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Scheurer JM, Fanta ML, Colbenson GA, Arbefeville S, Ferrieri P. Early-Onset Neonatal Sepsis Caused by Vertical Transmission of Pasteurella multocida. AJP Rep 2022; 12:e123-e126. [PMID: 35941964 PMCID: PMC9356768 DOI: 10.1055/a-1830-2903] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 04/05/2022] [Indexed: 11/22/2022] Open
Abstract
Early-onset neonatal sepsis contributes substantially to neonatal morbidity and mortality. Presenting signs and symptoms vary, and most causes are due to a limited number of common microbes. However, providers must be cognizant of unusual pathogens when treating early-onset sepsis (EOS). We report a case of a term neonate who presented with respiratory distress, lethargy, and hypoglycemia 5 hours after birth. He was treated for presumed EOS with blood culture, revealing an unusual pathogen, Pasteurella multocida . Sepsis from this pathogen is a rarely reported cause of early onset neonatal sepsis. Our report is one of few that implicate vertical transmission with molecular diagnostic confirmation of P . multocida , subspecies septica. The neonate was treated with antibiotics and supportive care and recovered without ongoing complications. Providers should maintain an index of suspicion for rare causes of neonatal EOS. For these unusual cases, precise microbial identification enables understanding to provide best clinical care and anticipation of complications.
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Affiliation(s)
| | - Meghan L Fanta
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota
| | | | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Patricia Ferrieri
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
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2
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Thomas SN, Altawallbeh G, Zaun CP, Pape KA, Peters JM, Titcombe PJ, Dileepan T, Rapp MJ, Bold TD, Schacker TW, Arbefeville S, Ferrieri P, Thyagarajan B, Jenkins MK, Karger AB. Initial determination of COVID-19 seroprevalence among outpatients and healthcare workers in Minnesota using a novel SARS-CoV-2 total antibody ELISA. Clin Biochem 2021; 90:15-22. [PMID: 33539808 PMCID: PMC7849522 DOI: 10.1016/j.clinbiochem.2021.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/08/2020] [Accepted: 01/21/2021] [Indexed: 01/19/2023]
Abstract
OBJECTIVES To avoid the significant risks posed by the use of COVID-19 serology tests with supply chain constraints or poor performance characteristics, we developed an in-house SARS-CoV-2 total antibody test. Our test was compared with three commercial methods, and was used to determine COVID-19 seroprevalence among healthcare workers and outpatients in Minnesota. METHODS Seventy-nine plasma and serum samples from 50 patients 4-69 days after symptom onset who tested positive by a SARS-CoV-2 PCR method using a nasopharyngeal (NP) swab were used to evaluate our test's clinical performance. Seropositive samples were analyzed for IgG titers in a follow-up assay. Thirty plasma and serum from 12 patients who tested negative by a SARS-CoV-2 PCR method using a nasopharyngeal (NP) swab and 210 negative pre-pandemic serum samples were also analyzed. Among samples from patients > 14 days after symptom onset, the assay had 100% clinical sensitivity and 100% clinical specificity, 100% positive predictive value and 100% negative predictive value. Analytical specificity was 99.8%, indicating minimal cross-reactivity. A screening study was conducted to ascertain COVID-19 seroprevalence among healthcare workers and outpatients in Minnesota. RESULTS Analysis of serum collected between April 13 and May 21, 2020 indicated a COVID-19 seroprevalence of 2.96% among 1,282 healthcare workers and 4.46% among 2,379 outpatients. CONCLUSIONS Our in-house SARS-CoV-2 total antibody test can be used to conduct reliable epidemiological studies to inform public health decisions during the COVID-19 pandemic.
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Affiliation(s)
- Stefani N Thomas
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA
| | - Ghaith Altawallbeh
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA
| | - Christopher P Zaun
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA
| | - Kathryn A Pape
- Department of Microbiology and Immunology, Center for Immunology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Jennifer M Peters
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA
| | - Philip J Titcombe
- Department of Medicine, Division of Rheumatology, Center for Immunology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Thamotharampillai Dileepan
- Department of Microbiology and Immunology, Center for Immunology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Michael J Rapp
- M Health Fairview University of Minnesota Medical Center West Bank Laboratory, Minneapolis, MN, USA
| | - Tyler D Bold
- Department of Medicine, Division of Infectious Diseases and International Medicine, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Timothy W Schacker
- Department of Medicine, Division of Infectious Diseases and International Medicine, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA
| | - Marc K Jenkins
- Department of Microbiology and Immunology, Center for Immunology, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Amy B Karger
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis MN, USA.
