Molecular characterization of Candida auris outbreak isolates in Qatar from patients with COVID-19 reveals the emergence of isolates resistant to three classes of antifungal drugs.

OBJECTIVES: During the COVID-19 pandemic in Qatar, many patients who were severely ill were colonized and infected by Candida auris, an invasive multidrug-resistant yeast pathogen that spreads through nosocomial transmission within healthcare facilities. Here, we investigated the molecular epidemiology of these C. auris isolates and the mechanisms associated with antifungal drug resistance. METHODS: Whole genomes of 76 clinical C. auris isolates, including 65 from patients with COVID-19 collected from March 2020 to June 2021, from nine major hospitals were sequenced on Illumina NextSeq. Single nucleotide polymorphisms were used to determine their epidemiological patterns and mechanisms for antifungal resistance. The data were compared with those published prior to the COVID-19 pandemic from 2018 to 2020 in Qatar. RESULTS: Genomic analysis revealed low genetic variability among the isolates from patients with and without COVID-19, confirming a clonal outbreak and ongoing dissemination of C. auris among various healthcare facilities. Based on antifungal susceptibility profiles, more than 70% (22/28) of isolates were resistant to both fluconazole and amphotericin B. Variant analysis revealed the presence of multi-antifungal resistant isolates with prominent amino acid substitutions: Y132F in ERG11 and V704L in CDR1 linked to reduced azole susceptibility and the emergence of echinocandin resistance samples bearing mutations in FKS1 in comparison with pre-COVID-19 pandemic samples. One sample (CAS109) was resistant to three classes of antifungal drugs with a unique premature stop codon in ERG3 and novel mutations in CDR2, which may be associated with elevated amphotericin B and azole resistance. DISCUSSION: Candida auris isolates from patients with COVID-19 and from most patient samples without COVID-19 in Qatar were highly clonal. The data demonstrated the emergence of multidrug-resistant strains that carry novel mutations linked to enhanced resistance to azoles, echinocandins, and amphotericin B. Understanding the epidemiology and drug resistance will inform the infection control strategy and drug therapy.

COVID-19 Hastalar?nda Candida auris ?nfeksiyonlar?: Bir Derleme

An increase in the incidence of invasive fungal infection, which can lead to serious complications and death, has been detected in some patients who had Coronavirus disease-2019 (COVID-19). Since the beginning of the COVID-19 pandemic, fungal infections increase the risk of mortality in long-term hospitalized COVID-19 patients. C. auris has emerged as a multidrug-resistant fungal pathogen iso-lated from healthcare-associated infections globally. Studies have reported an increase in C. auris isolation in COVID-19 patients who developed candidemia. They stated that C. auris is the most isolated Candida species in blood cultures since the beginning of the SARS-CoV-2 pandemic, replacing other Candida species. In the studies included in this study, the mean incidance of C. auris was found to be as 22.7% (74/325) in COVID-19 patients with suspected fungal infection. The aim of our study is to evaluate the literature published so far in Turkiye and in the world regarding the coexistence of C. auris and COVID-19, which was reported as an "immediate threat" by the Centers for Disease Control and Prevention (CDC). However, there is not enough information about the effect of C. auris coinfection on mortality and whether it is an indicator of the severity of COVID-19 infection. Well-designed and careful epidemiological studies are needed to define the true burden of invasive candidiasis in COVID-19 patients.

The Emergence and Persistence of Candida auris in Western New York With No Epidemiologic Links: A Failure of Stewardship?

Reports of Candida auris infection in patients without epidemiologic links to prior outbreaks are scarce. We describe the genomic epidemiology of such a case in Western New York. Before emergence, the patient received >60 days of excess antibiotics. Candida auris was recovered on near-patient surfaces after enhanced terminal cleanings.

Regional spread of Candida auris.

