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Mahmud B, Vargas RC, Sukhum KV, Patel S, Liao J, Hall LR, Kesaraju A, Le T, Kitchner T, Kronholm E, Koshalek K, Bendixsen CG, VanWormer JJ, Shukla SK, Dantas G. Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes. Nat Microbiol 2024; 9:1007-1020. [PMID: 38570675 DOI: 10.1038/s41564-024-01639-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.
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Affiliation(s)
- Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Rhiannon C Vargas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Kimberley V Sukhum
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Sanket Patel
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - James Liao
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Lindsey R Hall
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Akhil Kesaraju
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Thao Le
- Integrated Research Development Laboratory, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Terrie Kitchner
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Erik Kronholm
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Kyle Koshalek
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Casper G Bendixsen
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Jeffrey J VanWormer
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA.
- Computational Informatics in Biology and Medicine program, University of Wisconsin-Madison, Madison, WI, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
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Subramaniam S, Karunanandham K, Raja ASM, Shukla SK, Uthandi S. EnZolv delignification of cotton spinning mill waste and optimization of process parameters using response surface methodology (RSM). Biotechnol Biofuels Bioprod 2024; 17:37. [PMID: 38449061 PMCID: PMC10918963 DOI: 10.1186/s13068-024-02473-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND EnZolv is a novel enzyme-based, eco-friendly biomass pretreatment process that has shown great potential in the field of textile engineering and biotechnology. It employs laccase from Hexagonia hirta MSF2 and 2% ethanol in the process of delignification. The process is designed to evaluate optimal conditions to remove lignin and other impurities from cotton spinning mill waste (CSMW), without compromising the quality and strength of the fibers. CSMW is a low-cost and readily available source of cellulose, making it an ideal candidate for delignification using EnZolv. By optimizing the pretreatment conditions and harnessing the potential of enzymatic delignification, this research aims to contribute to more sustainable and efficient ways of utilizing lignocellulosic biomass in various industries for the production of biochemical and bioproducts. RESULTS The present study emphasizes the EnZolv pretreatment in the delignification of cotton spinning mill wastes irrespective of the cellulose content. EnZolv process parameters such as, moisture content, enzyme load, incubation time, incubation temperature, and shaking speed were optimized. Under pre-optimized conditions, the percent lignin reduction was 61.34%, 61.64%, 41.85%, 35.34%, and 35.83% in blowroom droppings (BD), flat strips (FS), lickerin fly (LF), microdust (MD) and comber noils (CN), respectively. Using response surface methodology (RSM), the statistically optimized EnZolv pretreatment conditions showed lignin reduction of 59.16%, 62.88%, 48.26%, 34.64%, and 45.99% in BD, FS, LF, MD, and CN, respectively. CONCLUSION Traditional chemical-based pretreatment methods often involve harsh chemicals and high energy consumption, which can have detrimental effects on the environment. In contrast, EnZolv offers a greener approach by utilizing enzymes that are biodegradable and more environmentally friendly. The resulting fibers from EnZolv treatment exhibit improved properties that make them suitable for various applications. Some of the key properties include enhanced cellulose recovery, reduced lignin content, and improved biophysical and structural characteristics. These improvements can contribute to the fiber's performance and processability in different industries and future thrust for the production of cellulose-derived and lignin-derived bioproducts.
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Affiliation(s)
- Santhoshkumar Subramaniam
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu, 625104, India
| | - Kumutha Karunanandham
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu, 625104, India
| | - A S M Raja
- ICAR-Central Institute for Research on Cotton Technology, Adenwala Road, Matunga, Mumbai, 400019, India
| | - S K Shukla
- ICAR-Central Institute for Research on Cotton Technology, Adenwala Road, Matunga, Mumbai, 400019, India
| | - Sivakumar Uthandi
- Biocatalysts Laboratory, Department of Agricultural Microbiology, Tamil Nadu Agricultural University (TNAU), Coimbatore, Tamil Nadu, 641003, India.
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Pereira L, Haidar CE, Haga SB, Cisler AG, Hall A, Shukla SK, Hebbring SJ, Leary EJW. Assessment of the current status of real-world pharmacogenomic testing: informed consent, patient education, and related practices. Front Pharmacol 2024; 15:1355412. [PMID: 38410134 PMCID: PMC10895424 DOI: 10.3389/fphar.2024.1355412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction: The practice of informed consent (IC) for pharmacogenomic testing in clinical settings varies, and there is currently no consensus on which elements of IC to provide to patients. This study aims to assess current IC practices for pharmacogenomic testing. Methods: An online survey was developed and sent to health providers at institutions that offer clinical germline pharmacogenomic testing to assess current IC practices. Results: Forty-six completed surveys representing 43 clinical institutions offering pharmacogenomic testing were received. Thirty-two (74%) respondents obtain IC from patients with variability in elements incorporated. Results revealed that twenty-nine (67%) institutions discuss the benefits, description, and purpose of pharmacogenomic testing with patients. Less commonly discussed elements included methodology and accuracy of testing, and laboratory storage of samples. Discussion: IC practices varied widely among survey respondents. Most respondents desire the establishment of consensus IC recommendations from a trusted pharmacogenomics organization to help address these disparities.
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Affiliation(s)
- Lucas Pereira
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield Clinic Health Systems, Marshfield, WI, United States
- Division of Genetics and Metabolism, Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Cyrine-Eliana Haidar
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Susanne B Haga
- Program in Precision Medicine, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States
| | - Anna G Cisler
- Medical Genetics, Marshfield Clinic Health Systems, Marshfield, WI, United States
| | - April Hall
- Division of Genetics and Metabolism, Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Center for Human Genomics and Precision Medicine, Wisconsin Institute for Medical Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Sanjay K Shukla
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield Clinic Health Systems, Marshfield, WI, United States
| | - Scott J Hebbring
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield Clinic Health Systems, Marshfield, WI, United States
| | - Emili J W Leary
- Marshfield Clinic Research Institute, Center for Precision Medicine Research, Marshfield Clinic Health Systems, Marshfield, WI, United States
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Yerukala Sathipati S, Aimalla N, Tsai MJ, Carter T, Jeong S, Wen Z, Shukla SK, Sharma R, Ho SY. Prognostic microRNA signature for estimating survival in patients with hepatocellular carcinoma. Carcinogenesis 2023; 44:650-661. [PMID: 37701974 DOI: 10.1093/carcin/bgad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/01/2023] [Accepted: 09/08/2023] [Indexed: 09/14/2023] Open
Abstract
OBJECTIVE Hepatocellular carcinoma (HCC) is one of the leading cancer types with increasing annual incidence and high mortality in the USA. MicroRNAs (miRNAs) have emerged as valuable prognostic indicators in cancer patients. To identify a miRNA signature predictive of survival in patients with HCC, we developed a machine learning-based HCC survival estimation method, HCCse, using the miRNA expression profiles of 122 patients with HCC. METHODS The HCCse method was designed using an optimal feature selection algorithm incorporated with support vector regression. RESULTS HCCse identified a robust miRNA signature consisting of 32 miRNAs and obtained a mean correlation coefficient (R) and mean absolute error (MAE) of 0.87 ± 0.02 and 0.73 years between the actual and estimated survival times of patients with HCC; and the jackknife test achieved an R and MAE of 0.73 and 0.97 years between actual and estimated survival times, respectively. The identified signature has seven prognostic miRNAs (hsa-miR-146a-3p, hsa-miR-200a-3p, hsa-miR-652-3p, hsa-miR-34a-3p, hsa-miR-132-5p, hsa-miR-1301-3p and hsa-miR-374b-3p) and four diagnostic miRNAs (hsa-miR-1301-3p, hsa-miR-17-5p, hsa-miR-34a-3p and hsa-miR-200a-3p). Notably, three of these miRNAs, hsa-miR-200a-3p, hsa-miR-1301-3p and hsa-miR-17-5p, also displayed association with tumor stage, further emphasizing their clinical relevance. Furthermore, we performed pathway enrichment analysis and found that the target genes of the identified miRNA signature were significantly enriched in the hepatitis B pathway, suggesting its potential involvement in HCC pathogenesis. CONCLUSIONS Our study developed HCCse, a machine learning-based method, to predict survival in HCC patients using miRNA expression profiles. We identified a robust miRNA signature of 32 miRNAs with prognostic and diagnostic value, highlighting their clinical relevance in HCC management and potential involvement in HCC pathogenesis.
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Affiliation(s)
| | - Nikhila Aimalla
- Department of Internal Medicine-Pediatrics, Marshfield Clinic Health System, Marshfield, WI 54449, USA
| | - Ming-Ju Tsai
- Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Tonia Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Sohyun Jeong
- Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Zhi Wen
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Rohit Sharma
- Department of Surgical Oncology, Marshfield Clinic Health System, Marshfield, WI 54449, USA
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
- Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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VanWormer JJ, Bendixsen CG, Shukla SK. Dairy Farm Work and Protection from Gastrointestinal Illness. J Agromedicine 2023; 28:640-646. [PMID: 37128886 PMCID: PMC10664175 DOI: 10.1080/1059924x.2023.2209091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Gastrointestinal (GI) disorders are a major public health burden in the United States. Due to close contact with animals, farmers may be a high risk subgroup for acute GI infections, though some studies suggest farm work is actually protective against GI illness. The purpose of this study was to examine associations between dairy farm work and GI symptoms over 3 years. A prospective, matched cohort study was used that included 70 adult dairy farm workers and 74 matched (age, gender, ZIP code) non-farm participants from central Wisconsin. The outcome was mean GI symptom scores for abdominal pain, diarrhea, constipation, dyspepsia, nausea, and reflux, per the 23-item Gastrointestinal Symptoms Severity Index (GISSI). After adjustment for potential confounding variables, linear regression results indicated dairy farm workers had significantly lower GISSI scores for abdominal pain (mean±SE = 4.3 ± 1.1 dairy vs. 7.6 ± 1.1 non-farm, p = .047), diarrhea (3.2 ± 1.0 dairy vs. 7.0 ± 1.0 non-farm, p = .010), constipation (2.0 ± 0.8 dairy vs. 6.6 ± 0.8 non-farm, p < .001), and dyspepsia (2.0 ± 0.6 dairy vs. 3.9 ± 0.5 non-farm, p = .026). Working on a dairy farm was associated with significantly less frequent and severe GI illness symptoms in adults. Future research should identify underlying causal pathways, including possible farm animal exposures, that influence beneficial gut microbiota that could inform therapeutic remedies to help prevent clinical GI disorders.
