1
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Lai Y, Tang W, Luo X, Zheng H, Zhang Y, Wang M, Yu G, Yang M. Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis. Front Immunol 2024; 15:1369116. [PMID: 38711505 PMCID: PMC11070502 DOI: 10.3389/fimmu.2024.1369116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/01/2024] [Indexed: 05/08/2024] Open
Abstract
Objective Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome-metabolome interface in AS. Based on prospective cohort studies, we further explored the impact of the tumor necrosis factor inhibitor (TNFi) on the gut microbiota and metabolites in AS. Methods To further understand the gut microbiota and metabolites in AS, along with the influence of TNFi, we initiated a prospective cohort study. Fecal samples were collected from 29 patients with AS before and after TNFi therapy and 31 healthy controls. Metagenomic and metabolomic experiments were performed on the fecal samples; moreover, validation experiments were conducted based on the association between the microbiota and metabolites. Results A total of 7,703 species were annotated using the metagenomic sequencing system and by profiling the microbial community taxonomic composition, while 50,046 metabolites were identified using metabolite profiling. Differential microbials and metabolites were discovered between patients with AS and healthy controls. Moreover, TNFi was confirmed to partially restore the gut microbiota and the metabolites. Multi-omics analysis of the microbiota and metabolites was performed to determine the associations between the differential microbes and metabolites, identifying compounds such as oxypurinol and biotin, which were correlated with the inhibition of the pathogenic bacteria Ruminococcus gnavus and the promotion of the probiotic bacteria Bacteroides uniformis. Through experimental studies, the relationship between microbes and metabolites was further confirmed, and the impact of these two types of microbes on the enterocytes and the inflammatory cytokine interleukin-18 (IL-18) was explored. Conclusion In summary, multi-omics exploration elucidated the impact of TNFi on the gut microbiota and metabolites and proposed a novel therapeutic perspective: supplementation of compounds to inhibit potential pathogenic bacteria and to promote potential probiotics, therefore controlling inflammation in AS.
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Affiliation(s)
- Yupeng Lai
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Wenli Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiao Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huihui Zheng
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanpeng Zhang
- Department of Laboratory, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Meiying Wang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Min Yang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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2
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Li J, Zhang Q, Li X, Liu J, Wang F, Zhang W, Liu X, Li T, Wang S, Wang Y, Zhang X, Meng Y, Ma Y, Wang H. QingXiaoWuWei decoction alleviates methicillin-resistant Staphylococcus aureus-induced pneumonia in mice by regulating metabolic remodeling and macrophage gene expression network via the microbiota-short-chain fatty acids axis. Microbiol Spectr 2023; 11:e0034423. [PMID: 37823635 PMCID: PMC10714818 DOI: 10.1128/spectrum.00344-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/06/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) colonizes the upper respiratory airways and is resistant to antibiotics. MRSA is a frequently acquired infection in hospital and community settings, including cases of MRSA-induced pneumonia. Multidrug-resistant Staphylococcus aureus and the limited efficacy of antibiotics necessitate alternative strategies for preventing or treating the infection. QingXiaoWuWei decoction (QXWWD) protects against both gut microbiota dysbiosis and MRSA-induced pneumonia. Furthermore, the QXWWD-regulated metabolic remodeling and macrophage gene expression network contribute to its protective effects through the microbiota-short-chain fatty acid axis. The results of this study suggest that QXWWD and its pharmacodynamic compounds might have the potential to prevent and treat pulmonary infections, especially those caused by multidrug-resistant organisms. Our study provides a theoretical basis for the future treatment of pulmonary infectious diseases by manipulating gut microbiota and their metabolites via traditional Chinese medicine.
