Last data update: May 06, 2024. (Total: 46732 publications since 2009)
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The National Wastewater Surveillance System (NWSS): From inception to widespread coverage, 2020-2022, United States
Adams C , Bias M , Welsh RM , Webb J , Reese H , Delgado S , Person J , West R , Shin S , Kirby A . Sci Total Environ 2024 171566 Wastewater surveillance is a valuable tool that can be used to track infectious diseases in a community. In September 2020, the Centers for Disease Control and Prevention (CDC) established the National Wastewater Surveillance System (NWSS) to coordinate and build the nation's capacity to detect and quantify concentrations of SARS-CoV-2 RNA in U.S. wastewater. This is the first surveillance summary of NWSS, covering September 1, 2020 to December 31, 2022. Through partnerships with state, tribal, local, and territorial health departments, NWSS became a national surveillance platform that can be readily expanded and adapted to meet changing public health needs. Beginning with 209 sampling sites in September 2020, NWSS rapidly expanded to >1500 sites by December 2022, covering ≈47 % of the U.S. population. As of December 2022, >152,000 unique wastewater samples have been collected by NWSS partners, primarily from wastewater treatment plants (WWTPs). WWTPs participating in NWSS tend to be larger than the average U.S. WWTP and serve more populated communities. In December 2022, ≈8 % of the nearly 16,000 U.S. WWTPs were participating in NWSS. NWSS partners used a variety of methods for sampling and testing wastewater samples; however, progress is being made to standardize these methods. In July 2021, NWSS partners started submitting SARS-CoV-2 genome sequencing data to NWSS. In October 2022, NWSS expanded to monkeypox virus testing, with plans to include additional infectious disease targets in the future. Through the rapid implementation and expansion of NWSS, important lessons have been learned. Wastewater surveillance programs should consider both surge and long-term capacities when developing an implementation plan, and early standardization of sampling and testing methods is important to facilitate data comparisons across sites. NWSS has proven to be a flexible and sustainable surveillance system that will continue to be a useful complement to case-based surveillance for guiding public health action. |
Finding Candida auris in public metagenomic repositories
Mario-Vasquez JE , Bagal UR , Lowe E , Morgulis A , Phan J , Sexton DJ , Shiryev S , Slatkevičius R , Welsh R , Litvintseva AP , Blumberg M , Agarwala R , Chow NA . PLoS One 2024 19 (1) e0291406 Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative effort between the U.S. Centers for Disease Control and Prevention, the National Center for Biotechnology Information, and GridRepublic (a volunteer computing platform) to identify C. auris sequences in publicly available metagenomic datasets. We developed the MetaNISH pipeline that uses SRPRISM to align sequences to a set of reference genomes and computes a score for each reference genome. We used MetaNISH to scan ~300,000 SRA metagenomic runs from 2010 onwards and identified five datasets containing C. auris reads. Finally, GridRepublic has implemented a prospective C. auris molecular monitoring system using MetaNISH and volunteer computing. |
Early detection and surveillance of the SARS-CoV-2 variant BA.2.86 - Worldwide, July-October 2023
Lambrou AS , South E , Ballou ES , Paden CR , Fuller JA , Bart SM , Butryn DM , Novak RT , Browning SD , Kirby AE , Welsh RM , Cornforth DM , MacCannell DR , Friedman CR , Thornburg NJ , Hall AJ , Hughes LJ , Mahon BE , Daskalakis DC , Shah ND , Jackson BR , Kirking HL . MMWR Morb Mortal Wkly Rep 2023 72 (43) 1162-1167 Early detection of emerging SARS-CoV-2 variants is critical to guiding rapid risk assessments, providing clear and timely communication messages, and coordinating public health action. CDC identifies and monitors novel SARS-CoV-2 variants through diverse surveillance approaches, including genomic, wastewater, traveler-based, and digital public health surveillance (e.g., global data repositories, news, and social media). The SARS-CoV-2 variant BA.2.86 was first sequenced in Israel and reported on August 13, 2023. The first U.S. COVID-19 case caused by this variant was reported on August 17, 2023, after a patient received testing for SARS-CoV-2 at a health care facility on August 3. In the following month, eight additional U.S. states detected BA.2.86 across various surveillance systems, including specimens from health care settings, wastewater surveillance, and traveler-based genomic surveillance. As of October 23, 2023, sequences have been reported from at least 32 countries. Continued variant tracking and further evidence are needed to evaluate the full public health impact of BA.2.86. Timely genomic sequence submissions to global public databases aided early detection of BA.2.86 despite the decline in the number of specimens being sequenced during the past year. This report describes how multicomponent surveillance and genomic sequencing were used in real time to track the emergence and transmission of the BA.2.86 variant. This surveillance approach provides valuable information regarding implementing and sustaining comprehensive surveillance not only for novel SARS-CoV-2 variants but also for future pathogen threats. |
Improving reporting standards for polygenic scores in risk prediction studies (preprint)
Wand H , Lambert SA , Tamburro C , Iacocca MA , O'Sullivan JW , Sillari C , Kullo IJ , Rowley R , Dron JS , Brockman D , Venner E , McCarthy MI , Antoniou AC , Easton DF , Hegele RA , Khera AV , Chatterjee N , Kooperberg C , Edwards K , Vlessis K , Kinnear K , Danesh JN , Parkinson H , Ramos EM , Roberts MC , Ormond KE , Khoury MJ , Janssens Acjw , Goddard KAB , Kraft P , MacArthur JAL , Inouye M , Wojcik GL . medRxiv 2020 2020.04.23.20077099 Polygenic risk scores (PRS), often aggregating the results from genome-wide association studies, can bridge the gap between the initial discovery efforts and clinical applications for disease risk estimation. However, there is remarkable heterogeneity in the reporting of these risk scores. This lack of adherence to reporting standards hinders the translation of PRS into clinical care. The ClinGen Complex Disease Working Group, in a collaboration with the Polygenic Score (PGS) Catalog, have updated the Genetic Risk Prediction (GRIPS) Reporting Statement to the current state of the field and to enable downstream utility. Drawing upon experts in epidemiology, statistics, disease-specific applications, implementation, and policy, this 22-item reporting framework defines the minimal information needed to interpret and evaluate a PRS, especially with respect to any downstream clinical applications. Items span detailed descriptions of the study population (recruitment method, key demographic and clinical