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Affiliation(s)
- Jeffrey J. VanWormer
- Center for Clinical Epidemiology & Population Health, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Casper G. Bendixsen
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | - Sanjay K. Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, USA
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Elsayed NS, Valenzuela RK, Kitchner T, Le T, Mayer J, Tang ZZ, Bayanagari VR, Lu Q, Aston P, Anantharaman K, Shukla SK. Genetic risk score in multiple sclerosis is associated with unique gut microbiome. Sci Rep 2023; 13:16269. [PMID: 37758833 PMCID: PMC10533555 DOI: 10.1038/s41598-023-43217-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Multiple sclerosis (MS) is a complex autoimmune disease in which both the roles of genetic susceptibility and environmental/microbial factors have been investigated. More than 200 genetic susceptibility variants have been identified along with the dysbiosis of gut microbiota, both independently have been shown to be associated with MS. We hypothesize that MS patients harboring genetic susceptibility variants along with gut microbiome dysbiosis are at a greater risk of exhibiting the disease. We investigated the genetic risk score for MS in conjunction with gut microbiota in the same cohort of 117 relapsing remitting MS (RRMS) and 26 healthy controls. DNA samples were genotyped using Illumina's Infinium Immuno array-24 v2 chip followed by calculating genetic risk score and the microbiota was determined by sequencing the V4 hypervariable region of the 16S rRNA gene. We identified two clusters of MS patients, Cluster A and B, both having a higher genetic risk score than the control group. However, the MS cases in cluster B not only had a higher genetic risk score but also showed a distinct gut microbiome than that of cluster A. Interestingly, cluster A which included both healthy control and MS cases had similar gut microbiome composition. This could be due to (i) the non-active state of the disease in that group of MS patients at the time of fecal sample collection and/or (ii) the restoration of the gut microbiome post disease modifying therapy to treat the MS. Our study showed that there seems to be an association between genetic risk score and gut microbiome dysbiosis in triggering the disease in a small cohort of MS patients. The MS Cluster A who have a higher genetic risk score but microbiome profile similar to that of healthy controls could be due to the remitting phase of the disease or due to the effect of disease modifying therapies.
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Affiliation(s)
- Noha S Elsayed
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
- Department of Pediatrics, Albert Einstein Medical College, New York, United States
| | - Robert K Valenzuela
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
| | - Terrie Kitchner
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
| | - Thao Le
- Integrated Research Development Laboratory, Marshfield Clinic Research Institute, Marshfield Clinic Health System, Marshfield, WI, 54449, USA
| | - John Mayer
- Office of Research Computing and Analytics, Marshfield Clinic Research Institute, Marshfield Clinic Health System, Marshfield, WI, 54449, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Vishnu R Bayanagari
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
- Roger Williams Medical Center, Boston University School of Medicine, Providence, RI, 02908, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Paula Aston
- Department of Neurology, Marshfield Clinic Health System, Marshfield, WI, 54449, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA.
- Computational and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Yerukala Sathipati S, Tsai MJ, Shukla SK, Ho SY. Artificial intelligence-driven pan-cancer analysis reveals miRNA signatures for cancer stage prediction. HGG Adv 2023; 4:100190. [PMID: 37124139 PMCID: PMC10130501 DOI: 10.1016/j.xhgg.2023.100190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
The ability to detect cancer at an early stage in patients who would benefit from effective therapy is a key factor in increasing survivability. This work proposes an evolutionary supervised learning method called CancerSig to identify cancer stage-specific microRNA (miRNA) signatures for early cancer predictions. CancerSig established a compact panel of miRNA signatures as potential markers from 4,667 patients with 15 different types of cancers for the cancer stage prediction, and achieved a mean performance: 10-fold cross-validation accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve of 84.27% ± 6.31%, 0.81 ± 0.12, 0.80 ± 0.10, and 0.80 ± 0.06, respectively. The pan-cancer analysis of miRNA signatures suggested that three miRNAs, hsa-let-7i-3p, hsa-miR-362-3p, and hsa-miR-3651, contributed significantly toward stage prediction across 8 cancers, and each of the 67 miRNAs of the panel was a biomarker of stage prediction in more than one cancer. CancerSig may serve as the basis for cancer screening and therapeutic selection..
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Affiliation(s)
- Srinivasulu Yerukala Sathipati
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
- Corresponding author
| | - Ming-Ju Tsai
- Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Sanjay K. Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Corresponding author
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Uhde M, Indart AC, Green PH, Yolken RH, Cook DB, Shukla SK, Vernon SD, Alaedini A. Suppressed immune and metabolic responses to intestinal damage-associated microbial translocation in myalgic encephalomyelitis/chronic fatigue syndrome. Brain Behav Immun Health 2023; 30:100627. [PMID: 37396339 PMCID: PMC10308215 DOI: 10.1016/j.bbih.2023.100627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 07/04/2023] Open
Abstract
The etiology and mechanism of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) are poorly understood and no biomarkers have been established. Specifically, the relationship between the immunologic, metabolic, and gastrointestinal abnormalities associated with ME/CFS and their relevance to established symptoms of the condition remain unclear. Relying on data from two independent pairs of ME/CFS and control cohorts, one at rest and one undergoing an exercise challenge, we identify a state of suppressed acute-phase innate immune response to microbial translocation in conjunction with a compromised gut epithelium in ME/CFS. This immunosuppression, along with observed enhancement of compensatory antibody responses to counter the microbial translocation, was associated with and may be mediated by alterations in glucose and citrate metabolism and an IL-10 immunoregulatory response. Our findings provide novel insights into mechanistic pathways, biomarkers, and potential therapeutic targets in ME/CFS, including in the context of exertion, with relevance to both intestinal and extra-intestinal symptoms.
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Affiliation(s)
- Melanie Uhde
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Alyssa C. Indart
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
| | - Peter H.R. Green
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
- Celiac Disease Center, Columbia University, New York, NY, USA
| | - Robert H. Yolken
- The Stanley Laboratory of Developmental Neurovirology, Johns Hopkins University, Baltimore, MD, USA
| | - Dane B. Cook
- Department of Kinesiology, University of Wisconsin - Madison, Madison, WI, USA
| | - Sanjay K. Shukla
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, WI, USA
| | | | - Armin Alaedini
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University, New York, NY, USA
- Institute of Human Nutrition, Columbia University, New York, NY, USA
- Celiac Disease Center, Columbia University, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, New York Medical College, Valhalla, NY, USA
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9
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Sachan D, Shukla SK, Bajpai PK, Srivastava DK, Kumar S, Jain PK, Pathak P. Validation of satisfaction questionnaire for services provided in the labour rooms of government health facilities. J Healthc Qual Res 2023; 38:76-83. [PMID: 36163149 DOI: 10.1016/j.jhqr.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 06/20/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
INTRODUCTION AND OBJECTIVES Using the assessment of satisfaction of patients of labour room services, the caregiver or policymakers can identify the gaps in the implemented programmes and health policies. This study was aimed to design a valid and reliable satisfaction questionnaire that will help in identifying the aspects of gaps that need improvement. METHODS A facility and community-based observational cross-sectional study was conducted in the district of western Uttar Pradesh (India) between January 2019 and August 2020. Validation of the structured questionnaire with 34 dichotomous questions categorized under five subscales was performed by evaluating its validity and reliability. A total of 380 beneficiaries were selected from 48 government health facilities. RESULTS The calculated Content validity index was calculated to be 9.5 which was adequate as per the guidelines. The reliability analysis of the questionnaire showed that the internal consistency was high with an overall Cronbach's alpha of 0.710. The variation in Cronbach's alpha on the elimination of any question from the questionnaire ranged from 0.676 to 0.767. The mean patient satisfaction score in the total surveyed population was 24.39±4.684 (total score=34) and there was a greater variation in the satisfaction score of infrastructure when compared with other subscales. CONCLUSION The findings from this study support the reliability and validity of the patient satisfaction questionnaire as it is capable of evaluating the satisfaction in terms of delivery services provided in labour rooms as a whole.
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Affiliation(s)
- D Sachan
- Department of Community Medicine, Uttar Pradesh University of Medical Sciences, Saifai, India
| | - S K Shukla
- Department of Community Medicine, Uttar Pradesh University of Medical Sciences, Saifai, India.
| | - P K Bajpai
- Department of Community Medicine, Uttar Pradesh University of Medical Sciences, Saifai, India
| | - D K Srivastava
- Department of Community Medicine, Uttar Pradesh University of Medical Sciences, Saifai, India
| | - S Kumar
- Department of Community Medicine, Uttar Pradesh University of Medical Sciences, Saifai, India
| | - P K Jain
- Department of Community Medicine, Uttar Pradesh University of Medical Sciences, Saifai, India
| | - P Pathak
- Department of Community Medicine, Uttar Pradesh University of Medical Sciences, Saifai, India
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10
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Budi ND, Godfrey JJ, Safdar N, Shukla SK, Rose WE. Efficacy of Omadacycline or Vancomycin Combined With Germinants for Preventing Clostridioides difficile Relapse in a Murine Model. J Infect Dis 2023; 227:622-630. [PMID: 35904942 PMCID: PMC9978312 DOI: 10.1093/infdis/jiac324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 07/15/2022] [Accepted: 07/27/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Clostridioides difficile infections (CDI) and recurrence (rCDI) are major health care burdens. Recurrence is likely caused by spores in the gastrointestinal tract that germinate after antibiotic therapy. This murine study explores germinant-antibiotic combinations for CDI. METHODS Previously described murine models were evaluated using C. difficile VPI 10463. The severe model compared omadacycline versus vancomycin in survival, weight loss, clinical scoring, and C. difficile toxin production. The nonsevere model compared these antibiotics with and without germinants (solution of sodium taurocholate, taurine, sodium docusate, calcium gluconate). Additionally, colon histopathology, bile acid analysis, environmental/spore shedding, and 16S sequencing was evaluated. RESULTS In the severe model, omadacycline-treated mice had 60% survival versus 13.3% with vancomycin (hazard ratio [HR], 0.327; 95% confidence interval [CI],.126-.848; P = .015) along with decreased weight loss, and disease severity. In the nonsevere model, all mice survived with antibiotic-germinant treatment versus 60% antibiotics alone (HR, 0.109; 95% CI, .02-.410; P = .001). Omadacycline resulted in less changes in bile acids and microbiota composition. Germinant-treated mice showed no signs of rCDI, spore shedding, or significant toxin production at 15 days. CONCLUSIONS In murine models of CDI, omadacycline improved survival versus vancomycin. Germinant-antibiotic combinations were more effective at preventing rCDI compared to antibiotics alone without inducing toxin production.
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Affiliation(s)
- Noah D Budi
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jared J Godfrey
- Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Nasia Safdar
- Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.,William S. Middleton Memorial Veterans Hospital, Madison, Wisconsin, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Warren E Rose
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
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11
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Elsayed NS, Aston P, Bayanagari VR, Shukla SK. The gut microbiome molecular mimicry piece in the multiple sclerosis puzzle. Front Immunol 2022; 13:972160. [PMID: 36045671 PMCID: PMC9420973 DOI: 10.3389/fimmu.2022.972160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/25/2022] [Indexed: 12/11/2022] Open
Abstract
The etiological complexity of multiple sclerosis, an immune-mediated, neurodegenerative disease with multifactorial etiology is still elusive because of an incomplete understanding of the complex synergy between contributing factors such as genetic susceptibility and aberrant immune response. Recently, the disease phenotypes have also been shown to be associated with dysbiosis of the gut microbiome, a dynamic reservoir of billions of microbes, their proteins and metabolites capable of mimicring the autoantigens. Microbial factors could potentially trigger the neuroinflammation and symptoms of MS. In this perspective article, we discussed how microbial molecules resulting from a leaky gut might mimic a host’s autoantigen, potentially contributing to the disease disequilibrium. It further highlights the importance of targeting the gut microbiome for alternate therapeutic options for the treatment of MS.
