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1. Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study

Author

Choi, JooHee, Thänert, Robert, Reske, Kimberly A., Nickel, Katelin B., Olsen, Margaret A., Hink, Tiffany, Thänert, Anna, Wallace, Meghan A., Wang, Bin, Cass, Candice, Barlet, Margaret H., Struttmann, Emily L., Iqbal, Zainab Hassan, Sax, Steven R., Fraser, Victoria J., Baker, Arthur W., Foy, Katherine R., Williams, Brett, Xu, Ben, Capocci-Tolomeo, Pam, Lautenbach, Ebbing, Burnham, Carey-Ann D., Dubberke, Erik R., Dantas, Gautam, and Kwon, Jennie H.

Published
2024
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2. Early Serial Echocardiographic and Ultrasonographic Findings in Critically Ill Patients With COVID-19

Author

Calhoun, Nicole, Herrick, Judy, Hoffman, Eric, McKillop, Amanda, Murthy, Kempapura, Smith, Michael, Zayed, Martha, De Souza, Lesley, Kindle, Ryan, Kozikowski, Lori-Ann, Ouellette, Scott, Thornton-Thompson, Sherell, Bolstad, Michael, Ciottone, Robert, Coviello, Brianna, Devilla, Arnaldo, Grafals, Ana, Higgins, Conor, Ottanelli, Carlo, Redman, Kimberly, Scaffidi, Douglas, Weingart, Alexander, Lewis, Nathaniel, Olson, Samantha, Ashok, Kiran, Brennan, Connery, Mehkri, Omar, Mitchell, Megan, Poynter, Bryan, Stanley, Nicholas, Lohuis, Caitlin ten, Caspers, Sean, Erikson, Heidi, Hendrickson, Audrey, Kaus, Olivia, Maruggi, Ellen, Scharber, Tyler, Tordsen, Walker, Aston, Valerie, Bowers, Robert, Jorgensen, Jeffrey, King, Jennifer, Ali, Harith, Rothman, Richard E., Nair, Rahul, Chen, Jen-Ting, Karow, Sarah, Robart, Emily, Maldonado, Paulo Nunes, Khan, Maryiam, So, Preston, Schwartz, Elizabeth, So, Madison, Weigand, Michael, Luong, Andrea, Martinez, Jesus, Huynh, Bao, Ibrahim, Habiba, Villanueva-Vargas, Cynthia, Jung, Haeun, Villanueva-Vargas, Juliana, Quadri, Suha, Gordon, Alexandra Jun, Levitt, Joe, Perez, Cynthia, Visweswaran, Anita, Roque, Jonasel, Rivera, Adreanne, Frankel, Trevor, Goff, Jennifer, Huynh, David, Jensen, Kelly, Driver, Conner, Chambers, Ian, Nassar, Paul, Stout, Lori, Sibenaller, Zita, Walter, Alicia, Mares, Jasmine, Olson, Logan, Clinansmith, Bradley, Gershengorn, Hayley, Rivas, Carolina, McSpadden, E.J., Truscon, Rachel, Kaniclides, Anne, Thomas, Lara, Bielak, Ramsay, Valvano, Weronika Damek, Fong, Rebecca, Fitzsimmons, William J., Blair, Christopher, Valesano, Andrew, Baker, Leigh, Gilbert, Julie, Crider, Christine D., Steinbock, Kyle A., Paulson, Thomas C., Anderson, Layla A., Kampe, Christy, Johnson, Jakea, Short, Laura L., Ezzell, Lauren J., Whitsett, Margaret E., McHenry, Rendie E., Hargrave, Samarian J., Blair, Marica, Luther, Jennifer L., Pulido, Claudia Guevara, Peterson, Bryan P.M., LaRose, Mary, Landreth, Leigha, Hicks, Madeline, Parks, Lisa, Bongu, Jahnavi, McDonald, David, Cass, Candice, Seiler, Sondra, Park, David, Hink, Tiffany, Wallace, Meghan, Burnham, Carey-Ann, Arter, Olivia G., Lanspa, Michael J., Dugar, Siddharth P., Prigmore, Heather L., Boyd, Jeremy S., Rupp, Jordan D., Lindsell, Chris J., Rice, Todd W., Qadir, Nida, Lim, George W., Shiloh, Ariel L., Dieiev, Vladyslav, Gong, Michelle N., Fox, Steven W., Hirshberg, Eliotte L., Khan, Akram, Kornfield, James, Schoeneck, Jacob H., Macklin, Nicholas, Files, D.Clark, Gibbs, Kevin W., Prekker, Matthew E., Parsons-Moss, Daniel, Bown, Mikaele, Olsen, Troy D., Knox, Daniel B., Cirulis, Meghan M., Duggal, Abhijit, Tenforde, Mark W., Patel, Manish M., Self, Wesley H., and Brown, Samuel M.