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Affiliation(s)
- Jun Li
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Qian Zhang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Xue Li
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Jing Liu
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Fang Wang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Wei Zhang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Xingyue Liu
- First Clinical Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Tiewei Li
- Zhengzhou Key Laboratory of Children’s Infection and Immunity, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital, Zhengzhou, China
| | - Shiqi Wang
- First Clinical Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Yuqi Wang
- First Clinical Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Xinyu Zhang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Yukun Meng
- First Clinical Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Yuheng Ma
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
| | - Huanyun Wang
- College of Pharmacy, Inner Mongolia Medical University, Hohhot, China
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3
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Psotta C, Nilsson EJ, Sjöberg T, Falk M. Bacteria-Infected Artificial Urine Characterization Based on a Combined Approach Using an Electronic Tongue Complemented with 1H-NMR and Flow Cytometry. BIOSENSORS 2023; 13:916. [PMID: 37887109 PMCID: PMC10605348 DOI: 10.3390/bios13100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023]
Abstract
The prevailing form of bacterial infection is within the urinary tract, encompassing a wide array of bacteria that harness the urinary metabolome for their growth. Through their metabolic actions, the chemical composition of the growth medium undergoes modifications as the bacteria metabolize urine compounds, leading to the subsequent release of metabolites. These changes can indirectly indicate the existence and proliferation of bacterial organisms. Here, we investigate the use of an electronic tongue, a powerful analytical instrument based on a combination of non-selective chemical sensors with a partial specificity for data gathering combined with principal component analysis, to distinguish between infected and non-infected artificial urine samples. Three prevalent bacteria found in urinary tract infections were investigated, Escherichia coli, Klebsiella pneumoniae, and Enterococcus faecalis. Furthermore, the electronic tongue analysis was supplemented with 1H NMR spectroscopy and flow cytometry. Bacteria-specific changes in compound consumption allowed for a qualitative differentiation between artificial urine medium and bacterial growth.
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Affiliation(s)
| | | | | | - Magnus Falk
- Biomedical Science, Faculty of Health and Society, and Biofilms Research Center, Malmö University, 205 06 Malmö, Sweden; (C.P.); (E.J.N.); (T.S.)
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4
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Hogins J, Xuan Z, Zimmern PE, Reitzer L. The distinct transcriptome of virulence-associated phylogenetic group B2 Escherichia coli. Microbiol Spectr 2023; 11:e0208523. [PMID: 37724859 PMCID: PMC10580932 DOI: 10.1128/spectrum.02085-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/28/2023] [Indexed: 09/21/2023] Open
Abstract
Escherichia coli strains of phylogenetic group B2 are often associated with urinary tract infections (UTIs) and several other diseases. Recent genomic and transcriptomic analyses have not suggested or identified specific genes required for virulence, but have instead suggested multiple virulence strategies and complex host-pathogen interactions. Previous analyses have not compared core gene expression between phylogenetic groups or between pathogens and nonpathogens within phylogenetic groups. We compared the core gene expression of 35 strains from three phylogenetic groups that included both pathogens and nonpathogens after growth in a medium that allowed comparable growth of both types of strains. K-means clustering suggested a B2 cluster with 17 group B2 strains and two group A strains; an AD cluster with six group A strains, five group D strains and one B2 strain; and four outliers which included the highly studied model uropathogenic E. coli strains UTI89 and CFT073. Half of the core genes were differentially expressed between B2 and AD cluster strains, including transcripts of genes for all aspects of macromolecular synthesis-replication, transcription, translation, and peptidoglycan synthesis-energy metabolism, and environmental-sensing transcriptional regulators. Notably, core gene expression between nonpathogenic and uropathogenic transcriptomes within phylogenetic groups did not differ. If differences between pathogens and nonpathogens exist, then the differences do not require transcriptional reprogramming. In summary, B2 cluster strains have a distinct transcription pattern that involves hundreds of genes. We propose that this transcription pattern is one factor that contributes to virulence. IMPORTANCE Escherichia coli is a diverse species and an opportunistic pathogen that is associated with various diseases, such as urinary tract infections. When examined, phylogenetic group B2 strains are more often associated with these diseases, but the specific properties that contribute to their virulence are not known. From a comparative transcriptomic analysis, we found that group B2 strains grown in a nutrient-rich medium had a distinct transcription pattern, which is the first evidence that core gene expression differs between phylogenetic groups. Understanding the consequences of group B2 transcription pattern will provide important information on basic E. coli biology, the basis for E. coli virulence, and possibly for developing therapies for a majority of urinary tract infections and other group B2-associated diseases.
