Stephen W. Peterson

Public Health Agency of Canada

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Jens C. Frisvad

Technical University of Denmark

Vít Hubka

Czech Academy of Sciences

Fernando E. Vega

Hospital Doctor Hernán Henríquez Aravena

Robert A. Samson

Westerdijk Fungal Biodiversity Institute

Miroslav Kolařík

Czech Academy of Sciences, Institute of Microbiology

Robert W. Lichtwardt

University of Kansas

Tetsuhisa Goto

Shinshu University

Francisco Posada

United States Department of Agriculture

Donald T. Wicklow

National Center for Agricultural Utilization Research

Bruce W. Horn

United States Department of Agriculture

Cooperative Institutions

Murdoch University

Westerdijk Fungal Biodiversity Institute

Universidade Federal de Pernambuco

Cornell University

Mae Fah Luang University

Agricultural Research Service

United States Department of Agriculture

University of Pretoria

Naturalis Biodiversity Center

National Center for Agricultural Utilization Research

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Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing

Genomics (2023)

Stephen W. Peterson Walter Demczuk Irene Martín Heather J. Adam Amrita Bharat

Bloodstream infections are a major cause of morbidity and mortality worldwide. Early administration of appropriate antimicrobial therapy can improve patient survival and prevent antimicrobial resistance (AMR). Whole genome sequencing (WGS) can provide information for pathogen identification, AMR prediction and sequence typing earlier than current phenotypic diagnostic methods. WGS was performed on 97 clinical blood specimens and matched culture isolate pairs. Specimen/isolate pairs were MLST sequence-typed and further characterization was performed on Streptococcus species. WGS correctly identified 91.7% of clinical specimens and 93.2% of matched isolates representing 35 different microbial species. MLST types were assigned for 89.9% of matched cultures and 21.7% of blood specimens, with higher success for blood culture specimens extracted within 3 days (52% characterized) than 7 days (9.3%). This study demonstrates the potential use of WGS for identification and characterization of pathogens directly from blood culture specimens to facilitate timely initiation of appropriate antimicrobial therapies.

Multilocus sequence typing

Blood Culture

10.1016/j.ygeno.2023.110580

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Citations (4)

Polycystic kidney disease, fungi, and bacterial endotoxin: shifting paradigms involving infection and diet

Reviews in Medical Microbiology (2000)

Thomas J. Hjelle Marcia A. Miller-Hjelle Deborah M. Nowak Mary Ann Dombrink-Kurtzman Stephen W. Peterson

The effort to understand the significance of ever-more numerous observations of fungal and bacterial components in tissues and fluids from patients with polycystic kidney disease (PKD) is the focus of this review. Could this second most common genetic disease in man be promoted or even caused by microbes or their components/toxins found in PKD patients? Findings include fungal glucans, fungal antigens, immunoglobulin E reactive with fungal antigens, fungal DNA, bacterial endotoxin from at least three genera, and a newly discovered class of bacteria,Nanobacterium.A new species of fungus,Penicillium pimiteouiense, has been isolated from PKD kidney cellsin vitro.What are the sources of these microbes or microbial parts and by what mechanism(s) do they alter those few cells that become the progenitors of all phenotypically cystic cells? Hypotheses concerning the interactions of microbial components with PKD biology are presented along with strategies to confirm and exploit therapeutically these ideas. The study of microbes and their parts in this prominent chronic, genetic disease may provide insights into other polymicrobic, multifactorial diseases. © 2000 Lippincott Williams & Wilkins

10.1097/00013542-200011010-00003

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Phylogenetic analysis ofAspergillusspecies using DNA sequences from four loci

Mycologia (2008)