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Affiliation(s)
- Noha S. Elsayed
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Paula Aston
- Department of Neurology, Marshfield Clinic Health System, Marshfield, WI, United States
| | - Vishnu R. Bayanagari
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
| | - Sanjay K. Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, United States
- *Correspondence: Sanjay K. Shukla,
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12
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Tripathi A, Ranjan MR, Verma DK, Singh Y, Shukla SK, Rajput VD, Minkina T, Mishra PK, Garg MC. Author Correction: ANN-GA based biosorption of As(III) from water through chemo-tailored and iron impregnated fungal biofilter system. Sci Rep 2022; 12:13228. [PMID: 35918382 PMCID: PMC9345897 DOI: 10.1038/s41598-022-17593-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- A Tripathi
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India.
| | - M R Ranjan
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India
| | - D K Verma
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P., 221005, India
| | - Y Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P., 221005, India
| | - S K Shukla
- Department of Transport Science and Technology, School of Engineering and Technology, Central University of Jharkhand, Ranchi, Jharkhand, 835222, India
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia, 344090
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia, 344090
| | - P K Mishra
- Department of Chemical Engineering, IIT BHU, Varanasi, U.P., 221005, India
| | - M C Garg
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India
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13
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Tripathi A, Ranjan MR, Verma DK, Singh Y, Shukla SK, Rajput VD, Minkina T, Mishra PK, Garg MC. ANN-GA based biosorption of As(III) from water through chemo-tailored and iron impregnated fungal biofilter system. Sci Rep 2022; 12:12414. [PMID: 35858932 PMCID: PMC9300712 DOI: 10.1038/s41598-022-14802-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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] [Received: 02/16/2022] [Accepted: 06/13/2022] [Indexed: 11/22/2022] Open
Abstract
The iron impregnated fungal bio-filter (IIFB) discs of luffa sponge containing Phanerochaete chrysosporium mycelia have been used for the removal of As(III) from water. Two different forms of same biomass viz. free fungal biomass (FFB) and modified free fungal biomass (chemically modified and iron impregnated; CFB and IIFB) have been simultaneously investigated to compare the performance of immobilization, chemo-tailoring and iron impregnation for remediation of As(III). IIFB showed highest uptake capacity and percentage removal of As(III), 1.32 mg/g and 92.4% respectively among FFB, CFB and IIFB. Further, the application of RSM and ANN-GA based mathematical model showed a substantial increase in removal i.e. 99.2% of As(III) was filtered out from water at optimised conditions i.e. biomass dose 0.72 g/L, pH 7.31, temperature 42 °C, and initial As(III) concentration 1.1 mg/L. Isotherm, kinetic and thermodynamic studies proved that the process followed monolayer sorption pattern in spontaneous and endothermic way through pseudo-second order kinetic pathway. Continuous mode of As(III) removal in IIFB packed bed bioreactor, revealed increased removal of As(III) from 76.40 to 88.23% with increased column height from 5 to 25 cm whereas the removal decreased from 88.23 to 69.45% while increasing flow rate from 1.66 to 8.30 mL/min. Moreover, the IIFB discs was regenerated by using 10% NaOH as eluting agent and evaluated for As(III) removal for four sorption–desorption cycles, showing slight decrease of their efficiency by 1–2%. SEM–EDX, pHzpc, and FTIR analysis, revealed the involvement of hydroxyl and amino surface groups following a non-electrostatic legend exchange sorption mechanism during removal of As(III).
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Affiliation(s)
- A Tripathi
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India.
| | - M R Ranjan
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India
| | - D K Verma
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P., 221005, India
| | - Y Singh
- School of Biochemical Engineering, Indian Institute of Technology (Banaras Hindu University), Varanasi, U.P., 221005, India
| | - S K Shukla
- Department of Transport Science and Technology, School of Engineering and Technology, Central University of Jharkhand, Ranchi, Jharkhand, 835222, India
| | - Vishnu D Rajput
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia, 344090
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, Russia, 344090
| | - P K Mishra
- Department of Chemical Engineering, IIT BHU, Varanasi, U.P., 221005, India
| | - M C Garg
- Amity Institute of Environmental Sciences, Amity University Uttar Pradesh, Noida-125, Gautam Buddha Nagar, U.P., 201303, India
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14
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Tiwari R, Chandra K, Shukla SK, Jaiswal VP, Amaresan N, Srivastava AK, Gaur A, Sahni D, Tiwari RK. Interference of bio-control Trichoderma to enhance physical and physiological strength of sugarcane during Pokkah boeng infection. World J Microbiol Biotechnol 2022; 38:139. [PMID: 35705749 DOI: 10.1007/s11274-022-03319-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/22/2022] [Indexed: 11/30/2022]
Abstract
Tremendous benefits have been derived from the use of fungicides but excessive use of chemical fungicides not only posing threat to human and animal life but also contaminates the prevailing environment. Damage by pathogenic fungi alone causes significant damage to crops like maize, rice, wheat, soybeans, and potatoes. Therefore, it becomes imperative that these diseases are checked and controlled, for which chemical pesticides are being sprayed on plants extensively. Considering the devastating damage and toxicity, the global focus has taken a drift from synthetic chemicals to nature-friendly biological control agents. The present study focuses on the use of biological control agents particularly Trichoderma in sugarcane during Pokkah boeng infection. In the present experiment, twenty promising Trichoderma strains were evaluated for plant growth promotion, lytic enzymes, and physiological and biocontrol activity. Out of the twenty, four potential Trichoderma strains were assessed in the pot experiment viz. T. harzianum strain T28, T41 and T49 and T. aureoviride strain T38. The T. harzianum (T28) showed efficient plant growth-promoting traits as it produced IAA (20.67 µg/ml), phosphorus solubilization (18.57 µg/ml), and cell wall degrading enzymes such as chitinase (24.98 µg/ml) and β-glucanase (29.98 µg/ml). The interference of biocontrol agent T. harzianum (T28) controlled the disease by 73.55%. Apart from this, the inoculation of Trichoderma (T28) enhanced growth attributes including germination percentage (26.61%), mean tiller number (8.28 tiller/pot), individual cane length (241.5 cm), single cane weight (1.13 kg) and the number of milleable canes (6.00 cane/pot). Improvements in physiological activities at different growth stages of the sugarcane crop were observed based on the photosynthetically active radiation (PAR) on the leaf surface, transpiration rate, stomatal conductance, and photosynthetic rate. Further, improvement in juice quality parameters was also observed as it recorded the highest 0brix, sucrose, and commercial cane sugar by 21.26%, 19.28%, and 13.50%, respectively, by applying T. harzianum strain T28. Thus, results proved that T. harzianum strain T28 may be an effective eco-friendly biocontrol tool for managing Pokkah boeng disease in sugarcane. This is the first report of the biocontrol potential of Trichoderma spp. against Fusarium proliferatum causing Pokkah boeng disease in sugarcane.
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Affiliation(s)
- Raghvendra Tiwari
- ICAR-Indian Institute of Sugarcane Research, Lucknow, 226008, India.,Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India
| | - Kajal Chandra
- Birbal Sahni Institute of Palaeosciences, Lucknow, 226007, India
| | - S K Shukla
- ICAR-Indian Institute of Sugarcane Research, Lucknow, 226008, India
| | - V P Jaiswal
- ICAR-Indian Institute of Sugarcane Research, Lucknow, 226008, India
| | - Natarajan Amaresan
- C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Surat, Gujarat, 394350, India
| | | | - Asha Gaur
- ICAR-Indian Institute of Sugarcane Research, Lucknow, 226008, India
| | - Divya Sahni
- ICAR-Indian Institute of Sugarcane Research, Lucknow, 226008, India
| | - Rajesh Kumar Tiwari
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India.
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15
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Sathipati SY, Ming-Ju-Tsai, Carter T, Shukla SK, Ho SY. SPIKES: Identification of physicochemical properties of spike proteins across diverse host species of SARS-CoV-2. STAR Protoc 2022; 3:101460. [PMID: 35726315 PMCID: PMC9127179 DOI: 10.1016/j.xpro.2022.101460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We describe a protocol to identify physicochemical properties using amino acid sequences of spike (S) proteins of SARS-CoV-2. We present an S protein prediction technique named SPIKES, incorporating an inheritable bi-objective combinatorial genetic algorithm to determine the host species specificity. This protocol addresses the S protein amino acid sequence data collection, preprocessing, methodology, and analysis. For complete details on the use and execution of this protocol, please refer to Yerukala Sathipati et al. (2022). Identify informative physicochemical properties of the SARS-CoV-2 spike protein SPIKES predicts the species specificity across diverse host species of SARS-CoV-2 This protocol addresses spike protein sequence retrieval and analysis procedures Differences exist in the S protein properties of diverse host species CoVs
Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
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16
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Yerukala Sathipati S, Tsai MJ, Shukla SK, Ho SY, Liu Y, Beheshti A. Author Correction: MicroRNA signature for estimating the survival time in patients with bladder urothelial carcinoma. Sci Rep 2022; 12:4990. [PMID: 35322184 PMCID: PMC8943119 DOI: 10.1038/s41598-022-09235-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Ming-Ju Tsai
- Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi Liu
- Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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17
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Yerukala Sathipati S, Tsai MJ, Shukla SK, Ho SY, Liu Y, Beheshti A. MicroRNA signature for estimating the survival time in patients with bladder urothelial carcinoma. Sci Rep 2022; 12:4141. [PMID: 35264666 PMCID: PMC8907292 DOI: 10.1038/s41598-022-08082-7] [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] [Received: 09/10/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Bladder urothelial carcinoma (BLC) is one of the most common cancers in men, and its heterogeneity challenges the treatment to cure this disease. Recently, microRNAs (miRNAs) gained promising attention as biomarkers due to their potential roles in cancer biology. Identifying survival-associated miRNAs may help identify targets for therapeutic interventions in BLC. This work aims to identify a miRNA signature that could estimate the survival in patients with BLC. We developed a survival estimation method called BLC-SVR based on support vector regression incorporated with an optimal feature selection algorithm to select a robust set of miRNAs as a signature to estimate the survival in patients with BLC. BLC-SVR identified a miRNA signature consisting of 29 miRNAs and obtained a mean squared correlation coefficient and mean absolute error of 0.79 ± 0.02 and 0.52 ± 0.32 year between actual and estimated survival times, respectively. The prediction performance of BLC-SVR had a better estimation capability than other standard regression methods. In the identified miRNA signature, 14 miRNAs, hsa-miR-432-5p, hsa-let-7e-3p, hsa-miR-652-3p, hsa-miR-629-5p, and hsa-miR-203a-3p, hsa-miR-129-5p, hsa-miR-769-3p, hsa-miR-570-3p, hsa-miR-320c, hsa-miR-642a-5p, hsa-miR-496, hsa-miR-5480-3p, hsa-miR-221-5p, and hsa-miR-7-1-3p, were found to be good biomarkers for BLC diagnosis; and the six miRNAs, hsa-miR-652-5p, hsa-miR-193b-5p, hsa-miR-129-5p, hsa-miR-143-5p, hsa-miR-496, and hsa-miR-7-1-3p, were found to be good biomarkers of prognosis. Further bioinformatics analysis of this miRNA signature demonstrated its importance in various biological pathways and gene ontology annotation. The identified miRNA signature would further help in understanding of BLC diagnosis and prognosis in the development of novel miRNA-target based therapeutics in BLC.