Published
2023
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4. Comparison of Clostridioides difficile nucleic acid amplification test (NAAT) results using fresh and frozen stool specimens and rectal swabs

Author

Dumm, Rebekah E., primary, Burnham, Carey-Ann D., additional, Hink, Tiffany, additional, Reske, Kimberly A., additional, Struttmann, Emily, additional, Iqbal, Zainab Hassan, additional, Cass, Candice, additional, Kwon, Jennie H., additional, Olsen, Margaret A., additional, and Dubberke, Erik R., additional

Published
2024
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5. 691. Association between Clostridioides difficile Colonization, Rectal Swab NAAT Positivity, and Environmental Contamination

Author

Lee, Mary Morgan, primary, Hink, Tiffany, additional, Newcomer, Erin, additional, Fishbein, Skye, additional, Reske, Kimberly, additional, Struttmann, Emily, additional, Iqbal, Zainab, additional, Cass, Candice, additional, Kwon, Jennie H, additional, Olsen, Margaret A, additional, Burnham, Carey-Ann, additional, Dantas, Gautam, additional, and Dubberke, Erik R, additional

Published
2023
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6. 981. Sink drain environmental hygiene intervention successfully reduces burden of AROs

Author

Newcomer, Erin, primary, O’Neal, Carrie, additional, Vogt, Lucy, additional, Macdonald, David, additional, Cass, Candice, additional, Wallace, Meghan, additional, Hink, Tiffany, additional, Yerbic, Francesca, additional, Muenks, Carol, additional, Gordon, Rebecca, additional, Stewart, Henry B, additional, Amor, Mostafa, additional, Jolani, Kevin, additional, Alvarado, Kelly, additional, Valencia, Alyssa, additional, Samuels, Carleigh, additional, Peacock, Kate, additional, Park, Daniel, additional, Struttman, Emily, additional, Sukhum, Kimberley, additional, Burnham, Carey-Ann, additional, Dantas, Gautam, additional, and Kwon, Jennie H, additional

Published
2023
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8. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections

Author

Robinson, John I., Weir, William H., Crowley, Jan R., Hink, Tiffany, Reske, Kimberly A., Kwon, Jennie H., Burnham, Carey-Ann D., Dubberke, Erik R., Mucha, Peter J., and Henderson, Jeffrey P.

Subjects
Hospital patients -- Health aspects, Branched chain amino acids -- Health aspects, Fermentation -- Health aspects, Antibiotics -- Health aspects, Microbial drug resistance -- Health aspects, Infection -- Health aspects, Diarrhea -- Health aspects, Deoxycholic acid -- Health aspects, Amino acids, Bile acids, Bacteria, Health care industry
Abstract

Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization., Introduction Each year in the United States, over 450,000 cases of Clostridioides difficile infection (CDI) are associated with over 29,000 associated deaths, with attributable costs of over $2 billion (1). [...]

Published
2019
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9. Sustained Effectiveness of Pfizer-BioNTech and Moderna Vaccines Against COVID-19 Associated Hospitalizations Among Adults — United States, March–July 2021