The geographical routes and time schedule of spread of C. auris - the fungus first identified in 2009 are discussed. Data on the increasing frequency of C. auris infections and rapid dissemination of the fungus from the regions of origin - southern Asia, eastern Asia, southern Africa and southern America - towards different regions of all continents except Antarctica, especially after 2016, are presented. Three different clades are encountered in Great Britain, all four clades - in the USA. South Asian clade is currently present in Russia: the introduction was associated with labor migration from Middle Asia. The necessity of C. auris surveillance, essential for the establishment of sources and routes of transmission and dissemination of different clades is emphasized. A window of possibilities is still present to prevent further spread of the fungus with the ability to cause outbreaks of hospital infections including intensive care departments. Rapid implementation of preventive measures during the pandemic of COVID-19 are needed taking into account introduction of fungus in new countries and clinics, as well as increased frequency of C. auris infections in some hospitals for patients infected with SARS-CoV-2 virus.Copyright © 2021, Interregional Association for Clinical Microbiology and Antimicrobial Chemotherapy. All rights reserved.

A Review on Candida Auris, an Emerging Drug-resistant Fungal Pathogen.

Candida auris, a multidrug-resistant yeast, can cause primary or secondary infections in a wide range of patients, including those diagnosed with the new coronavirus to even healthy individuals. The fungus has been reported in less than a decade on all six continents and in more than 45 countries. Ease of distribution, long shelf life, and resistance to several antifungal drugs have raised concerns about the prevention and management of patients with C. auris infection. Recent reports indicate serious challenges in identifying, understanding the mechanism of drug resistance, and preventing mortality from the infection with this microorganism. Given the prevalence of COVID-19 infection, it is important to identify patients colonized with C. auris correctly and at the early stages, to control and prevent a possible outbreak. In this article, the widespread occurrence of infections due to C. auris in the world and Iran, its clinical manifestations, risk factors, pathogenic mechanisms, diagnostic enhancements and challenges, drug resistance, treatment options, prevention, and control as well as concomitant C. auris infections in patients with COVID-19 virus, are reviewed.Copyright © 2022 Isfahan University of Medical Sciences(IUMS). All rights reserved.

Candida auris Infections in COVID-19 Patients: A Review.

An increase in the incidence of invasive fungal infection, which can lead to serious complications and death, has been detected in some patients who had Coronavirus disease-2019 (COVID-19). Since the beginning of the COVID-19 pandemic, fungal infections increase the risk of mortality in long-term hospitalized COVID-19 patients. C. auris has emerged as a multidrug-resistant fungal pathogen isolated from healthcare-associated infections globally. Studies have reported an increase in C. auris isolation in COVID-19 patients who developed candidemia. They stated that C. auris is the most isolated Candida species in blood cultures since the beginning of the SARSCoV-2 pandemic, replacing other Candida species. In the studies included in this study, the mean incidance of C. auris was found to be as 22.7% (74/325) in COVID-19 patients with suspected fungal infection. The aim of our study is to evaluate the literature published so far in Turkiye and in the world regarding the coexistence of C. auris and COVID-19, which was reported as an "immediate threat" by the Centers for Disease Control and Prevention (CDC). However, there is not enough information about the effect of C. auris coinfection on mortality and whether it is an indicator of the severity of COVID-19 infection. Well-designed and careful epidemiological studies are needed to define the true burden of invasive candidiasis in COVID-19 patients.Copyright © 2023 Bilimsel Tip Yayinevi. All rights reserved.

COVID-19 pandemic and the evolving epidemiology of Candidemia: A topic of concern!!!