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Affiliation(s)
| | - Ming-Ju Tsai
- Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA, USA.,Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI, 54449, USA
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi Liu
- Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
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18
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Yerukala Sathipati S, Shukla SK, Ho SY. Tracking the amino acid changes of spike proteins across diverse host species of severe acute respiratory syndrome coronavirus 2. iScience 2022; 25:103560. [PMID: 34877480 PMCID: PMC8638202 DOI: 10.1016/j.isci.2021.103560] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/02/2021] [Accepted: 11/30/2021] [Indexed: 12/14/2022] Open
Abstract
Knowledge of the host-specific properties of the spike protein is of crucial importance to understand the adaptability of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) to infect multiple species and alter transmissibility, particularly in humans. Here, we propose a spike protein predictor SPIKES incorporating with an inheritable bi-objective combinatorial genetic algorithm to identify the biochemical properties of spike proteins and determine their specificity to human hosts. SPIKES identified 20 informative physicochemical properties of the spike protein, including information measures for alpha helix and relative mutability, and amino acid and dipeptide compositions, which have shown compositional difference at the amino acid sequence level between human and diverse animal coronaviruses. We suggest that alterations of these amino acids between human and animal coronaviruses may provide insights into the development and transmission of SARS-CoV-2 in human and other species and support the discovery of targeted antiviral therapies. Differences exist in the amino acids within the S protein of diverse host species CoVs We developed SPIKES to identify informative properties of S protein SARS-CoV-2 variants have amino acid changes that alter infection and transmission The SPIKES identified changes in S protein properties from animal to human host CoVs
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Affiliation(s)
- Srinivasulu Yerukala Sathipati
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
- Corresponding author
| | - Sanjay K. Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- Center for intelligent Drug Systems and Smart Bio-Devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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19
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Kumar TK, Tewari M, Shukla SK, Mishra SP. Pancreatic exocrine insufficiency occurs in most patients following pancreaticoduodenectomy. Indian J Cancer 2022; 58:511-517. [PMID: 34975096 DOI: 10.4103/ijc.ijc_764_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Pancreatic exocrine insufficiency (PEI) is a well-defined complication of malignant diseases and pancreatic resection; however, study results of PEI are less consistent. Assessment of PEI by estimation of fecal elastase (FE)-1 in stool by enzyme-linked immunosorbent essay (ELISA) is a relatively inexpensive, noninvasive, and simple test. This study assessed exocrine function of pancreas following pancreaticoduodenectomy (PD) by estimating FE-1. Methods This prospective hospital-based study involved 30 patients who had undergone PD for malignancy. All 30 patients had an uneventful postoperative period under the unit's enhanced recovery after surgery (ERAS) protocol with no Grade B, C postoperative pancreatic fistula/postpancreatectomy hemorrhage as per the International Study Group of Pancreatic Surgery (ISGPS) definitions. Stool samples were collected postoperatively 3 months after surgery from all patients irrespective of clinical symptoms. The analysis was based on a solid phase ELISA used for the quantitative determination of human elastase 1 in feces. Fecal elastase was considered normal if >200 μg/gm stool, moderately reduced if 100-200 μg/gm stool, and severely reduced if <100 μg/gm stool. Results Among 30 patients included, fecal elastase levels were moderately reduced in 10 (33.33%) and severely reduced in 20 (66.67%) patients (P <0.0001). Mean (± standard deviation) of fecal elastase was 87.12 ± 38.76 with median of 74.6 μg/gm stool. There was no significant difference in the fecal elastase levels between men and women (P = 0.057), age (P = 0.48), pancreatic duct diameter (P = 0.609), pancreatic texture (P = 0.286), and presence or absence of clinical symptoms (P = 0.181). Conclusions PD was frequently associated with PEI. Unfortunately PEI is an under recognized and under treated long-term sequel of PD. Fecal elastase 1 should be performed routinely in both symptomatic and asymptomatic patients. Pancreatic enzyme replacement therapy should be considered in every patient after PD.
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Affiliation(s)
- Thogari K Kumar
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Mallika Tewari
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - S K Shukla
- Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - S P Mishra
- Department of Biochemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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20
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Yerukala Sathipati S, Tsai MJ, Carter T, Allaire P, Shukla SK, Beheshti A, Ho SY. Survival estimation in patients with stomach and esophageal carcinoma using miRNA expression profiles. Comput Struct Biotechnol J 2022; 20:4490-4500. [PMID: 36051876 PMCID: PMC9421182 DOI: 10.1016/j.csbj.2022.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Received: 06/03/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 11/27/2022] Open
Abstract
Identifying a miRNA signature associated with survival will open a new window for developing miRNA-targeted treatment strategies in stomach and esophageal cancers (STEC). Here, using data from The Cancer Genome Atlas on 516 patients with STEC, we developed a Genetic Algorithm-based Survival Estimation method, GASE, to identify a miRNA signature that could estimate survival in patients with STEC. GASE identified 27 miRNAs as a survival miRNA signature and estimated the survival time with a mean squared correlation coefficient of 0.80 ± 0.01 and a mean absolute error of 0.44 ± 0.25 years between actual and estimated survival times, and showed a good estimation capability on an independent test cohort. The miRNAs of the signature were prioritized and analyzed to explore their roles in STEC. The diagnostic ability of the identified miRNA signature was analyzed, and identified some critical miRNAs in STEC. Further, miRNA-gene target enrichment analysis revealed the involvement of these miRNAs in various pathways, including the somatotrophic axis in mammals that involves the growth hormone and transforming growth factor beta signaling pathways, and gene ontology annotations. The identified miRNA signature provides evidence for survival-related miRNAs and their involvement in STEC, which would aid in developing miRNA-target based therapeutics.
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Affiliation(s)
- Srinivasulu Yerukala Sathipati
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
- Corresponding author.
| | - Ming-Ju Tsai
- Hinda and Arthur Marcus Institute for Aging Research at Hebrew Senior Life, Boston, MA, USA
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Tonia Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Patrick Allaire
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Sanjay K. Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Afshin Beheshti
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
- College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
- Biomedical Engineering, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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Overmyer KA, Rhoads TW, Merrill AE, Ye Z, Westphall MS, Acharya A, Shukla SK, Coon JJ. Proteomics, lipidomics, metabolomics and 16S DNA sequencing of dental plaque from patients with diabetes and periodontal disease. Mol Cell Proteomics 2021; 20:100126. [PMID: 34332123 PMCID: PMC8426274 DOI: 10.1016/j.mcpro.2021.100126] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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] [Received: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 12/11/2022] Open
Abstract
Oral microbiome influences human health, specifically prediabetes and type 2 diabetes (Pre-DM/DM) and periodontal diseases (PDs), through complex microbial interactions. To explore these relations, we performed 16S rDNA sequencing, metabolomics, lipidomics, and proteomics analyses on supragingival dental plaque collected from individuals with Pre-DM/DM (n = 39), Pre-DM/DM and PD (n = 37), PD alone (n = 11), or neither (n = 10). We identified on average 2790 operational taxonomic units and 2025 microbial and host proteins per sample and quantified 110 metabolites and 415 lipids. Plaque samples from Pre-DM/DM patients contained higher abundance of Fusobacterium and Tannerella than plaques from metabolically healthy patients. Phosphatidylcholines, plasmenyl phosphatidylcholines, ceramides containing non-OH fatty acids, and host proteins related to actin filament rearrangement were elevated in plaques from PD versus non-PD samples. Cross-omic correlation analysis enabled the detection of a strong association between Lautropia and monomethyl phosphatidylethanolamine (PE-NMe), which is striking because synthesis of PE-NMe is uncommon in oral bacteria. Lipidomics analysis of in vitro cultures of Lautropia mirabilis confirmed the synthesis of PE-NMe by the bacteria. This comprehensive analysis revealed a novel microbial metabolic pathway and significant associations of host-derived proteins with PD. Patients with periodontal disease or diabetes have unique microbial dysbiosis. Proteomics and 16S data provide complementary information about microbial diversity. Cross-omic correlation reveals host signatures associated with periodontal disease. Multi-omic data lead to finding about microbially synthesized lipids.
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Affiliation(s)
- Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Timothy W Rhoads
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Anna E Merrill
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zhan Ye
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Amit Acharya
- Center for Oral and Systemic Health, Marshfield Clinic, Marshfield, WI 54449, USA
| | - Sanjay K Shukla
- Center for Oral and Systemic Health, Marshfield Clinic, Marshfield, WI 54449, USA; Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA.
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA.
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22
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Aswani VH, Shukla SK. An Early History of Phage Therapy in the United States: Is it Time to Reconsider? Clin Med Res 2021; 19:82-89. [PMID: 34172535 PMCID: PMC8231696 DOI: 10.3121/cmr.2021.1605] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 11/30/2020] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
Frederick William Twort and Felix d'Hérelle independently discovered bacteriophages in 1915 and 1917, respectively. This led to the early trials of using bacteriophages to treat infectious diseases worldwide. The earliest reported use of bacteriophages therapeutically in the United States was in 1922. With the subsequent discovery of antibiotics in the 1940s, and because of disappointing results of phage therapy in the next decade, use of bacteriophages as therapeutic agents declined in western countries. This paper addresses two questions in the field: what is the historical record of the successes and failures of phage therapy in the United States and, what led to abandoning phage therapy in the United States? We examined the literature from 1915 to 1965, and we present a numerical analysis of the papers published during that period. We report key historical factors leading to a decline in the use of phage therapy in the United States by the 1950s. Since bacteriophages were first used therapeutically, several changes have occurred: increased antimicrobial drug resistance and a better knowledge of the biology of bacteriophages are important examples. Early assessments leading to the rejection of phage therapy in the United States were perhaps appropriate. However, it is time to reconsider the role of bacteriophages in treatment of bacterial infections.
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Affiliation(s)
- Vijay H Aswani
- Department of Internal Medicine & Pediatrics, University at Buffalo, Buffalo, New York, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
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23
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Kumar N, Puri P, Shukla SK, Verma D. Impact of poor evidence management on DNA profiling in sexual assault and homicide: A case report. Med Leg J 2021; 89:58-60. [PMID: 33475030 DOI: 10.1177/0025817220966487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Increasing numbers of female victims of violent sexual assaults are being murdered with the aim of concealing the identity of the perpetrator. Proper handling and analysis of evidence is very important in gaining a conviction in many criminal cases. After evidence is collected, due precautions must be taken to ensure that the integrity of the sample is maintained, and chances of contamination are minimised. This paper presents a case study where improper handling of biological evidence led to loss of evidentiary value, and the semen could not be located on the vaginal swabs and victim's garments due to improper preservation of samples. However, the DNA from the nail of a decomposed finger helped identify the victim, and the suspect was apprehended based on the clues given by her family.
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Affiliation(s)
- Naresh Kumar
- Forensic Science Laboratory, Home Department, Government of NCT of Delhi, Delhi, India
| | - Pooja Puri
- Amity Institute of Forensic Science, Amity University Noida, Noida, India
| | - S K Shukla
- Amity Institute of Forensic Science, Amity University Noida, Noida, India
| | - Deepa Verma
- Forensic Science Laboratory, Home Department, Government of NCT of Delhi, Delhi, India
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24
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Kushwaha CS, Shukla SK. Potentiometric extractive sensing of lead ions over a nickel oxide intercalated chitosan-grafted-polyaniline composite. Dalton Trans 2020; 49:13862-13871. [PMID: 33006591 DOI: 10.1039/d0dt02687e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present research paper reports the extractive potentiometric sensing of lead ions over a chemically functionalized ternary nanocomposite of nickel oxide intercalated chitosan grafted polyaniline (NiO-in-CHIT-g-PANI) prepared by the in situ chemical polymerization and composite formation technique under optimized conditions. The structural, morphological, and physical properties of the composite material were investigated by Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), and other suitable ASTM methods. The obtained analytical result suggests the formation of a porous hybrid composite matrix with better electrical conductivity ∼ 5.25 × 10-3 S cm-1, free interactive carbonyl sites, and evolved aligned crystallinity. Furthermore, a film of the synthesized composite was cast on ITO coated glass by the spin coating technique for potentiometric sensing and the recovery of adsorbed Pb2+ ions from natural and artificial water solutions. Under optimum conditions of ∼pH = 7.0 and a temperature of 25 °C, the electrode exhibited potential responses for Pb2+ ions in concentrations ranging from 1.0 × 10-6 M to 1 × 10-3 M along with a sensitivity of 0.2379 mV μM-1 cm-2, response time of 40 s, recovery time of 10 s, and stability for 64 days. The adsorbed Pb2+ ions were recovered at a rate of 84% after applying an optimized reverse voltage on the above-used electrodes. The adsorption and desorption mechanism has been explained based on the induced potential due to the electrochemical surface interaction between Pb2+ and the NiO-in-CHIT-g-PANI based electrode. The analytical application of the fabricated electrode in the real sample was also explored for the sensing and recovery of the respective metal ions in wastewater samples along with the possibility of optimization of the required metal concentrations.
