From Pandemic to Epidemic: Lessons Learned From COVID-19 Applied to Mpox Outbreak Response, Westchester County, Metropolitan New York.

The COVID-19 pandemic vaccination infrastructure was redeployed to address the Mpox epidemic. The Westchester County Department of Health coordinated an effective vaccine distribution, tracking, and data collection process with community partners with real-time feedback of operational challenges and updated public health directives. Westchester County, which comprises 9% of the New York State population, administered 24% (6770 doses) of JYNNEOS (smallpox and monkeypox vaccine) across the state. Among first-dose recipients, 13% were Black and 25% were Hispanic, approaching countywide US Census race and ethnicity breakdowns. The operational template designed during COVID-19 can be readily redeployed for subsequent epidemics of even seemingly dissimilar infections like Mpox.

Development and Validation of TaqMan Chemistry Probe-Based Rapid Assay for the Detection of Echinocandin-Resistance in Candida auris.

Candida auris is a multidrug-resistant yeast pathogen causing outbreaks in health care facilities worldwide, and the emergence of echinocandin-resistant C. auris is a concern. Currently used Clinical and Laboratory Standards Institute (CLSI) and commercial antifungal susceptibility tests (AFST) are phenotype-based, slow, and not scalable, limiting their effectiveness in the surveillance of echinocandin-resistant C. auris. The urgent need for accurate and rapid methods of assessment of echinocandin resistance cannot be overstated, as this class of antifungal drugs is preferred for patient management. We report the development and validation of a TaqMan chemistry probe-based fluorescence melt curve analysis (FMCA) following asymmetric polymerase chain reaction (PCR) to assess mutations within the hot spot one (HS1) region of FKS1, the gene responsible for encoding 1,3-ß-d-glucan synthase that is a target for echinocandins. The assay correctly identified F635C, F635Y, F635del, F635S, S639F or S639Y, S639P, and D642H/R645T mutations. Of these mutations, F635S and D642H/R645T were not involved in echinocandin resistance, while the rest were, as confirmed by AFST. Of 31 clinical cases, the predominant mutation conferring echinocandin resistance was S639F/Y (20 cases) followed by S639P (4 cases), F635del (4 cases), F635Y (2 cases), and F635C (1 case). The FMCA assay was highly specific and did not cross-react with closely and distantly related Candida and other yeast and mold species. Structural modeling of the Fks1 protein, its mutants, and docked conformations of three echinocandin drugs suggest a plausible Fks1 binding orientation for echinocandins. These findings lay the groundwork for future evaluations of additional FKS1 mutations and their impact on the development of drug resistance. The TaqMan chemistry probe-based FMCA would allow rapid, high throughput, and accurate detection of FKS1 mutations conferring echinocandin resistance in C. auris.

Mpox in the New York metropolitan area, Summer 2022.

Early in the 2022 Mpox (MPX) global outbreak, caseloads in the New York Metropolitan area climbed rapidly before other US urban areas. This case series summarizes the authors' clinical experience detecting and treating MPX, during a quickly evolving outbreak. Clinical outcomes were recorded with a focus on varied clinical presentation and outcomes such as complications and response to experimental tecovirimat therapy. A focal or multifocal rash was the most common presenting symptom in 91% of patients. Almost two-thirds (62%) of patients had anogenital involvement. Proctitis was one of the most painful presentations with 75% requiring antiviral treatment and three patients needing hospitalization for pain management. Most patients responded promptly to antiviral treatment with tecovirimat. Five out of 10 patients treated with tecovirimat reported symptom resolution within 48-72 h of therapy and another three saw resolution within first 96 h. Two patients had poor response to tecovirimat. This series includes the only reported case of an HIV positive, immunocompetent patient who experienced recurrent anal ulcers due to Mpox and required a second course of tecovirimat. Other unique presentations included urethritis, abscess formation and MPX infection postvaccination. Control of this current Mpox outbreak was possible due to timely diagnosis and the availability of both a licensed vaccine and an investigational drug.