Author

Tenforde, Mark W., Self, Wesley H., Naioti, Eric A., Ginde, Adit A., Douin, David J., Olson, Samantha M., Talbot, H. Keipp, Casey, Jonathan D., Mohr, Nicholas M., Zepeski, Anne, Gaglani, Manjusha, McNeal, Tresa, Ghamande, Shekhar, Shapiro, Nathan I., Gibbs, Kevin W., Files, D. Clark, Hager, David N., Shehu, Arber, Prekker, Matthew E., Erickson, Heidi L., Gong, Michelle N., Mohamed, Amira, Henning, Daniel J., Steingrub, Jay S., Peltan, Ithan D., Brown, Samuel M., Martin, Emily T., Monto, Arnold S., Khan, Akram, Hough, Catherine L., Busse, Laurence W., ten Lohuis, Caitlin C., Duggal, Abhijit, Wilson, Jennifer G., Gordon, Alexandra June, Qadir, Nida, Chang, Steven Y., Mallow, Christopher, Rivas, Carolina, Babcock, Hilary M., Kwon, Jennie H., Exline, Matthew C., Halasa, Natasha, Chappell, James D., Lauring, Adam S., Grijalva, Carlos G., Rice, Todd W., Jones, Ian D., Stubblefield, William B., Baughman, Adrienne, Womack, Kelsey N., Lindsell, Christopher J., Hart, Kimberly W., Zhu, Yuwei, Stephenson, Meagan, Schrag, Stephanie J., Kobayashi, Miwako, Verani, Jennifer R., Patel, Manish M., Calhoun, Nicole, Murthy, Kempapura, Herrick, Judy, McKillop, Amanda, Hoffman, Eric, Zayed, Martha, Smith, Michael, Settele, Natalie, Ettlinger, Jason, Priest, Elisa, Thomas, Jennifer, Arroliga, Alejandro, Beeram, Madhava, Kindle, Ryan, Kozikowski, Lori-Ann, De Souza, Lesley, Ouellette, Scott, Thornton-Thompson, Sherell, Tyler, Patrick, Mehkri, Omar, Ashok, Kiran, Gole, Susan, King, Alexander, Poynter, Bryan, Stanley, Nicholas, Hendrickson, Audrey, Maruggi, Ellen, Scharber, Tyler, Jorgensen, Jeffrey, Bowers, Robert, King, Jennifer, Aston, Valerie, Armbruster, Brent, Rothman, Richard E., Nair, Rahul, Chen, Jen-Ting (Tina), Karow, Sarah, Robart, Emily, Maldonado, Paulo Nunes, Khan, Maryiam, So, Preston, Levitt, Joe, Perez, Cynthia, Visweswaran, Anita, Roque, Jonasel, Rivera, Adreanne, Frankel, Trevor, Howell, Michelle, Friedel, Jennifer, Goff, Jennifer, Huynh, David, Tozier, Michael, Driver, Conner, Carricato, Michael, Foster, Alexandra, Nassar, Paul, Stout, Lori, Sibenaller, Zita, Walter, Alicia, Mares, Jasmine, Olson, Logan, Clinansmith, Bradley, Gershengorn, Hayley, McSpadden, EJ, Truscon, Rachel, Kaniclides, Anne, Thomas, Lara, Bielak, Ramsay, Valvano, Weronika Damek, Fong, Rebecca, Fitzsimmons, William J., Blair, Christopher, Valesano, Andrew L., Gilbert, Julie, Crider, Christine D., Steinbock, Kyle A., Paulson, Thomas C., Anderson, Layla A., Kampe, Christy, Johnson, Jakea, McHenry, Rendie, Blair, Marcia, Conway, Douglas, LaRose, Mary, Landreth, Leigha, Hicks, Madeline, Parks, Lisa, Bongu, Jahnavi, McDonald, David, Cass, Candice, Seiler, Sondra, Park, David, Hink, Tiffany, Wallace, Meghan, Burnham, Carey-Ann, and Arter, Olivia G.

Subjects
Adult, Male, medicine.medical_specialty, 2019-20 coronavirus outbreak, Health (social science), COVID-19 Vaccines, Time Factors, Coronavirus disease 2019 (COVID-19), Adolescent, Epidemiology, Health, Toxicology and Mutagenesis, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Young Adult, Health Information Management, Internal medicine, Medicine, Humans, Full Report, Young adult, Aged, Vaccines, Synthetic, business.industry, Vaccination, COVID-19, General Medicine, High effectiveness, Middle Aged, Confidence interval, United States, Hospitalization, Female, business
Abstract