characteristics, inclusion/exclusion criteria, and outcome definition), statistical methods for both PRS development and validation, and considerations for potential limitations of the published risk score and downstream clinical utility. Additionally, emphasis has been placed on data availability and transparency to facilitate reproducibility and benchmarking against other PRS, such as deposition in the publicly available PGS Catalog. By providing these criteria in a structured format that builds upon existing standards and ontologies, the use of this framework in publishing PRS will facilitate translation of PRS into clinical care and progress towards defining best practices.Summary In recent years, polygenic risk scores (PRS) have increasingly been used to capture the genome-wide liability underlying many human traits and diseases, hoping to better inform an individual’s genetic risk. However, a lack of adherence to existing reporting standards has hindered the translation of this important tool into clinical and public health practice; in particular, details necessary for benchmarking and reproducibility are underreported. To address this gap, the ClinGen Complex Disease Working Group and Polygenic Score (PGS) Catalog have updated the Genetic Risk Prediction (GRIPS) Reporting Statement into the 22-item Polygenic Risk Score Reporting Statement (PRS-RS). This framework provides the minimal information expected of authors to promote the validity, transparency, and reproducibility of PRS by encouraging authors to detail the study population, statistical methods, and potential clinical utility of a published score. The widespread adoption of this framework will encourage rigorous methodological consideration and facilitate benchmarking to ensure high quality scores are translated into the clinic.Competing Interest StatementMIM is on the advisory panels Pfizer, Novo Nordisk, and Zoe Global; Honoraria: Merck, Pfizer, Novo Nordisk, and Eli Lilly; Research funding: Abbvie, Astra Zeneca, Boehringer Ingelheim, Eli Lilly, Janssen, Merck, Novo Nordisk, Pfizer, Roche, Sanofi Aventis, Servier & Takeda. As of June 2019, he is an employee of Genentech with stock and stock options in Roche. No other authors have competing interests to declare.Funding StatementClinGen is primarily funded by the National Human Genome Research Institute (NHGRI), through the following three grants: U41HG006834, U41HG009649, U41HG009650. ClinGen also receives support for content curation from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), through the following three grants: U24HD093483, U24HD093486, U24HD093487. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Additionally, the views expressed in this article are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health. Research reported in this publication was supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number U41HG007823 (EBI-NHGRI GWAS Catalog, PGS Catalog). In addition, we acknowledge funding from the European Molecular Biology Laboratory. Individuals were funded from the following sources: MIM was a Wellcome Investigator and an NIHR Senior Investigator with funding from NIDDK (U01-DK105535); Wellcome (090532, 098381, 106130, 203141, 212259). MI, SAL, and JD were supported by core funding from: the UK Medical Research Council (MR/L003120/1), the British Heart Foundation (RG/13/13/30194; RG/18/13/33946) and the National Institute for Health Research (Cambridge Biomedical Research Centre at the Cambridge University Hospitals NHS Foundation Trust). SAL is supported by a Canadian Institutes of Health Research postdoctoral fellowship (MFE-171279). JD holds a British Heart Foundation Personal Chair and a National Institute for Health Research Senior Investigator Award. This work was also supported by Health Data Research UK, which is funded by the UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation and Wellcome.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:N/AAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesN/A |
Chromosomal rearrangements and loss of subtelomeric adhesins linked to clade-specific phenotypes in Candida auris (preprint)
Muñoz JF , Welsh RM , Shea T , Batra D , Gade L , Litvintseva AP , Cuomo CA . bioRxiv 2019 754143 Candida auris is an emerging fungal pathogen of rising concern due to its increasing incidence, its ability to cause healthcare-associated outbreaks and antifungal resistance. Genomic analysis revealed that early cases of C. auris that were detected contemporaneously were geographically stratified into four major clades. Clade II, also termed East Asian clade, consists of the initial isolates described from cases of ear infection, is less frequently resistant to antifungal drugs and to date, the isolates from this group have not been associated with outbreaks. Here, we generate nearly complete genomes (“telomere-to-telomere”) of an isolate of this clade and of the more widespread Clade IV. By comparing these to genome assemblies of the other two clades, we find that the Clade II genome appears highly rearranged, with 2 inversions and 9 translocations resulting in a substantially different karyotype. In addition, large subtelomeric regions have been lost from 10 of 14 chromosome ends in the Clade II genomes. We find that shorter telomeres and genome instability might be a consequence of a naturally occurring loss-of-function mutation in DCC1 exclusively found in Clade II isolates, resulting in a hypermutator phenotype. We also determine that deleted subtelomeric regions might be linked to clade-specific adaptation as these regions are enriched in Hyr/Iff-like cell surface proteins, novel candidate cell surface proteins, and an ALS-like adhesin. The presence of these cell surface proteins in the clades responsible for global outbreaks causing invasive infections suggests an explanation for the different phenotypes observed between clades.IMPORTANCE Candida auris was unknown prior to 2009 and since then it has quickly spread around the world, causing outbreaks in healthcare facilities and representing a high fraction of candidemia cases in some regions. The emergence of C. auris is a major concern, since it is often multidrug-resistant, easily spread between patients, and causes invasive infections. While isolates from three global clades cause invasive infections, isolates from Clade II primarily cause ear infections and have not been implicated in outbreaks, though cases of Clade II infections have been reported on different continents. Here, we describe genetic differences between Clade II and Clades I, III and IV, including a loss-of-function mutation in a gene associated with telomere length maintenance and genome stability, and the loss of cell wall proteins involved in adhesion and biofilm formation, that may suggest an explanation for the lower virulence and potential for transmission of Clade II isolates. |
Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses (preprint)
