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1. Fungal Whole-Genome Sequencing for Species Identification: From Test Development to Clinical Utilization.

Author

Salem-Bango, Zackary, Price, Travis K, Chan, June L, Chandrasekaran, Sukantha, Garner, Omai B, and Yang, Shangxin

Subjects
28S rRNA, ITS, beta-tubulin, fungal infections, fungal species identification, k-mer tree, next-generation sequencing, whole-genome sequencing, Infectious Diseases, Genetics, Human Genome, Biotechnology, Detection, screening and diagnosis, 4.2 Evaluation of markers and technologies, Good Health and Well Being
Abstract

Using next-generation sequencing (NGS), we developed and validated a whole-genome sequencing (WGS)-based clinical test for fungal species identification on clinical isolates. The identification is mainly based on the fungal ribosomal internal transcribed spacer (ITS) region as the primary marker, and additional marker and genomic analysis applied for species within the Mucorales family (using the 28S rRNA gene) and Aspergillus genus (using the beta-tubulin gene and k-mer tree-based phylogenetic clustering). The validation study involving 74 unique fungal isolates (22 yeasts, 51 molds, and 1 mushroom-forming fungus) showed high accuracy, with 100% (74/74) concordance on the genus-level identifications and 89.2% (66/74) concordance on the species level. The 8 discrepant results were due to either the limitation of conventional morphology-based methodology or taxonomic changes. After one year of implementation in our clinical laboratory, this fungal NGS test was utilized in 29 cases; the majority of them were transplant and cancer patients. We demonstrated the utility of this test by detailing five case studies, in which accurate fungal species identification led to correct diagnosis, treatment adjustment or was ruled out for hospital acquired infection. This study provides a model for validation and implementation of WGS for fungal identification in a complex health system that serves a large immunocompromised patient population.

Published
2023

2. Case Report: Symptomatic Herpes Simplex Virus Type 2 and Monkeypox Coinfection in an Adult Male.

Author

Prabaker, Kavitha K, de St Maurice, Annabelle, Uslan, Daniel Z, Yen, George C, Manavi, Shadi, Gray, Hannah K, Caldera, Juan R, Chan, June L, Garner, Omai B, and Yang, Shangxin

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Rare Diseases, Infection, Adult, Male, Humans, Herpesvirus 2, Human, Coinfection, Monkeypox, Polymerase Chain Reaction, Medical and Health Sciences, Tropical Medicine, Biomedical and clinical sciences, Health sciences
Abstract

A 39-year-old man presented with a history of fatigue, malaise, and rash with varied morphology on his perianal region. Polymerase chain reaction testing of the lesions confirmed coinfection with monkeypox and herpes simplex virus type 2. We emphasize the difficulty in distinguishing between monkeypox virus and herpes simplex virus type 2 based on history and examination alone.

Published
2022

6. Bacteroides fragilis Toxin Coordinates a Pro-carcinogenic Inflammatory Cascade via Targeting of Colonic Epithelial Cells

Author

Chung, Liam, Orberg, Erik Thiele, Geis, Abby L, Chan, June L, Fu, Kai, Shields, Christina E DeStefano, Dejea, Christine M, Fathi, Payam, Chen, Jie, Finard, Benjamin B, Tam, Ada J, McAllister, Florencia, Fan, Hongni, Wu, Xinqun, Ganguly, Sudipto, Lebid, Andriana, Metz, Paul, Van Meerbeke, Sara W, Huso, David L, Wick, Elizabeth C, Pardoll, Drew M, Wan, Fengyi, Wu, Shaoguang, Sears, Cynthia L, and Housseau, Franck

Subjects
Biochemistry and Cell Biology, Biomedical and Clinical Sciences, Biological Sciences, Digestive Diseases, Colo-Rectal Cancer, Cancer, Adenomatous Polyposis Coli Protein, Animals, Bacterial Toxins, Bacteroides fragilis, Carcinogenesis, Cell Line, Tumor, Colon, Colorectal Neoplasms, Enzyme Activation, Epithelial Cells, Female, Gene Deletion, HT29 Cells, Humans, Inflammation, Interleukin-17, Male, Metalloendopeptidases, Mice, Mice, Inbred C57BL, Mice, Knockout, Myeloid Cells, Receptors, Interleukin-17, Receptors, Interleukin-8B, STAT3 Transcription Factor, Transcription Factor RelA, Nf-κB, STAT-3, colorectal cancer, inflammation, mucosal immunology, myeloid cells, Microbiology, Medical Microbiology, Immunology, Biochemistry and cell biology, Medical microbiology
Abstract