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Affiliation(s)
- Jacob Hogins
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Zhenyu Xuan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Philippe E. Zimmern
- Department of Urology, The University of Texas Southwestern, Dallas, Texas, USA
| | - Larry Reitzer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
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5
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Rahman M, Schellhorn HE. Metabolomics of infectious diseases in the era of personalized medicine. Front Mol Biosci 2023; 10:1120376. [PMID: 37275959 PMCID: PMC10233009 DOI: 10.3389/fmolb.2023.1120376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/08/2023] [Indexed: 06/07/2023] Open
Abstract
Infectious diseases continue to be a major cause of morbidity and mortality worldwide. Diseases cause perturbation of the host's immune system provoking a response that involves genes, proteins and metabolites. While genes are regulated by epigenetic or other host factors, proteins can undergo post-translational modification to enable/modify function. As a result, it is difficult to correlate the disease phenotype based solely on genetic and proteomic information only. Metabolites, however, can provide direct information on the biochemical activity during diseased state. Therefore, metabolites may, potentially, represent a phenotypic signature of a diseased state. Measuring and assessing metabolites in large scale falls under the omics technology known as "metabolomics". Comprehensive and/or specific metabolic profiling in biological fluids can be used as biomarkers of disease diagnosis. In addition, metabolomics together with genomics can be used to differentiate patients with differential treatment response and development of host targeted therapy instead of pathogen targeted therapy where pathogens are more prone to mutation and lead to antimicrobial resistance. Thus, metabolomics can be used for patient stratification, personalized drug formulation and disease control and management. Currently, several therapeutics and in vitro diagnostics kits have been approved by US Food and Drug Administration (FDA) for personalized treatment and diagnosis of infectious diseases. However, the actual number of therapeutics or diagnostics kits required for tailored treatment is limited as metabolomics and personalized medicine require the involvement of personnel from multidisciplinary fields ranging from technological development, bioscience, bioinformatics, biostatistics, clinicians, and biotechnology companies. Given the significance of metabolomics, in this review, we discussed different aspects of metabolomics particularly potentials of metabolomics as diagnostic biomarkers and use of small molecules for host targeted treatment for infectious diseases, and their scopes and challenges in personalized medicine.
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6
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Edwards G, Seeley A, Carter A, Patrick Smith M, Cross ELA, Hughes K, Van den Bruel A, Llewelyn MJ, Verbakel JY, Hayward G. What is the Diagnostic Accuracy of Novel Urine Biomarkers for Urinary Tract Infection? Biomark Insights 2023; 18:11772719221144459. [PMID: 36761839 PMCID: PMC9902898 DOI: 10.1177/11772719221144459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/31/2022] [Indexed: 01/26/2023] Open
Abstract
Background Urinary tract infection (UTI) affects half of women at least once in their lifetime. Current diagnosis involves urinary dipstick and urine culture, yet both methods have modest diagnostic accuracy, and cannot support decision-making in patient populations with high prevalence of asymptomatic bacteriuria, such as older adults. Detecting biomarkers of host response in the urine of hosts has the potential to improve diagnosis. Objectives To synthesise the evidence of the diagnostic accuracy of novel biomarkers for UTI, and of their ability to differentiate UTI from asymptomatic bacteriuria. Design A systematic review. Data Sources and Methods We searched MEDLINE, EMBASE, CINAHL and Web of Science for studies of novel biomarkers for the diagnosis of UTI. We excluded studies assessing biomarkers included in urine dipsticks as these have been well described previously. We included studies of adult patients (≥16 years) with a suspected or confirmed urinary tract infection using microscopy and culture as the reference standard. We excluded studies using clinical signs and symptoms, or urine dipstick only as a reference standard. Quality appraisal was performed using QUADAS-2. We summarised our data using point estimates and data accuracy statistics. Results We included 37 studies on 4009 adults measuring 66 biomarkers. Study quality was limited by case-control design and study size; only 4 included studies had a prospective cohort design. IL-6 and IL-8 were the most studied biomarkers. We found plausible evidence to suggest that IL-8, IL-6, GRO-a, sTNF-1, sTNF-2 and MCR may benefit from more rigorous evaluation of their potential diagnostic value for UTI. Conclusions There is insufficient evidence to recommend the use of any novel biomarker for UTI diagnosis at present. Further evaluation of the more promising candidates, is needed before they can be recommended for clinical use.