Stephen W. Peterson

DNA sequences were determined for beta tubulin (BT2), calmodulin (CF), ITS and lsu rDNA (ID) and RNA polymerase II (RPB2) from ca. 460 Aspergillus isolates. RPB2 and rDNA sequences were combined and analyzed to determine relationships in the genus and in the family Trichocomaceae. Eupenicillium species form a statistically supported clade with origins among the Aspergillus clades. A. crystallinus, A. malodoratus and H. paradoxus are members of the Eupenicillium clade. A. zonatus, A. clavatoflvus and W. spinulosa occur in a clade along with Hamigera sp. Other than these exceptional species, Aspergillus species and sections occur on three strongly supported clades that descend from a polytomy. Section Versicolores as a monophyletic group includes only A. versicolor and A. sydowii and is superfluous. The other sections were retained but modified. All four loci were used in genealogical concordance analysis of species boundaries. Fennellia flavipes and F. nivea are not conspecific with their supposed anamorphs A. flavipes and A. nivea. Synonymies were found for some species and more than 20 undescribed taxa were identified in genealogical concordance analysis. Newly discovered taxa will be described elsewhere. Possibly paralogous gene fragments were amplified with the BT2 primers in sections Nidulantes, Usti and Nigri. Use of nonhomologous sequences in genealogical concordance analysis could lead to false conclusions and so BT2 sequences were not used in analysis of those sections.

Monophyly

10.1080/15572536.2008.11832477

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Citations (174)

Polycystic Kidney Disease: An Unrecognized Emerging Infectious Disease?

Emerging infectious diseases (1997)

Marcia A. Miller-Hjelle J. Thomas Hjelle Margaret T. Jones W R Mayberry Mary Ann Dombrink-Kurtzman

Polycystic kidney disease (PKD) is one of the most common genetic diseases in humans. We contend that it may be an emerging infectious disease and/or microbial toxicosis in a vulnerable human subpopulation. Use of a differential activation protocol for the Limulus amebocyte lysate (LAL) assay showed bacterial endotoxin and fungal (1-->3)-beta-D-glucans in cyst fluids from human kidneys with PKD. Fatty acid analysis of cyst fluid confirmed the presence of 3-hydroxy fatty acids characteristic of endotoxin. Tissue and cyst fluid from three PKD patients were examined for fungal components. Serologic tests showed Fusarium, Aspergillus, and Candida antigens. IgE, but not IgG, reactive with Fusarium and Candida were also detected in cyst fluid. Fungal DNA was detected in kidney tissue and cyst fluid from these three PKD patients, but not in healthy human kidney tissue. We examine the intertwined nature of the actions of endotoxin and fungal components, sphingolipid biology in PKD, the structure of PKD gene products, infections, and integrity of gut function to establish a mechanistic hypothesis for microbial provocation of human cystic disease. Proof of this hypothesis will require identification of the microbes and microbial components involved and multifaceted studies of PKD cell biology.

Cystic kidney disease

10.3201/eid0302.970204

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Citations (15)

Increasing the species diversity in the Aspergillus section Nidulantes: Six novel species mainly from the indoor environment

Figshare (2020)

F. Sklenář Ž Jurjević Stephen W. Peterson Miroslav Kolařík Alena Nováková

Aspergillus section Nidulantes encompasses almost 80 homothallic and anamorphic species, mostly isolated from soil, plant material, or the indoor environment. Some species are clinically relevant or produce mycotoxins. This study reevaluated the species boundaries within several clades of section Nidulantes. Five data sets were assembled, each containing presumptive new species and their closest relatives, and phylogenetic and phenotypic analyses were performed. We tested the hypotheses that the newly isolated or reexamined strains constitute separate species (splitting approach) or should be treated as part of broadly defined species (lumping approach). Four DNA sequence loci were amplified, internal transcribed spacer (ITS) and large subunit (LSU) regions of the rDNA and partial sequences of the β-tubulin (benA), calmodulin (CaM), and RNA polymerase II second largest subunit (RPB2) genes. The latter three loci were used for the phylogenetic analysis and served as input for single-locus (GMYC, bGMYC, PTP, and bPTP) and multilocus (STACEY and BP&P) species delimitation analyses. The phenotypic analysis comprised macro- and micromorphology (including scanning electron microscopy) and comparison of cardinal growth temperatures. The phylogenetic analysis supported the splitting hypothesis in all cases, and based on the combined approach, we propose six new species, four that are homothallic and two anamorphic. Four new species were isolated from the indoor environment (Jamaica, Trinidad and Tobago, USA), one originated from soil (Australia), and one from a kangaroo rat cheek pouch (USA).