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Affiliation(s)
- Chandra Shekhar Kushwaha
- Department of Polymer Science, Bhaskaracharya College of Applied Sciences, University of Delhi, Delhi-110075, India.
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25
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Miller LS, Fowler VG, Shukla SK, Rose WE, Proctor RA. Development of a vaccine against Staphylococcus aureus invasive infections: Evidence based on human immunity, genetics and bacterial evasion mechanisms. FEMS Microbiol Rev 2020; 44:123-153. [PMID: 31841134 PMCID: PMC7053580 DOI: 10.1093/femsre/fuz030] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Invasive Staphylococcus aureus infections are a leading cause of morbidity and mortality in both hospital and community settings, especially with the widespread emergence of virulent and multi-drug resistant methicillin-resistant S. aureus strains. There is an urgent and unmet clinical need for non-antibiotic immune-based approaches to treat these infections as the increasing antibiotic resistance is creating a serious threat to public health. However, all vaccination attempts aimed at preventing S. aureus invasive infections have failed in human trials, especially all vaccines aimed at generating high titers of opsonic antibodies against S. aureus surface antigens to facilitate antibody-mediated bacterial clearance. In this review, we summarize the data from humans regarding the immune responses that protect against invasive S. aureus infections as well as host genetic factors and bacterial evasion mechanisms, which are important to consider for the future development of effective and successful vaccines and immunotherapies against invasive S. aureus infections in humans. The evidence presented form the basis for a hypothesis that staphylococcal toxins (including superantigens and pore-forming toxins) are important virulence factors, and targeting the neutralization of these toxins are more likely to provide a therapeutic benefit in contrast to prior vaccine attempts to generate antibodies to facilitate opsonophagocytosis.
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Affiliation(s)
- Lloyd S Miller
- Immunology, Janssen Research and Development, 1400 McKean Road, Spring House, PA, 19477, USA.,Department of Dermatology, Johns Hopkins University School of Medicine, 1550 Orleans Street, Cancer Research Building 2, Suite 209, Baltimore, MD, 21231, USA.,Department of Medicine, Division of Infectious Diseases, Johns Hopkins University School of Medicine, 1830 East Monument Street, Baltimore, MD, 21287, USA.,Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, 601 North Caroline Street, Baltimore, MD, 21287, USA.,Department of Materials Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Vance G Fowler
- Department of Medicine, Division of Infectious Diseases, Duke University Medical Center, 315 Trent Drive, Hanes House, Durham, NC, 27710, USA.,Duke Clinical Research Institute, Duke University Medical Center, 40 Duke Medicine Circle, Durham, NC, 27710, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 North Oak Avenue, Marshfield, WI, 54449, USA.,Computation and Informatics in Biology and Medicine, University of Wisconsin, 425 Henry Mall, Room 3445, Madison, WI, 53706, USA
| | - Warren E Rose
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA.,Pharmacy Practice Division, University of Wisconsin-Madison, 777 Highland Avenue, 4123 Rennebohm Hall, Madison, WI, 53705 USA
| | - Richard A Proctor
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI, 53705, USA.,Department of Medical Microbiology and Immunology, University of Wisconsin-Madison School of Medicine and Public Health, 1550 Linden Drive, Microbial Sciences Building, Room 1334, Madison, WI, 53705, USA
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26
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Shukla SK, Carter TC, Ye Z, Pantrangi M, Rose WE. Modeling of Effective Antimicrobials to Reduce Staphylococcus aureus Virulence Gene Expression Using a Two-Compartment Hollow Fiber Infection Model. Toxins (Basel) 2020; 12:toxins12020069. [PMID: 31979087 PMCID: PMC7076779 DOI: 10.3390/toxins12020069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/20/2020] [Indexed: 11/17/2022] Open
Abstract
Toxins produced by community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) contribute to virulence. We developed a statistical approach to determine an optimum sequence of antimicrobials to treat CA-MRSA infections based on an antimicrobial’s ability to reduce virulence. In an in vitro pharmacodynamic hollow fiber model, expression of six virulence genes (lukSF-PV, sek, seq, ssl8, ear, and lpl10) in CA-MRSA USA300 was measured by RT-PCR at six time points with or without human-simulated, pharmacokinetic dosing of five antimicrobials (clindamycin, minocycline, vancomycin, linezolid, and trimethoprim/sulfamethoxazole (SXT)). Statistical modeling identified the antimicrobial causing the greatest decrease in virulence gene expression at each time-point. The optimum sequence was SXT at T0 and T4, linezolid at T8, and clindamycin at T24–T72 when lukSF-PV was weighted as the most important gene or when all six genes were weighted equally. This changed to SXT at T0–T24, linezolid at T48, and clindamycin at T72 when lukSF-PV was weighted as unimportant. The empirical p-value for each optimum sequence according to the different weights was 0.001, 0.0009, and 0.0018 with 10,000 permutations, respectively, indicating statistical significance. A statistical method integrating data on change in gene expression upon multiple antimicrobial exposures is a promising tool for identifying a sequence of antimicrobials that is effective in sustaining reduced CA-MRSA virulence.
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Affiliation(s)
- Sanjay K. Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA; (T.C.C.); (Z.Y.); (M.P.)
- Correspondence:
| | - Tonia C. Carter
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA; (T.C.C.); (Z.Y.); (M.P.)
| | - Zhan Ye
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA; (T.C.C.); (Z.Y.); (M.P.)
| | - Madhulatha Pantrangi
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA; (T.C.C.); (Z.Y.); (M.P.)
| | - Warren E. Rose
- Pharmacy Practice Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA;
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27
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Puri P, Kumar N, Sharma D, Shukla SK. Differential organic DNA extraction of semen sample contaminated with blood for the identification of a serial sexual offender: A case report. Med Leg J 2019; 87:32-35. [PMID: 30070156 DOI: 10.1177/0025817218789569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In many cases of sexual assault, traces of semen are left behind on the victim's body, clothes and the area in which the assault has taken place. The positive identification of semen is instrumental in supporting such cases. There are several methods of forensic examination of semen reported in literature, but the presence of blood complicates the identification of semen stains. This paper presents one such case study where the presence of blood makes DNA profiling more challenging as the PCR amplification becomes complicated, and the absolute differential isolation is the only way to get the clear profile using identifiler kits.
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Affiliation(s)
- Pooja Puri
- 1 Amity Institute of Forensic Sciences, Amity University, Noida, India
| | - Naresh Kumar
- 2 Biology Division, Forensic Science Laboratory, Home Department, GNCT of Delhi, Rohini, New Delhi, India
| | - Dhruv Sharma
- 2 Biology Division, Forensic Science Laboratory, Home Department, GNCT of Delhi, Rohini, New Delhi, India
| | - S K Shukla
- 1 Amity Institute of Forensic Sciences, Amity University, Noida, India
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28
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Abstract
Teeth may provide useful forensic evidence owing to features like uniqueness, stability and comparability. Moreover, the human dentition is heterodont, i.e. all the teeth have different morphology - incisors, canines, premolars and molars. There are sometimes deviations from normal morphology, such as the presence of extra teeth, variation in their shape and size eg the presence of an extra cusp, fractured crown/root, Carabelli's cusp, peg laterals, transpositions, fusion, etc. These differences can help forensic personnel identify bodies, especially where other methods of identification like facial features, fingerprints or DNA typing cannot yield satisfactory results as in cases of badly decomposed bodies, burnt remains, mass disasters, etc. Identification from dentition is based on the direct comparison of post-mortem dental profiles with ante-mortem dental records of the deceased. This article aims to review these developmental and morphological dental traits and their role in post-mortem identification.
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Affiliation(s)
- Pooja Puri
- 1 Amity Institute of Forensic Science, Amity University, Uttar Pradesh, India
| | - S K Shukla
- 1 Amity Institute of Forensic Science, Amity University, Uttar Pradesh, India
| | - I Haque
- 2 Directorate of Forensic Science Services, Ministry of Home Affairs, Govt. of India, New Delhi, India
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29
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Aswani V, Najar F, Pantrangi M, Mau B, Schwan WR, Shukla SK. Virulence factor landscape of a Staphylococcus aureus sequence type 45 strain, MCRF184. BMC Genomics 2019; 20:123. [PMID: 30736742 PMCID: PMC6368776 DOI: 10.1186/s12864-018-5394-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background We describe the virulence factors of a methicillin-sensitive Staphylococcus aureus sequence type (ST) 45 strain, MCRF184, (spa type t917), that caused severe necrotizing fasciitis in a 72-year-old diabetic male. The genome of MCRF184 possesses three genomic islands: a relatively large type III νSaα with 42 open reading frames (ORFs) that includes superantigen- and lipoprotein-like genes, a truncated νSaβ that consists mostly of the enterotoxin gene cluster (egc), and a νSaγ island with 18 ORFs including α-toxin. Additionally, the genome has two phage-related regions: phage φSa3 with three genes of the immune evasion cluster (IEC), and an incomplete phage that is distinct from other S. aureus phages. Finally, the region between orfX and orfY harbors a putative efflux pump, acetyltransferase, regulators, and mobilization genes instead of genes of SCCmec. Results Virulence factors included phenol soluble modulins (PSMs) α1 through α4 and PSMs β1 and β2. Ten ORFs identified in MCRF184 had not been reported in previously sequenced S. aureus strains. Conclusion The dire clinical outcome in the patient and the described virulence factors all suggest that MCRF184, a ST45 strain is a highly virulent strain of S. aureus. Electronic supplementary material The online version of this article (10.1186/s12864-018-5394-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vijay Aswani
- Department of Internal Medicine & Pediatrics, University at Buffalo, Buffalo, New York, USA
| | - Fares Najar
- Department of Chemistry & Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Madhulatha Pantrangi
- Center for Human Genetics, 1000 North Oak Avenue # MLR, Marshfield, WI, 54449, USA
| | - Bob Mau
- Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, USA
| | - William R Schwan
- Department of Microbiology, University of Wisconsin -La Crosse, La Crosse, WI, USA
| | - Sanjay K Shukla
- Center for Human Genetics, 1000 North Oak Avenue # MLR, Marshfield, WI, 54449, USA.