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Obeid KM, Grzywacz B, Ferrieri P, Arbefeville S, Slungaard A, Betts B. Hemophagocytic lymphohistiocytosis induced by Toxoplasma gondii infection diagnosed by a bone marrow biopsy and DNA next-generation sequencing in an allogeneic hematopoietic stem cell transplant recipient. Transpl Infect Dis 2021; 23:e13610. [PMID: 33783930 DOI: 10.1111/tid.13610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/08/2021] [Accepted: 03/21/2021] [Indexed: 11/28/2022]
Abstract
In the United States, toxoplasmosis following allogeneic hematopoietic stem transplant (allo-HCT) is very rare with a rate only between 0.5% and 2%. The reported rates of hemophagocytic lymphohistiocytosis (HLH) following allo-HCT range between 0.3% and 17%. Secondary HLH due to toxoplasmosis infection is extremely rare. Herein, we report a case of secondary HLH due to toxoplasmosis following allo-HCT. The diagnosis was reached by a bone marrow biopsy and confirmed by DNA next generation sequencing and immunohistochemical (IHC) staining. The IHC staining included CD1a, a stain previously known to react with cells infected by Leishmania, here we show CD1a staining of macrophages infected with Toxoplasma gondii. Our report highlights the utility of bone marrow biopsy in diagnosing parasitic infection underlying HLH in post-transplant settings. The pre-transplant evaluation of patients from low endemic countries, is a great opportunity to obtain a travel history to determine the risks and the preventative measures against opportunistic infections including toxoplasmosis.
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Affiliation(s)
- Karam M Obeid
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Bartosz Grzywacz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Arne Slungaard
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Brian Betts
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
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4
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Arbefeville S, Ferrieri P. Role of Multiplex Molecular Diagnosis for Acute Gastroenteritis. Curr Infect Dis Rep 2020. [DOI: 10.1007/s11908-020-0718-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Chauhan A, Gruenberg J, Arbefeville S, Mettler T, Brent CH, Ferrieri P. Disseminated Hormographiella aspergillata Infection with Lung and Brain Involvement after Allogenic Hematopoietic Stem-Cell Transplantation in a 54-Year-Old Man. Lab Med 2020; 50:426-431. [PMID: 31065690 DOI: 10.1093/labmed/lmz018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hormographiella is a rare fungal pathogen in humans; however, case reports have described disseminated infection in immunocompromised hosts. This pathogen has been described to yield poor prognosis in patients who harbor it. Herein, we present a case report of autopsy-proven disseminated Hormographiella aspergillata infection, confirmed by DNA sequencing, in a patient experiencing a relapse of leukemia. This 54-year-old Caucasian man with chronic myelogenous leukemia (CML) that had been diagnosed in 1989, after having received a hematopoietic cell allotransplant from a compatible sibling donor, had B-cell lymphoid-blast phase of CML in April of 2013, with multiple relapses. His most recent relapse was in September of 2016, when bone marrow biopsy showed 90% blasts. The results of bronchoalveolar lavage (BAL) cultures were positive for filamentous fungus infection. The patient developed encephalopathy and worsening respiratory statusand tachycardia with flutter and hypotension, which resulted in his death. At autopsy, bilateral pleural effusions, multiple right pleural nodules, and subarachnoid hemorrhage were noted. Angioinvasive hyphal fungi were found in the right frontal lobe of the brain and the right upper lobe of the lung. Morphologically, the fungi had multiseptate, branching hyphae. The bronchoalveolar lavage specimen grew a fungus for which the colony morphologic characteristics and microscopic features were compatible with a Hormographiella species. H. aspergillata from the bronchoalveolar lavage was further identified by sequencing the D2 hypervariable region of the large-subunit (LSU) ribosomal DNA gene and the full internal transcribed spacer (ITS) regions.
