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Medeiros MCD, The S, Bellile E, Russo N, Schmitd L, Danella E, Singh P, Banerjee R, Bassis C, Murphy GR, Sartor MA, Lombaert I, Schmidt TM, Eisbruch A, Murdoch-Kinch CA, Rozek L, Wolf GT, Li G, Chen GY, D'Silva NJ. Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer. Microbiome 2023; 11:268. [PMID: 38037123 PMCID: PMC10687843 DOI: 10.1186/s40168-023-01677-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/26/2023] [Indexed: 12/02/2023]
Abstract
BACKGROUND Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and examined how microbiome changes correlated with the expression of an anti-microbial protein. RESULTS Treatment of SCC was associated with a reduction in overall bacterial richness and diversity. There were significant changes in the microbial community structure, including a decrease in the abundance of Porphyromonaceae and Prevotellaceae and an increase in Lactobacillaceae. There were also significant changes in the microbial community structure before and after treatment with chemoradiotherapy, but not with surgery alone. In patients treated with chemoradiotherapy alone, several bacterial populations were differentially abundant between responders and non-responders before and after therapy. Microbiome changes were associated with a change in the expression of DMBT1, an anti-microbial protein in human saliva. Additionally, we found that salivary DMBT1, which increases after treatment, could serve as a post-treatment salivary biomarker that links to microbial changes. Specifically, post-treatment increases in human salivary DMBT1 correlated with increased abundance of Gemella spp., Pasteurellaceae spp., Lactobacillus spp., and Oribacterium spp. This is the first longitudinal study to investigate treatment-associated changes (chemoradiotherapy and surgery) in the oral microbiome in patients with SCC along with changes in expression of an anti-microbial protein in saliva. CONCLUSIONS The composition of the oral microbiota may predict treatment responses; salivary DMBT1 may have a role in modulating the oral microbiome in patients with SCC. After completion of treatment, 6 months after diagnosis, patients had a less diverse and less rich oral microbiome. Leptotrichia was a highly prevalent bacteria genus associated with disease. Expression of DMBT1 was higher after treatment and associated with microbiome changes, the most prominent genus being Gemella Video Abstract.
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Affiliation(s)
- Marcell Costa de Medeiros
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Stephanie The
- Cancer Data Science Shared Resource, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Emily Bellile
- Cancer Data Science Shared Resource, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Nickole Russo
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Ligia Schmitd
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Erika Danella
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Priyanka Singh
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Rajat Banerjee
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA
| | - Christine Bassis
- Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 331248109, USA
| | - George R Murphy
- Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA
- Biointerfaces Institute, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Computational Medicine and Bioinformatics, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Isabelle Lombaert
- Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, 1011 N. University Ave, Ann Arbor, MI, USA
- Biointerfaces Institute, Ann Arbor, MI, USA
| | - Thomas M Schmidt
- Microbiology and Immunology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Avi Eisbruch
- Radiation Oncology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Carol Anne Murdoch-Kinch
- Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, 1011 North Michigan St, Indianapolis, IN, USA
| | - Laura Rozek
- Environmental Health Sciences, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Gregory T Wolf
- Otolaryngology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Gen Li
- Biostatistics, University of Michigan School of Public Health, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA
| | - Grace Y Chen
- Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 331248109, USA.
| | - Nisha J D'Silva
- Periodontics and Oral Medicine, University of Michigan School of Dentistry, 1011 North University Ave, Room G018, Ann Arbor, MI, 48109-1078, USA.
- Pathology, University of Michigan Medical School, 1500 E. Medical Center Dr, Ann Arbor, MI, USA.
- Rogel Cancer Center, Ann Arbor, MI, USA.