Real-world evaluations have demonstrated high effectiveness of vaccines against COVID-19-associated hospitalizations (1-4) measured shortly after vaccination; longer follow-up is needed to assess durability of protection. In an evaluation at 21 hospitals in 18 states, the duration of mRNA vaccine (Pfizer-BioNTech or Moderna) effectiveness (VE) against COVID-19-associated hospitalizations was assessed among adults aged ≥18 years. Among 3,089 hospitalized adults (including 1,194 COVID-19 case-patients and 1,895 non-COVID-19 control-patients), the median age was 59 years, 48.7% were female, and 21.1% had an immunocompromising condition. Overall, 141 (11.8%) case-patients and 988 (52.1%) controls were fully vaccinated (defined as receipt of the second dose of Pfizer-BioNTech or Moderna mRNA COVID-19 vaccines ≥14 days before illness onset), with a median interval of 65 days (range = 14-166 days) after receipt of second dose. VE against COVID-19-associated hospitalization during the full surveillance period was 86% (95% confidence interval [CI] = 82%-88%) overall and 90% (95% CI = 87%-92%) among adults without immunocompromising conditions. VE against COVID-19- associated hospitalization was 86% (95% CI = 82%-90%) 2-12 weeks and 84% (95% CI = 77%-90%) 13-24 weeks from receipt of the second vaccine dose, with no significant change between these periods (p = 0.854). Whole genome sequencing of 454 case-patient specimens found that 242 (53.3%) belonged to the B.1.1.7 (Alpha) lineage and 74 (16.3%) to the B.1.617.2 (Delta) lineage. Effectiveness of mRNA vaccines against COVID-19-associated hospitalization was sustained over a 24-week period, including among groups at higher risk for severe COVID-19; ongoing monitoring is needed as new SARS-CoV-2 variants emerge. To reduce their risk for hospitalization, all eligible persons should be offered COVID-19 vaccination.

Published
2021

11. Persisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements

Author

Thänert, Robert, primary, Choi, JooHee, additional, Reske, Kimberly A., additional, Hink, Tiffany, additional, Thänert, Anna, additional, Wallace, Meghan A., additional, Wang, Bin, additional, Seiler, Sondra, additional, Cass, Candice, additional, Bost, Margaret H., additional, Struttmann, Emily L., additional, Iqbal, Zainab Hassan, additional, Sax, Steven R., additional, Fraser, Victoria J., additional, Baker, Arthur W., additional, Foy, Katherine R., additional, Williams, Brett, additional, Xu, Ben, additional, Capocci-Tolomeo, Pam, additional, Lautenbach, Ebbing, additional, Burnham, Carey-Ann D., additional, Dubberke, Erik R., additional, Kwon, Jennie H., additional, and Dantas, Gautam, additional

Published
2022
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15. Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults

Author

Anthony, Winston E., primary, Wang, Bin, additional, Sukhum, Kimberley V., additional, D’Souza, Alaric W., additional, Hink, Tiffany, additional, Cass, Candice, additional, Seiler, Sondra, additional, Reske, Kimberly A., additional, Coon, Christopher, additional, Dubberke, Erik R., additional, Burnham, Carey-Ann D., additional, Dantas, Gautam, additional, and Kwon, Jennie H., additional

Published
2022
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18. The Impact of Universal Glove and Gown Use on Clostridioides Difficile Acquisition: A Cluster-Randomized Trial.

Author

Morgan, Daniel J, Dubberke, Erik R, Hink, Tiffany, Paszkiewicz, Gwen, Burnham, Carey-Ann D, Pineles, Lisa, Magder, Larry, Johnson, J Kristie, Leekha, Surbhi, and Harris, Anthony D

Subjects
CROSS infection prevention, INTENSIVE care units, HOSPITALS, PUBLIC health surveillance, HOSPITAL patients, ANUS, PROTECTIVE clothing, CLOSTRIDIUM diseases, GLOVES, ROOMS, DESCRIPTIVE statistics, RESEARCH funding, DRUG resistance in microorganisms, SECONDARY analysis
Abstract