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30
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Bucholtz GA, Salzman SA, Bersalona FB, Boyle TR, Ejercito VS, Penno L, Peterson DW, Stone GE, Urquhart A, Shukla SK, Burmester JK. PCR Analysis of Nasal Polyps, Chronic Sinusitis, and Hypertrophied Turbinates for DNA Encoding Bacterial 16S rRNA. ACTA ACUST UNITED AC 2018. [DOI: 10.1177/194589240201600309] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background Nasal polyps are considered to result from chronic inflammation, but the initial or persisting stimulus for the inflammation is not known. A variety of bacteria and fungi have been cultured from nasal polyps, but ∼35% have sterile cultures. Previously, Mycoplasma pneumoniae–specific DNA was detected in human nasal polyps using polymerase chain reaction (PCR) techniques, suggesting M. pneumoniae as a causative agent in the etiology of nasal polyps. Methods In this study, we tested for the presence of bacterial DNA in nasal polyps resected from 40 patients, in nasal mucosa membrane from 9 patients undergoing turbinectomy for hypertrophy, and in sinus mucosa membrane from 6 patients undergoing endoscopic surgery for chronic sinusitis. Tissue DNA was extracted and analyzed by PCR using M. pneumoniae specific primers for DNA that encode the 16S rRNA gene in 41 specimens (31 polyps, 6 turbinates, and 4 sinus), and by consensus sequence-based PCR using broad range primers for most eubacterial DNA encoding the 16S rRNA gene in 38 specimens (26 polyps, 7 turbinates, and 5 sinuses). Results Only two samples were positive for bacterial DNA encoding 16S rRNA: Streptococcus sp. DNA was isolated from one polyp specimen and Pseudomonas aeruginosa DNA was isolated in one maxillary sinusitis specimen. No evidence of M. pneumoniae–specific DNA encoding 16S rRNA was found in any of the tissues. Conclusions This study suggests that chronic bacterial infection is not a major component of nasal polyp etiology.
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Affiliation(s)
| | - Sherry A. Salzman
- Departments of Marshfield Medical Research and Education Foundation, A Division of Marshfield Clinic, Marshfield, Wisconsin
| | | | - Timothy R. Boyle
- Departments of Otolaryngology, Marshfield Clinic, Marshfield, Wisconsin
| | | | - Linda Penno
- Departments of Otolaryngology, Marshfield Clinic, Marshfield, Wisconsin
| | | | - Gwen E. Stone
- Departments of Otolaryngology, Marshfield Clinic, Marshfield, Wisconsin
| | - Andrew Urquhart
- Departments of Otolaryngology, Marshfield Clinic, Marshfield, Wisconsin
| | - Sanjay K. Shukla
- Departments of Marshfield Medical Research and Education Foundation, A Division of Marshfield Clinic, Marshfield, Wisconsin
| | - James K. Burmester
- Departments of Marshfield Medical Research and Education Foundation, A Division of Marshfield Clinic, Marshfield, Wisconsin
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Eggers S, Malecki KMC, Peppard P, Mares J, Shirley D, Shukla SK, Poulsen K, Gangnon R, Duster M, Kates A, Suen G, Sethi AK, Safdar N. Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods. BMJ Open 2018; 8:e019450. [PMID: 29588324 PMCID: PMC5875638 DOI: 10.1136/bmjopen-2017-019450] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Prevention of multidrug-resistant organism (MDRO) infections, such as those caused by methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, fluoroquinolone-resistant Gram-negative bacteria and Clostridium difficile is crucial. Evidence suggests that dietary fibre increases gut microbial diversity, which may help prevent colonisation and subsequent infection by MDROs. The aim of the Winning the War on Antibiotic Resistance (WARRIOR) project is to examine associations of dietary fibre consumption with the composition of the gut microbiota and gut colonisation by MDROs. The secondary purpose of the study is to create a biorepository of multiple body site specimens for future microbiota research. METHODS AND ANALYSIS The WARRIOR project collects biological specimens, including nasal, oral and skin swabs and saliva and stool samples, along with extensive data on diet and MDRO risk factors, as an ancillary study of the Survey of the Health of Wisconsin (SHOW). The SHOW is a population-based health survey collecting data on several different health determinants and outcomes, as well as objective body measurements and biological specimens. WARRIOR participants include 600 randomly selected Wisconsin residents age 18 and over. Specimens are screened for MDRO colonisation and DNA is extracted for 16S ribosomal RNA-based microbiota sequencing. Data will be analysed to assess the relationship between dietary fibre, the gut microbiota composition and gut MDRO colonisation. ETHICS AND DISSEMINATION The WARRIOR project is approved by the University of Wisconsin Institutional Review Board. The main results of this study will be published in a peer-reviewed scientific journal.
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Affiliation(s)
- Shoshannah Eggers
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kristen MC Malecki
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Paul Peppard
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Julie Mares
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Daniel Shirley
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sanjay K Shukla
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin, USA
| | - Keith Poulsen
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ronald Gangnon
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biostatistics and Medical Informatics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Megan Duster
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ashley Kates
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Garret Suen
- Department of Bacteriology, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ajay K Sethi
- Department of Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nasia Safdar
- Division of Infectious Disease, Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- William S. Middleton Veterans Affairs Medical Center, Madison, Wisconsin, USA
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32
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Rose WE, Shukla SK, Berti AD, Hayney MS, Henriquez KM, Ranzoni A, Cooper MA, Proctor RA, Nizet V, Sakoulas G. Increased Endovascular Staphylococcus aureus Inoculum Is the Link Between Elevated Serum Interleukin 10 Concentrations and Mortality in Patients With Bacteremia. Clin Infect Dis 2018; 64:1406-1412. [PMID: 28205673 DOI: 10.1093/cid/cix157] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 02/15/2017] [Indexed: 12/12/2022] Open
Abstract
Background Cell wall peptidoglycan stimulates interleukin 10 (IL-10) production in Staphylococcus aureus bacteremia (SaB) animal models, but clinical data are not available. This study evaluates the impact of intravascular bacterial cell numbers (ie, the level of bacteremia), in patients at the time of clinical presentation on IL-10 production and its association with S. aureus bacteremia (SaB) mortality. Methods Blood and isolates were collected in 133 consecutive SaB patients. Serum IL-10 was quantified by an electrochemoluminescence assay. Bacterial inoculum was measured in patient sera with elevated (n = 8) or low (n = 8) IL-10 using a magnetic bacterial capture assay. Staphylococcus aureus from these 2 groups were introduced into whole blood ex vivo to determine IL-10 production with variable inocula. Results IL-10 serum concentration was higher in SaB patient mortality (n = 27) vs survival (n = 106) (median, 36.0 pg/mL vs 10.4 pg/mL, respectively, P < .001). Patients with elevated IL-10 more often had endovascular SaB sources. The inoculum level of SaB was higher in patients with elevated serum IL-10 vs patients with low IL-10 (35.5 vs 0.5 median CFU/mL; P = .044). Ex vivo studies showed that 108 CFU/mL yielded greater IL-10 than did 103 CFU/mL (4.4 ± 1.8 vs 1.0 ± 0.6 pg/mL; P < .01). Conclusions Elevated IL-10 serum concentrations at clinical presentation of SaB were highly associated with mortality. High intravascular peptidoglycan concentration, driven by a higher level of bacteremia, is a key mediator of IL-10 anti-inflammatory response that portends poor clinical outcome. Using IL-10 as an initial biomarker, clinicians may consider more aggressive antimicrobials for rapid bacterial load reduction in high-risk SaB patients.
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Affiliation(s)
- Warren E Rose
- School of Pharmacy, University of Wisconsin-Madison, and
| | | | - Andrew D Berti
- School of Pharmacy, University of Wisconsin-Madison, and
| | - Mary S Hayney
- School of Pharmacy, University of Wisconsin-Madison, and
| | | | - Andrea Ranzoni
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Matthew A Cooper
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Richard A Proctor
- Departments of Medicine and Medical Microbiology/Immunology, University of Wisconsin School of Medicine and Public Health, Madison, and
| | - Victor Nizet
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla
| | - George Sakoulas
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla
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Singh VK, Ring RP, Aswani V, Stemper ME, Kislow J, Ye Z, Shukla SK. Phylogenetic distribution and expression of a penicillin-binding protein homologue, Ear and its significance in virulence of Staphylococcus aureus. J Med Microbiol 2017; 66:1811-1821. [PMID: 29099691 DOI: 10.1099/jmm.0.000630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Staphylococcus aureus is an opportunistic human pathogen that can cause serious infections in humans. A plethora of known and putative virulence factors are produced by staphylococci that collectively orchestrate pathogenesis. Ear protein (Escherichia coli ampicillin resistance) in S. aureus is an exoprotein in COL strain, predicted to be a superantigen, and speculated to play roles in antibiotic resistance and virulence. The goal of this study was to determine if expression of ear is modulated by single nucleotide polymorphisms in its promoter and coding sequences and whether this gene plays roles in antibiotic resistance and virulence. METHODOLOGY Promoter, coding sequences and expression of the ear gene in clinical and carriage S. aureus strains with distinct genetic backgrounds were analysed. The JE2 strain and its isogenic ear mutant were used in a systemic infection mouse model to determine the competiveness of the ear mutant.Results/Key findings. The ear gene showed a variable expression, with USA300FPR3757 showing a high-level expression compared to many of the other strains tested including some showing negligible expression. Higher expression was associated with agr type 1 but not correlated with phylogenetic relatedness of the ear gene based upon single nucleotide polymorphisms in the promoter or coding regions suggesting a complex regulation. An isogenic JE2 (USA300 background) ear mutant showed no significant difference in its growth, antibiotic susceptibility or virulence in a mouse model. CONCLUSION Our data suggests that despite being highly expressed in a USA300 genetic background, Ear is not a significant contributor to virulence in that strain.
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Affiliation(s)
- Vineet K Singh
- A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Robert P Ring
- A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Vijay Aswani
- The State University of New York, Buffalo, NY, USA
| | | | | | - Zhan Ye
- Marshfield Clinic Research Institute, Marshfield, WI, USA
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Shukla SK, Ye Z, Sandberg S, Reyes I, Fritsche TR, Keifer M. The nasal microbiota of dairy farmers is more complex than oral microbiota, reflects occupational exposure, and provides competition for staphylococci. PLoS One 2017; 12:e0183898. [PMID: 28850578 PMCID: PMC5574581 DOI: 10.1371/journal.pone.0183898] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022] Open
Abstract
Allergic and autoimmune diseases had been attributed to lack of exposure to biodiversity, an important factor in regulating immune homeostasis in a healthy host. We posit that the microbiome of healthy dairy farmers (DF) will be richer than non-farmers (NF) living in urban settings due to exposure to a greater biodiversity in the dairy environment. However, no studies have investigated the relationships between microbiota of dairy farmers (DF) compared with urban non-farmers (NF). We compared the nasal and oral microbiota of dairy farmers (N_DF, O_DF, respectively) with nasal and oral microbiota of NF in the same geographical area. The N_DF showed high microbial diversity with hundreds of unique genera that reflected environmental/occupational exposures. The nasal and oral microbiomes clustered separately from each other using Principal Coordinate Analysis, and with DF harboring two-fold and 1.5-fold greater exclusive genera in their nose and mouth respectively, than did non-farmers. Additionally, the N_DF group had a lower burden of Staphylococcus spp. suggesting a correlation between higher microbial diversity and competition for colonization by staphylococci. The N_DF samples were negative for the mecA gene, a marker of methicillin-resistance in staphylococci. The lower burden of staphylococci was found to be independent of the abundance of Corynebacterium spp. Exposure to greater biodiversity could enhance microbial competition, thereby reducing colonization with opportunistic pathogens. Future studies will analyze whether exposure to livestock microbiomes offers protection from acute and chronic diseases.