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Affiliation(s)
- George Edwards
- NIHR Community Healthcare Medtech and IVD Cooperative, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK,George Edwards, Nuffield Department of Primary Care Health Sciences, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK.
| | - Anna Seeley
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Adam Carter
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Maia Patrick Smith
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Elizabeth LA Cross
- Department of Global Health and Infection, Brighton and Sussex Medical School, Falmer, UK
| | - Kathryn Hughes
- PRIME Centre Wales, Division of Population Medicine, Cardiff University, Cardiff, UK
| | - Ann Van den Bruel
- EPI-Centre, Academic Centre for General Practice, KU Leuven, Leuven, Belgium
| | - Martin J Llewelyn
- Department of Global Health and Infection, Brighton and Sussex Medical School, Falmer, UK
| | - Jan Y Verbakel
- NIHR Community Healthcare Medtech and IVD Cooperative, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK,EPI-Centre, Academic Centre for General Practice, KU Leuven, Leuven, Belgium
| | - Gail Hayward
- NIHR Community Healthcare Medtech and IVD Cooperative, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
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7
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Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the two major analytical platforms in the field of metabolomics, the other being mass spectrometry (MS). NMR is less sensitive than MS and hence it detects a relatively small number of metabolites. However, NMR exhibits numerous unique characteristics including its high reproducibility and non-destructive nature, its ability to identify unknown metabolites definitively, and its capabilities to obtain absolute concentrations of all detected metabolites, sometimes even without an internal standard. These characteristics outweigh the relatively low sensitivity and resolution of NMR in metabolomics applications. Since biological mixtures are highly complex, increased demand for new methods to improve detection, better identify unknown metabolites, and provide more accurate quantitation continues unabated. Technological and methodological advances to date have helped to improve the resolution and sensitivity and detection of a larger number of metabolite signals. Efforts focused on measuring unknown metabolite signals have resulted in the identification and quantitation of an expanded pool of metabolites including labile metabolites such as cellular redox coenzymes, energy coenzymes, and antioxidants. This chapter describes quantitative NMR methods in metabolomics with an emphasis on recent methodological developments, while highlighting the benefits and challenges of NMR-based metabolomics.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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8
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Zhang L, Wang B, Yin G, Wang J, He M, Yang Y, Wang T, Tang T, Yu XA, Tian J. Rapid Fluorescence Sensor Guided Detection of Urinary Tract Bacterial Infections. Int J Nanomedicine 2022; 17:3723-3733. [PMID: 36061124 PMCID: PMC9428933 DOI: 10.2147/ijn.s377575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/21/2022] [Indexed: 11/23/2022] Open
Abstract
Introduction Urinary tract infections (UTI) are one of the most serious human bacterial infections affecting millions of people every year. Therefore, simple and reliable identification of the urinary tract pathogenic bacteria within a few minutes would be of great significance for diagnosis and treatment of clinical patients with UTIs. In this study, the fluorescence sensor was reported to guide the detection of urinary tract bacterial infections rapidly. Methods The Ami-AuNPs-DNAs sensor was fabricated by the amino-modified Au nanoparticles (Ami-AuNPs) and six DNAs signal molecules, which bound to the urinary tract pathogenic bacteria and generated corresponding response signals. Further, based on the collected response signals, identification was performed by principal component analysis (PCA) and linear discriminant analysis (LDA). The Ami-AuNPs and Ami-AuNPs-DNAs were characterized by transmission electron microscopy, UV−vis absorption spectrum, Fourier transform infrared spectrum, dynamic light scattering and zeta potentials. Thereafter, the Ami-AuNPs-DNAs sensor was used to discriminate and identify five kinds of urinary tract pathogenic bacteria. Moreover, the quantitative analysis performance towards individual bacteria at different concentrations were also evaluated. Results The Ami-AuNPs-DNAs sensor were synthesized successfully in terms of spherical, well-dispersed and uniform in size, which could well discriminate five main urinary tract pathogenic bacteria with unique fingerprint-like patterns and was sufficiently sensitive to determine individual bacteria with a detection limit to 1×107 cfu/mL. Furthermore, the sensor had also been successfully applied to identify bacteria in urine samples collected from clinical UTIs. Conclusion The developed fluorescence sensor could be applied to rapid and accurate discrimination of urinary tract pathogenic bacteria and holds great promise for the diagnosis of the disease caused by bacterial infection.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu Province, 211198, People’s Republic of China
| | - Bing Wang
- NMPA Key Laboratory for Bioequivalence Research of Generic Drug Evaluation, Shenzhen Institute for Drug Control, Shenzhen, Guangdong Province, 518057, People’s Republic of China
| | - Guo Yin
- NMPA Key Laboratory for Bioequivalence Research of Generic Drug Evaluation, Shenzhen Institute for Drug Control, Shenzhen, Guangdong Province, 518057, People’s Republic of China