Antifungal Resistance Trends of Candida auris Clinical Isolates in New York and New Jersey from 2016 to 2020.

About 55% of U.S. Candida auris clinical cases were reported from New York and New Jersey from 2016 through 2020. Nearly all New York-New Jersey clinical isolates (99.8%) were fluconazole resistant, and 50% were amphotericin B resistant. Echinocandin resistance increased from 0% to 4% and pan-resistance increased from 0 to <1% for New York C. auris clinical isolates but not for New Jersey, highlighting the regional differences.

Candida auris Pan-Drug-Resistant to Four Classes of Antifungal Agents.

Candida auris is an urgent antimicrobial resistance threat due to its global emergence, high mortality, and persistent transmissions. Nearly half of C. auris clinical and surveillance cases in the United States are from the New York and New Jersey Metropolitan area. We performed genome, and drug-resistance analysis of C. auris isolates from a patient who underwent multi-visceral transplantation. Whole-genome comparisons of 19 isolates, collected over 72 days, revealed closed similarity (Average Nucleotide Identity > 0.9996; Aligned Percentage > 0.9764) and a distinct subcluster of NY C. auris South Asia Clade I. All isolates had azole-linked resistance in ERG11(K143R) and CDR1(V704L). Echinocandin resistance first appeared with FKS1(S639Y) mutation and then a unique FKS1(F635C) mutation. Flucytosine-resistant isolates had mutations in FCY1, FUR1, and ADE17. Two pan-drug-resistant C. auris isolates had uracil phosphoribosyltransferase deletion (FUR1[1Δ33]) and the elimination of FUR1 expression, confirmed by a qPCR test developed in this study. Besides ERG11 mutations, four amphotericin B-resistant isolates showed no distinct nonsynonymous variants suggesting unknown genetic elements driving the resistance. Pan-drug-resistant C. auris isolates were not susceptible to two-drug antifungal combinations tested by checkerboard, Etest, and time-kill methods. The fungal population pattern, discerned from SNP phylogenetic analysis, was consistent with in-hospital or inpatient evolution of C. auris isolates circulating locally and not indicative of a recent introduction from elsewhere. The emergence of pan-drug-resistance to four major classes of antifungals in C. auris is alarming. Patients at high risk for drug-resistant C. auris might require novel therapeutic strategies and targeted pre-and/or posttransplant surveillance.

Reverse Transcription-Quantitative Real-Time PCR (RT-qPCR) Assay for the Rapid Enumeration of Live Candida auris Cells from the Health Care Environment.

Ongoing health care-associated outbreaks of the multidrug-resistant yeast Candida auris have prompted the development of several rapid DNA-based molecular diagnostic tests. These tests do not distinguish between live and dead C. auris cells, limiting their use for environmental surveillance and containment efforts. We addressed this critical gap by developing a reverse transcription (RT)-quantitative real-time PCR (RT-qPCR) assay to rapidly detect live C. auris in health care environments. This assay targeted the internal transcribed spacer 2 (ITS2) ribosomal gene by obtaining pure RNA followed by reverse transcription (ITS2 cDNA) and qPCR. ITS2 cDNA was not detectable in bleach-killed cells but was detectable in heat- and ethanol-killed C. auris cells. The assay was highly sensitive, with a detection limit of 10 CFU per RT-qPCR. Validation studies yielded positive cycle threshold (CT) values from sponge matrix samples spiked with 102 to 105 CFU of live C. auris, while dead (bleach-killed) C. auris (105/mL) or other live Candida species (105/mL) had no CT values. Finally, 33 environmental samples positive for C. auris DNA but negative by culture were all negative by RT-qPCR assay, confirming the concordance between culture and the PCR assay. The RT-qPCR assay appears highly reproducible, robust, and specific for detecting live C. auris from environmental samples. The Candida auris RT-qPCR assay could be an invaluable tool in surveillance efforts to control the spread of live C. auris in health care environments.