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Affiliation(s)
- Sanjay K. Shukla
- Molecular Microbiology Laboratory, Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
- * E-mail:
| | - Zhan Ye
- Biomedical Informatics Research Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
| | - Scott Sandberg
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
| | - Iris Reyes
- National Farm Medicine Center, Marshfield Clinic Research Institute, Marshfield, Wisconsin, United States of America
| | - Thomas R. Fritsche
- Division of Laboratory Medicine, Marshfield Clinic, Marshfield, Wisconsin, United States of America
| | - Matthew Keifer
- VA Puget Sound, Seattle, Washington, United States of America
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Abstract
Human anaplasmosis (HA) is an emerging tick-borne disease that may present as a mild flu-like illness or a life threatening, sepsis-like condition. Although disease severity is hypothesized to relate to immunopathology and immune dysfunction in humans, studies to directly measure immune responses in infected humans have been very limited. We quantified cytokines in 80 confirmed HA patients using a multiplex chemiluminescence immunoassay system and compared similarly measured responses in 1000 control subjects. Pro-inflammatory cytokines were significantly elevated in HA patients (all seven p<0.0001). Interferon gamma (IFN-γ) concentrations were particularly high, with average concentrations 7.8 times higher in the HA patients than the controls. A subset of cytokines consisting of IL-1β, IL-8, IL-6, TNF-α, and IL-10 was also coordinately high and significantly associated with severity of thrombocytopenia in HA patients. Patients with infections in the very acute stage (≤ 4 days ill) tended to have the highest IFN-γ, IL-12p70, and IL-2 levels. Higher concentrations of IL-13 and IL-5 were associated with diarrhea and vomiting. Our findings support a pathophysiological role for a pro-inflammatory response in HA, especially with regard to the modulation of hematopoiesis and subsequent hematopoietic complications.
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Affiliation(s)
- Anna M. Schotthoefer
- Marshfield Clinic Research Institute, Marshfield Clinic, Marshfield, Wisconsin, United States of America
- * E-mail:
| | - Steven J. Schrodi
- Marshfield Clinic Research Institute, Marshfield Clinic, Marshfield, Wisconsin, United States of America
| | - Jennifer K. Meece
- Marshfield Clinic Research Institute, Marshfield Clinic, Marshfield, Wisconsin, United States of America
| | - Thomas R. Fritsche
- Marshfield Labs, Marshfield Clinic, Marshfield, Wisconsin, United States of America
- Microbiology Department, University of Wisconsin-La Crosse, La Crosse, Wisconsin, United States of America
| | - Sanjay K. Shukla
- Marshfield Clinic Research Institute, Marshfield Clinic, Marshfield, Wisconsin, United States of America
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Marcel N, Perumalsamy LR, Shukla SK, Sarin A. The lysine deacetylase Sirtuin 1 modulates the localization and function of the Notch1 receptor in regulatory T cells. Sci Signal 2017; 10:10/473/eaah4679. [PMID: 28377411 DOI: 10.1126/scisignal.aah4679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The ability to tune cellular functions in response to nutrient availability has important consequences for immune homeostasis. The activity of the receptor Notch in regulatory T (Treg) cells, which suppress the functions of effector T cells, is indispensable for Treg cell survival under conditions of diminished nutrient supply. Anti-apoptotic signaling induced by the Notch1 intracellular domain (NIC) originates from the cytoplasm and is spatially decoupled from the nuclear, largely transcriptional functions of NIC. We showed that Sirtuin 1 (Sirt1), which is an NAD+ (nicotinamide adenine dinucleotide)-dependent lysine deacetylase that inhibits NIC-dependent gene transcription, stabilized NIC proximal to the plasma membrane to promote the survival and function of activated Treg cells. Sirt1 was required for NIC-dependent protection from apoptosis in cell lines but not for the activity of the anti-apoptotic protein Bcl-xL. In addition, a variant NIC protein in which four lysines were mutated to arginines (NIC4KR) retained anti-apoptotic activity, but was not regulated by Sirt1, and reconstituted the functions of nonnuclear NIC in Notch1-deficient Treg cells. Loss of Sirt1 compromised Treg cell survival, resulting in antigen-induced T cell proliferation and inflammation in two mouse models. Thus, the Sirt1-Notch interaction may constitute an important checkpoint that tunes noncanonical Notch1 signaling.
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Affiliation(s)
- Nimi Marcel
- National Centre for Biological Sciences, Bengaluru, Karnataka 560065, India.,Manipal University, Manipal, Karnataka, India
| | | | - Sanjay K Shukla
- National Centre for Biological Sciences, Bengaluru, Karnataka 560065, India.,Manipal University, Manipal, Karnataka, India
| | - Apurva Sarin
- National Centre for Biological Sciences, Bengaluru, Karnataka 560065, India. .,Institute for Stem Cell Biology and Regenerative Medicine, Bengaluru, Karnataka 560065, India
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Agger WA, Schauberger CW, Burmester JK, Shukla SK. Developing Research Priorities for Prediction and Prevention of Preterm Birth. Clin Med Res 2016; 14:123-125. [PMID: 27565514 PMCID: PMC5302454 DOI: 10.3121/cmr.2016.1330] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/11/2016] [Accepted: 08/22/2016] [Indexed: 01/10/2023]
Affiliation(s)
- William A Agger
- Infectious Disease Section, Gundersen Health System, La Crosse, Wisconsin
- Department of Medical Research, Gundersen Medical Foundation, La Crosse, Wisconsin
| | - Charles W Schauberger
- Department of Obstetrics & Gynecology, Gundersen Health System, La Crosse, Wisconsin
| | - James K Burmester
- Department of Medical Research, Gundersen Medical Foundation, La Crosse, Wisconsin
| | - Sanjay K Shukla
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin
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Jackson KL, Mbagwu M, Pacheco JA, Baldridge AS, Viox DJ, Linneman JG, Shukla SK, Peissig PL, Borthwick KM, Carrell DA, Bielinski SJ, Kirby JC, Denny JC, Mentch FD, Vazquez LM, Rasmussen-Torvik LJ, Kho AN. Performance of an electronic health record-based phenotype algorithm to identify community associated methicillin-resistant Staphylococcus aureus cases and controls for genetic association studies. BMC Infect Dis 2016; 16:684. [PMID: 27855652 PMCID: PMC5114817 DOI: 10.1186/s12879-016-2020-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 11/11/2016] [Indexed: 12/25/2022] Open
Abstract
Background Community associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is one of the most common causes of skin and soft tissue infections in the United States, and a variety of genetic host factors are suspected to be risk factors for recurrent infection. Based on the CDC definition, we have developed and validated an electronic health record (EHR) based CA-MRSA phenotype algorithm utilizing both structured and unstructured data. Methods The algorithm was validated at three eMERGE consortium sites, and positive predictive value, negative predictive value and sensitivity, were calculated. The algorithm was then run and data collected across seven total sites. The resulting data was used in GWAS analysis. Results Across seven sites, the CA-MRSA phenotype algorithm identified a total of 349 cases and 7761 controls among the genotyped European and African American biobank populations. PPV ranged from 68 to 100% for cases and 96 to 100% for controls; sensitivity ranged from 94 to 100% for cases and 75 to 100% for controls. Frequency of cases in the populations varied widely by site. There were no plausible GWAS-significant (p < 5 E −8) findings. Conclusions Differences in EHR data representation and screening patterns across sites may have affected identification of cases and controls and accounted for varying frequencies across sites. Future work identifying these patterns is necessary. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-2020-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathryn L Jackson
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Michael Mbagwu
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | | | - Daniel J Viox
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Emory University School of Medicine, Atlanta, GA, USA
| | - James G Linneman
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | | | - Peggy L Peissig
- Biomedical Informatics Research Center, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | | | - David A Carrell
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | | | - Jacqueline C Kirby
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Frank D Mentch
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lyam M Vazquez
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Abel N Kho
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Behera MK, Dixit VK, Shukla SK, Ghosh JK, Abhilash VB, Asati PK, Jain AK. Solitary rectal ulcer syndrome: clinical, endoscopic, histological and anorectal manometry findings in north Indian patients. ACTA ACUST UNITED AC 2016; 36:244-50. [PMID: 27509702 DOI: 10.7869/tg.298] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Solitary rectal ulcer syndrome (SRUS) is a chronic, benign defecation disorder often related to excessive straining. SRUS is diagnosed on the basis of clinical symptoms, endoscopic and histological findings. METHODS All patients diagnosed with SRUS by colonoscopy and confirmed by histopathology from October 2012 to August 2014 in the Department of Gastroenterology, Institute of Medical Sciences, Banaras Hindu University, India, were included in the study. Out of 92 patients, thirty-four patients underwent anorectal manometry. Twenty age-matched healthy volunteers were also studied with anorectal manometry to serve as controls. RESULTS Mean age of the group was 41 ± 19 years with age range of 10-82 years; males were 58 (63%) with male to female ratio of 1.7:1. Bleeding per rectum was present in 83%, constipation in 46.7%, abdominal pain in 27.2%, and diarrhea in 25% of the patients. On endoscopy, ulcerative lesions were seen in 83% patients of whom solitary and multiple lesions were present in 44% and 39%, respectively. Polypoidal lesions were reported in 17.4% whilst rectal polyps and erythematous mucosa were found in 5.4% and 2.2%, respectively. Histological examination revealed fibromuscular obliteration in 100% of patients, surface ulceration in 70.6% and crypt distortion in 20.65% of patients. Anal relaxation and balloon expulsion test was significantly abnormal in SRUS patients compared to healthy controls (53% vs. 20%, p < 0.01). CONCLUSION Rectal bleeding was the most common symptom and ulcerative lesions the most common endoscopic finding. Fecal evaluation disorder was more prevalent inpatients with SRUS.
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Tripathi A, Shukla SK, Singh A, Prasad KN. Prevalence, outcome and risk factor associated with vancomycin-resistant Enterococcus faecalis and Enterococcus faecium at a Tertiary Care Hospital in Northern India. Indian J Med Microbiol 2016; 34:38-45. [DOI: 10.4103/0255-0857.174099] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Glurich I, Acharya A, Brilliant MH, Shukla SK. Progress in oral personalized medicine: contribution of 'omics'. J Oral Microbiol 2015; 7:28223. [PMID: 26344171 PMCID: PMC4561229 DOI: 10.3402/jom.v7.28223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Precision medicine (PM), representing clinically applicable personalized medicine, proactively integrates and interprets multidimensional personal health data, including clinical, 'omics', and environmental profiles, into clinical practice. Realization of PM remains in progress. OBJECTIVE The focus of this review is to provide a descriptive narrative overview of: 1) the current status of oral personalized medicine; and 2) recent advances in genomics and related 'omic' and emerging research domains contributing to advancing oral-systemic PM, with special emphasis on current understanding of oral microbiomes. DESIGN A scan of peer-reviewed literature describing oral PM or 'omic'-based research conducted on humans/data published in English within the last 5 years in journals indexed in the PubMed database was conducted using mesh search terms. An evidence-based approach was used to report on recent advances with potential to advance PM in the context of historical critical and systematic reviews to delineate current state-of-the-art technologies. Special focus was placed on oral microbiome research associated with health and disease states, emerging research domains, and technological advances, which are positioning realization of PM. RESULTS This review summarizes: 1) evolving conceptualization of personalized medicine; 2) emerging insight into roles of oral infectious and inflammatory processes as contributors to both oral and systemic diseases; 3) community shifts in microbiota that may contribute to disease; 4) evidence pointing to new uncharacterized potential oral pathogens; 5) advances in technological approaches to 'omics' research that will accelerate PM; 6) emerging research domains that expand insights into host-microbe interaction including inter-kingdom communication, systems and network analysis, and salivaomics; and 7) advances in informatics and big data analysis capabilities to facilitate interpretation of host and microbiome-associated datasets. Furthermore, progress in clinically applicable screening assays and biomarker definition to inform clinical care are briefly explored. CONCLUSION Advancement of oral PM currently remains in research and discovery phases. Although substantive progress has been made in advancing the understanding of the role of microbiome dynamics in health and disease and is being leveraged to advance early efforts at clinical translation, further research is required to discern interpretable constituency patterns in the complex interactions of these microbial communities in health and disease. Advances in biotechnology and bioinformatics facilitating novel approaches to rapid analysis and interpretation of large datasets are providing new insights into oral health and disease, potentiating clinical application and advancing realization of PM within the next decade.