| | - Jue Wang
- NMPA Key Laboratory for Bioequivalence Research of Generic Drug Evaluation, Shenzhen Institute for Drug Control, Shenzhen, Guangdong Province, 518057, People’s Republic of China
| | - Ming He
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou Province, 550002, People’s Republic of China
| | - Yuqi Yang
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou Province, 550002, People’s Republic of China
| | - Tiejie Wang
- NMPA Key Laboratory for Bioequivalence Research of Generic Drug Evaluation, Shenzhen Institute for Drug Control, Shenzhen, Guangdong Province, 518057, People’s Republic of China
| | - Ting Tang
- Dermatology Department, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou Province, 550002, People’s Republic of China
| | - Xie-An Yu
- NMPA Key Laboratory for Bioequivalence Research of Generic Drug Evaluation, Shenzhen Institute for Drug Control, Shenzhen, Guangdong Province, 518057, People’s Republic of China
- Correspondence: Xie-An Yu; Jiangwei Tian, Email ;
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu Province, 211198, People’s Republic of China
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9
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Hasandka A, Singh AR, Prabhu A, Singhal HR, Nandagopal MSG, Mani NK. Paper and thread as media for the frugal detection of urinary tract infections (UTIs). Anal Bioanal Chem 2022; 414:847-865. [PMID: 34668042 PMCID: PMC8724062 DOI: 10.1007/s00216-021-03671-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/02/2021] [Accepted: 09/15/2021] [Indexed: 12/22/2022]
Abstract
Urinary tract infections (UTIs) make up a significant proportion of the global burden of disease in vulnerable groups and tend to substantially impair the quality of life of those affected, making timely detection of UTIs a priority for public health. However, economic and societal barriers drastically reduce accessibility of traditional lab-based testing methods for critical patient groups in low-resource areas, negatively affecting their overall healthcare outcomes. As a result, cellulose-based materials such as paper and thread have garnered significant interest among researchers as substrates for so-called frugal analytical devices which leverage the material's portability and adaptability for facile and reproducible diagnoses of UTIs. Although the field may be only in its infancy, strategies aimed at commercial penetration can appreciably increase access to more healthcare options for at-risk people. In this review, we catalogue recent advances in devices that use cellulose-based materials as the primary housing or medium for UTI detection and chart out trends in the field. We also explore different modalities employed for detection, with particular emphasis on their ability to be ported onto discreet casings such as sanitary products.
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Affiliation(s)
- Amrutha Hasandka
- Microfluidics, Sensors and Diagnostics Laboratory (μSenD), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ankita Ramchandran Singh
- Microfluidics, Sensors and Diagnostics Laboratory (μSenD), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Anusha Prabhu
- Microfluidics, Sensors and Diagnostics Laboratory (μSenD), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Hardik Ramesh Singhal
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - M S Giri Nandagopal
- Department of Mechanical Engineering, Indian Institute of Technology, Kharagpur, Kharagpur, 721302, India
| | - Naresh Kumar Mani
- Microfluidics, Sensors and Diagnostics Laboratory (μSenD), Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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Schlatterer K, Peschel A, Kretschmer D. Short-Chain Fatty Acid and FFAR2 Activation - A New Option for Treating Infections? Front Cell Infect Microbiol 2021; 11:785833. [PMID: 34926327 PMCID: PMC8674814 DOI: 10.3389/fcimb.2021.785833] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/09/2021] [Indexed: 01/05/2023] Open
Abstract
The human innate immune system is equipped with multiple mechanisms to detect microbe-associated molecular patterns (MAMPs) to fight bacterial infections. The metabolite short-chain fatty acids (SCFAs) acetate, propionate and butyrate are released by multiple bacteria or are food ingredients. SCFA production, especially acetate production, is usually essential for bacteria, and knockout of pathways involved in acetate production strongly impairs bacterial fitness. Because host organisms use SCFAs as MAMPs and alter immune reactions in response to SCFAs, interventions that modulate SCFA levels can be a new strategy for infection control. The interaction between SCFAs and host cells has been primarily investigated in the intestinal lumen because of the high local levels of SCFAs released by bacterial microbiome members. However, members of not only the intestinal microbiome but also the skin microbiome produce SCFAs, which are known ligands of the seven-transmembrane G-protein-coupled receptor FFAR2. In addition to enterocytes, FFAR2 is expressed on other human cell types, including leukocytes, especially neutrophils. This finding is in line with other research that determined that targeted activation of FFAR2 diminishes susceptibility toward various types of infection by bacteria such as Klebsiella pneumonia, Citrobacter rodentium, and Staphylococcus aureus but also by viruses such as respiratory syncytial and influenza viruses. Thus, our immune system appears to be able to use FFAR2-dependent detection of SCFAs for perceiving and even averting severe infections. We summarize recent advances in understanding the role of SCFAs and FFAR2 in various infection types and propose the manipulation of this receptor as an additional therapeutic strategy to fight infections.