Pro-carcinogenic bacteria have the potential to initiate and/or promote colon cancer, in part via immune mechanisms that are incompletely understood. Using ApcMin mice colonized with the human pathobiont enterotoxigenic Bacteroides fragilis (ETBF) as a model of microbe-induced colon tumorigenesis, we show that the Bacteroides fragilis toxin (BFT) triggers a pro-carcinogenic, multi-step inflammatory cascade requiring IL-17R, NF-κB, and Stat3 signaling in colonic epithelial cells (CECs). Although necessary, Stat3 activation in CECs is not sufficient to trigger ETBF colon tumorigenesis. Notably, IL-17-dependent NF-κB activation in CECs induces a proximal to distal mucosal gradient of C-X-C chemokines, including CXCL1, that mediates the recruitment of CXCR2-expressing polymorphonuclear immature myeloid cells with parallel onset of ETBF-mediated distal colon tumorigenesis. Thus, BFT induces a pro-carcinogenic signaling relay from the CEC to a mucosal Th17 response that results in selective NF-κB activation in distal colon CECs, which collectively triggers myeloid-cell-dependent distal colon tumorigenesis.

Published
2018

9. Supplementary Table from Human Colon Cancer–Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice

Author

Drewes, Julia L., primary, Chen, Jie, primary, Markham, Nicholas O., primary, Knippel, Reece J., primary, Domingue, Jada C., primary, Tam, Ada J., primary, Chan, June L., primary, Kim, Lana, primary, McMann, Madison, primary, Stevens, Courtney, primary, Dejea, Christine M., primary, Tomkovich, Sarah, primary, Michel, John, primary, White, James R., primary, Mohammad, Fuad, primary, Campodónico, Victoria L., primary, Heiser, Cody N., primary, Wu, Xinqun, primary, Wu, Shaoguang, primary, Ding, Hua, primary, Simner, Patricia, primary, Carroll, Karen, primary, Shrubsole, Martha J., primary, Anders, Robert A., primary, Walk, Seth T., primary, Jobin, Christian, primary, Wan, Fengyi, primary, Coffey, Robert J., primary, Housseau, Franck, primary, Lau, Ken S., primary, and Sears, Cynthia L., primary

Published
2023
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10. Data from Human Colon Cancer–Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice

Author

Drewes, Julia L., primary, Chen, Jie, primary, Markham, Nicholas O., primary, Knippel, Reece J., primary, Domingue, Jada C., primary, Tam, Ada J., primary, Chan, June L., primary, Kim, Lana, primary, McMann, Madison, primary, Stevens, Courtney, primary, Dejea, Christine M., primary, Tomkovich, Sarah, primary, Michel, John, primary, White, James R., primary, Mohammad, Fuad, primary, Campodónico, Victoria L., primary, Heiser, Cody N., primary, Wu, Xinqun, primary, Wu, Shaoguang, primary, Ding, Hua, primary, Simner, Patricia, primary, Carroll, Karen, primary, Shrubsole, Martha J., primary, Anders, Robert A., primary, Walk, Seth T., primary, Jobin, Christian, primary, Wan, Fengyi, primary, Coffey, Robert J., primary, Housseau, Franck, primary, Lau, Ken S., primary, and Sears, Cynthia L., primary

Published
2023
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11. Supplementary Figure from Human Colon Cancer–Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice

Author

Drewes, Julia L., primary, Chen, Jie, primary, Markham, Nicholas O., primary, Knippel, Reece J., primary, Domingue, Jada C., primary, Tam, Ada J., primary, Chan, June L., primary, Kim, Lana, primary, McMann, Madison, primary, Stevens, Courtney, primary, Dejea, Christine M., primary, Tomkovich, Sarah, primary, Michel, John, primary, White, James R., primary, Mohammad, Fuad, primary, Campodónico, Victoria L., primary, Heiser, Cody N., primary, Wu, Xinqun, primary, Wu, Shaoguang, primary, Ding, Hua, primary, Simner, Patricia, primary, Carroll, Karen, primary, Shrubsole, Martha J., primary, Anders, Robert A., primary, Walk, Seth T., primary, Jobin, Christian, primary, Wan, Fengyi, primary, Coffey, Robert J., primary, Housseau, Franck, primary, Lau, Ken S., primary, and Sears, Cynthia L., primary