Chow NA , Munoz JF , Gade L , Berkow EL , Li X , Welsh RM , Forsberg K , Lockhart SR , Adam R , Alanio A , Alastruey-Izquierdo A , Althawadi S , Arauz AB , Ben-Ami R , Bharat A , Calvo B , Desnos-Ollivier M , Escandon P , Gardam D , Gunturu R , Heath CH , Kurzai O , Martin R , Litvintseva AP , Cuomo CA . bioRxiv 2020 2020.01.06.896548 Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (Clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in over 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; Clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single healthcare facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 339 years; outbreak-causing clusters from Clades I, III, and IV originated 34-35 years ago. We observed high rates of antifungal resistance in Clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in Clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris.Importance In less than a decade, C. auris has emerged in healthcare settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology. |
Reporting Rates for VAERS Death Reports Following COVID-19 Vaccination, December 14, 2020-November 17, 2021 (preprint)
Day B , Menschik D , Thompson D , Jankosky C , Su J , Moro P , Zinderman C , Welsh K , Nair N . medRxiv 2022 07 Background: Despite widely available safety information for the COVID-19 vaccines, vaccine hesitancy remains a challenge. In some cases, vaccine hesitancy may be related to concerns about the number of reports of death to the Vaccine Adverse Event Reporting System (VAERS). Objective(s): To provide information and context about reports of death to VAERS following COVID-19 vaccination. Design(s): Descriptive study; reporting rates for VAERS death reports. Setting(s): United States; December 14, 2020, to November 17, 2021. Participant(s): COVID-19 vaccine recipients. Measurements: Reporting rates for death events per million persons vaccinated; adverse event counts; data mining signals of disproportionate reporting. Result(s): 9,201 death events were reported for COVID-19 vaccine recipients aged five years and older (or age unknown). Reporting rates for death events increased with increasing age, and males generally had higher reporting rates than females. For death events within seven days and 42 days of vaccination, respectively, observed reporting rates were lower than the expected all-cause death rates. Reporting rates for Ad26.COV2.S vaccine were generally higher than for mRNA COVID-19 vaccines, but still lower than the expected all-cause death rates. Reported adverse events were nonspecific or reflected the known leading causes of death. Limitation(s): VAERS data are subject to several limitations such as reporting bias (underreporting and stimulated reporting), missing or inaccurate information, and lack of a control group. Reported diagnoses, including deaths, are not causally verified diagnoses. Conclusion(s): Reporting rates for death events were lower than the expected all-cause mortality rates. Trends in reporting rates reflected known trends in background mortality rates. These findings do not suggest an association between vaccination and overall increased mortality. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. |
Reporting rates for VAERS death reports following COVID-19 vaccination, December 14, 2020-November 17, 2021
Day B , Menschik D , Thompson D , Jankosky C , Su J , Moro P , Zinderman C , Welsh K , Dimova RB , Nair N . Pharmacoepidemiol Drug Saf 2023 32 (7) 763-772 PURPOSE: Despite widely available safety information for the COVID-19 vaccines, vaccine hesitancy remains a challenge. In some cases, vaccine hesitancy may be related to concerns about the number of reports of death to the Vaccine Adverse Event Reporting System (VAERS). We aimed to provide information and context about reports of death to VAERS following COVID-19 vaccination. METHODS: This is a descriptive study evaluating reporting rates for VAERS death reports for COVID-19 vaccine recipients in the United States between December 14, 2020, and November 17, 2021. Reporting rates were calculated as death events per million persons vaccinated and compared to expected all-cause (background) death rates. RESULTS: 9,201 death events were reported for COVID-19 vaccine recipients aged five years and older (or age unknown). Reporting rates for death events increased with increasing age, and males generally had higher reporting rates than females. For death events within seven days and 42 days of vaccination, respectively, observed reporting rates were lower than the expected all-cause death rates. Reporting rates for Ad26.COV2.S vaccine were generally higher than for mRNA COVID-19 vaccines, but still lower than the expected all-cause death rates. Limitations of VAERS data include potential reporting bias, missing or inaccurate information, lack of a control group, and reported diagnoses, including deaths, are not causally verified diagnoses. CONCLUSIONS: Reporting rates for death events were lower than the all-cause death rates expected in the general population. Trends in reporting rates reflected known trends in background death rates. These findings do not suggest an association between vaccination and overall increased mortality. This article is protected by copyright. All rights reserved. |
Rapid implementation of high-frequency wastewater surveillance of SARS-CoV-2
Holst MM , Person J , Jennings W , Welsh RM , Focazio MJ , Bradley PM , Schill WB , Kirby AE , Marsh ZA . ACS ES T Water 2022 2 (11) 2201-2210 There have been over 507 million cases of COVID-19, the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in 6 million deaths globally. Wastewater surveillance has emerged as a valuable tool in understanding SARS-CoV-2 burden in communities. The National Wastewater Surveillance System (NWSS) partnered with the United States Geological Survey (USGS) to implement a high-frequency sampling program. This report describes basic surveillance and sampling statistics as well as a comparison of SARS-CoV-2 trends between high-frequency sampling 3-5 times per week, referred to as USGS samples, and routine sampling 1-2 times per week, referred to as NWSS samples. USGS samples provided a more nuanced impression of the changes in wastewater trends, which could be important in emergency response situations. Despite the rapid implementation time frame, USGS samples had similar data quality and testing turnaround times as NWSS samples. Ensuring there is a reliable sample collection and testing plan before an emergency arises will aid in the rapid implementation of a high-frequency sampling approach. High-frequency sampling requires a constant flow of information and supplies throughout sample collection, testing, analysis, and data sharing. High-frequency sampling may be a useful approach for increased resolution of disease trends in emergency response. © 2022 American Chemical Society. All rights reserved. |
MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris.