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Affiliation(s)
- Ingrid Glurich
- Institute for Oral Systemic Health, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Amit Acharya
- Institute for Oral Systemic Health, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA;
| | - Sanjay K Shukla
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
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Shukla SK, Murali NS, Brilliant MH. Personalized medicine going precise: from genomics to microbiomics. Trends Mol Med 2015; 21:461-2. [PMID: 26129865 DOI: 10.1016/j.molmed.2015.06.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Sanjay K Shukla
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA.
| | | | - Murray H Brilliant
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
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Shukla SK, Rose W, Schrodi SJ. Complex host genetic susceptibility to Staphylococcus aureus infections. Trends Microbiol 2015; 23:529-36. [PMID: 26112911 DOI: 10.1016/j.tim.2015.05.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/11/2015] [Accepted: 05/22/2015] [Indexed: 12/20/2022]
Abstract
Understanding of the host genetic susceptibility to carriage of, and infections, due to Staphylococcus aureus, a nosocomial pathogen, is still in its nascent stages. Mouse models show variable susceptibility to S. aureus infections across mouse strains and disease models with roles for signaling pathways involving Toll-like receptors (TLR-1, TLR-2, and TLR-6), interleukins (IL-4, IL-6, IL-10, and IL-13), chemokines [CXC ligand (CXCL)-1 and CXCL-2], and T helper (Th)1/Th2 responses. Genome-wide association studies (GWASs) for carriage in humans identified SNPs in IL4, DEFB1, CRP, and VDR for persistent nasal carriage. NR3C1 haplotypes may either enhance risk or provide protection from colonization. GWASs for all S. aureus diseases have suggested roles for DAPK3, a kinase, and XRN1, a nuclease, while CDON could have a role in complicated bacteremia. More studies are needed to identify host susceptibility genes along with confirmation from functional assays.
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Affiliation(s)
- Sanjay K Shukla
- Center for Human Genetics, Marshfield Clinic Research Foundation, 1000 North Oak Avenue-MLR, Marshfield, WI, USA.
| | - Warren Rose
- Pharmacy Practice Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - Steven J Schrodi
- Center for Human Genetics, Marshfield Clinic Research Foundation, 1000 North Oak Avenue-MLR, Marshfield, WI, USA
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Pantrangi M, Singh VK, Shukla SK. Regulation of Staphylococcal Superantigen-Like Gene, ssl8, Expression in Staphylococcus aureus strain, RN6390. Clin Med Res 2015; 13:7-11. [PMID: 24899694 PMCID: PMC4435084 DOI: 10.3121/cmr.2014.1226] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/02/2014] [Indexed: 01/23/2023]
Abstract
Staphylococcal superantigen-like (SSL) proteins, which are encoded by a cluster of eleven ssl genes, contribute to the Staphylococcus aureus virulence. Recently we reported ssl8 expression profiles in seven clinically important strains-MW2, USA300FPR3757, MSSA476, Newman, RN6390, Mu50, and N315-and showed the differential expression of ssl8 in Newman, RN6390, and USA300FPR3757 strains, despite harboring identical allelic forms of ssl8, suggesting the roles for different regulatory elements for this gene in different S. aureus strains. In this communication, using RN6390, a common laboratory S. aureus strain and its isogenic knockout mutant strains of agr, sae, sarA, sigB, rot, and the agr-/sigB (-) double mutant, we showed that SarA and Rot are inducer and repressor, respectively, for ssl8 expression in RN6390. This is in contrast to the Newman strain, where ssl8 is positively regulated by Sae but negatively by Agr, indicating the variable expression of ssl8 in clinical strains is more likely due to strain-specific regulatory elements.
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Affiliation(s)
| | - Vineet K Singh
- A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Sanjay K Shukla
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin USA
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Singh VK, Vaish M, Johansson TR, Baum KR, Ring RP, Singh S, Shukla SK, Moskovitz J. Significance of four methionine sulfoxide reductases in Staphylococcus aureus. PLoS One 2015; 10:e0117594. [PMID: 25680075 PMCID: PMC4334518 DOI: 10.1371/journal.pone.0117594] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/29/2014] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and emergence of antibiotic resistance in clinical staphylococcal isolates raises concerns about our ability to control these infections. Cell wall-active antibiotics cause elevated synthesis of methionine sulfoxide reductases (Msrs: MsrA1 and MsrB) in S. aureus. MsrA and MsrB enzymes reduce S-epimers and R-epimers of methionine sulfoxide, respectively, that are generated under oxidative stress. In the S. aureus chromosome, there are three msrA genes (msrA1, msrA2 and msrA3) and one msrB gene. To understand the precise physiological roles of Msr proteins in S. aureus, mutations in msrA1, msrA2 and msrA3 and msrB genes were created by site-directed mutagenesis. These mutants were combined to create a triple msrA (msrA1, msrA2 and msrA3) and a quadruple msrAB (msrA1, msrA2, msrA3, msrB) mutant. These mutants were used to determine the roles of Msr proteins in staphylococcal growth, antibiotic resistance, adherence to human lung epithelial cells, pigment production, and survival in mice relative to the wild-type strains. MsrA1-deficient strains were sensitive to oxidative stress conditions, less pigmented and less adherent to human lung epithelial cells, and showed reduced survival in mouse tissues. In contrast, MsrB-deficient strains were resistant to oxidants and were highly pigmented. Lack of MsrA2 and MsrA3 caused no apparent growth defect in S. aureus. In complementation experiments with the triple and quadruple mutants, it was MsrA1 and not MsrB that was determined to be critical for adherence and phagocytic resistance of S. aureus. Overall, the data suggests that MsrA1 may be an important virulence factor and MsrB probably plays a balancing act to counter the effect of MsrA1 in S. aureus.
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Affiliation(s)
- Vineet K. Singh
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
- * E-mail:
| | - Manisha Vaish
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
| | - Trintje R. Johansson
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
| | - Kyle R. Baum
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
| | - Robert P. Ring
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
| | - Saumya Singh
- Department of Microbiology and Immunology, A.T. Still University of Health Sciences, Kirksville, Missouri, United States of America
| | - Sanjay K. Shukla
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin, United States of America
| | - Jackob Moskovitz
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas, United States of America
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Singh SK, Singh R, Singh P, Shukla SK. Effect of integrated nutrient management modules on yield and soil properties of Indian mustard (Brassica juncea). ACTA ACUST UNITED AC 2015. [DOI: 10.5958/2394-4471.2015.00009.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Agger WA, Siddiqui D, Lovrich SD, Callister SM, Borgert AJ, Merkitch KW, Mason TC, Baumgardner DJ, Burmester JK, Shukla SK, Welter JD, Stewart KS, Washburn M, Bailey HH. Epidemiologic factors and urogenital infections associated with preterm birth in a midwestern U.S. population. Obstet Gynecol 2014; 124:969-977. [PMID: 25437726 PMCID: PMC4251709 DOI: 10.1097/aog.0000000000000470] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE To correlate epidemiologic factors with urogenital infections associated with preterm birth. METHODS Pregnant women were sequentially included from four Wisconsin cohorts: large urban, midsize urban, small city, and rural city. Demographic, clinical, and current pregnancy data were collected. Cervical and urine specimens were analyzed by microscopy, culture, and polymerase chain reaction for potential pathogens. RESULTS Six hundred seventy-six women were evaluated. Fifty-four (8.0%) had preterm birth: 12.1% (19/157) large urban, 8.8% (15/170) midsize urban, 9.4% (16/171) small city, and 2.3% (4/178) rural city. Associated host factors and infections varied significantly among sites. Urogenital infection rates, especially Mycoplasma hominis and Ureaplasma parvum, were highest at the large urban site. Large urban site, minority ethnicity, multiple infections, and certain historical factors were associated with preterm birth by univariable analysis. By multivariable analysis, preterm birth was associated with prior preterm birth (adjusted odds ratio [aOR] 2.76, 95% confidence interval [CI] 1.27-6.02) and urinary tract infection (aOR 2.62, 95% CI 1.32-519), and negatively associated with provider-assessed good health (aOR 0.42, 95% CI 0.23-0.76) and group B streptococcal infection treatment (surrogate for health care use) (aOR 0.38, 95% CI 0.15-.99). Risk and protective factors were similar for women with birth at less than 35 weeks, and additionally associated with M hominis (aOR 3.6, 95% CI 1.4-9.7). CONCLUSION These measured differences among sites are consistent with observations that link epidemiologic factors, both environmental and genetic, with minimally pathogenic vaginal bacteria, inducing preterm birth, especially at less than 35 weeks of gestation.
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Affiliation(s)
- William A. Agger
- Gundersen Health System, La Crosse
- Gundersen Medical Foundation, La Crosse
| | | | | | | | | | | | | | | | | | | | | | | | - M.J. Washburn
- Wisconsin Network for Health Research Central Administration, Madison
| | - Howard H. Bailey
- University of Wisconsin, Madison
- Wisconsin Network for Health Research Central Administration, Madison
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Mangwani N, Shukla SK, Kumari S, Rao TS, Das S. Characterization of Stenotrophomonas acidaminiphila NCW-702 biofilm for implication in the degradation of polycyclic aromatic hydrocarbons. J Appl Microbiol 2014; 117:1012-24. [PMID: 25040365 DOI: 10.1111/jam.12602] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 07/07/2014] [Accepted: 07/15/2014] [Indexed: 11/30/2022]
Abstract
AIMS Biofilm formation and polycyclic aromatic hydrocarbons (PAHs) degradation by a marine bacterium Stenotrophomonas acidaminihila NCW-702 was investigated. METHODS AND RESULTS The biofilm structure was studied by confocal laser scanning microscopy (CLSM). Both planktonic and biofilm cultures were used for PAHs (phenanthrene and pyrene) degradation. In 7 days, Sten. acidaminiphila biofilm culture efficiently degraded 71·1 ± 3·1% and 40·2 ± 2·4% of phenanthrene and pyrene, respectively, whereas 38·7 ± 2·5% of phenanthrene and 29·7 ± 1% of pyrene degradation was observed in planktonic culture. The presence of phenolic intermediates in the culture supernatant during degradation process was evaluated by Folin-Ciocalteu reagent. The average thickness and diffusion distance of Sten. acidaminiphila NCW-702 biofilm was found to be 23·94 ± 2·62 μm and 2·68 ± 0·7 μm, respectively. Bacterial biofilms have numerous metabolic features that aid in the degradation of hydrophobic organic pollutants. CONCLUSIONS Biofilm of Sten. acidaminiphila NCW-702 was able to degrade PAHs more efficiently as compared to planktonic cells. The findings support the efficacy of biofilms over planktonic culture in bioremediation applications. SIGNIFICANCE AND IMPACT OF THE STUDY The study provides a constructive application of bacterial biofilms for the bioremediation of hydrophobic organic contaminants. The biofilm mode remediation process has the advantage of reusability of bacterial biomass and is also a low cost process as compared to cell immobilization techniques.
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Affiliation(s)
- N Mangwani
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Odisha, India
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