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Ambrosio FJ, Scribner MR, Wright SM, Otieno JR, Doughty EL, Gorzalski A, Siao DD, Killian S, Hua C, Schneider E, Tran M, Varghese V, Libuit KG, Pandori M, Sevinsky JR, Hess D. TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization. Front Public Health 2023; 11:1198213. [PMID: 37593727 PMCID: PMC10428623 DOI: 10.3389/fpubh.2023.1198213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/04/2023] [Indexed: 08/19/2023] Open
Abstract
Introduction The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens. Methods TheiaEuk was designed using containerized components and written in the workflow description language (WDL) to facilitate deployment on the cloud-based open bioinformatics platform Terra. This species-agnostic workflow enables the analysis of fungal genomes without requiring coding, thereby reducing the entry barrier for laboratory scientists. To demonstrate the usefulness of this pipeline, an ongoing outbreak of C. auris in southern Nevada was investigated. We performed whole-genome sequence analysis of 752 new C. auris isolates from this outbreak. Furthermore, TheiaEuk was utilized to observe the accumulation of mutations in the FKS1 gene over the course of the outbreak, highlighting the utility of TheiaEuk as a monitor of emerging public health threats when combined with whole-genome sequencing surveillance of fungal pathogens. Results A primary result of this work is a curated fungal database containing 5,667 unique genomes representing 245 species. TheiaEuk also incorporates taxon-specific submodules for specific species, including clade-typing for Candida auris (C. auris). In addition, for several fungal species, it performs dynamic reference genome selection and variant calling, reporting mutations found in genes currently associated with antifungal resistance (FKS1, ERG11, FUR1). Using genome assemblies from the ATCC Mycology collection, the taxonomic identification module used by TheiaEuk correctly assigned genomes to the species level in 126/135 (93.3%) instances and to the genus level in 131/135 (97%) of instances, and provided zero false calls. Application of TheiaEuk to actual specimens obtained in the course of work at a local public health laboratory resulted in 13/15 (86.7%) correct calls at the species level, with 2/15 called at the genus level. It made zero incorrect calls. TheiaEuk accurately assessed clade type of Candida auris in 297/302 (98.3%) of instances. Discussion TheiaEuk demonstrated effectiveness in identifying fungal species from whole genome sequence. It further showed accuracy in both clade-typing of C. auris and in the identification of mutations known to associate with drug resistance in that organism.
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Affiliation(s)
| | | | | | | | | | | | | | - Steve Killian
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | - Chi Hua
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Emily Schneider
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Michael Tran
- Public Health Laboratories, Division of Disease Control and Health Statistics, Washington State Department of Health, Shoreline, WA, United States
| | - Vici Varghese
- Alameda County Public Health Laboratory, Oakland, CA, United States
| | | | - Mark Pandori
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
- Department of Microbiology and Immunology, Reno School of Medicine, University of Nevada, Reno, NV, United States
| | | | - David Hess
- Nevada State Public Health Laboratory, Reno, NV, United States
- Department of Pathology and Laboratory Medicine, Reno School of Medicine, University of Nevada, Reno, NV, United States
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Olivier MR, Killian S, Chiliza B, Asmal L, Schoeman R, Oosthuizen PP, Kidd M, Emsley R. Cognitive performance during the first year of treatment in first-episode schizophrenia: a case-control study. Psychol Med 2015; 45:2873-2883. [PMID: 25998030 DOI: 10.1017/s0033291715000860] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Several questions remain unanswered regarding the magnitude and time course of cognitive improvement in response to antipsychotic treatment. The purpose of this study was to assess changes in cognitive performance in antipsychotic-naive or minimally medicated patients with first-episode schizophrenia during the first 12 months of treatment, in a case-control design. Patients were treated with flupenthixol decanoate depot injection, according to a standard algorithm. The primary outcome measure was change in MATRICS Cognitive Consensus Battery (MCCB) composite score over 12 months. METHOD The sample comprised 92 patients and 100 healthy controls matched for age, sex, ethnicity and educational status. Cognitive function was assessed by means of the MCCB. RESULTS A mixed-effects model identified a significant group × time effect (p ≤ 0.0001) for the MCCB composite score, with patients showing a greater degree of change than the controls. For the other MCCB domains there were significant group × time effects at adjusted significance level for attention and vigilance (p ≤ 0.0001), visual learning (p ≤ 0.0001), verbal learning (p = 0.005) and working memory (p ≤ 0.0001), but not for reasoning and problem solving (p = 0.04), speed of processing (p = 0.03) and social cognition (p = 0.06). There were moderate correlations between change in MCCB composite score and change in symptomatology as assessed by Positive and Negative Syndrome Scale factor analysis-derived domains. CONCLUSIONS Substantial improvements in cognitive function were observed over and above a practice effect, and were significantly correlated with improvements in psychopathology and functionality.