Published
2023
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12. Supplementary Table S5 from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Author

DeStefano Shields, Christina E., primary, White, James R., primary, Chung, Liam, primary, Wenzel, Alyssa, primary, Hicks, Jessica L., primary, Tam, Ada J., primary, Chan, June L., primary, Dejea, Christine M., primary, Fan, Hongni, primary, Michel, John, primary, Maiuri, Ashley R., primary, Sriramkumar, Shruthi, primary, Podicheti, Ram, primary, Rusch, Douglas B., primary, Wang, Hao, primary, De Marzo, Angelo M., primary, Besharati, Sepideh, primary, Anders, Robert A., primary, Baylin, Stephen B., primary, O'Hagan, Heather M., primary, Housseau, Franck, primary, and Sears, Cynthia L., primary

Published
2023
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13. Data from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Author

DeStefano Shields, Christina E., primary, White, James R., primary, Chung, Liam, primary, Wenzel, Alyssa, primary, Hicks, Jessica L., primary, Tam, Ada J., primary, Chan, June L., primary, Dejea, Christine M., primary, Fan, Hongni, primary, Michel, John, primary, Maiuri, Ashley R., primary, Sriramkumar, Shruthi, primary, Podicheti, Ram, primary, Rusch, Douglas B., primary, Wang, Hao, primary, De Marzo, Angelo M., primary, Besharati, Sepideh, primary, Anders, Robert A., primary, Baylin, Stephen B., primary, O'Hagan, Heather M., primary, Housseau, Franck, primary, and Sears, Cynthia L., primary

Published
2023
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14. Supplementary Figures S1-S6, Table S4, Table S6 from Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Author

DeStefano Shields, Christina E., primary, White, James R., primary, Chung, Liam, primary, Wenzel, Alyssa, primary, Hicks, Jessica L., primary, Tam, Ada J., primary, Chan, June L., primary, Dejea, Christine M., primary, Fan, Hongni, primary, Michel, John, primary, Maiuri, Ashley R., primary, Sriramkumar, Shruthi, primary, Podicheti, Ram, primary, Rusch, Douglas B., primary, Wang, Hao, primary, De Marzo, Angelo M., primary, Besharati, Sepideh, primary, Anders, Robert A., primary, Baylin, Stephen B., primary, O'Hagan, Heather M., primary, Housseau, Franck, primary, and Sears, Cynthia L., primary

Published
2023
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15. Human Colon Cancer–Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice

Author

Drewes, Julia L., primary, Chen, Jie, additional, Markham, Nicholas O., additional, Knippel, Reece J., additional, Domingue, Jada C., additional, Tam, Ada J., additional, Chan, June L., additional, Kim, Lana, additional, McMann, Madison, additional, Stevens, Courtney, additional, Dejea, Christine M., additional, Tomkovich, Sarah, additional, Michel, John, additional, White, James R., additional, Mohammad, Fuad, additional, Campodónico, Victoria L., additional, Heiser, Cody N., additional, Wu, Xinqun, additional, Wu, Shaoguang, additional, Ding, Hua, additional, Simner, Patricia, additional, Carroll, Karen, additional, Shrubsole, Martha J., additional, Anders, Robert A., additional, Walk, Seth T., additional, Jobin, Christian, additional, Wan, Fengyi, additional, Coffey, Robert J., additional, Housseau, Franck, additional, Lau, Ken S., additional, and Sears, Cynthia L., additional

Published
2022
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16. Prevalence of carbapenemase‐producing organisms among hospitalized solid organ transplant recipients, five US hospitals, 2019–2020

Author

Chan, June L., primary, Nazarian, Elizabeth, additional, Musser, Kimberlee A., additional, Snavely, Emily A., additional, Fung, Monica, additional, Doernberg, Sarah B., additional, Pouch, Stephanie M., additional, Leekha, Surbhi, additional, Anesi, Judith A., additional, Kodiyanplakkal, Rosy Priya L., additional, Turbett, Sarah E., additional, Spalding Walters, Maroya, additional, and Epstein, Lauren, additional