Bagal UR , Phan J , Welsh RM , Misas E , Wagner D , Gade L , Litvintseva AP , Cuomo CA , Chow NA . Methods Mol Biol 2022 2517 215-228 Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris. |
Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater - United States, November-December 2021.
Kirby AE , Welsh RM , Marsh ZA , Yu AT , Vugia DJ , Boehm AB , Wolfe MK , White BJ , Matzinger SR , Wheeler A , Bankers L , Andresen K , Salatas C , Gregory DA , Johnson MC , Trujillo M , Kannoly S , Smyth DS , Dennehy JJ , Sapoval N , Ensor K , Treangen T , Stadler LB , Hopkins L . MMWR Morb Mortal Wkly Rep 2022 71 (3) 103-105 The United States designated the B.1.1.529 (Omicron) variant of SARS-CoV-2 (the virus that causes COVID-19) a variant of concern on November 30, 2021, and the first U.S. Omicron COVID-19 case was reported on December 1 (1). By December 18, Omicron was estimated to account for 37.9% of U.S. COVID-19 cases.* Early warning systems, such as sewage (wastewater) surveillance,† can help track the spread of SARS-CoV-2 variants across communities (2). | | The National Wastewater Surveillance System (NWSS) comprises 43 health departments funded by CDC to provide data on presence of and trends in SARS-CoV-2 infections that are independent of clinical testing. In addition to total SARS-CoV-2 testing, some health departments track SARS-CoV-2 variants by detecting variant-associated mutations in wastewater. Health departments in four states (California, Colorado, New York, and Texas) were the first wastewater surveillance programs to detect evidence of Omicron in community wastewater. This report describes the initial detections in wastewater during November 21–December 16, 2021, and the interpretative framework for these types of data. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.§ |
Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.
Huang X , Welsh RM , Deming C , Proctor DM , Thomas PJ , Gussin GM , Huang SS , Kong HH , Bentz ML , Vallabhaneni S , Chiller T , Jackson BR , Forsberg K , Conlan S , Litvintseva AP , Segre JA . mSphere 2021 6 (4) e0028721 Candida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term care hospitals and nursing homes. Skin is the primary site of colonization for C. auris. To accelerate research studies, we developed microbiome sequencing protocols, including amplicon and metagenomic sequencing, directly from patient samples at health care facilities with ongoing C. auris outbreaks. We characterized the skin mycobiome with a database optimized to classify Candida species and C. auris to the clade level. While Malassezia species were the predominant skin-associated fungi, nursing home residents also harbored Candida species, including C. albicans, and C. parapsilosis. Amplicon sequencing was concordant with culturing studies to identify C. auris-colonized patients and provided further resolution that distinct clades of C. auris are colonizing facilities in New York and Illinois. Shotgun metagenomic sequencing from a clinical sample with a high fungal bioburden generated a skin-associated profile of the C. auris genome. Future larger scale clinical studies are warranted to more systematically investigate the effects of commensal microbes and patient risk factors on the colonization and transmission of C. auris. IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable. In this study, we developed microbiome sequencing protocols directly from surveillance samples, including amplicon and metagenomic sequencing, demonstrating concordance between sequencing results and culturing. |
Integrated genomic, epidemiologic investigation of Candida auris skin colonization in a skilled nursing facility.
Proctor DM , Dangana T , Sexton DJ , Fukuda C , Yelin RD , Stanley M , Bell PB , Baskaran S , Deming C , Chen Q , Conlan S , Park M , Welsh RM , Vallabhaneni S , Chiller T , Forsberg K , Black SR , Pacilli M , Kong HH , Lin MY , Schoeny ME , Litvintseva AP , Segre JA , Hayden MK . Nat Med 2021 27 (8) 1401-1409 Candida auris is a fungal pathogen of high concern due to its ability to cause healthcare-associated infections and outbreaks, its resistance to antimicrobials and disinfectants and its persistence on human skin and in the inanimate environment. To inform surveillance and future mitigation strategies, we defined the extent of skin colonization and explored the microbiome associated with C. auris colonization. We collected swab specimens and clinical data at three times points between January and April 2019 from 57 residents (up to ten body sites each) of a ventilator-capable skilled nursing facility with endemic C. auris and routine chlorhexidine gluconate (CHG) bathing. Integrating microbial-genomic and epidemiologic data revealed occult C. auris colonization of multiple body sites not targeted commonly for screening. High concentrations of CHG were associated with suppression of C. auris growth but not with deleterious perturbation of commensal microbes. Modeling human mycobiome dynamics provided insight into underlying alterations to the skin fungal community as a possible modifiable risk factor for acquisition and persistence of C. auris. Failure to detect the extensive, disparate niches of C. auris colonization may reduce the effectiveness of infection-prevention measures that target colonized residents, highlighting the importance of universal strategies to reduce C. auris transmission. |
Positive correlation between Candida auris skin-colonization burden and environmental contamination at a ventilator-capable skilled nursing facility in Chicago
Sexton DJ , Bentz ML , Welsh RM , Derado G , Furin W , Rose LJ , Noble-Wang J , Pacilli M , McPherson TD , Black S , Kemble SK , Herzegh O , Ahmad A , Forsberg K , Jackson B , Litvintseva AP . Clin Infect Dis 2021 73 (7) 1142-1148 BACKGROUND: Candida auris is an emerging multidrug-resistant yeast that contaminates healthcare environments causing healthcare-associated outbreaks. The mechanisms facilitating contamination are not established. METHODS: C. auris was quantified in residents' bilateral axillary/inguinal composite skin swabs and environmental samples during a point-prevalence survey at a ventilator-capable skilled-nursing facility (vSNF A) with documented high colonization prevalence. Environmental samples were collected from all doorknobs, windowsills and handrails of each bed in 12 rooms. C. auris concentrations were measured using culture and C. auris-specific qPCR. The relationship between C. auris concentrations in residents' swabs and associated environmental samples were evaluated using Kendall's tau-b (τb) correlation coefficient. RESULTS: C. auris was detected in 70 /100 tested environmental samples and 31/ 57 tested resident skin swabs. The mean C. auris concentration in skin swabs was 1.22 x 10 5 cells/mL by culture and 1.08 x 10 6 cells/mL by qPCR. C. auris was detected on all handrails of beds occupied by colonized residents, as well as 10/24 doorknobs and 9/12 windowsills. A positive correlation was identified between the concentrations of C. auris in skin swabs and associated handrail samples based on culture (τb = 0.54, p = 0.0004) and qPCR (τb = 0.66, p = 3.83e -6). Two uncolonized residents resided in beds contaminated with C. auris. CONCLUSIONS: Colonized residents can have high C. auris burdens on their skin, which was positively related with contamination of their surrounding healthcare environment. These findings underscore the importance of hand hygiene, transmission-based precautions, and particularly environmental disinfection in preventing spread in healthcare facilities. |
Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines
Welsh RM , Misas E , Forsberg K , Lyman M , Chow NA . J Fungi (Basel) 2021 7 (3) Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster C. auris surveillance networks moving forward. Laboratories conducting genomic surveillance need to be able to compare analyses from various national and international surveillance partners to ensure that results are mutually trusted and understood. Therefore, we established an empirical outbreak benchmark dataset consisting of 23 C. auris genomes to help validate comparisons of genomic analyses and facilitate communication among surveillance networks. Our outbreak benchmark dataset represents a polyclonal phylogeny with three subclades. The genomes in this dataset are from well-vetted studies that are supported by multiple lines of evidence, which demonstrate that the whole-genome sequencing data, phylogenetic tree, and epidemiological data are all in agreement. This C. auris benchmark set allows for standardized comparisons of phylogenomic pipelines, ultimately promoting effective C. auris collaborations. |
Clade-specific chromosomal rearrangements and loss of subtelomeric adhesins in Candida auris.
Muñoz JF , Welsh RM , Shea T , Batra D , Gade L , Howard D , Rowe LA , Meis JF , Litvintseva AP , Cuomo CA . Genetics 2021 218 (1) Candida auris is an emerging fungal pathogen of rising concern due to global spread, the ability to cause healthcare-associated outbreaks, and antifungal resistance. Genomic analyses revealed that early contemporaneously detected cases of C. auris were geographically stratified into four major clades. While Clades I, III, and IV are responsible for ongoing outbreaks of invasive and multidrug-resistant infections, Clade II, also termed the East Asian clade, consists primarily of cases of ear infection, is often susceptible to all antifungal drugs, and has not been associated with outbreaks. Here, we generate chromosome-level assemblies of twelve isolates representing the phylogenetic breadth of these four clades and the only isolate described to date from Clade V. This Clade V genome is highly syntenic with those of Clades I, III, and IV, although the sequence is highly divergent from the other clades. Clade II genomes appear highly rearranged, with translocations occurring near GC-poor regions, and large subtelomeric deletions in most chromosomes, resulting in a substantially different karyotype. Rearrangements and deletion lengths vary across Clade II isolates, including two from a single patient, supporting ongoing genome instability. Deleted subtelomeric regions are enriched in Hyr/Iff-like cell-surface proteins, novel candidate cell wall proteins, and an ALS-like adhesin. Cell wall proteins from these families and other drug-related genes show clade-specific signatures of selection in Clades I, III, and IV. Subtelomeric dynamics and the conservation of cell surface proteins in the clades responsible for global outbreaks causing invasive infections suggest an explanation for the different phenotypes observed between clades. |
Myopericarditis after vaccination, Vaccine Adverse Event Reporting System (VAERS), 1990-2018.
Su JR , McNeil MM , Welsh KJ , Marquez PL , Ng C , Yan M , Cano MV . Vaccine 2021 39 (5) 839-845 BACKGROUND: Myopericarditis after vaccination has been sporadically reported in the medical literature. Here, we present a thorough descriptive analysis of reports to a national passive vaccine safety surveillance system (VAERS) of myopericarditis after vaccines licensed for use in the United States. METHODS: We identified U.S. reports of myopericarditis received by VAERS during 1990-2018 that met a published case definition for myopericarditis or were physician-diagnosed. We stratified analysis by age group (<19, 19-49, ≥50 years), describing reports by serious/non-serious status, sex, time to symptom onset after vaccination, vaccine(s) administered, and exposure to other known causes of myopericarditis. We used Empirical Bayesian data mining to detect disproportionate reporting of myopericarditis after vaccination. RESULTS: VAERS received 620,195 reports during 1990-2018: 708 (0.1%) met the case definition or were physician-diagnosed as myopericarditis. Most (79%) myopericarditis reports described males; 69% were serious; 72% had symptom onset ≤ 2 weeks postvaccination. Overall, smallpox (59%) and anthrax (23%) vaccines were most commonly reported. By age, among persons aged < 19 years, Haemophilus influenzae type b (22, 22%) and hepatitis B (18, 18%); among persons aged 19-49 years smallpox (387, 79%); among persons aged ≥ 50 years inactivated influenza (31, 36%) and live attenuated zoster (19, 22%) vaccines were most commonly reported. The vaccines most commonly reported remained unchanged when excluding 138 reports describing other known causes of myopericarditis. Data mining revealed disproportionate reporting of myopericarditis only after smallpox vaccine. CONCLUSIONS: Despite the introduction of new vaccines over the years, myopericarditis remains rarely reported after vaccines licensed for use in the United States. In this analysis, myopericarditis was most commonly reported after smallpox vaccine, and less commonly after other vaccines. |
Early use of the palliative approach to improve patient outcomes in HIV disease: Insights and findings from the Care and Support Access (CASA) Study 2013-2019