Utility of CHROMagar™ Candida Plus for presumptive identification of Candida auris from surveillance samples.

Candida auris is a nosocomial fungal pathogen of prime importance due to its global emergence and rapid spread in healthcare facilities worldwide. One important concern is that routine, conventional methods fail to identify C. auris. While molecular and protein-based assays accurately detect/identify C. auris, these methods are time-consuming, expensive, and require expertise. Therefore, the objective of the present study was to assess the potential use of a novel chromogenic medium, CHROMagar™ Candida Plus, as an economical alternative to expensive and laborious diagnostic tests. We compared CHROMagar™ Candida Plus with the standard enrichment (salt Sabouraud Dulcitol broth) medium to test the recovery efficiency of C. auris from surveillance samples. We also tested CHROMagar™ Candida Plus for its ability to distinguish C. auris from other yeast species. One hundred surveillance samples were cultured on CHROMagar™ Candida Plus and Dulcitol broth and incubated at 37 °C and 40 °C, respectively. Additionally, 32 Candida and yeast species were cultured on CHROMagar™ Candida Plus at 37 °C for three days to rule out any close resemblance to C. auris. Of 100 surveillance samples tested, 69 yielded presumptive positive C. auris exhibiting creamy pink colonies with a blue halo on CHROMagar™ Candida Plus within three days of incubation, and MALDI-TOF MS confirmed all by day 4. On the other hand, 69 of 100 surveillance samples yielded turbidity in Dulcitol broth by days 3-14 with final MALDI identification by days 5 to 17. Both media failed to identify one sample each, resulting in assay sensitivity and specificity of 99% and 97%, respectively. Of Candida and yeast species tested, 75-80% of C. metapsilosis and C. orthospilosis were misidentified as C. auris. However, previous studies indicated that these species are rarely detected in surveillance screening of C. auris. Naganishia diffluens also resembled C. auris, although it required different temperature growth (30 °C). In conclusion, CHROMagar™ Candida Plus provides rapid presumptive identification of C. auris. It would be another valuable tool in surveillance efforts to control the spread of C. auris in healthcare.

Development of a Duplex Real-Time PCR Assay for the Differentiation of Blastomyces dermatitidis and Blastomyces gilchristii and a Retrospective Analysis of Culture and Primary Specimens from Blastomycosis Cases from New York (2005 to 2019).

Blastomycosis due to Blastomyces dermatitidis and Blastomyces gilchristii is a significant cause of respiratory mycoses in North America with occasional reported outbreaks. We developed a highly sensitive, specific, and reproducible TaqMan duplex real-time PCR assay for the differentiation of B. dermatitidis and B. gilchristii The new assay permitted retrospective analysis of Blastomyces cultures (2005 to 2019) and primary clinical specimens from blastomycosis cases (2013 to 2019) from New York patients. We identified B. dermatitidis as the predominant pathogen in 38 cases of blastomycosis, while B. gilchristii was a minor pathogen involved in five cases; these findings expand understanding of blastomycosis in New York. The duplex real-time PCR assay could be implemented in reference and public health laboratories to further understand the ecology and epidemiology of blastomycosis due to B. dermatitidis and B. gilchristii.

Mycopathologia 2020: Legacy and Change to Remain Relevant for Content, Creation, and Communication.

The 2020 COVID-19 pandemic had a profound impact on the publishing landscape. The 'pre-peer-review' publication model is likely to become common as a lag in publishing is not acceptable in a pandemic or other time! Mycopathologia is well placed to adopt such changes with its improved editorial processes, article formats, author engagements, and published articles' access and citation. Mycopathologia had an improved journal impact factor and article downloads in 2018-2019. A limited sampling suggested a slight decrease in the total submissions in 2019 (352 articles) compared to 2018 (371 articles). However, the acceptance rate improved to 30% in 2019 from 19% in 2018. Nearly half of all submissions in 2019 were rejected before peer-review or transferred to other Springer Nature journals. The published articles were contributed from 34 different countries, with authors from China, the USA, and Brazil among the top three contributors. An enhanced editorial oversight allowed peer-reviewers to focus on fewer articles that were well-matched to their expertise, which led to lower rejection rates post-peer-review. The introduction of MycopathologiaGENOME and MycopathologiaIMAGE article types received a good reception with notable downloads and citations.