Published
2022
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18. Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Author

DeStefano Shields, Christina E., primary, White, James R., additional, Chung, Liam, additional, Wenzel, Alyssa, additional, Hicks, Jessica L., additional, Tam, Ada J., additional, Chan, June L., additional, Dejea, Christine M., additional, Fan, Hongni, additional, Michel, John, additional, Maiuri, Ashley R., additional, Sriramkumar, Shruthi, additional, Podicheti, Ram, additional, Rusch, Douglas B., additional, Wang, Hao, additional, De Marzo, Angelo M., additional, Besharati, Sepideh, additional, Anders, Robert A., additional, Baylin, Stephen B., additional, O'Hagan, Heather M., additional, Housseau, Franck, additional, and Sears, Cynthia L., additional

Published
2021
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19. 918. Pilot Surveillance for Carbapenemase Gene-positive Organisms Among Hospitalized Solid Organ Transplant Recipients

Author

Chan, June L, primary, Nazarian, Elizabeth, additional, Musser, Kimberlee A, additional, Fung, Monica, additional, Doernberg, Sarah B, additional, Pouch, Stephanie M, additional, Leekha, Surbhi, additional, Anesi, Judith A, additional, Kodiyanplakkal, Rosy Priya, additional, Turbett, Sarah, additional, Walters, Maroya Spalding, additional, and Epstein, Lauren, additional

Published
2020
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23. 629 – Colorectal Cancer-Associated Bacteria Induce Th1 and Th17 Mucosal Immune Responses in Germ-Free Mice

Author

Domingue, Jada C., primary, Drewes, Julia L., additional, Stevens, Courtney, additional, Chan, June L., additional, McMann, Madison, additional, Ding, Hua, additional, Bourdas, Dimitrios, additional, Ellis, Brandon, additional, Simner, Patricia, additional, Carroll, Karen, additional, Llosa, Nicolas, additional, Housseau, Franck, additional, and Sears, Cynthia L., additional

Published
2019
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24. Su1983 – Lack of Preventive Dental Care is Associated with Sessile Serrated Polyps in a Screening Colonoscopy Cohort

Author

Rifkin, Samara, primary, Drewes, Julia L., additional, McMann, Madison, additional, Chan, June L., additional, Spence, Emma, additional, Levine, Louis, additional, Stevens, Courtney, additional, Gills, Joell J., additional, Schearer, Pamela, additional, Gerhart, Stacy, additional, Schiller, Amy L., additional, Donato, Karin, additional, Bourdas, Dimitrios, additional, Ellis, Brandon, additional, Simner, Patricia, additional, Carroll, Karen, additional, Kafonek, David, additional, Cromwell, David, additional, Bedine, Marshall, additional, Mullin, Gerard, additional, Gonzalez-Velez, Eduardo, additional, Veloso, Hazel Marie Galon, additional, Luna, Louis La, additional, Hylind, Linda, additional, Giardiello, Francis, additional, and Sears, Cynthia L., additional

Published
2019
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26. 1058 - The Probiotic Potential of Non-Toxigenic Bacteroides Fragilis to Prevent Colitis and Tumorigenesis

Author

Chan, June L., primary, Wu, Shaoguang, additional, Geis, Abby L., additional, Chan, Gabrielle V., additional, Gomes, Talles A., additional, Beck, Sarah E., additional, Wu, Xinqun, additional, Fan, Hongni, additional, Tam, Ada, additional, Ding, Hua, additional, Pardoll, Drew, additional, Housseau, Franck, additional, and Sears, Cynthia L., additional

Published
2018
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27. Non-toxigenic Bacteroides fragilis(NTBF) administration reduces bacteria-driven chronic colitis and tumor development independent of polysaccharide A

Author

Chan, June L., Wu, Shaoguang, Geis, Abby L., Chan, Gabrielle V., Gomes, Talles A.M., Beck, Sarah E., Wu, Xinqun, Fan, Hongni, Tam, Ada J., Chung, Liam, Ding, Hua, Wang, Hao, Pardoll, Drew M., Housseau, Franck, and Sears, Cynthia L.