Alexander CS , Raveis VH , Karus D , Carrero-Tagle M , Lee MC , Pappas G , Lockman K , Brotemarkle R , Memiah P , Mulasi I , Hossain BM , Welsh C , Henley Y , Piet L , N'Diaye S , Murray R , Haltiwanger D , Smith CR , Flynn C , Redfield R , Silva CL , Amoroso A , Selwyn P . Am J Hosp Palliat Care 2020 38 (4) 332-339 Young men of color who have sex with men (yMSM) living with human immunodeficiency virus (HIV) in syndemic environments have been difficult-to-retain in care resulting in their being at-risk for poor health outcomes despite availability of effective once-daily antiretroviral treatment (ART). Multiple methods have been implemented to improve outcomes for this cohort; none with sustainable results. Outpatient HIV staff themselves may be a contributing factor. We introduced multidisciplinary staff to the concept of using a palliative approach early (ePA) in outpatient HIV care management to enable them to consider the patient-level complexity of these young men. Young MSM (18-35 years of age) enrolled in and cared for at the intervention site of the Care and Support Access Study (CASA), completed serial surveys over 18 months. Patients' Global and Summary quality of life (QoL) increased during the study at the intervention site (IS) where staff learned about ePA, compared with patients attending the control site (CS) (p=.021 and p=.018, respectively). Using serial surveys of staff members, we found that in the era of HIV disease control, outpatient staff are stressed more by environmental factors than by patients' disease status seen historically in the HIV epidemic. A Community Advisory Panel of HIV stakeholders contributed to all phases of this study and altered language used in educational activities with staff members to describe the patient cohort. |
Evaluation of nine surface disinfectants against Candida auris using a quantitative disk carrier method: EPA SOP-MB-35
Sexton DJ , Welsh RM , Bentz ML , Forsberg K , Jackson B , Berkow EL , Litvintseva AP . Infect Control Hosp Epidemiol 2020 41 (10) 1-3 We tested 9 disinfectants against Candida auris using the quantitative disk carrier method EPA-MB-35-00: 5 products with hydrogen peroxide or alcohol-based chemistries were effective and 4 quaternary ammonium compound-based products were not. This work supported a FIFRA Section 18 emergency exemption granted by the US Environmental Protection Agency to expand disinfectant guidance for C. auris. |
Performance evaluation of culture-independent SYBR Green Candida auris qPCR diagnostics on anterior nares surveillance swabs
Georgacopoulos O , Nunnally NS , Le N , Lysen C , Welsh RM , Kordalewska M , Perlin DS , Berkow EL , Sexton DJ . J Clin Microbiol 2020 58 (9) Early identification of Candida auris is important for timely implementation of infection prevention and control actions. Here, we evaluated performance of the C. auris-specific SYBR Green qPCR assay on a panel of 70 anterior nares swabs. Enrichment broth culture was used as "gold standard". After performing a receiver operating curve (ROC) to optimize signal threshold, we found perfect agreement between culture and qPCR. Additionally, we found no indication of inhibitors in the anterior nares swabs. |
Tracing the Evolutionary History and Global Expansion of Candida auris Using Population Genomic Analyses.
Chow NA , Munoz JF , Gade L , Berkow EL , Li X , Welsh RM , Forsberg K , Lockhart SR , Adam R , Alanio A , Alastruey-Izquierdo A , Althawadi S , Arauz AB , Ben-Ami R , Bharat A , Calvo B , Desnos-Ollivier M , Escandon P , Gardam D , Gunturu R , Heath CH , Kurzai O , Martin R , Litvintseva AP , Cuomo CA . mBio 2020 11 (2) Candida auris has emerged globally as a multidrug-resistant yeast that can spread via nosocomial transmission. An initial phylogenetic study of isolates from Japan, India, Pakistan, South Africa, and Venezuela revealed four populations (clades I, II, III, and IV) corresponding to these geographic regions. Since this description, C. auris has been reported in more than 30 additional countries. To trace this global emergence, we compared the genomes of 304 C. auris isolates from 19 countries on six continents. We found that four predominant clades persist across wide geographic locations. We observed phylogeographic mixing in most clades; clade IV, with isolates mainly from South America, demonstrated the strongest phylogeographic substructure. C. auris isolates from two clades with opposite mating types were detected contemporaneously in a single health care facility in Kenya. We estimated a Bayesian molecular clock phylogeny and dated the origin of each clade within the last 360 years; outbreak-causing clusters from clades I, III, and IV originated 36 to 38 years ago. We observed high rates of antifungal resistance in clade I, including four isolates resistant to all three major classes of antifungals. Mutations that contribute to resistance varied between the clades, with Y132F in ERG11 as the most widespread mutation associated with azole resistance and S639P in FKS1 for echinocandin resistance. Copy number variants in ERG11 predominantly appeared in clade III and were associated with fluconazole resistance. These results provide a global context for the phylogeography, population structure, and mechanisms associated with antifungal resistance in C. auris IMPORTANCE In less than a decade, C. auris has emerged in health care settings worldwide; this species is capable of colonizing skin and causing outbreaks of invasive candidiasis. In contrast to other Candida species, C. auris is unique in its ability to spread via nosocomial transmission and its high rates of drug resistance. As part of the public health response, whole-genome sequencing has played a major role in characterizing transmission dynamics and detecting new C. auris introductions. Through a global collaboration, we assessed genome evolution of isolates of C. auris from 19 countries. Here, we described estimated timing of the expansion of each C. auris clade and of fluconazole resistance, characterized discrete phylogeographic population structure of each clade, and compared genome data to sensitivity measurements to describe how antifungal resistance mechanisms vary across the population. These efforts are critical for a sustained, robust public health response that effectively utilizes molecular epidemiology. |
Candida auris: A review of recommendations for detection and control in healthcare settings
Caceres DH , Forsberg K , Welsh RM , Sexton DJ , Lockhart SR , Jackson BR , Chiller T . J Fungi (Basel) 2019 5 (4) Candida auris is an emerging multidrug-resistant fungal pathogen. Since first reported in 2009, C. auris has caused healthcare outbreaks around the world, often involving high mortality. Identification of C. auris has been a major challenge as many common conventional laboratory methods cannot accurately detect it. Early detection and implementation of infection control practices can prevent its spread. The aim of this review is to describe recommendations for the detection and control of C. auris in healthcare settings. |
On the Origins of a Species: What Might Explain the Rise of Candida auris ?