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Affiliation(s)
- M R Olivier
- Department of Psychiatry,Faculty of Medicine and Health Sciences,Stellenbosch University,Tygerberg Campus,Cape Town,South Africa
| | - S Killian
- Department of Psychiatry,Faculty of Medicine and Health Sciences,Stellenbosch University,Tygerberg Campus,Cape Town,South Africa
| | - B Chiliza
- Department of Psychiatry,Faculty of Medicine and Health Sciences,Stellenbosch University,Tygerberg Campus,Cape Town,South Africa
| | - L Asmal
- Department of Psychiatry,Faculty of Medicine and Health Sciences,Stellenbosch University,Tygerberg Campus,Cape Town,South Africa
| | - R Schoeman
- Department of Psychiatry,Faculty of Medicine and Health Sciences,Stellenbosch University,Tygerberg Campus,Cape Town,South Africa
| | - P P Oosthuizen
- Department of Psychiatry,Faculty of Medicine and Health Sciences,Stellenbosch University,Tygerberg Campus,Cape Town,South Africa
| | - M Kidd
- Centre for Statistical Consultation,Stellenbosch University,South Africa
| | - R Emsley
- Department of Psychiatry,Faculty of Medicine and Health Sciences,Stellenbosch University,Tygerberg Campus,Cape Town,South Africa
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Abstract
Reconstituting the immune response will be critical for the survival of HIV-infected individuals once viral load is brought under control. While the adult thymus was previously thought to be relatively inactive, new data suggest it may play a role in T cell reconstitution. We examined thymopoiesis in adults up to 56 years of age and found active T cell receptor (TCR) rearrangement, generating a diverse TCR Vbeta repertoire. The resulting thymocytes are functional and are capable of responding to costimulatory signals. These data demonstrate that the adult thymus remains active late in life and contributes functional T cells to the peripheral lymphoid pool.
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Affiliation(s)
- B D Jamieson
- Department of Medicine, UCLA School of Medicine and Jonsson Comprehensive Cancer Center, Los Angeles, California 90095-1678, USA.
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Espinel-Ingroff A, Pfaller M, Messer SA, Knapp CC, Killian S, Norris HA, Ghannoum MA. Multicenter comparison of the sensititre YeastOne Colorimetric Antifungal Panel with the National Committee for Clinical Laboratory standards M27-A reference method for testing clinical isolates of common and emerging Candida spp., Cryptococcus spp., and other yeasts and yeast-like organisms. J Clin Microbiol 1999; 37:591-5. [PMID: 9986817 PMCID: PMC84481 DOI: 10.1128/jcm.37.3.591-595.1999] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
National Committee for Clinical Laboratory Standards (NCCLS) standard guidelines are available for the antifungal susceptibility testing of common Candida spp. and Cryptococcus neoformans, but NCCLS methods may not be the most efficient and convenient procedures for use in the clinical laboratory. MICs of amphotericin B, fluconazole, flucytosine, itraconazole, and ketoconazole were determined by the commercially prepared Sensititre YeastOne Colorimetric Antifungal Panel and by the NCCLS M27-A broth microdilution method for 1,176 clinical isolates of yeasts and yeast-like organisms, including Blastoschizomyces capitatus, Cryptococcus spp., 14 common and emerging species of Candida, Hansenula anomala, Rhodotorula spp., Saccharomyces cerevisiae, Sporobolomyces salmonicolor, and Trichosporon beigelii. Colorimetric MICs of amphotericin B corresponded to the first blue well (no growth), and MICs of the other agents corresponded to the first purple or blue well. Three comparisons of MIC pairs by the two methods were evaluated to obtain percentages of agreement: 24- and 48-h MICs and 24-h colorimetric versus 48-h reference MICs. The best performance of the YeastOne panel was with 24-h MICs (92 to 100%) with the azoles and flucytosine for all the species tested, with the exception of C. albicans (87 to 90%). For amphotericin B, the best agreement between the methods was with 48-h MIC pairs (92 to 99%) for most of the species tested. The exception was for isolates of C. neoformans (76%). These data suggest the potential value of the YeastOne panel for use in the clinical laboratory.
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Affiliation(s)
- A Espinel-Ingroff
- Medical College of Virginia of Virginia Commonwealth University, Richmond, Virginia, USA.
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Tomori O, Bertolli J, Rollin PE, Fleerackers Y, Guimard Y, De Roo A, Feldmann H, Burt F, Swanepoel R, Killian S, Khan AS, Tshioko K, Bwaka M, Ndambe R, Peters CJ, Ksiazek TG. Serologic survey among hospital and health center workers during the Ebola hemorrhagic fever outbreak in Kikwit, Democratic Republic of the Congo, 1995. J Infect Dis 1999; 179 Suppl 1:S98-101. [PMID: 9988171 DOI: 10.1086/514307] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
From May to July 1995, a serologic and interview survey was conducted to describe Ebola hemorrhagic fever (EHF) among personnel working in 5 hospitals and 26 health care centers in and around Kikwit, Democratic Republic of the Congo. Job-specific attack rates estimated for Kikwit General Hospital, the epicenter of the EHF epidemic, were 31% for physicians, 11% for technicians/room attendants, 10% for nurses, and 4% for other workers. Among 402 workers who did not meet the EHF case definition, 12 had borderline positive antibody test results; subsequent specimens from 4 of these tested negative. Although an old infection with persistent Ebola antibody production or a recent atypical or asymptomatic infection cannot be ruled out, if they occur at all, they appear to be rare. This survey demonstrated that opportunities for transmission of Ebola virus to personnel in health facilities existed in Kikwit because blood and body fluid precautions were not being universally followed.
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Affiliation(s)
- O Tomori
- World Health Organization, Harare, Zimbabwe
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