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Bloom PP, Rao K, Bassis C, Nojkov B, Young VB, Lok ASF. Regional changes in intestinal permeability in cirrhosis are associated with mucosal bacteria. Hepatol Commun 2023; 7:e0221. [PMID: 37756036 PMCID: PMC10531369 DOI: 10.1097/hc9.0000000000000221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Several complications of cirrhosis are theorized to result from the translocation of bacteria or their products across the intestinal epithelium. We aimed to assess epithelial permeability and associations with mucosal bacteria in patients with cirrhosis. APPROACH AND RESULTS We collected 247 duodenum, ileum, and colon biopsies from 58 consecutive patients with cirrhosis and 33 controls during clinically indicated endoscopies. Patients with cirrhosis were similarly aged to controls (60 vs. 58 y) and had a median Model for End-stage Liver Disease of 8 (interquartile range 7, 10). Biopsies underwent 16S rRNA-encoding gene amplicon sequencing to determine mucosal bacteria composition and transepithelial electrical resistance (TEER) to determine epithelial permeability. In the entire cohort, there were regional differences in TEER with the lowest TEER (ie, more permeable) in the ileum; duodenum TEER was 43% higher and colon TEER 20% higher than ileum TEER (ANOVA p = 0.0004). When comparing patients with cirrhosis and controls, both TEER (26% lower in cirrhosis, p = 0.006) and alpha diversity differed in the duodenum (27% lower in cirrhosis, p = 0.01) but not ileum or colon. A beta-binomial model found that 26 bacteria were significantly associated with TEER. Bifidobacteriaceae Bifidobacterium in duodenal mucosa was protective of epithelial permeability and future hospitalization for hepatic decompensation. CONCLUSIONS Duodenal epithelial permeability was higher, and mucosal bacteria alpha diversity was lower in cirrhosis compared to controls, while no such differences were seen in the ileum or colon. Specific bacteria were associated with epithelial permeability and future hepatic decompensation.
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Affiliation(s)
- Patricia P. Bloom
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Christine Bassis
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Borko Nojkov
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna SF Lok
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA
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Miles-Jay A, Snitkin ES, Lin MY, Shimasaki T, Schoeny M, Fukuda C, Dangana T, Moore N, Sansom SE, Yelin RD, Bell P, Rao K, Keidan M, Standke A, Bassis C, Hayden MK, Young VB. Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit. Nat Med 2023; 29:2526-2534. [PMID: 37723252 PMCID: PMC10579090 DOI: 10.1038/s41591-023-02549-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023]
Abstract
Despite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States. Current prevention strategies are limited by their failure to account for patients who carry C. difficile asymptomatically, who may act as hidden reservoirs transmitting infections to other patients. To improve the understanding of asymptomatic carriers' contribution to C. difficile spread, we conducted admission and daily longitudinal culture-based screening for C. difficile in a US-based intensive care unit over nine months and performed whole-genome sequencing on all recovered isolates. Despite a high burden of carriage, with 9.3% of admissions having toxigenic C. difficile detected in at least one sample, only 1% of patients culturing negative on admission to the unit acquired C. difficile via cross-transmission. While patients who carried toxigenic C. difficile on admission posed minimal risk to others, they themselves had a 24-times greater risk for developing a healthcare-onset C. difficile infection than noncarriers. Together, these findings suggest that current infection prevention practices can be effective in preventing nosocomial cross-transmission of C. difficile, and that decreasing C. difficile infections in hospitals further will require interventions targeting the transition from asymptomatic carriage to infection.