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Affiliation(s)
- Katja Schlatterer
- Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence Cluster of Excellence (EXC) 2124 Controlling Microbes to Fight Infections, University of Tuebingen, Tübingen, Germany
| | - Andreas Peschel
- Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence Cluster of Excellence (EXC) 2124 Controlling Microbes to Fight Infections, University of Tuebingen, Tübingen, Germany
| | - Dorothee Kretschmer
- Infection Biology, Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Tübingen, Germany.,German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany.,Cluster of Excellence Cluster of Excellence (EXC) 2124 Controlling Microbes to Fight Infections, University of Tuebingen, Tübingen, Germany
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11
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Panunzio A, Tafuri A, Princiotta A, Gentile I, Mazzucato G, Trabacchin N, Antonelli A, Cerruto MA. Omics in urology: An overview on concepts, current status and future perspectives. Urologia 2021; 88:270-279. [PMID: 34169788 DOI: 10.1177/03915603211022960] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent technological advances in molecular biology have led to great progress in the knowledge of structure and function of cells and their main constituents. In this setting, 'omics' is standing out in order to significantly improve the understanding of etiopathogenetic mechanisms of disease and contribute to the development of new biochemical diagnostics and therapeutic tools. 'Omics' indicates the scientific branches investigating every aspect of cell's biology, including structures, functions and dynamics pathways. The main 'omics' are genomics, epigenomics, proteomics, transcriptomics, metabolomics and radiomics. Their diffusion, success and proliferation, addressed to many research fields, has led to many important acquisitions, even in Urology. Aim of this narrative review is to define the state of art of 'omics' application in Urology, describing the most recent and relevant findings, in both oncological and non-oncological diseases, focusing the attention on urinary tract infectious, interstitial cystitis, urolithiasis, prostate cancer, bladder cancer and renal cell carcinoma. In Urology the majority of 'omics' applications regard the pathogenesis and diagnosis of the investigated diseases. In future, its role should be implemented in order to develop specific predictors and tailored treatments.
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Affiliation(s)
- Andrea Panunzio
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Alessandro Tafuri
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy.,Department of Neuroscience, Imaging and Clinical Science, Physiology and Physiopathology division, "G. D'Annunzio" University, Chieti, Italy
| | - Alessandro Princiotta
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Ilaria Gentile
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Giovanni Mazzucato
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Nicolò Trabacchin
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Alessandro Antonelli
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Maria Angela Cerruto
- Department of Urology, University of Verona, Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
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12
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Li X, Zhou K, Wang J, Guo J, Cao Y, Ren J, Guan T, Sheng W, Zhang M, Yao Z, Wang Q. Diagnostic Value of the Fimbriae Distribution Pattern in Localization of Urinary Tract Infection. Front Med (Lausanne) 2021; 8:602691. [PMID: 34222269 PMCID: PMC8249706 DOI: 10.3389/fmed.2021.602691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/26/2021] [Indexed: 01/16/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common infectious diseases. UTIs are mainly caused by uropathogenic Escherichia coli (UPEC), and are either upper or lower according to the infection site. Fimbriae are necessary for UPEC to adhere to the host uroepithelium, and are abundant and diverse in UPEC strains. Although great progress has been made in determining the roles of different types of fimbriae in UPEC colonization, the contributions of multiple fimbriae to site-specific attachment also need to be considered. Therefore, the distribution patterns of 22 fimbrial genes in 90 UPEC strains from patients diagnosed with upper or lower UTIs were analyzed using PCR. The distribution patterns correlated with the infection sites, an XGBoost model with a mean accuracy of 83.33% and a mean area under the curve (AUC) of the receiver operating characteristic (ROC) of 0.92 demonstrated that fimbrial gene distribution patterns could predict the localization of upper and lower UTIs.