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Affiliation(s)
- Aastha Chauhan
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Jessica Gruenberg
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Tetyana Mettler
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Clark H Brent
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
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6
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Arbefeville S, Lynch M, Ferrieri P. Evaluation of a Multiplex Fully Automated Treponemal and Nontreponemal (Rapid Plasma Reagin) Assay. Am J Clin Pathol 2019; 152:230-236. [PMID: 31139835 DOI: 10.1093/ajcp/aqz034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES In June 2017, Bio-Rad Laboratories received US Food and Drug Administration clearance for its BioPlex 2200 Syphilis Total & RPR (rapid plasma reagin) assay. It is the first fully automated treponemal/nontreponemal multiplex flow immunoassay, simultaneously detecting Treponema pallidum and reagin antibodies and an RPR titer. We compared the performance of the BioPlex Syphilis Total & RPR assay with the LIAISON Treponema Assay and the manual BD Macro-Vue RPR 18-mm Circle Test. METHODS In total, 314 serum specimens were tested for treponemal immunoglobulin G/immunoglobulin M and RPR with the LIAISON Treponema Assay, the BioPlex 2200 Syphilis Total & RPR assay, and the manual BD Macro-Vue RPR card test. All discordant results were further tested with the T pallidum particle agglutination assay from Fujirebio Diagnostics. RESULTS The overall percent agreement for the BioPlex assay for treponemal antibodies with the LIAISON Treponema Assay was 96.1%. Sensitivity and specificity for the BioPlex RPR assay were 90.5% and 97.2%, respectively (the manual RPR assay was considered the gold standard). CONCLUSIONS The BioPlex 2200 Syphilis Total & RPR assay performance was comparable to the LIAISON Treponema Assay and the manual RPR test. Compared with the manual RPR, the automation of RPR testing offered labor savings, objective result reporting, and improved workflow.
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Affiliation(s)
- Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
- Infectious Diseases Diagnostic Laboratory, Medical Center and Fairview Health System, University of Minnesota, Minneapolis
| | - Maureen Lynch
- Infectious Diseases Diagnostic Laboratory, Medical Center and Fairview Health System, University of Minnesota, Minneapolis
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
- Infectious Diseases Diagnostic Laboratory, Medical Center and Fairview Health System, University of Minnesota, Minneapolis
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7
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Ferrieri P, Nelson K, Thonen-Kerr E, Arbefeville S. Prospective Evaluation of Xpert Xpress Strep A Automated PCR Assay vs Solana Group A Streptococcal NAAT vs Conventional Throat Culture. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqy112.367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Arbefeville S, Nelson K, Thonen-Kerr E, Ferrieri P. Prospective Postimplementation Study of Solana Group A Streptococcal Nucleic Acid Amplification Test vs Conventional Throat Culture. Am J Clin Pathol 2018; 150:333-337. [PMID: 29982326 DOI: 10.1093/ajcp/aqy051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES We evaluated the Solana Group A Streptococcus Assay (Quidel, San Diego, CA), a nucleic acid amplification test (NAAT), as a substitute for backup culture on throat specimens with a negative rapid group A Streptococcus (GAS) antigen assay. METHODS During October 2016, all throat swabs from patients with a negative GAS antigen assay from local urgent care centers were processed by NAAT and conventional culture in real time. RESULTS The overall agreement of the 2,090 tested throat swab specimens of the NAAT with the culture was 2,050 (98%) of 2,090. Sensitivity, specificity, positive predictive value, and negative predictive value were 91.4%, 98.5%, 78.0%, and 99.5%, respectively. CONCLUSIONS In summary, this postimplementation study supported high sensitivity and specificity of the GAS NAAT as a backup test for negative rapid GAS antigen tests.
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Affiliation(s)
- Sophie Arbefeville
- Infectious Diseases Diagnostic Laboratory, University of Minnesota Medical Center and Fairview Health System, Minneapolis
- University of Minnesota Medical School, Minneapolis
| | - Kari Nelson
- Infectious Diseases Diagnostic Laboratory, University of Minnesota Medical Center and Fairview Health System, Minneapolis
| | - Elizabeth Thonen-Kerr
- Infectious Diseases Diagnostic Laboratory, University of Minnesota Medical Center and Fairview Health System, Minneapolis
| | - Patricia Ferrieri
- Infectious Diseases Diagnostic Laboratory, University of Minnesota Medical Center and Fairview Health System, Minneapolis
- University of Minnesota Medical School, Minneapolis
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Barnes AMT, Crespo-Diaz RJ, Cohenour J, Kirsch JD, Arbefeville S, Ferrieri P. A Noninvasive Rhizopus Infection With a Bladder Fungal Ball in a Patient With Poorly Controlled Diabetes Mellitus. Lab Med 2018; 49:75-79. [PMID: 29069422 DOI: 10.1093/labmed/lmx060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Here we present the first reported case of a noninvasive Rhizopus fungal ball confined to the bladder of a patient with poorly controlled diabetes and right flank pain. The patient developed bilateral hydronephrosis after several hospital admissions for urinary tract infections with multiple failed courses of antibiotics. During cystoscopy to replace a ureteral stent, he was found to harbor a fungal ball in the bladder that was removed and grew Rhizopus in culture. Patient received treatment with amphotericin B and transitioned to long-term posaconazole therapy. This case highlights the importance of considering fungal agents in urinary tract infections, especially in persistent or refractory cases, and the role of the clinical microbiology laboratory in correct identification of the infectious source.