Foodborne Botulism Outbreak Associated With Commercial Nacho Cheese Sauce From a Gas Station Market.

BACKGROUND: Botulism is a rare and potentially fatal paralytic disease caused by botulinum neurotoxin (BoNT). In April 2017, 4 California residents from 2 adjacent counties were hospitalized with suspected foodborne botulism, precipitating an investigation by state and local public health departments in California. METHODS: We interviewed suspected botulism patients and their families, inspected the suspect establishment, and collected suspect food. We tested patient sera, stool, and gastric aspirates using mouse bioassay for BoNT and/or culture for Clostridium botulinum. We tested suspect food and environmental samples for BoNT and confirmed presumptive positives using direct mouse bioassay and culture. We performed whole-genome sequencing on food and clinical isolates. RESULTS: From April 2017 through May 2017, 10 patients in the Sacramento area were hospitalized with laboratory-confirmed botulism; 7 required mechanical ventilation, and 1 died. Of 9 patients with information, all had visited Gas Station X before illness onset, where 8 reported consuming a commercial cheese sauce. BoNT/A and/or BoNT/A-producing C. botulinum were detected from each patient and from leftover cheese sauce. Clostridium botulinum isolates from 4 patients were closely related to cheese sauce isolates by whole-genome high-quality single-nucleotide polymorphism analysis. No other botulism cases associated with this cheese sauce were reported elsewhere in the United States. CONCLUSIONS: This large foodborne botulism outbreak in California was caused by consumption of commercial cheese sauce dispensed at a gas station market. The epidemiologic and laboratory evidence confirmed the cheese sauce as the outbreak source. The cheese sauce was likely locally contaminated, although the mechanism is unclear.

In Vitro Evaluation of Antifungal Drug Combinations against Multidrug-Resistant Candida auris Isolates from New York Outbreak.

Since 2016, New York hospitals and health care facilities have faced an unprecedented outbreak of the pathogenic yeast Candida auris We tested over 1,000 C. auris isolates from affected facilities and found high resistance to fluconazole (MIC > 256 mg/liter) and variable resistance to other antifungal drugs. Therefore, we tested if two-drug combinations are effective in vitro against multidrug-resistant C. auris Broth microdilution antifungal combination plates were custom manufactured by TREK Diagnostic System. We used 100% inhibition endpoints for the drug combination as reported earlier for the intra- and interlaboratory agreements against Candida species. The results were derived from 12,960 readings, for 15 C. auris isolates tested against 864 two-drug antifungal combinations for nine antifungal drugs. Flucytosine (5FC) at 1.0 mg/liter potentiated the most combinations. For nine C. auris isolates resistant to amphotericin B (AMB; MIC ≥ 2.0 mg/liter), AMB-5FC (0.25/1.0 mg/liter) yielded 100% inhibition. Six C. auris isolates resistant to three echinocandins (anidulafungin [AFG], MIC ≥ 4.0 mg/liter; caspofungin [CAS], MIC ≥ 2.0 mg/liter; and micafungin [MFG], MIC ≥ 4.0 mg/liter) were 100% inhibited by AFG-5FC and CAS-5FC (0.0078/1 mg/liter) and MFG-5FC (0.12/1 mg/liter). None of the combinations were effective for C. auris 18-1 and 18-13 (fluconazole [FLC] > 256 mg/liter, 5FC > 32 mg/liter) except MFG-5FC (0.1/0.06 mg/liter). Thirteen isolates with a high voriconazole (VRC) MIC (>2 mg/liter) were 100% inhibited by the VRC-5FC (0.015/1 mg/liter). The simplified two-drug combination susceptibility test format would permit laboratories to provide clinicians and public health experts with additional data to manage multidrug-resistant C. auris.