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Affiliation(s)
- Xiao Li
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Xuzhou Key Laboratory of Laboratory Diagnostics, School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Kaichen Zhou
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jingyu Wang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiahe Guo
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yang Cao
- Department of Clinical Laboratory, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jie Ren
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tao Guan
- China Unicom Software Research Institute, Xi'an, China
| | - Wenchao Sheng
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mingyao Zhang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhi Yao
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Quan Wang
- Key Laboratory of Immune Microenvironment and Disease of the Educational Ministry of China, Tianjin Key Laboratory of Cellular and Molecular Immunology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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Heidrich D, Koehler A, Ramírez-Castrillón M, Pagani DM, Ferrão MF, Scroferneker ML, Corbellini VA. Rapid classification of chromoblastomycosis agents genera by infrared spectroscopy and chemometrics supervised by sequencing of rDNA regions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 254:119647. [PMID: 33744705 DOI: 10.1016/j.saa.2021.119647] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Chromoblastomycosis (CBM) is a skin and subcutaneous infection caused by species of seven fungal genera. Identification of CBM species is performed by DNA sequencing of one or more genes, which becomes a time-consuming work. Fourier Transform Infrared Spectroscopy (FTIR) has been used for the identification of other microorganisms, however, only one CBM genus was evaluated by FTIR analysis to date. Therefore, the study is aimed to differentiate the CBM agents for identification at genera level using FTIR supervised by Internal Transcribed Spacer (ITS) rDNA region. Seventy-seven isolates of the main five CBM genera were prepared for Attenuated Total Reflection FTIR (ATR-FTIR) with a new methodology using slices of dry fungus in glass fixing-modeling proposed in this study. The algorithm Hierarchical Cluster Analysis (HCA) was used to analyze the differences and similarities between species through the spectra. Orthogonal Partial Least Square Discriminant Analysis (OPLS-DA) allowed to correctly classify all samples of five CBM genera. The ATR-FTIR/OPLS-DA models highlighted important contributions of regions attributed to NH and OH stretching, amide I of proteins, polysaccharides bands and fingerprint region for the complete differentiation of the genera investigated. Thus, FTIR can be a fast and inexpensive alternative for identification of CBM agents.
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Affiliation(s)
- Daiane Heidrich
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2400, CEP: 90035-003 Porto Alegre, RS, Brazil
| | - Alessandra Koehler
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2400, CEP: 90035-003 Porto Alegre, RS, Brazil
| | - Mauricio Ramírez-Castrillón
- Postgraduate Program in Molecular and Cellular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, CEP: 91501-970 Porto Alegre, RS, Brazil.
| | - Danielle Machado Pagani
- Postgraduate Program in Agricultural and Environmental Microbiology, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, CEP: 90050-170 Porto Alegre, RS, Brazil
| | - Marco Flores Ferrão
- Department of Inorganic Chemistry, Chemistry Institute, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, CEP: 91501-970 Porto Alegre, RS, Brazil.
| | - Maria Lúcia Scroferneker
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2400, CEP: 90035-003 Porto Alegre, RS, Brazil; Department of Microbiology, Immunology and Parasitology, ICBS, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, CEP: 90050-170 Porto Alegre, RS, Brazil.
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities and Education, Postgraduate Program in Health Promotion, Postgraduate Program in Environmental Technology, Universidade de Santa Cruz do Sul, Avenida Independência, 2293, CEP: 96815-900 Santa Cruz do Sul, RS, Brazil.
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14
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a major analytical method used in the growing field of metabolomics. Although NMR is relatively less sensitive than mass spectrometry, this analytical platform has numerous characteristics including its high reproducibility and quantitative abilities, its nonselective and noninvasive nature, and the ability to identify unknown metabolites in complex mixtures and trace the downstream products of isotope labeled substrates ex vivo, in vivo, or in vitro. Metabolomic analysis of highly complex biological mixtures has benefitted from the advances in both NMR data acquisition and analysis methods. Although metabolomics applications span a wide range of disciplines, a majority has focused on understanding, preventing, diagnosing, and managing human diseases. This chapter describes NMR-based methods relevant to the rapidly expanding metabolomics field.