Section (typography)

10.6084/m9.figshare.11874159

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Penicillium thiersii, Penicillium angulare and Penicillium decaturense, New Species Isolated from Wood-Decay Fungi in North America and Their Phylogenetic Placement from Multilocus DNA Sequence Analysis

Mycologia (2004)

Stephen W. Peterson Eileen M. Bayer Donald T. Wicklow

We describe three new fungicolous species on the basis of phenotypic and phylogenetic differences from known species. Penicillium thiersii, P. angulare and Penicillium decaturense are described. Penicillium thiersii phenotypically is identified on the basis of several characteristics including growth rates, vesicle size and condium shape and roughening. Penicillium angulare is related most closely to P. adametzioides but differs from it by restricted growth rates and conidiophores greater than 60 μm in length. Penicillium decaturense is related most closely to P. miczynskii but differs from that species by growth rate, minimum growth temperature and pigment production on MEA. Multilocus phylogenetic analysis confirmed the genetic distinctiveness of P. decaturense and the closely related species P. miczynskii, P. chrzaszczii and P. manginii. Penicillium rivolii is a synonym of P. waksmanii on the basis of this analysis. Analysis of the EF-1α gene shows rapid changes of position, number and length of introns between the species, suggesting a recent evolutionary origin for the introns.

10.2307/3762145

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Citations (17)

Journal of Clinical Microbiology (2014)

Janyce A. Sugui Stephen W. Peterson Figat Abigail Bryan Hansen Robert A. Samson

ABSTRACT Aspergillus section Fumigati contains 12 clinically relevant species. Among these Aspergillus species, A. fumigatus is the most frequent agent of invasive aspergillosis, followed by A. lentulus and A. viridinutans . Genealogical concordance and mating experiments were performed to examine the relationship between phylogenetic distance and mating success in these three heterothallic species. Analyses of 19 isolates from section Fumigati revealed the presence of three previously unrecognized species within the broadly circumscribed species A. viridinutans . A single mating type was found in the new species Aspergillus pseudofelis and Aspergillus pseudoviridinutans , but in Aspergillus parafelis , both mating types were present. Reciprocal interspecific pairings of all species in the study showed that the only successful crosses occurred with the MAT1-2 isolates of both A. parafelis and A. pseudofelis . The MAT1-2 isolate of A. parafelis was fertile when paired with the MAT1-1 isolates of A. fumigatus , A. viridinutans , A. felis , A. pseudoviridinutans , and A. wyomingensis but was not fertile with the MAT1-1 isolate of A. lentulus . The MAT1-2 isolates of A. pseudofelis were fertile when paired with the MAT1-1 isolate of A. felis but not with any of the other species. The general infertility in the interspecies crossings suggests that genetically unrelated species are also biologically incompatible, with the MAT1-2 isolates of A. parafelis and A. pseudofelis being the exception. Our findings underscore the importance of genealogical concordance analysis for species circumscription, as well as for accurate species identification, since misidentification of morphologically similar pathogens with differences in innate drug resistance may be of grave consequences for disease management.

10.1128/jcm.01704-14

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Citations (78)

A reappraisal of Aspergillus section Nidulantes with descriptions of two new sterigmatocystin-producing species

Plant Systematics and Evolution (2016)

Vít Hubka Alena Nováková Stephen W. Peterson Jens C. Frisvad F. Sklenář

Monophyly

Subgenus

Sterigmatocystin

Sister group

10.1007/s00606-016-1331-5

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Citations (46)

The Talaromyces pinophilus species complex

Fungal Biology (2019)

Stephen W. Peterson Željko Jurjević

Species complex

10.1016/j.funbio.2019.06.007

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Citations (22)

Penicillium pimiteouiense: A New Species Isolated from Polycystic Kidney Cell Cultures

Mycologia (1999)

Stephen W. Peterson Sylvia Corneli J. Thomas Hjelle Marcia A. Miller-Hjelle Deborah M. Nowak

As part of a study of polycystic kidney disease (PKD), epithelial cells were isolated and propagated from cyst walls of human kidneys obtained at nephrectomy. A Penicillium species was found growing with the epithelial cells in some culture flasks. It was monoverticillate and somewhat resembled P. restrictum but differed morphologically from this and all other Penicillium species. Two strains of this fungus were isolated in pure culture and described as the new species Penicillium pimiteouiense. Ochratoxin A production was not detected in P. pimiteouiense. The role, if any, that this fungus plays in polycystic kidney disease is not known.

Laboratory flask

10.2307/3761372

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Citations (11)