In Vitro Activity of Manogepix against Multidrug-Resistant and Panresistant Candida auris from the New York Outbreak.

An ongoing Candida auris outbreak in the New York metropolitan area is the largest recorded to date in North America. Laboratory surveillance revealed NY C. auris isolates are resistant to fluconazole, with variable resistance to other currently used broad-spectrum antifungal drugs, and that several isolates are panresistant. Thus, there is an urgent need for new drugs with a novel mechanism of action to combat the resistance challenge. Manogepix (MGX) is a first-in-class agent that targets the fungal Gwt1 enzyme. The prodrug fosmanogepix is currently in phase 2 clinical development for the treatment of fungal infections. We evaluated the susceptibility of 200 New York C. auris isolates to MGX and 10 comparator drugs using CLSI methodology. MGX demonstrated lower MICs than comparators (MIC50 and MIC90, 0.03 mg/liter; range, 0.004 to 0.06 mg/liter). The local epidemiological cutoff value (ECV) for MGX indicated all C. auris isolates were within the population of wild-type (WT) strains; 0.06 mg/liter defines the upper limit of wild type (UL-WT). MGX was 8- to 32-fold more active than the echinocandins, 16- to 64-fold more active than the azoles, and 64-fold more active than amphotericin B. No differences were found in the MGX or comparators' MIC50, MIC90, or geometric mean (GM) values when subsets of clinical, surveillance, and environmental isolates were evaluated. The range of MGX MIC values for six C. auris panresistant isolates was 0.008 to 0.015 mg/liter, and the median and mode MIC values were 0.015 mg/liter, demonstrating that MGX retains activity against these isolates. These data support further clinical evaluation of fosmanogepix for the treatment of C. auris infections, including highly resistant isolates.

Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018: Impact and Lessons Learned.

Candida auris is a multidrug-resistant yeast which has emerged in health care facilities worldwide; however, little is known about identification methods, patient colonization, environmental survival, spread, and drug resistance. Colonization on both biotic (patients) and abiotic (health care objects) surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in New York (NY) from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/nonselective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of the internal transcribed spacer (ITS) and D1/D2 regions of the ribosomal gene for C. auris genotyping. Results included (a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates as well as identification of 277 clinical cases and 350 colonized cases from 151 health care facilities, including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, (b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, (c) demonstration of relatively heavier colonization of C. auris in nares than in the axilla/groin, and (d) predominance of the South Asia clade I with intrinsic resistance to fluconazole and elevated MIC to voriconazole (81%), amphotericin B (61%), flucytosine (5FC) (3%), and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.

Candida auris Isolates Resistant to Three Classes of Antifungal Medications - New York, 2019.

Candida auris is a globally emerging yeast that causes outbreaks in health care settings and is often resistant to one or more classes of antifungal medications (1). Cases of C. auris with resistance to all three classes of commonly prescribed antifungal drugs (pan-resistance) have been reported in multiple countries (1). C. auris has been identified in the United States since 2016; the largest number (427 of 911 [47%]) of confirmed clinical cases reported as of October 31, 2019, have been reported in New York, where C. auris was first detected in July 2016 (1,2). As of June 28, 2019, a total of 801 patients with C. auris were identified in New York, based on clinical cultures or swabs of skin or nares obtained to detect asymptomatic colonization (3). Among these patients, three were found to have pan-resistant C. auris that developed after receipt of antifungal medications, including echinocandins, a class of drugs that targets the fungal cell wall. All three patients had multiple comorbidities and no known recent domestic or foreign travel. Although extensive investigations failed to document transmission of pan-resistant isolates from the three patients to other patients or the environment, the emergence of pan-resistance is concerning. The occurrence of these cases underscores the public health importance of surveillance for C. auris, the need for prudent antifungal prescribing, and the importance of conducting susceptibility testing on all clinical isolates, including serial isolates from individual patients, especially those treated with echinocandin medications. This report summarizes investigations related to the three New York patients with pan-resistant infections and the subsequent actions conducted by the New York State Department of Health and hospital and long-term care facility partners.