Jackson BR , Chow N , Forsberg K , Litvintseva AP , Lockhart SR , Welsh R , Vallabhaneni S , Chiller T . J Fungi (Basel) 2019 5 (3) Candida auris is an emerging multidrug-resistant yeast first described in 2009 that has since caused healthcare-associated outbreaks of severe human infections around the world. In some hospitals, it has become a leading cause of invasive candidiasis. C. auris is markedly different from most other pathogenic Candida species in its genetics, antifungal resistance, and ability to spread between patients. The reasons why this fungus began spreading widely in the last decade remain a mystery. We examine available data on C. auris and related species, including genomic epidemiology, phenotypic characteristics, and sites of detection, to put forth hypotheses on its possible origins. C. auris has not been detected in the natural environment; related species have been detected in in plants, insects, and aquatic environments, as well as from human body sites. It can tolerate hypersaline environments and higher temperatures than most Candida species. We explore hypotheses about the pre-emergence niche of C. auris, whether in the environmental or human microbiome, and speculate on factors that might have led to its spread, including the possible roles of healthcare, antifungal use, and environmental changes, including human activities that might have expanded its presence in the environment or caused increased human contact. |
Insights into the Unique Nature of the East Asian Clade of the Emerging Pathogenic Yeast, Candida auris .
Welsh RM , Sexton DJ , Forsberg K , Vallabhaneni S , Litvintseva A . J Clin Microbiol 2019 57 (4) The emerging yeast Candida auris can be highly drug resistant, cause invasive infections, and large outbreaks. C. auris went from an unknown pathogen a decade ago to being reported in over thirty countries on six continents. C. auris consists of four discrete clades, based on where the first isolates of the clade were reported: South Asian (Clade I), East Asian (Clade II), African (Clade III), and South American (Clade IV). These have unique genetic and biochemical characteristics, which are important to understand and inform the global response to C. auris Clade II has been underrepresented in the literature despite being the first one discovered. In this issue of the Journal of Clinical Microbiology, Y. J. Kwon et al. (J Clin Microbiol 57:e01624-18, 2019, https://doi.org/10.1128/JCM.01624-18) describe the largest collection of clinical isolates from Clade II, which is also the longest running span of clinical cases, 20 years, from any single region to date. Clade II appears to have a propensity for the ear that is uncharacteristic of the other clades, which typically cause invasive infections and large-scale outbreaks. This study provides new information on an understudied lineage of C. auris and has important implications for future surveillance. |
Phenotypic switching in newly emerged multidrug-resistant pathogen Candida auris
Bentz ML , Sexton DJ , Welsh RM , Litvintseva AP . Med Mycol 2018 57 (5) 636-638 Candida auris is an emerging, multidrug-resistant yeast that can spread rapidly in healthcare settings. Phenotypic switching has been observed in other Candida species and can potentially interfere with correct identification. The aim of this study is to address misidentification of C. auris by describing alternate phenotypes after broth enrichment and subculturing on CHROMagar Candida. Each isolate displayed different frequencies of phenotypic switching, suggesting a strain to strain variability. Increased knowledge of the multiple phenotypes of C. auris increases the chance of isolating and identifying C. auris by reducing the risk of discarding false negative alternate colony morphologies. |
Direct detection of emergent fungal pathogen Candida auris in clinical skin swabs by SYBR Green qPCR assay
Sexton DJ , Kordalewska M , Bentz ML , Welsh RM , Perlin DS , Litvintseva AP . J Clin Microbiol 2018 56 (12) The recent emergence of the multidrug-resistant and pathogenic yeast Candida auris continues to cause public health concern worldwide. C. auris is alarming because it causes healthcare-associated outbreaks and can establish invasive infections with high mortality rates. Transmission between patients is facilitated by the ability of C. auris to persistently colonize multiple body sites, including the skin, and survive for weeks on surfaces in healthcare settings. Rapid identification of colonized patients is needed to implement timely infection control measures. Currently, CDC laboratories use an enrichment culture-based approach that can take up to two weeks to identify C. auris from composite swabs from the bilateral axillae and groin. A rapid SYBR Green qPCR assay that can identify C. auris in a single day was recently described. In this study, we developed the SYBR Green qPCR assay further by incorporating a DNA extraction procedure for skin swabs and by including an internal amplification control based on the distinguishable melt curve of a lambda DNA amplicon. The assay was evaluated using 103 clinical axilla/groin skin swab samples. Using the enrichment culture-based approach as a gold standard, we determined the SYBR Green C. auris qPCR has a sensitivity of 0.93 and specificity of 0.96. Overall, we found the SYBR Green C. auris qPCR assay can be successfully applied for rapid and accurate detection of C. auris in patient skin swabs, thereby increasing diagnostic options for this emerging pathogen. |
Challenges in identifying Candida auris in hospital clinical laboratories: a need for hospital and public health laboratory collaboration in rapid identification of an emerging pathogen
Durante AJ , Maloney MH , Leung VH , Razeq JH , Banach DB . Infect Control Hosp Epidemiol 2018 39 (8) 1-2 Candida auris is an emerging fungus that poses a considerable threat to US healthcare facilities and their patients. Patients exposed to C. auris can develop invasive infection, which can be fatal,Reference Lockhart, Etienne and Vallabhaneni 1 or can become colonized, which poses long-term transmission risks. Once introduced into a healthcare facility, C. auris can spread through contact with affected patients and contaminated surfaces.Reference Tsay, Welsh and Adams 2 The organism can persist in the environment,Reference Welsh, Bentz and Shams 3 and quaternary ammonium disinfectants demonstrate poor activity against it.Reference Cadnum, Shaikh, Piedrahita and Sankar 4 Candida auris is often multidrug-resistant,Reference Lockhart, Etienne and Vallabhaneni 1 , Reference Cadnum, Shaikh, Piedrahita and Sankar4 and its detection is challenging because it can be misidentified by some biochemically based identification methods. For example, the API 20 C (bioMerieux, Marcy-l’Etoile, France) can misidentify C. auris as C. sake or Rhodotorula glutinis, and the Vitek 2 (bioMerieux) can misidentify C. auris as C. haemulonii or C. duobushaemulonii.Reference Mizusawa, Miller and Green 5 Rapid and accurate C. auris detection would help hospitals to guide infection control activities intended to prevent the spread of the fungus within and between facilities and to properly plan antifungal treatment. We surveyed laboratories that serve Connecticut’s acute-care hospitals to assess their capability to identify C. auris. The information was collected to guide statewide hospital prevention efforts. |