Candidemia is the most common recorded invasive fungal infection worldwide. During the last couple of years, the world has been struggling with the COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV-2), during which an increase in the incidence of candidemia and Candida auris cases were reported by several researchers. This study aimed to address how the entire landscape evolved during the downslide of the COVID-19 pandemic over the study period that spanned five years, including the pre-pandemic, peak, and waning of the COVID-19 pandemic. This retrospective observational study was conducted on a cohort of 1450 tertiary care cases in a University hospital in Jaipur, India, from July, 2017 to November, 2021. During the study period, all blood cultures of the suspected sepsis cases were screened for candidemia. Identification and antifungal susceptibility testing of Candida isolates were carried out using the standard assays. A consistent increase in the prevalence of candidemia has been observed during the current study period. Despite this, the prevalence of Non albicans Candida has remained almost steady. A sharp increase in C. auris candidemia during the COVID-19 pandemic was observed. The waning of the COVID-19 pandemic has brought the epidemiology of candidemia back to the pre-pandemic times, and C. tropicalis has become the predominant clinical isolate again. There is a slight fall in resistance to fluconazole. Echinocandins, which is considered as a remedy till few years back, has also showed first signs of emerging resistance in patients attending to Mahatma Gandhi University of Medical Sciences & Technology (MGUMST), Jaipur, Rajasthan, India. Due to the extreme overlapping of the associated disease/ risk factors observed between COVID-19 and candidemia, these two disease entities have definitely influenced the epidemiology of each other's. However, how the landscape will evolve in the aftermath of the COVID-19 pandemic is yet to be detected. © 2022, Egyptian Association for Medical Mycologists (EAMM). All rights reserved.

An Investigation into the Presence of Pathogens on Inanimate Surfaces in the Hospital Environment

Background The hospital environment is understood to play an important role in the transmission of nosocomial pathogens, with inanimate surfaces facilitating pathogen movement and persistence in the environment. The majority of studies of surface contamination have been carried out in outbreak conditions or on high-dependency wards. Current surface cleaning guidance only requires surfaces to be visually clean. Microbiological standards for cleanliness have been proposed however they are not widely adopted and little implementation guidance is available. Evidence-based surface sampling protocols are required for the transmission risk surfaces pose to be adequately quantified and addressed. Methods Environmental surface samples will be collected in a number of in- and outpatient settings staff and public areas, such as waiting rooms. This will be done before and after cleaning. Pathogens associated with nosocomial infection (e.g., ESKAPE pathogens Clostridioides difficile and Candida auris) will be identified through culture methods and MALDI-ToF mass spectrometry. Antimicrobial susceptibility profiles of isolates will be determined following EUCAST protocols. Realtime PCR will be utilized to identify viral pathogens (including norovirus adenovirus influenza and SARS-CoV-2) present. Following this samples will be collected for community composition sequencing allowing for non-culturable microorganisms to be identified. Whole genome sequencing will be performed on any pathogens of interest isolated during this investigation. Results and Conclusion Fewer microorganisms are expected to be isolated after cleaning than prior and samples from inpatient environments will have higher proportions of pathogens. The hospital microbiome has rarely been investigated outside of outbreak conditions. This study presents a novel, systematic approach to assess the microorganisms present in the hospital environment and how they are impacted by current cleaning measures. This will build a comprehensive picture of the hospital microflora and provide an evidence base for the development of surface sampling protocols helping inform clinical risk assessments and subsequently improving patient outcomes.

Phenotypic and genotypic characterization of Candida auris, an emerging pathogen isolated from blood

Introduction: Candida auris has been reported from various health care settings and has recently gained importance because of its intrinsic resistance to many classes of antifungal agents and to disinfection. The outbreak potential and high mortality associated with Candida auris infection reinforces the need for speciation. Routine conventional methods are cumbersome and automated systems are unable to confirm up to species level. Materials and Methods: Candida auris isolates from consecutive non-repetitive blood cultures over a 1-year period were speciated based on phenotypic, physiological and biochemical tests and VITEK. Molecular confirmation was done by PCR-RFLP and MALDI-TOF. Anti- fungal susceptibility test was performed according to CLSI guidelines (2021), using suitable controls. Virulence factors such as production of Hemolysin, Phospholipase, Esterase and Bio-film production were demonstrated. RT-PCR was used to screen the COVID-19 status using SD-Biosensor kit. Baseline data and clinical history were collected and analysed. Results: Of 3632 blood cultures (0.77%), 28 Candida sp. were isolated including 9 Candida auris, (9/28, 32.14%). Of these 8 were from COVID-19 positive patients (88.89%), while 1 was from COVID-19 negative patient (11.11%). Two patients survived, while the remaining 7 patients succumbed to the disease. Conclusion: The increasing incidence of Candidiasis especially during the COVID-19 pandemic has raised the concern for early speciation. Through multi-modal strategies such as quick and correct identification, active surveillance, guided reporting, stringent infection control measures and correct use of anti-fungals through proper susceptibility testing, we can prevent the occurrence and spread of new Candida auris cases in the future.