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Affiliation(s)
- Aaron M T Barnes
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN.,Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, MN
| | - Ruben J Crespo-Diaz
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Justin Cohenour
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Jonathan D Kirsch
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN
| | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN
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10
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Vahidi S, Beckman A, Albrecht K, Arbefeville S, Ferrieri P, Amin K. Urinary tract blastomycosis diagnosed by urine cytology. Diagn Cytopathol 2018; 46:698-701. [PMID: 29573229 DOI: 10.1002/dc.23929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/27/2018] [Accepted: 03/06/2018] [Indexed: 11/08/2022]
Abstract
Urinary tract blastomycosis is an uncommon manifestation of disseminated Blastomyces infection. Here, we report a 50-year-old male with common variable immunodeficiency who presented with urinary symptoms and a renal mass concerning for a kidney neoplasm. Urine cytology revealed typical broad-based budding yeasts with thick-walled refractile capsules, leading to diagnosis of urinary tract blastomycosis. In this case, urine cultures were negative, and urine cytology was the main method of diagnosis of blastomycosis. Thus, urine cytology represents a rapid and reliable method of diagnosing blastomycosis, which in the current case led to prompt treatment of this potentially life threatening infection.
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Affiliation(s)
- Shifteh Vahidi
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Amy Beckman
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Kellen Albrecht
- Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
| | - Khalid Amin
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota
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Bhaskaran A, Obeid KM, Arbefeville S, Ferrieri P. Trichosporon loubieri Fungemia in a 39-Year-Old Caucasian Woman With B-Cell Lymphoblastic Leukemia. Lab Med 2018; 47:255-8. [PMID: 27406143 DOI: 10.1093/labmed/lmw026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report a case of Trichosporon loubieri (T. loubieri) fungemia with likely liver involvement in a 39-year-old Caucasian patient with relapsed B-cell acute lymphoblastic leukemia after an allogeneic hematopoietic cell transplant. This is the fifth published case of T. loubieri infection and only the third case of T. loubieri fungemia, to our knowledge. All 3 cases of T. loubieri infection with fungemia had liver involvement.
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Affiliation(s)
| | - Karam M Obeid
- Division of Infectious Diseases and International Medicine
| | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
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12
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Arbefeville S, Thonen-Kerr E, Ferrieri P. Prospective and Retrospective Evaluation of the Performance of the FDA-Approved Cepheid Xpert Flu/RSV XC Assay. Lab Med 2017; 48:e53-e56. [DOI: 10.1093/labmed/lmx038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Arbefeville S, Harris A, Ferrieri P. Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species. J Microbiol Methods 2017. [PMID: 28647582 DOI: 10.1016/j.mimet.2017.06.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
CONTEXT Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. OBJECTIVE The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data. DESIGN 85 common and uncommon clinically relevant fungi isolated from clinical specimens were sequenced for the D2 region of the large subunit (LSU) of ribosomal RNA (rRNA) gene with the MicroSEQ® Kit and the ITS regions with the in house developed assay. The generated sequenced data were analyzed with the online GenBank and MycoBank public databases. RESULTS The D2 region of the LSU rRNA gene identified 89.4% or 92.9% of the 85 isolates to the genus level and the full ITS region (f-ITS) 96.5% or 100%, using GenBank or MycoBank, respectively, when compared to the consensus ID. When comparing species-level designations to the consensus ID, D2 region of the LSU rRNA gene aligned with 44.7% (38/85) or 52.9% (45/85) of these isolates in GenBank or MycoBank, respectively. By comparison, f-ITS possessed greater specificity, followed by ITS1, then ITS2 regions using GenBank or MycoBank. Using GenBank or MycoBank, D2 region of the LSU rRNA gene outperformed phenotypic based ID at the genus level. Comparing rates of ID between D2 region of the LSU rRNA gene and the ITS regions in GenBank or MycoBank at the species level against the consensus ID, f-ITS and ITS2 exceeded performance of the D2 region of the LSU rRNA gene, but ITS1 had similar performance to the D2 region of the LSU rRNA gene using MycoBank. CONCLUSION Our results indicated that the MicroSEQ® D2 LSU rDNA Fungal Identification Kit was equivalent to the in-house developed ITS regions assay to identify fungi at the genus level. The MycoBank database gave a better curated database and thus allowed a better genus and species identification for both D2 region of the LSU rRNA gene and ITS regions.