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Affiliation(s)
- Arianna Miles-Jay
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
| | - Michael Y Lin
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Teppei Shimasaki
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Michael Schoeny
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Christine Fukuda
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Thelma Dangana
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Nicholas Moore
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sarah E Sansom
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Rachel D Yelin
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Pamela Bell
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Micah Keidan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Standke
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Christine Bassis
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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4
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Sansom S, Lin MY, Schoeny M, Fukuda C, Bassis C, Shimasaki T, Dangana TE, Moore NM, Yelin R, Liu S, Young VB, Rhee Y, Tabith L, Sheng J, Cisneros EC, Murray J, Chang K, Lolans K, Ariston M, Rotunno W, Ramos H, Li H, Aboushaala K, Iwai N, Hayden MK. 919. Understanding Intermittent Detection of Multidrug-Resistant Organisms (MDROs) in Rectally Colonized Patients. Open Forum Infect Dis 2020. [PMCID: PMC7777592 DOI: 10.1093/ofid/ofaa439.1107] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Background MDRO detection in colonized patients may be intermittent for reasons that are incompletely understood. We examined temporal patterns of gut MDRO colonization after initial MDRO detection by rectal swab screening, and determined the relationship of culture positivity to the relative abundance of corresponding MDRO operational taxonomic units (OTUs) identified by 16S rRNA gene sequence analysis. Methods Rectal or fecal swabs were collected daily from MICU patients 1/11/2017-1/11/2018. First MICU admissions with ≥2 swabs and MICU stays ≥3 days were studied. Samples were cultured for vancomycin-resistant enterococci (VRE), carbapenem-resistant Enterobacteriaceae (CRE) and P. aeruginosa (CRPA), and extended-spectrum β-lactamase-producing (ESBL) Enterobacteriaceae by selective media. Resistance mechanisms were confirmed by phenotypic methods and/or PCR. Limit of detection was similar for different MDROs (24-52 CFU/sample). OTU categories corresponding to MDRO species were identified by taxonomy and BLAST. Multilevel regression models estimated the association between MDRO detection and relative abundance of the corresponding OTU. Results 796 unique patients with 3519 swabs were studied. Median (IQR) age was 64 (51-74) years, MICU length of stay was 5 (3-8) days, and number of samples-per-patient was 3 (2-5). Following initial MDRO detection, the probability of subsequent detection varied by MDRO type, and was highest for VRE and lowest for CRPA [Figure 1]. Within each sample, we found a significant association between MDRO detection and relative abundance of the corresponding OTU [Table 1]. In contrast, relative OTU abundance in the first sample with MDRO detection was not predictive of odds of future MDRO detection (p >0.05 for all comparisons). Carriage of >1 MDRO did not affect the odds of MDRO detection in later samples. Figure 1. Probability of Subsequent MDRO Detection after First Positive Varies by MDRO Type ![]()
Table 1. Higher Mean Corresponding OTU Relative Abundance Within Each Sample is Associated with MDRO Detection ![]()
Conclusion MDRO culture positivity in rectally colonized patients was correlated with relative abundance of the corresponding OTU in the same sample. Serial detection of different MDRO types was variable, possibly due to distinct microbial community dynamics of different MDRO types. Intermittent failure to detect MDROs could result in misattribution of MDRO acquisition, resulting in inappropriate investigation or intervention. Disclosures All Authors: No reported disclosures
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Sophia Liu
- University of Michigan-Ann Arbor, Ann Arbor, Michigan
| | | | - Yoona Rhee
- Rush University Medical Center, Berwyn, IL
| | | | | | | | | | - Kyle Chang
- Rush University Medical Center, Berwyn, IL
| | | | | | | | | | - Haiying Li
- Rush University Medical Center, Berwyn, IL
| | | | - Naomi Iwai
- Rush University Medical Center, Berwyn, IL
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McKee KS, Carter KA, Bassis C, Young VB, Reed B, Harper DM, Ruffin MT, Bell JD. The vaginal microbiota, high-risk human papillomavirus infection, and cervical cytology: results from a population-based study. Gynecol Pelvic Med 2020; 3. [PMID: 35252846 PMCID: PMC8896808 DOI: 10.21037/gpm-20-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background: The relationship between the vaginal microbiota, high-risk human papillomavirus infection, and abnormal cervical cytology has not been well characterized. Our objective was to characterize the vaginal microbiota in a stratified random sample of women from a population-based study in Appalachia. Methods: We analyzed a random sample of 308 women in the Community Access, Resources and Education: Project 3 study across 16 clinics in Ohio and West Virginia. Using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we characterized the vaginal microbiota among (I) 109 women randomly chosen with abnormal cervical cytology (i.e., the majority were atypical squamous cells of undetermined significance (n=55) and low-grade squamous intraepithelial lesions (n=45) while n=6 were high-grade squamous intraepithelial lesions and n=3 were atypical glandular cells); (II) 110 high-risk human papillomavirus infection only without cytologic abnormality; and (III) 89 women from a stratified random sample without cytologic abnormalities (negative for intraepithelial lesion or malignancy or any human papillomavirus infection). Among the women with abnormal cervical cytology (n=109), 80 had human papillomavirus infection, the majority of which were positive for a high-risk type (n=61). Results: Nearly all of the women were non-Hispanic White (94.5%), and the mean age was 26 (IQR=21–39) years. Women with abnormal cervical cytology or who were HPV+ were more likely to have a diverse vaginal microbiota characterized by higher Gardnerella vaginalis relative abundance, compared to women without cytologic abnormalities whose communities were more likely to be Lactobacillus spp. dominant (P<0.04). Women without cytologic abnormalities had a higher prevalence of L. iners dominated communities than women with abnormal cervical cytology and HR HPV+ respectively (P<0.04), and L. gasseri relative abundance was differentially greater among these women compared to women with abnormal cervical cytology or who were high-risk HPV+ (Linear discriminant analysis effect size =4.17; P=0.0009). After adjustment for age, white race, current smoking, and ≥2 male partners in the last year, however, we did not detect differences in the vaginal microbiota community states across the three outcome groups. Conclusions: Compared to women without cytologic abnormalities, the vaginal microbiota of women with abnormal cervical cytology or who were high-risk HPV+ were characterized by a diverse community with increased relative abundance of G. vaginalis and reduced relative abundance of L. gasseri. However, these differences were attenuated after adjustment for other factors. Further study and validation of these differences for prognostic use is warranted.
