one in-house clinical C. auris isolate. Bruker's protocol was used for database creation, and the direct on-plate extraction method was used for target preparation (7). The CMdb was evaluated on 23 clinical C. auris isolates, 20 CDC strains, 52 isolates of 10 other yeast species, and 28 isolates of 16 bacterial species.

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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.

AimsAcid-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.MethodsThe 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.ResultsBoth 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.ConclusionsThe PCR-Seq method provided specific identification of various AFB species or complexes from FFPE tissues.