Background Clostridioides difficile is the most common cause of healthcare-associated infections in the United States. It is unknown whether universal gown and glove use in intensive care units (ICUs) decreases acquisition of C. difficile. Methods This was a secondary analysis of a cluster-randomized trial in 20 medical and surgical ICUs in 20 US hospitals from 4 January 2012 to 4 October 2012. After a baseline period, ICUs were randomized to standard practice for glove and gown use versus the intervention of all healthcare workers being required to wear gloves and gowns for all patient contact and when entering any patient room (contact precautions). The primary outcome was acquisition of toxigenic C. difficile determined by surveillance cultures collected on admission and discharge from the ICU. Results A total of 21 845 patients had both admission and discharge perianal swabs cultured for toxigenic C. difficile. On admission, 9.43% (2060/21 845) of patients were colonized with toxigenic C. difficile. No significant difference was observed in the rate of toxigenic C. difficile acquisition with universal gown and glove use. Differences in acquisition rates in the study period compared with the baseline period in control ICUs were 1.49 per 100 patient-days versus 1.68 per 100 patient-days in universal gown and glove ICUs (rate difference, −0.28; generalized linear mixed model, P =.091). Conclusions Glove and gown use for all patient contact in medical and surgical ICUs did not result in a reduction in the acquisition of C. difficile compared with usual care. Clinical Trials Registration NCT01318213. [ABSTRACT FROM AUTHOR]

Published
2023
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24. Additional file 5 of Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study

Author

Langdon, Amy, Schwartz, Drew J., Bulow, Christopher, Xiaoqing Sun, Hink, Tiffany, Reske, Kimberly A., Jones, Courtney, Carey-Ann D. Burnham, Dubberke, Erik R., and Dantas, Gautam

Abstract

Additional file 5 Fig. S8. Relative abundance of ASVs corresponding to A) Enterobacter, B) Escherichia, C) Citrobacter, and D) Enterococcus tracked temporally after second dose of RBX2660 in the RI group. Fig. S9. Patient origin ARGs over time after A) first RBX2660 and B) second RBX2660 in the RI group. All comparisons non-significant as determined by pairwise Wilcoxon with Benjamini Hochberg correction. n = 17 total patients with A) 27 and B) 45 samples. Fig. S10. Abundance of resistance genes in each metagenomic sample compared to their DFD for resistance genes that were not detected in patients’ day 0 samples or in the donors. For these genes, their abundance and the distance from donor are uncorrelated.

Published
2021
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25. Additional file 1 of Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study

Author

Langdon, Amy, Schwartz, Drew J., Bulow, Christopher, Xiaoqing Sun, Hink, Tiffany, Reske, Kimberly A., Jones, Courtney, Carey-Ann D. Burnham, Dubberke, Erik R., and Dantas, Gautam

Abstract

Additional file 1: Fig. S1. Study protocol for Phase II clinical trial NCT01925417 adapted from reference [25]. Samples specifically used for this study depicted in Fig. 1. Fig. S2. The relative abundance of bacterial phyla in all patients are shown at day 0 (panel A) and in all donor samples from the 4 donors (panel B). The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug and in red if they required repeat intervention. A) Patient ID is listed after the letter A on the x axis with relative abundance of each phylum in stacked bar chart format on the y-axis. B) Donor samples are named as donor number.samplenumber followed by DS for donor substance. Fig. S3. linear discriminant analysis compares functional pathway abundance, as annotated by HUMAnN2 and visualized with LEfSe, at day 7 between the two outcome groups. In red are pathways more enriched in the reintervention (RI) group, while those patients who recovered after a single treatment had a significantly higher abundance of the pathways in green. Fig. S4. Shown are the HUMAnN2 functional pathway abundances for all patients with both day 0 and day 7 samples. Fig. S5. The relative abundance of Akkermansia muciniphila ASV 2 is shown over time stratified by outcome. A) The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug, in red if they required repeat intervention, and black if they come from the donor. B) Akkermansia muciniphila ASV2 abundance after re-intervention. Fig. S6. The PCA analysis from Main Fig. 2 is reproduced here via the dual principal component function of phyloseq, which uses Euclidean distances. The overall taxonomic composition is graphed in Panel A, while Panel B shows the directionality of the influence of individual taxa upon those samples. Fig. S7. A) The relative abundance of Clostridioides difficile is tracked here using species-specific toxin genes detected in metagenomic sequences via ShortBRED. The gene count was normalized to the number of metagenomic reads and expressed in terms of copies per metagenome. B) The relative abundance for the ASV corresponding to C. difficile is shown in the bottom panel. The patient IDs are marked in gray if symptoms resolved in a single dose of the study drug and in red if they required repeat intervention.