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Affiliation(s)
- Kimberly S. McKee
- Department of Family Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kayla A. Carter
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Christine Bassis
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B. Young
- Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Barbara Reed
- Department of Family Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Diane M. Harper
- Department of Family Medicine, University of Michigan, Ann Arbor, MI, USA
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mack T. Ruffin
- Department of Family and Community Medicine, Penn State Health, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Jason D. Bell
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA
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McKee K, Carter K, Bassis C, Young V, Reed B, Harper D, Ruffin M, Bell J. The vaginal microbiota, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia: results from a population-based study. Am J Obstet Gynecol 2019. [DOI: 10.1016/j.ajog.2019.10.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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McKee K, Bassis C, Murali S, Bell J, Young V. The vaginal microbiota in pregnancy and spontaneous preterm birth. Am J Obstet Gynecol 2019. [DOI: 10.1016/j.ajog.2019.10.060] [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: 11/28/2022]
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Bassis C, Seekatz A, Dangana TE, Shimasaki T, Yelin RD, Schoeny M, Rhee Y, Ariston M, Lolans K, Cornejo Cisneros E, Aboushaala K, Thabit L, Murray J, Sheng J, Ollison S, Bell PB, Fogg L, Weinstein RA, Lin MY, Young VB, Hayden MK. 2849. Gut Microbiota Differences at the Time of Medical Intensive Care Unit (MICU) Admission Are Associated with Acquisition of Multi-drug-Resistant Organisms (MDROs) Among Patients Not Already Colonized with an MDRO. Open Forum Infect Dis 2019. [PMCID: PMC6808848 DOI: 10.1093/ofid/ofz359.154] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Among hospitalized patients, underlying variation in gut microbiota may confer differential risk for gut MDRO acquisition. Methods Rectal swab samples were collected from patients ≤2 days of MICU admission and then daily in the 27-bed MICU of an acute care hospital in Chicago, IL over 1 year. Patients were screened for MDRO colonization by selective culture (see Figure 1 for MDRO types); those with ≥2 swabs and MICU stays ≥3 days were studied. Bacterial 16S rRNA gene amplicon sequences were used for microbiota analysis. Medical records were reviewed. Results In preliminary analysis, 2,480 samples were collected from 627 patients who acquired 170 MDROs (Figure 1). Debilitation, co-morbidities, and certain medical devices were associated with MDRO acquisition, though admission MDRO status was not (table). While no interactions were detected between admission MDRO status and clinical predictors of MDRO acquisition, there were significant differences in gut microbiota composition at the time of MICU admission between patients colonized with an MDRO on admission and those not colonized (P < 0.001, using analysis of molecular variance (AMOVA) on distances). Therefore, we stratified our analysis by admission MDRO colonization status. For patients MDRO-colonized at admission, there were no significant differences in microbiota of patients who later did or did not acquire a new MDRO (AMOVA P-value = 0.32). For patients not MDRO-colonized on admission, there was a significant difference in microbiota of patients who later acquired an MDRO and those who did not (AMOVA P-value: 0.026). Differentially abundant operational taxonomic units (OTUs, based on 3% sequence difference) included OTUs classified as Anaerococcus and as other Clostridiales (higher in patients who remained uncolonized) and as Enterococcus (higher in patients who acquired an MDRO) (Figure 2). Diversity was also higher in patients who remained uncolonized (Wilcoxon test P-value: 0.035) (Figure 3). Conclusion Among patients not already colonized with an MDRO on admission, we identified gut microbiota differences associated with MDRO acquisition that could help explain patient-level variation in MDRO colonization resistance. ![]()
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Disclosures All Authors: No reported Disclosures.