Invasive fungal infections in COVID-19 patients from Pakistan

Objective: The objective of this study is to report the frequency and clinical characteristic of IFI in COVID-19 patients. Method(s): This observational study was conducted in Karachi, Pakistan from March 2020-April 2021. Patients with COVID-19 associated aspergillosis (CAPA) were diagnosed using ECMM/ISHAM criteria modified to include tracheal aspirate culture and/or Galactomannan Index (GMI) >4.5 in the possible CAPA category. COVID-19 associated candidemia (CAC) was defined by isolation of Candida species from blood cultures. COVID-19 associated mucormycosis (CAM) was defined as updated EORTC/MSG criteria with inclusion of COVID-19 as host factor. Pneumocystis jirovecii pneumonia (PJP) was defined by consistent clinical and radiological features and PCR positivity. Result(s): During the study period a total of 123 (3.3%) IFI in 3506 hospitalized COVID-19 patients were identified. This included 78 (2.2%) CAPA patients (42 probable;36 possible), 29 (0.8%) CAC (5 C. auris;24 non-C. auris), 10 (0.3%) CAM (7 pulmonary;3 rhinocerebral), 3 (0.08%) PJP and three (0.08%) cases of rare invasive fungal infections (2 C. neoformans;1 Trichosporon asahii). Outcome data was available on 117/123 patients. Of these 117 patients, 78 expired (66.7%). These include 52/74 (70%) CAPA patients, 17/27 (63%) CAC patients, 7/10 (70%) CAM patients and 2/3 (67%) PJP patients. Conclusion(s): We report a rate of 3.3% IFI amongst hospitalized COVID-19 patients at our center. We consider this rate to be an underestimate due to less bronchoscopic procedures and inclusion of only candidemia cases. We also report higher mortality rate with IFI in our patients than global data probably due to delayed diagnosis, co-infections and limited therapeutic options.

Candida auris as an Emergent Public Health Problem: A Current Update on European Outbreaks and Cases.

Candida auris is considered to be an emerging fungal pathogen and is related to high mortality rates, persistent candidemia, inconsistencies in susceptibility testing results and misidentification by available commercial identification systems. Multidrug-resistant (MDR) and pandrug-resistant (PDR) strains are increasingly detected. In Europe, hospital outbreaks caused by C. auris have been reported in the United Kingdom (UK), Italy and Spain; however, several cases have been sporadically detected in all European countries. C. auris is difficult to control despite enhanced control measures due to its ability to survive for a long time in environments and colonize patients for prolonged periods. An adequate laboratory diagnostic capacity and national surveillance are fundamental to rapidly detect new C. auris cases and to apply the correct measures to circumscribe them and prevent their spread. Our narrative review aims to highlight the primary C. auris outbreaks and case reports that have occurred in Europe.

Candida auris and COVID-19: A health threatening combination.

Since its first emergence in December 2019, due to its fast distribution throughout the world, SARS-COV-2 become a global concern. With the extremely increased number of hospitalized patients, this situation provided a potential basis for the transmission of nosocomial infections. Candida auris is a multidrug-resistant pathogen with improved transmission dynamics and resistance traits. During the worldwide spread of COVID-19, cases or outbreaks of C. auris colonization or infection have been reported. Resistance to antifungal drugs has been observed in the causative agents of the majority of such cases. The focus in this review is on COVID-19-associated C. auris infections (case studies/outbreaks) and the pandemic's potential effect on antifungal drug resistance.

Candida auris Discovery through Community Wastewater Surveillance during Healthcare Outbreak, Nevada, USA, 2022.