Published
2021
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27. Additional file 1 of Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

Author

Kwak, Suryang, Choi, JooHee, Hink, Tiffany, Reske, Kimberly A., Blount, Kenneth, Jones, Courtney, Bost, Margaret H., Xiaoqing Sun, Carey-Ann D. Burnham, Dubberke, Erik R., and Dantas, Gautam

Abstract

Additional file 1: Figure S1. Taxonomic overview of patient stool samples at the genus level. Figure S2. Taxonomic shift by treatments (related Fig. 2). Figure S3. The effect of antibiotics prior to study drug on taxonomic shift by RBX2660 (related Fig. 2 and 3). Figure S4. Bray-Curtis dissimilarities between patients and respective RBX2660 (DR) or other random RBX2660 (DO). Figure S5. Changes in the Bray-Curtis dissimilarities between a patient and corresponding donor. Figure S6. Transplantation indices (TIs) and pseudo transplantation indices (pTIs). Figure S7. Additional discriminative features of the obstinate patients (related Fig. 3). Figure S8. Comparison of resistome compositions. Figure S9. Random forest classifier successfully distinguished between donor and patient baseline resistomes (related Fig. 5). Figure S10. Average nucleotide identity (ANI) and core genome phylogeny of E. coli isolates. Figure S11. Average nucleotide identity (ANI) and core genome phylogeny of VRE isolates. Figure S12. Antibiotic susceptibility testing (AST).

Published
2020
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28. The Gut Microbiome and Resistome of Healthy Volunteers are Restructured After Short Courses of Antibiotics

Author

Anthony, Winston, primary, Sukhum, Kimberley, additional, Cass, Candice, additional, Reske, Kimberly, additional, Seiler, Sondra, additional, Hink, Tiffany, additional, Coon, Christopher, additional, D'Souza, Alaric, additional, Wang, Bin, additional, Sun, Sherry, additional, Dubberke, Erik, additional, Burnham, Carey-Ann, additional, Dantas, Gautam, additional, and Kwon, Jennie H., additional

Published
2020
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29. Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile.

Author

Kwon, Jennie H, O'Neil, Caroline A, Hink, Tiffany, Reske, Kimberly A, Bosserman, Rachel E, Dubberke, Erik R, and Burnham, Carey-Ann D

Subjects
ROTAVIRUSES, DIARRHEA, NOROVIRUS diseases, CLOSTRIDIOIDES difficile, ENZYME-linked immunosorbent assay, ROTAVIRUS diseases, SYMPTOMS, HOSPITAL patients, AGAR plates
Abstract

Background: Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C. difficile toxin enzyme immunoassay (tEIA) testing after an initial tEIA test was negative. Methods: For patients age ≥18 years who had a second C. difficile tEIA test ordered within 96 h after a negative tEIA test, remnant fecal specimens from the first (negative) tEIA test were evaluated using the BioFire FilmArray Gastrointestinal Panel PCR, C. difficile toxigenic culture, and culture on a blood agar plate (BAP) to identify other potential causes of infectious diarrhea. Growth of organisms on the BAP was also used to assess potential disruptions in the gastrointestinal microbiota. Results: Among 84 remnant specimens, toxigenic C. difficile was identified in 9 (11%) by culture or PCR, while potential alternative causes of infectious diarrhea, including norovirus, rotavirus, enteropathogenic Escherichia coli, and Salmonella, were identified in 11 specimens (13%) by PCR. For the majority of patients, no infectious cause of diarrhea was identified, but 84% exhibited disrupted gastrointestinal microbiota, which may contribute to diarrhea. Conclusions: When a hospitalized patient has a negative C. difficile tEIA test but continues to have diarrhea, alternative infectious and noninfectious causes of diarrhea should be considered. If the patient has clinical signs and symptoms suggestive of infection or risk factors for gastrointestinal infection, laboratory testing for other etiologic agents may be appropriate. [ABSTRACT FROM AUTHOR]

Published
2022
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30. Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

Author

Kwak, Suryang, primary, Choi, JooHee, additional, Hink, Tiffany, additional, Reske, Kimberly A., additional, Blount, Kenneth, additional, Jones, Courtney, additional, Bost, Margaret H., additional, Sun, Xiaoqing, additional, Burnham, Carey-Ann D., additional, Dubberke, Erik R., additional, and Dantas, Gautam, additional