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Affiliation(s)
| | | | | | | | | | | | - Yoona Rhee
- Rush University Medical Center, Chicago, Illinois
| | | | - Karen Lolans
- Rush University Medical Center, Chicago, Illinois
| | | | | | | | - John Murray
- Rush University Medical Center, Chicago, Illinois
| | | | | | | | - Louis Fogg
- Rush University Medical Center, Chicago, Illinois
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Aslam MN, Bassis C, Bergin I, Knuver K, Sen A, Turgeon DK, Varani J. Abstract LB-250: The alteration of the colonic microbial community and metabolomic profile in humans: Results from a 90-day double-blinded, randomized interventional trial. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-250] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The bacteria making up the microbial community of the gastrointestinal tract, by virtue of their ability to produce pro-carcinogenic bile acids and anti-carcinogenic short chain fatty acids (SCFA), are thought to influence the colonic health.
Methods: Thirty healthy human subjects (at risk for colorectal cancer) were enrolled in a three-arm, 90-day double-blinded, randomized interventional trial in which Aquamin, a calcium- and magnesium-rich, multi-mineral product was compared to calcium alone and placebo for effects on the colonic microbial community and metabolomic profile. Aquamin and calcium (carbonate) alone groups provided 800 mg of calcium per day from the respective sources. Colonic tissue and stool samples were obtained endoscopically from unpreped sigmoid colon with a flexible sigmoidoscope before and after the intervention and were subjected to microbial and metabolomic analysis. Illumina® MiSeq sequencing of the V4 region of 16S rRNA genes was used to assess the bacterial populations represented in both colon mucosal biopsies and fecal material and qPCR was used to obtain an estimate of total bacterial DNA in each tissue and stool specimen. In parallel, a 2-step extraction procedure followed by liquid chromatography-mass spectrometry was used to assess bile acids and SCFA.
Results: As far as safety and tolerability is concerned, there were no serious adverse events to report during the trial with Aquamin or calcium. Compared to pretreatment values from both colonic biopsies and stool specimens, intervention with Aquamin led to a reduction in total bacterial load (based on qPCR). Treatment with calcium alone produced intermediary changes in total bacterial DNA while no reduction was observed with placebo. Based on sequencing of the V4 region of 16S rRNA genes, there were significant pre-post differences, but intra-subject variability was less than the variability between individuals. In spite of the high variability, greater pre-post interventional differences were seen with Aquamin relative to calcium alone and placebo. Differences between Aquamin and calcium alone reached statistical significance. Several operational taxonomic units representing major microbial phyla present in the colon (i.e., actinobacteria, bacteroidetes, and firmicutes) were reduced in response to Aquamin compared to placebo. Reductions were also seen with calcium but these were intermediary between Aquamin and placebo. In parallel with microbial changes, we observed a reduction in total bile acid levels and an increase in the level of acetate (an SCFA) in stool specimens from Aquamin-treated subjects. No or minimal change in bile acids or SCFAs was observed with calcium alone or placebo. Some of the primary bile acids (cholate and Chenodeoxycholate/deoxycholate) and the secondary bile acids (alpha-Murocholate, hyocholate, hyodeoxycholate, and omega-Muricholate) were significantly reduced with Aquamin. Additionally, on eicosanoids assessment in colon biopsies, 13S-HODE was reduced with Aquamin.
Conclusion: The combination of calcium, magnesium and additional trace elements (as present in Aquamin) can produce alterations in the colonic microbial community and the attendant metabolomic profile that could be beneficial to colonic health in subjects at risk for colorectal cancer.
