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Gillrie M, Chow B, Griener T, Johnson A, Church D. Hepatosplenic mucormycosis due to Rhizomucor pusillus identified by panfungal PCR/sequencing of ribosomal ITS2 and LSU regions in a patient with acute myelogenous leukemia: A case report. Journal of the Association of Medical Microbiology and Infectious Disease Canada 2023; 8:105-110. [PMID: 37008581 PMCID: PMC10052907 DOI: 10.3138/jammi-2022-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 03/29/2023]
Abstract
Background: Angioinvasive Rhizomucor pusillus infection with dissemination to the liver and spleen is exceedingly uncommon, representing less than 1% of reported cases of mucormycosis. Methods: Diagnosis of mucormycosis is often difficult using conventional methods that rely on broad-based non-septate hyphae present on histologic examination and morphological identification of the cultured organism. Our laboratory also uses an in-house panfungal molecular assay to rapidly diagnose invasive fungal infection when conventional methods do not provide definitive results. Results: Herein we present a case of disseminated mucormycosis with hepatosplenic involvement in a 49-year-old female with acute myelogenous leukemia following induction chemotherapy. But in this case repeated tissue biopsy cultures were negative. R. pusillus infection was diagnosed using an in-house panfungal PCR/sequencing assay based on dual priming oligonucleotide primers. Conclusions: New molecular assays facilitate prompt diagnosis of invasive fungal infections.
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Affiliation(s)
- Mark Gillrie
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Barbara Chow
- Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Thomas Griener
- Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrew Johnson
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Deirdre Church
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Correspondence: Deirdre Church, Departments of Pathology & Laboratory Medicine and Medicine, University of Calgary, 9-3535 Research Road NW, Calgary, Alberta T2N 2K8 Canada. Telephone: 403-770-3281. E-mail:
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Church DL, Griener T, Gregson D. Multi-year comparison of VITEK® MS and 16S rRNA gene sequencing performance for the identification of rarely encountered anaerobes causing invasive human infections in a large Canadian region: can our laboratory abandon 16S rRNA gene sequencing? Anaerobe 2022; 78:102640. [PMID: 36126828 DOI: 10.1016/j.anaerobe.2022.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/13/2022] [Accepted: 09/07/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Our large regional laboratory routinely provides a definitive identification (ID) for 800-1,200 anaerobic bacteria per annum that cause invasive human infections. An increasing number of isolates (i.e., 10-13%) recovered from clinical specimens from these cases were more unusual or rarely isolated genera and/or species (i.e., ≤5 individual cases/annum). METHODS VITEK® MS (MALDI-TOF MS)is done initially on all anaerobic bacteria, but rare isolates undergo in-house PCR/sequencing when proteomics provides a wrong ID or no results despite repeat testing. A clinical microbiologist in consultation with the Infectious Diseases service approves molecular analyses. This multi-year comparison (2014-19) of the performance of MALDI-TOF MS and 16S rRNA gene sequencing using the IDNS Smart Gene bacterial dataset shows both method's abilities to provide a genus-level and/or species-level ID for rare isolates. RESULTS 489 rare anaerobes were recovered from a variety of clinical specimens: 57% blood cultures, 19% other sterile fluids, 14% sterile tissues, 8% deep wounds/abscesses, and 2% prosthetic implants. 16S rRNA gene sequencing gave an accurate genus-vs. species level ID for 487/489 (99.6%) and 401/489 (82.0%) of isolates respectively. Accurate genus-vs species-level ID were obtained by MALDI-TOF MS for 269/489 (53.4%) and 187/489 (37.3%) of isolates respectively. MALDI-TOF MS gave wrong or no results for 35.1% of Gram-negative anaerobic cocci (GNAC), 62% of Gram-negative anaerobic bacilli (GNAB), 30.8% of Gram-positive anaerobic cocci (GPAC) and 46.3% of Gram-positive anaerobic bacilli (GPAB). Neither method gave an ID for one GNAB and one GPAC isolate. MALDI-TOF MS genus-level ID of GNAC and genus/species-level ID of GPAB improved during the study but its performance remained stable for genus- or species-level ID of other organism groups. CONCLUSIONS MALDI-TOF MS provides accurate ID for most common anaerobes, but molecular analyses need to be available for rare isolates. Large complex laboratories should have a workflow for sending rare isolates for 16S rRNA gene sequencing in invasive cases where a definitive ID is clinically required.