Onygenalean Fungi as Major Human and Animal Pathogens.

During the last two decades, many onygenalean pathogens were discovered, redefined, or re-classified from existing taxa into clusters of micro-species, among which the original genotypes often appeared to be uncommon and exceptional. The impact of these developments on the diagnosis and treatment of fungal diseases remains to be determined in most instances. This exciting collection of invited articles provides a full flavor of ongoing changes in the knowledge about taxonomy, genetics, ecology, epidemiology, and clinical spectra of human and animal pathogens classified in the order Onygenales. Recent developments have set the stage for an ambitious translational research agenda. Diagnostic mycology laboratories now need MALDI-TOF-MS spectra, PCR probes, and other specific tools to assist them in the rapid diagnosis of new species. Similarly, an educational set of type materials of new species needs to be readily available for enhanced expertise among the wider medical mycology community. As several new species were discovered retrospectively, it is crucial to expand the re-sampling to other fungal culture collections and archived paraffin tissues. Finally, clinical and laboratory investigations are needed to get an accurate assessment of the prevalence and impact of new pathogens as the cause of major fungal diseases.

Characterization of Clinical Isolates of Talaromyces marneffei and Related Species, California, USA.

Talaromyces marneffei and other Talaromyces species can cause opportunistic invasive fungal infections. We characterized clinical Talaromyces isolates from patients in California, USA, a non-Talaromyces-endemic area, by a multiphasic approach, including multigene phylogeny, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and phenotypic methods. We identified 10 potentially pathogenic Talaromyces isolates, 2 T. marneffei.

Talaromycosis (Penicilliosis) Due to Talaromyces (Penicillium) marneffei: Insights into the Clinical Trends of a Major Fungal Disease 60 Years After the Discovery of the Pathogen.

Talaromycosis (penicilliosis) is a major fungal disease endemic across a narrow band of tropical countries of South and Southeast Asia. The etiologic agent is a thermally dimorphic fungus Talaromyces (Penicillium) marneffei, which was first isolated from a bamboo rat in Vietnam in 1956, but no formal description was published. In 1959, Professor Gabriel Segretain formally described it as a novel species Talaromyces (Penicillium) marneffei, and the human pathogenic potential of the fungus in Mycopathologia. The first natural human case of talaromycosis (penicillosis) was reported in 1973 and involved an American minister with Hodgkin's disease who lived in Southeast Asia. Sixty years after the discovery of the pathogen, talaromycosis caused by T. marneffei is recognized as an important human disease with the potential to cause high mortality in the absence of proper diagnosis and prompt treatment. Talaromycosis remains a significant infectious complication in HIV/AIDS patients and in patients with other immune defects. The disease is being recognized with an increasing frequency well beyond the traditional endemic areas. The natural reservoirs of T. marneffei in wild rodents are well-defined, which links the ecology with the epidemiology of talaromycosis in endemic areas. There is an urgent unmet need for rapid and affordable point-of-care diagnostic tests. We also need more clinical studies to define the best therapeutic options for the management of talaromycosis patients.

MycopathologiaGENOMES: The New 'Home' for the Publication of Fungal Genomes.

The wider availability of information on genomes has become essential for future advances in fungal biology, pathogenesis and epidemiology, and for the discovery of new drugs and diagnostics. MycopathologiaGENOMES is designed for the rapid publication of new genomes of human and animal pathogenic fungi using a checklist-based, standardized format.