Candida auris transmission is steadily increasing across the United States. We report culture-based detection of C. auris in wastewater and the epidemiologic link between isolated strains and southern Nevada, USA, hospitals within the sampled sewershed. Our results illustrate the potential of wastewater surveillance for containing C. auris.

Increasing Number of Cases Due to Candida auris in North Italy, July 2019-December 2022.

Candida auris is an emerging fungus that represents a serious health threat globally. In Italy, the first case was detected in July 2019. Then, one case was reported to the Ministry of Health (MoH) on January 2020. Nine months later, a huge number of cases were reported in northern Italy. Overall, 361 cases were detected in 17 healthcare facilities between July 2019 and December 2022 in the Liguria, Piedmont, Emilia-Romagna, and Veneto regions, including 146 (40.4%) deaths. The majority of cases (91.8%) were considered as colonised. Only one had a history of travel abroad. Microbiological data on seven isolates showed that all but one strain (85.7%) were resistant to fluconazole. All the environmental samples tested negative. Weekly screening of contacts was performed by the healthcare facilities. Infection prevention and control (IPC) measures were applied locally. The MoH nominated a National Reference Laboratory to characterise C. auris isolates and store the strains. In 2021, Italy posted two messages through the Epidemic Intelligence Information System (EPIS) to inform on the cases. On February 2022, a rapid risk assessment indicated a high risk for further spread within Italy, but a low risk of spread to other countries.

The first case of clade I Candida auris candidemia in a patient with COVID-19 in Japan.

Candida auris is a health hazard because of its antifungal resistance and the potential to cause healthcare-associated outbreaks. To our knowledge, no previous cases of candidemia caused by C. auris have been reported in Japan. Herein, we report the first known case of clade I C. auris candidemia in a Japanese man with coronavirus disease 2019 (COVID-19) infection who was medically evacuated from the Philippines. A 71-year-old Japanese man traveled to Cebu Island in the Philippines 5 months before admission to our hospital. He contracted severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the Philippines and was admitted to the intensive care unit (ICU) in a local hospital. During his medical evacuation, we implemented precautions given his history of COVID-19 and pneumonia caused by multi-drug-resistant Acinetobacter baumannii complex. His blood culture revealed that C. auris infection was treated with antifungal agents but he did not survive. No evidence of nosocomial transmission was found among other patients in the ICU. This case study determines that accurate detection of C. auris, appropriate antifungal agent selection, precautions, and patient isolation are crucial to prevent nosocomial outbreaks, especially in patients with a history of multidrug-resistant organism (MDRO) colonization or international hospitalization. Medical professionals should recognize the risk of MDROs in international medical evacuation settings, considering the recent resumption of cross-border travel after the COVID-19 pandemic.

Emergence of Clonally-Related South Asian Clade I Clinical Isolates of Candida auris in a Greek COVID-19 Intensive Care Unit.

Candida auris has recently emerged as a multidrug-resistant yeast implicated in various healthcare-associated invasive infections and hospital outbreaks. In the current study, we report the first five intensive care unit (ICU) cases affected by C. auris isolates in Greece, during October 2020-January 2022. The ICU of the hospital was converted to a COVID-19 unit on 25 February 2021, during the third wave of COVID-19 in Greece. Identification of the isolates was confirmed by Matrix Assisted Laser Desorption Ionization Time of Flight mass spectroscopy (MALDI-TOF]. Antifungal susceptibility testing was performed by the EUCAST broth microdilution method. Based on the tentative CDC MIC breakpoints, all five C. auris isolates were resistant to fluconazole (≥32 µg/mL), while three of them exhibited resistance to amphotericin B (≥2 µg/mL). The environmental screening also revealed the dissemination of C. auris in the ICU. Molecular characterization of C. auris clinical and environmental isolates was performed by MultiLocus Sequence Typing (MLST) of a set of four genetic loci, namely ITS, D1/D2, RPB1 and RPB2, encoding for the internal transcribed spacer region (ITS) of the ribosomal subunit, the large ribosomal subunit region and the RNA polymerase II largest subunit, respectively. MLST analysis showed that all isolates possessed identical sequences in the four genetic loci and clustered with the South Asian clade I strains. Additionally, PCR amplification and sequencing of the CJJ09_001802 genetic locus, encoding for the "nucleolar protein 58" that contains clade-specific repeats was performed. Sanger sequence analysis of the TCCTTCTTC repeats within CJJ09_001802 locus also assigned the C. auris isolates to the South Asian clade I. Our study confirms that C. auris is an emerging yeast pathogen in our region, especially in the setting of the ongoing COVID-19 worldwide pandemic. Adherence to strict infection control is needed to restrain further spread of the pathogen.

