Confronting the COVID-19 Pandemic: A View from the Laboratory

A retrospective review of salient features of the early-to-mid phases COVID-19 pandemic is provided from the perspective of the clinical laboratory. Lessons learned and possible improvements are opined. These include the importance of maintaining a robust laboratory infrastructure, increased public health funding, the partnership between public health and hospital/commercial laboratories, and the critical importance of sound scientific assessment even during a pandemic crisis

Multicenter study evaluating the Vitek MS system for identification of medically important yeasts

The optimal management of fungal infections is correlated with timely organism identification. Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry (MS) is revolutionizing the identification of yeasts isolated from clinical specimens. We present a multicenter study assessing the performance of the Vitek MS system (bioMérieux) in identifying medically important yeasts. A collection of 852 isolates was tested, including 20 Candida species (626 isolates, including 58 C. albicans, 62 C. glabrata, and 53 C. krusei isolates), 35 Cryptococcus neoformans isolates, and 191 other clinically relevant yeast isolates; in total, 31 different species were evaluated. Isolates were directly applied to a target plate, followed by a formic acid overlay. Mass spectra were acquired using the Vitek MS system and were analyzed using the Vitek MS v2.0 database. The gold standard for identification was sequence analysis of the D2 region of the 26S rRNA gene. In total, 823 isolates (96.6%) were identified to the genus level and 819 isolates (96.1%) were identified to the species level. Twenty-four isolates (2.8%) were not identified, and five isolates (0.6%) were misidentified. Misidentified isolates included one isolate of C. albicans (n = 58) identified as Candida dubliniensis, one isolate of Candida parapsilosis (n = 73) identified as Candida pelliculosa, and three isolates of Geotrichum klebahnii (n = 6) identified as Geotrichum candidum. The identification of clinically relevant yeasts using MS is superior to the phenotypic identification systems currently employed in clinical microbiology laboratories

Antifungal Susceptibilities of Cryptococcus neoformans

Susceptibility profiles of medically important fungi in less-developed countries remain uncharacterized. We measured the MICs of amphotericin B, 5-flucytosine, fluconazole, itraconazole, and ketoconazole for Cryptococcus neoformans clinical isolates from Thailand, Malawi, and the United States and found no evidence of resistance or MIC profile differences among the countries

North American Paragonimiasis (Caused by Paragonimus kellicotti) in the Context of Global Paragonimiasis

Summary: Paragonimus species are highly evolved parasites with a complex life cycle that involves at least three different hosts, i.e., snails, crustaceans, and mammals. The adult forms of Paragonimus species reside and mate in the lungs of a variety of permissive mammalian hosts, including humans. Although human paragonimiasis is uncommonly encountered in North America, both autochthonous and imported disease may be encountered. Paragonimus kellicotti, the species endemic to North America, is a well-known pathogen in wild and domestic animals. Five patients with North American paragonimiasis have been reported in the recent medical literature. The biologic, clinical, radiologic, and laboratory features of paragonimiasis are reviewed, with emphasis on North American paragonimiasis whenever possible

North American paragonimiasis: A case report

Paragonimiasis is a parasitic infection with a predilection for pulmonary involvement. Paragonimus species occur throughout the world and exist in nature in a snail-crustacean-mammalian life cycle. Human disease is most frequently encountered in cultures that ingest raw or undercooked crustaceans. North American paragonimiasis, caused by an endemic Paragonimus species, Paragonimus kellicotti, predominantly causes disease in carnivorous and omnivorous animals but may cause human disease if the intermediate host, the crayfish, is ingested raw or undercooked. CASE: A previously healthy, 21-year-old male was infected with P kellicotti and developed parasitic hemoptysis. The disease was contracted through the ingestion of local, undercooked crayfish. Diagnosis was established through the morphologic examination of eggs in the cytologic preparation of bronchioalveolar lavage fluid. The patient was successfully treated with praziquantel and recovered without incident. CONCLUSION: Paragonimiasis is a cause of parasitic hemoptysis worldwide. Paragonimiasis is infrequently encountered in North America and is usually not considered in the differential diagnosis of hemoptysis unless specific risk factors are known. The cytologist or cytopathologist, therefore, may be the first to encounter the diagnostic eggs and should be familiar with this disease

Molecular Diagnostics for Invasive Fungal Infections: A Call for Refinement and Implementation

This Commentary discusses the role of molecular diagnostics in fungal infections

Rapid Identification of Staphylococcus aureus Directly from Blood Cultures by Fluorescence In Situ Hybridization with Peptide Nucleic Acid Probes

A new fluorescence in situ hybridization (FISH) method with peptide nucleic acid (PNA) probes for identification of Staphylococcus aureus directly from positive blood culture bottles that contain gram-positive cocci in clusters (GPCC) is described. The test (the S. aureus PNA FISH assay) is based on a fluorescein-labeled PNA probe that targets a species-specific sequence of the 16S rRNA of S. aureus. Evaluations with 17 reference strains and 48 clinical isolates, including methicillin-resistant and methicillin-susceptible S. aureus species, coagulase-negative Staphylococcus species, and other clinically relevant and phylogenetically related bacteria and yeast species, showed that the assay had 100% sensitivity and 96% specificity. Clinical trials with 87 blood cultures positive for GPCC correctly identified 36 of 37 (97%) of the S. aureus-positive cultures identified by standard microbiological methods. The positive and negative predictive values were 100 and 98%, respectively. It is concluded that this rapid method (2.5 h) for identification of S. aureus directly from blood culture bottles that contain GPCC offers important information for optimal antibiotic therapy