Published
2020
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31. The effect of microbiota-based investigational drug RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

Author

Kwak, Suryang, primary, Choi, JooHee, additional, Hink, Tiffany, additional, Reske, Kimberly A., additional, Blount, Kenneth, additional, Jones, Courtney, additional, Bost, Margaret H., additional, Sun, Xiaoqing, additional, Burnham, Carey-Ann D., additional, Dubberke, Erik R., additional, and Dantas, Gautam, additional

Published
2020
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35. 2847. Comparative Genomics and Clonal Tracking of Multi-drug-Resistant Uropathogens Implicates the Fecal Microbiome as a Potential Reservoir for Recurrent Urinary Tract Infections

Author

Thanert, Robert, primary, Reske, Kimberly, additional, Hink, Tiffany, additional, Wallace, Meghan, additional, Wang, Bin, additional, Schwartz, Drew, additional, Burnham, Carey-Ann, additional, Seiler, Sondra, additional, Cass, Candice, additional, Dubberke, Erik R, additional, Dantas, Gautam, additional, and Kwon, Jennie H, additional

Published
2019
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36. A randomized controlled trial of Lactobacillus rhamnosusGG on antimicrobial-resistant organism colonization

Author

Rauseo, Adriana M., Hink, Tiffany, Reske, Kimberly A., Seiler, Sondra M., Bommarito, Kerry M., Fraser, Victoria J., Burnham, Carey-Ann D., and Dubberke, Erik R.

Abstract

AbstractObjective:Alteration of the colonic microbiota following antimicrobial exposure allows colonization by antimicrobial-resistant organisms (AROs). Ingestion of a probiotic, such as Lactobacillus rhamnosusGG (LGG), could prevent colonization or infection with AROs by promoting healthy colonic microbiota. The purpose of this trial was to determine the effect of LGG administration on ARO colonization in hospitalized patients receiving antibiotics.Design:Prospective, double-blinded, randomized controlled trial of LGG versus placebo among patients receiving broad-spectrum antibiotics.Setting:Tertiary care center.Patients:In total, 88 inpatients receiving broad-spectrum antibiotics were enrolled.Intervention:Patients were randomized to receive 1 capsule containing 1×1010cells of LGG twice daily (n = 44) or placebo (n = 44), stratified by ward type. Stool or rectal-swab specimens were collected for culture at enrollment, during admission, and at discharge. Using selective media, specimens were cultured for Clostridioides difficile, vancomycin-resistant Enterococcusspp (VRE), and antibiotic-resistant gram-negative bacteria. The primary outcome was any ARO acquisition. Secondary outcomes included loss of any ARO if colonized at enrollment, and acquisition or loss of individual ARO.Results:ARO colonization prevalence at study enrollment was similar (LGG 39% vs placebo 39%). We detected no difference in any ARO acquisition (LGG 30% vs placebo 33%; OR,1.19; 95% CI, 0.38–3.75) nor for any individual ARO acquisition. There was no difference in the loss of any ARO (LGG 18% vs placebo 24%; OR, 1.44; 95% CI, 0.27–7.68) nor for any individual ARO.Conclusion:LGG administration neither prevented acquisition of ARO nor accelerated loss of ARO colonization.

Published
2022
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37. Comparative Genomics of Antibiotic-Resistant Uropathogens Implicates Three Routes for Recurrence of Urinary Tract Infections

Author

Thänert, Robert, primary, Reske, Kimberly A., additional, Hink, Tiffany, additional, Wallace, Meghan A., additional, Wang, Bin, additional, Schwartz, Drew J., additional, Seiler, Sondra, additional, Cass, Candice, additional, Burnham, Carey-Ann D., additional, Dubberke, Erik R., additional, Kwon, Jennie H., additional, and Dantas, Gautam, additional

Published
2019
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38. Impact of Amoxicillin-Clavulanate followed by Autologous Fecal Microbiota Transplantation on Fecal Microbiome Structure and Metabolic Potential

Author

Bulow, Christopher, primary, Langdon, Amy, additional, Hink, Tiffany, additional, Wallace, Meghan, additional, Reske, Kimberly A., additional, Patel, Sanket, additional, Sun, Xiaoqing, additional, Seiler, Sondra, additional, Jones, Susan, additional, Kwon, Jennie H., additional, Burnham, Carey-Ann D., additional, Dantas, Gautam, additional, and Dubberke, Erik R., additional

Published
2018
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40. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study.