Colonized patients by Candida auris: Third and largest outbreak in Brazil and impact of biofilm formation.

Objective: To describe the clinical-epidemiological features of patients colonized by Candida auris in the largest outbreak in Brazil and to show the biofilm formation capacity of yeast strains. Methods: Clinical yeasts suspected of C. auris isolated from urine and surveillance samples were seeded on chromogenic media at 30°C and Sabouraud agar at 42°C. matrix-assisted laser desorption/ionization-time of flight mass spectometry was used for reliable identification. After proteomic confirmation, the genomic approach and culture on Chromagar Candida Plus media were carried out. Biofilm formation was investigated based on metabolic activity, and the clinical-epidemiological profile of patients was described. Results: A total of 11 C. auris clinical yeasts from nine patients were identified between the end of December 2021 and March 2022. Two clinical yeasts were isolates from urine and nine clinical yeasts were isolates from axillary and inguinal surveillance swabs. No case is related to previous Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, all the yeasts showed a high ability of biofilm formation. Conclusion: C. auris requires great vigilance as its high capacity to colonize and form biofilms contributes to its dissemination. The rapid and precise identification of this species is essential for the management, control, and prevention of infections.

Protective Efficacy of Anti-Hyr1p Monoclonal Antibody against Systemic Candidiasis Due to Multi-Drug-Resistant Candida auris.

Candida auris is a multi-drug-resistant fungal pathogen that can survive outside the host and can easily spread and colonize the healthcare environment, medical devices, and human skin. C. auris causes serious life-threatening infections (up to 60% mortality) in immunosuppressed patients staying in such contaminated healthcare facilities. Some isolates of C. auris are resistant to virtually all clinically available antifungal drugs. Therefore, alternative therapeutic approaches are urgently needed. Using in silico protein modeling and analysis, we identified a highly immunogenic and surface-exposed epitope that is conserved between C. albicans hyphal-regulated protein (Cal-Hyr1p) and Hyr1p/Iff-like proteins in C. auris (Cau-HILp). We generated monoclonal antibodies (MAb) against this Cal-Hyr1p epitope, which recognized several clinical isolates of C. auris representing all four clades. An anti-Hyr1p MAb prevented biofilm formation and enhanced opsonophagocytic killing of C. auris by macrophages. When tested for in vivo efficacy, anti-Hyr1p MAb protected 55% of mice against lethal systemic C. auris infection and showed significantly less fungal burden. Our study is highly clinically relevant and provides an effective alternative therapeutic option to treat infections due to MDR C. auris.

The Impact of the COVID-19 Pandemic on the Prevalence of Multidrug-resistant Organisms in Veterans Affairs Nursing Homes