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Affiliation(s)
- S Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, MMC 609 Mayo, 420 Delaware St. S.E., Minneapolis, MN 55455, USA.
| | - A Harris
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, MMC 609 Mayo, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
| | - P Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, MMC 609 Mayo, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
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14
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Arbefeville S, Ferrieri P. Epidemiologic Analysis of Respiratory Viral Infections Mainly in Hospitalized Children and Adults in a Midwest University Medical Center After the Implementation of a 14-Virus Multiplex Nucleic Acid Amplification Test. Am J Clin Pathol 2017; 147:43-49. [PMID: 28028115 PMCID: PMC7109917 DOI: 10.1093/ajcp/aqw185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To investigate the etiology of viral respiratory tract infections mainly in hospitalized children and adults over a 12-month consecutive period after implementation of a 14-virus multiplex nucleic acid amplification test. METHODS From January 2014 to January 2015, a total of 2,237 respiratory samples were analyzed with the US Food and Drug Administration-cleared eSensor Respiratory Viral Panel (GenMark Diagnostics, Carlsbad, CA). RESULTS Of the 2,237 specimens tested, 788 specimens were positive for at least one virus, giving a positivity rate of 35.2%, and because of viral codetection, a total of 862 viral targets were identified. The age groups with the highest positivity rates were the 0- to 1-year (73.5%) and 2- to 6-year (78.4%) age groups. The overall viral codetection rate was 9.1%. Human rhinovirus (HRV) was the most prevalent respiratory virus found in children and adults. The peak of HRV seen in September 2014 represented a combination of HRV and enterovirus D68, 2014 epidemic respiratory infections. CONCLUSION The ability to detect a wider range of respiratory viruses gave us a better understanding of the etiology of respiratory infections in our population, particularly for HRV and enhanced our ability to detect viral coinfection.
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Affiliation(s)
- Sophie Arbefeville
- From the Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
- Corresponding author: Sophie Arbefeville, MD, Dept of Laboratory Medicine and Pathology, University of Minnesota Medical School, B203-3 Mayo Building, MMC 609 Mayo, 420 Delaware St SE, Minneapolis, MN 55455; . Presented in part at the 115th General Meeting, American Society for Microbiology; May 30 to June 2, 2015; New Orleans, LA
| | - Patricia Ferrieri
- From the Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
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15
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Arbefeville S, Harris A, Dittes S, Ferrieri P. Pasteurella multocida Bacteremia With Associated Knee Arthroplasty Infection in an 80-Year-Old Caucasian Man. Lab Med 2016; 47:241-5. [PMID: 27378482 DOI: 10.1093/labmed/lmw034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To identify the gram-negative rods grown from blood cultures and a right-knee fluid aspirate from an 80-year-old caucasian man who had undergone a total right knee arthroplastic procedure 6 years ago, and to assess the genetic similarity between the 2 isolates. METHODS We used 3 different approaches: biochemical testing, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, and 16S ribosomal RNA (rRNA) gene sequencing. RESULTS The 3 methods identified the gram-negative rods as Pasteurella multocida; 16S rRNA gene sequencing further identified the organisms as P. multocida subsp. septica. CONCLUSION A concordant identification of P. multocida was observed using biochemical testing, mass spectrometry, and 16S rRNA gene sequencing. Only 16S rRNA sequencing was able to determine the subspecies of P. multocida and to determine the genetic relatedness of the 2 isolates.