Author

Langdon, Amy, Schwartz, Drew J., Bulow, Christopher, Sun, Xiaoqing, Hink, Tiffany, Reske, Kimberly A., Jones, Courtney, Burnham, Carey-Ann D., Dubberke, Erik R., and Dantas, Gautam

Subjects
SHOTGUN sequencing, DRUG efficacy, GUT microbiome, GENES, DRUG resistance in bacteria, BACTERIA, INFECTION
Abstract

Background: Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI. Methods: An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms. Results: Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted. Conclusions: Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others. Trial registration: ClinicalTrials.gov, NCT01925417; registered on August 19, 2013. [ABSTRACT FROM AUTHOR]

Published
2021
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43. 2322

Author

Elizabeth Langdon, Amy, primary, Bulow, Christopher, additional, Reske, Kim, additional, Sun, Sherry, additional, Hink, Tiffany, additional, Jones, Courtney, additional, Burnham, Carey-Ann D., additional, Dubberke, Erik R., additional, and Dantas, Gautam, additional

Published
2017
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47. Assessment of antibiotic-resistant organism transmission among rooms of hospitalized patients, healthcare personnel, and the hospital environment utilizing surrogate markers and selective bacterial cultures

Author

Kwon, Jennie H., Reske, Kimberly, O’Neil, Caroline A., Cass, Candice, Seiler, Sondra, Wallace, Meghan A., Hink, Tiffany, Liang, Stephen Y., Fraser, Victoria J., Burnham, Carey-Ann D., and Dubberke, Erik R.

Abstract

AbstractObjective:To assess potential transmission of antibiotic-resistant organisms (AROs) using surrogate markers and bacterial cultures.Design:Pilot study.Setting:A 1,260-bed tertiary-care academic medical center.Participants:The study included 25 patients (17 of whom were on contact precautions for AROs) and 77 healthcare personnel (HCP).Methods:Fluorescent powder (FP) and MS2 bacteriophage were applied in patient rooms. HCP visits to each room were observed for 2–4 hours; hand hygiene (HH) compliance was recorded. Surfaces inside and outside the room and HCP skin and clothing were assessed for fluorescence, and swabs were collected for MS2 detection by polymerase chain reaction (PCR) and selective bacterial cultures.Results:Transfer of FP was observed for 20 rooms (80%) and 26 HCP (34%). Transfer of MS2 was detected for 10 rooms (40%) and 15 HCP (19%). Bacterial cultures were positive for 1 room and 8 HCP (10%). Interactions with patients on contact precautions resulted in fewer FP detections than interactions with patients not on precautions (P< .001); MS2 detections did not differ by patient isolation status. Fluorescent powder detections did not differ by HCP type, but MS2 was recovered more frequently from physicians than from nurses (P= .03). Overall, HH compliance was better among HCP caring for patients on contact precautions than among HCP caring for patients not on precautions (P= .003), among nurses than among other nonphysician HCP at room entry (P= .002), and among nurses than among physicians at room exit (P= .03). Moreover, HCP who performed HH prior to assessment had fewer fluorescence detections (P= .008).Conclusions:Contact precautions were associated with greater HCP HH compliance and reduced detection of FP and MS2.

Published
2020
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48. Impact of an electronic hard-stop clinical decision support tool to limit repeat Clostridioides difficiletoxin enzyme immunoassay testing on test utilization

Author

Kwon, Jennie H., Reske, Kimberly A., Hink, Tiffany, Jackups, Ronald, Burnham, Carey-Ann D., and Dubberke, Erik R.

Abstract

AbstractWe performed an intervention evaluating the impact of an electronic hard-stop clinical decision support tool on repeat Clostridioides difficile(CD) toxin enzyme immunoassay (T-EIA) testing. The CD testing rate and number of admissions with repeat tests decreased significantly postintervention (P< .01 for both); the percentage of positive tests was unchanged (P= .27).

Published
2019
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