Evaluation of a new T2 Magnetic Resonance assay for rapid detection of emergent fungal pathogen Candida auris on clinical skin swab samples
Sexton DJ , Bentz ML , Welsh RM , Litvintseva AP . Mycoses 2018 61 (10) 786-790 Candida auris is a multidrug-resistant pathogenic yeast whose recent emergence is of increasing public-health concern. C. auris can colonize multiple body sites, including patients' skin, and survive for weeks in the healthcare environment, facilitating patient-to-patient transmission and fueling healthcare-associated outbreaks. Rapid and accurate detection of C. auris colonization is essential for timely implementation of infection control measures and prevent transmission. Currently, axilla/groin composite swabs, used to assess colonization status, are processed using a culture-based method that is sensitive and specific but requires 14 days. This delay limits the opportunity to respond and highlights the need for a faster alternative. The culture-independent T2 Magnetic Resonance (T2MR) system is a rapid diagnostic platform shown to detect target pathogens of interest from unprocessed blood samples in <5 hours. In this study, a new C. auris-specific T2 assay was evaluated for screening of the skin surveillance samples. Inclusivity and limit of detection of the T2 C. auris assay were assessed with spiked samples in a representative skin flora background. The T2 C. auris assay recognized isolates from each of the 4 known clades of C. auris and consistently detected cells at 5 CFU/mL. Finally, 89 clinical axilla/groin swab samples were processed with the T2 C. auris assay. The culture-based diagnostic assay was used as a gold standard to determine performance statistics including sensitivity (0.89) and specificity (0.98). Overall, the T2 C. auris assay performed well as a rapid diagnostic and could help expedite the detection of C. auris in patient skin swabs. This article is protected by copyright. All rights reserved. |
Molecular epidemiology of Candida auris in Colombia reveals a highly-related, country-wide colonization with regional patterns in Amphotericin B resistance.
Escandon P , Chow NA , Caceres DH , Gade L , Berkow EL , Armstrong P , Rivera S , Misas E , Duarte C , Moulton-Meissner H , Welsh RM , Parra C , Pescador LA , Villalobos N , Salcedo S , Berrio I , Varon C , Espinosa-Bode A , Lockhart SR , Jackson BR , Litvintseva AP , Beltran M , Chiller TM . Clin Infect Dis 2018 68 (1) 15-21 Background: Candida auris is a multidrug-resistant yeast associated with hospital outbreaks worldwide. During 2015-2016, multiple outbreaks were reported in Colombia. We aimed to understand the extent of contamination in healthcare settings and to characterize the molecular epidemiology of C. auris in Colombia. Methods: We sampled patients, patient contacts, healthcare workers, and the environment in four hospitals with recent C. auris outbreaks. Using standardized protocols, people were swabbed at different body sites. Patient and procedure rooms were sectioned into four zones and surfaces were swabbed. We performed whole-genome sequencing (WGS) and antifungal susceptibility testing (AFST) on all isolates. Results: Seven (41%) of the 17 people swabbed were found to be colonized. C. auris was isolated from 37/322 (12%) environmental samples. These were collected from a variety of items in all four zones. WGS and AFST revealed that although isolates were similar throughout the country, isolates from the northern region were genetically distinct and more resistant to amphotericin B (AmB) than the isolates from central Colombia. Four novel non-synonymous mutations were found to be significantly associated with AmB resistance. Conclusions: Our results show that extensive C. auris contamination can occur and highlight the importance of adherence to appropriate infection control practices and disinfection strategies. Observed genetic diversity supports healthcare transmission and a recent expansion of C. auris within Colombia with divergent AmB susceptibility. |
Survival, persistence, and isolation of the emerging multidrug-resistant pathogenic yeast Candida auris on a plastic healthcare surface
Welsh RM , Bentz ML , Shams A , Houston H , Lyons A , Rose LJ , Litvintseva AP . J Clin Microbiol 2017 55 (10) 2996-3005 The emerging multidrug-resistant pathogenic yeast Candida auris represents a serious threat to global health. Unlike most other Candida species, this organism appears to be commonly transmitted within healthcare facilities and is capable of causing healthcare-associated outbreaks. To better understand the epidemiology of this emerging pathogen we investigated the ability of C. auris to persist on plastic surfaces common in healthcare settings and compared with that of Candida parapsilosis, a species known to colonize the skin and plastics. Specifically, we compiled comparative and quantitative data essential to understanding the vehicles of spread and the ability of both species to survive and persist on plastic surfaces under controlled conditions (25 degrees C & 57% relative humidity), such as those found in healthcare settings. When a test suspension of 104 cells was applied and dried on plastic surfaces, C. auris remained viable for at least 14 days and C. parapsilosis 28 days, as measured by colony forming units (CFU). However, survival measured by esterase activity was higher for C. auris than C. parapsilosis throughout the 28 day study. Given the notable length of time Candida survive and persist outside their host, we developed methods to more effectively culture C. auris from patients and their environment. Using our enrichment protocol, public health laboratories and researchers can now readily isolate C. auris from complex microbial communities (such as patient skin, nasopharynx, and stool) as well as environmental biofilms, in order to better understand and prevent C. auris colonization and transmission. |
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