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Affiliation(s)
- D L Church
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada.
| | - T Griener
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
| | - D Gregson
- Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Department of Medicine, Cummings School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary Alta. T2N 4B1, Canada; Calgary Laboratory Services (now Alberta Precision Laboratories), Research Rd NW, Calgary Alberta T2L 2K8, 9-3535, Canada
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Mohon AN, Oberding L, Hundt J, van Marle G, Pabbaraju K, Berenger BM, Lisboa L, Griener T, Czub M, Doolan C, Servellita V, Chiu CY, Greninger AL, Jerome KR, Pillai DR. Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2. J Virol Methods 2020; 286:113972. [PMID: 32941977 PMCID: PMC7490281 DOI: 10.1016/j.jviromet.2020.113972] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/04/2020] [Accepted: 09/11/2020] [Indexed: 01/10/2023]
Abstract
A novel reverse-transcriptase loop mediated amplification (RT-LAMP) method targeting genes encoding the Spike (S) protein and RNA-dependent RNA polymerase (RdRP) of SARS-CoV-2 has been developed. The LAMP assay achieves a comparable limit of detection (25-50 copies per reaction) to commonly used RT-PCR protocols using clinical samples quantified by digital droplet PCR. Precision, cross-reactivity, inclusivity, and limit of detection studies were performed according to regulatory standards. Clinical validation of dual-target RT-LAMP (S and RdRP gene) achieved a PPA of 98.48 % (95 % CI 91.84%-99.96%) and NPA 100.00 % (95 % CI 93.84%-100.00%) based on the E gene and N2 gene reference RT-PCR methods. The method has implications for development of point of care technology using isothermal amplification.
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Affiliation(s)
- Abu Naser Mohon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, AB, Canada
| | - Lisa Oberding
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, AB, Canada
| | - Jana Hundt
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, AB, Canada; Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Guido van Marle
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, AB, Canada
| | - Kanti Pabbaraju
- Alberta Public Health Laboratory, Alberta Precision Laboratory, Calgary, AB, Canada
| | - Byron M Berenger
- Alberta Public Health Laboratory, Alberta Precision Laboratory, Calgary, AB, Canada; Clinical Section of Microbiology, Alberta Precision Laboratories, Calgary, AB, Canada
| | - Luiz Lisboa
- Clinical Section of Microbiology, Alberta Precision Laboratories, Calgary, AB, Canada; Department Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Thomas Griener
- Clinical Section of Microbiology, Alberta Precision Laboratories, Calgary, AB, Canada; Department Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Markus Czub
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Venice Servellita
- Department Pathology and Laboratory Medicine, University of California, San Francisco, USA
| | - Charles Y Chiu
- Department Pathology and Laboratory Medicine, University of California, San Francisco, USA
| | | | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Dylan R Pillai
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, AB, Canada; Clinical Section of Microbiology, Alberta Precision Laboratories, Calgary, AB, Canada; Department Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada; Department of Medicine, University of Calgary, Calgary, AB, Canada.
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Diaz Pallares C, Griener T, Vaughan S. Ureaplasma urealyticum disseminated multifocal abscesses in an immunocompromised adult patient: a case report. BMC Infect Dis 2020; 20:47. [PMID: 31941460 PMCID: PMC6964043 DOI: 10.1186/s12879-020-4771-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/07/2020] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Ureaplasma urealyticum is a fastidious bacteria which lacks a cell wall. Extragenital infections are rare in immunocompetent adults. There are few literature reports of perinephric abscess. We present a case of non-resolving multifocal "culture-negative" abscesses in a hypogammaglobulinemic adult female due to U. urealyticum. CASE PRESENTATION 66-year-old female with a one-week history of fever, malaise and new right hip and leg pain. Past medical history was notable for chronic pancytopenia secondary to in remission B cell follicular lymphoma, ESRD on intermittent hemodialysis with bilateral nephrostomy tubes and Crohn's. CT abdomen/pelvis revealed a small left perinephric hematoma and proximal right femur fluid collection. Persistent right thigh pain led to additional ultrasound with anterior thigh collection and CT revealed an irregular rim-enhancing fluid collection in the left posterior pararenal space. Antimicrobial therapy included ertapenem and vancomycin followed by meropenem, trimethoprim-sulfamethoxazole, daptomycin and metronidazole in setting of persistent culture-negative results and clinical deterioration. Following detection of U. urealyticum by 16S rDNA PCR in both left pararenal and right trochanteric bursa abscesses doxycycline was started. Despite this, the patient died four days later. CONCLUSIONS Disseminated infection by U. urealyticum has been documented in immunocompromised adult patients with few reports of perinephric abscess. We propose that ascending genitourinary route led to perinephric abscess. The multiple disseminated fluid collections make it highly suspicious for hematogenous spread given the lack of radiographic enhancement to suggest contiguous spread. Diagnosis and treatment of U. urealyticum-disseminated infection is extremely challenging as culture is laborious and not routinely performed. Furthermore, the lack of cell wall renders beta-lactams and vancomycin ineffective and therefore requirement for "atypical" coverage. Early diagnosis and treatment are key to prevent further complications and death.
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Affiliation(s)
- Carolina Diaz Pallares
- University of Calgary Cumming School of Medicine, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada.
| | - Thomas Griener
- University of Calgary Cumming School of Medicine, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
| | - Stephen Vaughan
- University of Calgary Cumming School of Medicine, 3330 Hospital Dr NW, Calgary, AB, T2N 4N1, Canada
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