Abstract

Polysaccharide A (PSA), an immunogenic capsular component of non-toxigenic Bacteroides fragilis(NTBF) strain NCTC 9343, is reported to promote mucosal immune development and suppress colitis. Contrastingly, enterotoxigenic Bacteroides fragilis(ETBF) is highly associated with inflammatory bowel disease (IBD) and colorectal cancer (CRC), rapidly inducing IL-17-dependent murine colitis and tumorigenesis. In specific-pathogen-free (SPF) C57BL/6 wild-type (WT) and multiple intestinal neoplasia (MinApc716+/−) mice, we show that sequential treatment of the NTBF strain, 9343, followed by the ETBF strain, 86-5443-2-2 (86), diminished colitis and tumorigenesis. Mice treated simultaneously with 9343 and 86 exhibited both severe colitis and tumorigenesis. Abrogated disease severity in sequentially treated mice was attributed to 9343 strain dominance and decreased IL-17A, but 86 colonization prior to or simultaneous with 9343 mitigated the anti-inflammatory effect of 9343. Remarkably, 9343-mediated protection was independent of PSA, as sequentially treated mice receiving ΔPSA 9343 exhibited similar protection. Further, SPF WT and Min mice colonized with PSA-competent or PSA-deficient 9343 exhibited similar IL-10, IL-17, and IFN-γ responses. Treatment of 86-colonized mice with 9343 failed to disrupt 86 pathogenesis. Our findings demonstrate that 9343 colonization, independent of PSA, offers prophylaxis against colitis-inducing 86 but may not be a valid therapy once colitis is established.

Published
2019
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30. Development of a Rapid and High Throughput Multiplex Real-time PCR Assay for Mycoplasma hominisand Ureaplasmaspecies

Author

Chan, June L., Cerón, Stacey, Horiuchi, Stephanie M., Yap, Jewell P., Chihuahua, Erika G., Tsan, Allison T., Kamau, Edwin, and Yang, Shangxin

Abstract

Bacterial commensals of the human genitourinary tract, Mycoplasma hominisand Ureaplasmaspecies (parvumand urealyticum) can be sexually transmitted, with the potential to cause non-gonococcal urethritis, pelvic inflammatory disease, and infertility. M. hominisand Ureaplasmaspp. may also cause severe invasive infections in immunocompromised patients. Current culture-based methods for Mycoplasma/Ureaplasmaidentification are costly and laborious, with a turnaround time between 1-2 weeks. We developed a high-throughput, real-time multiplex PCR assay for the rapid detection of M. hominisand Ureaplasmaspp. in urine, genital swab, body fluid, and tissue. In total, 282 specimens were tested by PCR and compared with historical culture results; a molecular reference method was used to moderate discrepancies. Overall result agreement was 99% for M. hominis(97% positive percent agreement (PPA), 100% negative percent agreement (NPA)) and 96% for Ureaplasmaspp. (96% PPA, 97% NPA). Specimen stability was validated for up to 7 days at room temperature. This multiplex molecular assay was designed for implementation in a high-complexity clinical microbiology lab. With this method, >90 samples can be tested in one run, with a turnaround time of 4-5 hours from specimen extraction to reporting of results. This PCR test is also more labor- and cost-effective than the conventional culture-based test, thus improving laboratory efficiency and alleviating strains due to labor shortages.

Published
2023
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33. Subinhibitory Concentrations of Protein Synthesis-Inhibiting Antibiotics Promote Increased Expression of the agrVirulence Regulator and Production of Phenol-Soluble Modulin Cytolysins in Community-Associated Methicillin-Resistant Staphylococcus aureus

Author

Joo, Hwang-Soo, Chan, June L., Cheung, Gordon Y. C., and Otto, Michael

Abstract

ABSTRACTTetracycline, clindamycin, and other protein synthesis inhibitors at subinhibitory concentrations significantly increased the expression of the pivotal virulence regulator agrand production of the agr-regulated cytolytic phenol-soluble modulins in the community-associated methicillin-resistant Staphylococcus aureus(CA-MRSA) strain USA300. Our results suggest that such protein synthesis inhibitors may exacerbate the progression of CA-MRSA disease when applied at concentrations that are too low or when treating infections caused by strains resistant to those antibiotics.

Published
2010
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