Citation Format: Muhammad N. Aslam, Christine Bassis, Ingrid Bergin, Karsten Knuver, Ananda Sen, Danielle Kim Turgeon, James Varani. The alteration of the colonic microbial community and metabolomic profile in humans: Results from a 90-day double-blinded, randomized interventional trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-250.
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Shimasaki T, Seekatz A, Bassis C, Rhee Y, Yelin RD, Fogg L, Dangana T, Cisneros EC, Weinstein RA, Okamoto K, Lolans K, Schoeny M, Lin MY, Moore NM, Young VB, Hayden MK. Increased Relative Abundance of Klebsiella pneumoniae Carbapenemase-producing Klebsiella pneumoniae Within the Gut Microbiota Is Associated With Risk of Bloodstream Infection in Long-term Acute Care Hospital Patients. Clin Infect Dis 2019; 68:2053-2059. [PMID: 30239622 PMCID: PMC6541703 DOI: 10.1093/cid/ciy796] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND An association between increased relative abundance of specific bacterial taxa in the intestinal microbiota and bacteremia has been reported in some high-risk patient populations. METHODS We collected weekly rectal swab samples from patients at 1 long-term acute care hospital (LTACH) in Chicago from May 2015 to May 2016. Samples positive for Klebsiella pneumoniae carbapenemase-producing Klebsiella pneumoniae (KPC-Kp) by polymerase chain reaction and culture underwent 16S rRNA gene sequence analysis; relative abundance of the operational taxonomic unit containing KPC-Kp was determined. Receiver operator characteristic (ROC) curves were constructed using results from the sample with highest relative abundance of KPC-Kp from each patient admission, excluding samples collected after KPC-Kp bacteremia. Cox regression analysis was performed to evaluate risk factors associated with time to achieve KPC-Kp relative abundance thresholds calculated by ROC curve analysis. RESULTS We collected 2319 samples from 562 admissions (506 patients); KPC-Kp colonization was detected in 255 (45.4%) admissions and KPC-Kp bacteremia in 11 (4.3%). A relative abundance cutoff of 22% predicted KPC-Kp bacteremia with sensitivity 73%, specificity 72%, and relative risk 4.2 (P = .01). In a multivariable Cox regression model adjusted for age, Charlson comorbidity index, and medical devices, carbapenem receipt was associated with achieving the 22% relative abundance threshold (P = .044). CONCLUSION Carbapenem receipt was associated with increased hazard for high relative abundance of KPC-Kp in the gut microbiota. Increased relative abundance of KPC-Kp was associated with KPC-Kp bacteremia. Whether bacteremia arose directly from bacterial translocation or indirectly from skin contamination followed by bloodstream invasion remains to be determined.
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Affiliation(s)
- Teppei Shimasaki
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Anna Seekatz
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor
| | - Christine Bassis
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor
| | - Yoona Rhee
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Rachel D Yelin
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Louis Fogg
- Department of Nursing, Rush University Medical Center, Chicago, Illinois
| | - Thelma Dangana
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Enrique Cornejo Cisneros
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
- Hospital Nacional Cayetano Heredia, Lima, Peru
| | - Robert A Weinstein
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Koh Okamoto
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
- University of Tokyo Hospital, Japan
| | - Karen Lolans
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Michael Schoeny
- Department of Nursing, Rush University Medical Center, Chicago, Illinois
| | - Michael Y Lin
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Nicholas M Moore
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor
| | - Mary K Hayden
- Department of Internal Medicine, Division of Infectious Diseases, Rush University Medical Center, Chicago, Illinois
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Hummel SL, Bassis C, Marolt C, Konerman M, Schmidt TM. GUT MICROBIOME DIFFERS BETWEEN HEART FAILURE WITH PRESERVED EJECTION FRACTION AND AGE-MATCHED CONTROLS. J Am Coll Cardiol 2019. [DOI: 10.1016/s0735-1097(19)31358-0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Carter K, Bassis C, McKee K, Bullock K, Eastman A, Young V, Bell J. The impact of tampon use on the vaginal microbiota across four menstrual cycles. Am J Obstet Gynecol 2018. [DOI: 10.1016/j.ajog.2018.10.078] [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: 10/27/2022]
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