Background. Multidrug-resistant organisms (MDRO) in long-term care facilities are prevalent and pose a major health concern for their residents. During the COVID-19 pandemic, infection control measures were justifiably heightened in every aspect of health care, including nursing homes. There are reports depicting decreasing prevalence of MDRO in hospital settings during the pandemic. We compared the prevalence of MDRO in our facility's nursing homes in the two-year period before vs. the two years of the pandemic. Methods. Northport Veterans Affairs Medical Center provides long-term nursing home care structured as community living centers including mental health and hospice care;a 139 total bed capacity. A retrospective review of culture data collected by infection control preventionists comparing the prevalence of MDROs between 1 March 2018 to 28 February 2022 was performed. Data included: Nasopharyngeal MRSA swabs, urine, wound, blood, sputum cultures, C. difficile toxin and PCR assays. MDRO included ESBL E. coli, K. pneumoniae, P. mirabilis, MDR Pseudomonas spp (resistance to 2/3 antibiotics: cefepime/piperacillin-tazobactam/ciprofloxacin), carbapenem-resistant Pseudomonas spp, and vancomycin-resistant Enterococcus spp. Results. There were 75209 bed days of care from 1 March 2018 to 28 February 2020 vs. 77531 from 1 March 2020 to 28 February 2022. The MRSA rate per 1000 patient days decreased from 4.98 pre-COVID to 2.70 during-COVID, P < 0.001. Similarly, there was a decrease in C. difficile 0.69 vs. 0.13, P< 0.001, ESBL E. coli 0.53 vs. 0.51, P< 0.001 and S. maltophilia (no cases during COVID). There was an increase in ESBL K. pneumoniae 0.51 vs. 0.63, P< 0.001, MDR Pseudomonas 0.05 vs. 0.49, P< 0.001, carbapenem-resistant Pseudomonas 0.026 vs. 0.077, P< 0.001 and VRE 0.22 vs. 0.31, P< 0.001. There were no Candida auris or Acinetobacter spp detected in the study period. MDRO occurrences before and during COVID-19 pandemic Conclusion. While increased awareness and implementation of infection control measures during the years of the COVID-19 pandemic led to decrease in certain infections in our nursing homes, like C. difficile, a surprising uptick in ESBL K. pneumoniae and MDR Pseudomonas was noted. This is a concerning trend that merits further study to identify molecular factors and increase stewardship efforts in diligent use of carbapenems.

Standing up FungiNet: Genomic epidemiology and surveillance of fungal diseases

Objectives: With the advent of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing, the public health landscape for genomic epidemiology and surveillance has transformed for a variety of pathogens. For fungal diseases, the U. S. Centers for Disease Control and Prevention (CDC) is working with global partners to stand up FungiNet, a network that aims to equip scientists with laboratory, bioinformatics, and informatics resources to harness genomic data. FungiNet partners will use genomic and epidemiologic data to detect outbreaks, identify introductions, and characterize transmission of fungal infections. In 2022, FungiNet aims to onboard nine state and local health departments in the United States and two global partners, the Instituto Nacional de Salud in Colombia and the National Institute for Communicable Diseases in South Africa, with a focus on Candida auris. Method(s): To streamline the onboarding process, CDC generated standardized operating procedures (SOPs) specific to C. auris. For DNA extraction, SOPs were created for workflows using the Zymo Research Quick-DNA TM (ZR) Fungal/Bacterial Miniprep, Qiagen Dneasy Blood and Tissue, and Epicentre (Illumina) MasterPure Yeast DNA Purification kits. For library preparation and Illumina sequencing, PulseNet methods used for foodborne pathogens were validated for C. auris. For NCBI data submissions, required data elements were defined. For SNP and phylogenetic analyses, the bioinformatics workflow My-coSNP was adapted to use Nextflow software and the Terra platform. For visualization with epidemiologic data, guidance documents and tutorials for Microreact were created. Finally, for data reporting, processes are being designed in REDCap and in laboratory information management systems to rapidly share genomic-related data. Result(s): To date, 11 partners have committed to building capacity for C. auris genomic sequencing and analysis as a FungiNet partner. Of these, seven have validated methods for DNA extraction, and nine have generated high-quality sequencing data. Only one partner has installed and locally run MycoSNP, and none have submitted raw sequence data to NCBI. Conclusion(s): Currently, 11 FungiNet partners are working to onboard C. auris genomic sequencing and bioinformatics analysis in 2022. This process is complex, requiring several laboratories, bioinformatics, and informatics workflows. For many partners, bioinformatics analysisand NCBIsubmission are themost challenging activities with the installationof MycoSNPand the ability to batch upload data to NCBI as the main barriers. Next steps will focus on the validation of informatics methods to link genomic and epidemiologic data.