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Affiliation(s)
- Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School
| | - Anthony Harris
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School
| | | | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School
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Arbefeville S, Thonen-Kerr E, Ferrieri P. 30: Prospective and Retrospective Evaluation of the Performance of the Newly FDA-Approved Cepheid Xpert Flu/RSV XC Assay. Am J Clin Pathol 2015. [DOI: 10.1093/ajcp/143.suppl1.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School
| | | | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School
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McAllister SC, Schleiss MR, Arbefeville S, Steiner ME, Hanson RS, Pollock C, Ferrieri P. Epidemic 2014 enterovirus D68 cross-reacts with human rhinovirus on a respiratory molecular diagnostic platform. PLoS One 2015; 10:e0118529. [PMID: 25799541 PMCID: PMC4370466 DOI: 10.1371/journal.pone.0118529] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022] Open
Abstract
Enterovirus D68 (EV-D68) is an emerging virus known to cause sporadic disease and occasional epidemics of severe lower respiratory tract infection. However, the true prevalence of infection with EV-D68 is unknown, due in part to the lack of a rapid and specific nucleic acid amplification test as well as the infrequency with which respiratory samples are analyzed by enterovirus surveillance programs. During the 2014 EV-D68 epidemic in the United States, we noted an increased frequency of “low-positive” results for human rhinovirus (HRV) detected in respiratory tract samples using the GenMark Diagnostics eSensor respiratory viral panel, a multiplex PCR assay able to detect 14 known respiratory viruses but not enteroviruses. We simultaneously noted markedly increased admissions to our Pediatric Intensive Care Unit for severe lower respiratory tract infections in patients both with and without a history of reactive airway disease. Accordingly, we hypothesized that these “low-positive” RVP results were due to EV-D68 rather than rhinovirus infection. Sequencing of the picornavirus 5’ untranslated region (5’-UTR) of 49 samples positive for HRV by the GenMark RVP revealed that 33 (67.3%) were in fact EV-D68. Notably, the mean intensity of the HRV RVP result was significantly lower in the sequence-identified EV-D68 samples (20.3 nA) compared to HRV (129.7 nA). Using a cut-off of 40 nA for the differentiation of EV-D68 from HRV resulted in 94% sensitivity and 88% specificity. The robust diagnostic characteristics of our data suggest that the cross-reactivity of EV-D68 and HRV on the GenMark Diagnostics eSensor RVP platform may be an important factor to consider in making accurate molecular diagnosis of EV-D68 at institutions utilizing this system or other molecular respiratory platforms that may also cross-react.
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Affiliation(s)
- Shane C. McAllister
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Infectious Disease and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Mark R. Schleiss
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Infectious Disease and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Marie E. Steiner
- Division of Pediatric Hematology and Oncology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Division of Pediatric Critical Care, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Ryan S. Hanson
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Infectious Disease and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Catherine Pollock
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Center for Infectious Disease and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Patricia Ferrieri
- Division of Pediatric Infectious Diseases and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
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Arbefeville S, Levi MH, Ferrieri P. Development of a multiplex real-time PCR assay for the detection of Bordetella pertussis and Bordetella parapertussis in a single tube reaction. J Microbiol Methods 2013; 97:15-9. [PMID: 24333686 DOI: 10.1016/j.mimet.2013.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 12/01/2022]
Abstract
Pertussis is an infectious respiratory disease caused by the fastidious bacterium Bordetella pertussis, which may infect unvaccinated, previously vaccinated children, and adults in whom immunity has waned. Infants are at a particular risk for severe disease and complications. Bordetella parapertussis may cause a similar illness, however the symptoms are less severe and of shorter duration. Pertussis is a highly contagious disease and early diagnosis is essential. Studies have shown that PCR is 2-4 times more likely than culture to detect Bordetella pertussis. We developed a multiplex, real-time PCR assay using analyte-specific reagent (ASR) primers and probes dispensed in a convenient lyophilized bead format that targeted the multi-copy insertion sequences IS481 and IS1001 of B. pertussis and B. parapertussis, respectively. These specific ASRs were used in conjunction with Cepheid Smartmix. Included in the ASRs is a competitive internal control to evaluate the performance of the PCR reaction. After DNA extraction, amplification and detection were done on the Smart Cycler System, which performs integrated amplification and detection automatically in a single step. Specificity of the assay was confirmed using multiple distinct bacterial strains. Sensitivity of the assay and extraction efficiency were evaluated on DNA isolated from pure bacterial cultures and on spiked respiratory specimens. We also spiked different swab types and transport media to evaluate for interfering substances. To assess accuracy, we studied different patient specimen types received from two outside laboratories that used similar or different methods to detect B. pertussis and B. parapertussis. The sensitivity and the specificity of the assay for B. pertussis were 90% and 96%, respectively, and for B. parapertussis 71% (only 7 positive specimens were available for testing) and 100%, respectively. Our assay was found to be a valid method for the simultaneous detection of B. pertussis and B. parapertussis.
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Affiliation(s)
- Sophie Arbefeville
- Department of Laboratory Medicine and Pathology, U. of Minnesota Medical School, Minneapolis, MN, United States.
| | - Michael H Levi
- Division of Pathology, Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY, United States
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology, U. of Minnesota Medical School, Minneapolis, MN, United States
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