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Diray-Arce J, Conti MG, Petrova B, Kanarek N, Angelidou A, Levy O. Integrative Metabolomics to Identify Molecular Signatures of Responses to Vaccines and Infections. Metabolites 2020; 10:E492. [PMID: 33266347 PMCID: PMC7760881 DOI: 10.3390/metabo10120492] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Approaches to the identification of metabolites have progressed from early biochemical pathway evaluation to modern high-dimensional metabolomics, a powerful tool to identify and characterize biomarkers of health and disease. In addition to its relevance to classic metabolic diseases, metabolomics has been key to the emergence of immunometabolism, an important area of study, as leukocytes generate and are impacted by key metabolites important to innate and adaptive immunity. Herein, we discuss the metabolomic signatures and pathways perturbed by the activation of the human immune system during infection and vaccination. For example, infection induces changes in lipid (e.g., free fatty acids, sphingolipids, and lysophosphatidylcholines) and amino acid pathways (e.g., tryptophan, serine, and threonine), while vaccination can trigger changes in carbohydrate and bile acid pathways. Amino acid, carbohydrate, lipid, and nucleotide metabolism is relevant to immunity and is perturbed by both infections and vaccinations. Metabolomics holds substantial promise to provide fresh insight into the molecular mechanisms underlying the host immune response. Its integration with other systems biology platforms will enhance studies of human health and disease.
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Affiliation(s)
- Joann Diray-Arce
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
| | - Maria Giulia Conti
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Maternal and Child Health, Sapienza University of Rome, 5, 00185 Rome, Italy
| | - Boryana Petrova
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Naama Kanarek
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Pathology, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Asimenia Angelidou
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Department of Neonatology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Division of Infectious Diseases, Boston Children’s Hospital, Boston, MA 02115, USA; (M.G.C.); (A.A.)
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; (B.P.); (N.K.)
- Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
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16
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Horváth J, Wullt B, Naber KG, Köves B. Biomarkers in urinary tract infections - which ones are suitable for diagnostics and follow-up? GMS INFECTIOUS DISEASES 2020; 8:Doc24. [PMID: 33299741 PMCID: PMC7705555 DOI: 10.3205/id000068] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Urinary tract infections (UTIs) are one of the most common infections worldwide. Under special circumstances, clinicians must rely on laboratory findings, which might have a weak predicting value, misguiding the practitioners and leading to incorrect diagnosis and overuse of antibiotics. Therefore, there is an urgent need for reliable biomarkers in UTIs. Methods: We performed a literature search for biomarkers used in UTIs from January 1999 until May 2020. We used "urinary tract infection" and "biomarker" as the main key words in the PubMed, Medline and Cochrane databases. After peer review, we excluded the duplicates and identified the suitable articles, from which we collected the data and divided the available biomarkers into 5 groups: i) conventional markers; ii) promising, thoroughly studied biomarkers; iii) promising biomarkers that need further studies; iv) biomarkers of unknown significance; v) controversial, not useful markers. Results: We found 131 articles, mostly from the paediatric population. Neutrophil gelatinase-associated lipocalin (NGAL) and interleukins (IL) have a leading role in diagnosing and differentiating UTIs based on a lot of observational, comparative trials. Heparin Binding Protein (HBP), Lactoferrin (LF), Heat-Shock Protein-70 (HSP-70), Human Defensin-5 (HD-5), Lipopolysaccharide Binding Protein (LBP) and mass spectrometry studies are promising, but confirming data are lacking. The measurable components of the innate immune system and local host cell response could be appropriate biomarkers, but their significance is currently unknown. Conclusions: Conventional biomarkers for UTIs have low specificity. The use of urinary NGAL and interleukins could improve the sensitivity and specificity of laboratory diagnosis of UTIs.
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Affiliation(s)
- József Horváth
- BKMK SZTE ÁOK Okt. Kh. Urológiai Osztálya, Kecskemét, Hungary
| | - Björn Wullt
- Division of Microbiology, Immunology and Glycobiology, Lund University, Lund, Sweden
| | - Kurt G. Naber
- Department of Urology, Technical University of Munich, Munich, Germany
| | - Béla Köves
- Jahn Ferenc Dél-pesti Kórház és Rendelőintézet, Budapest, Hungary
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17
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Malodorous biogenic amines in Escherichia coli-caused urinary tract infections in women-a metabolomics approach. Sci Rep 2020; 10:9703. [PMID: 32546787 PMCID: PMC7297715 DOI: 10.1038/s41598-020-66662-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/21/2020] [Indexed: 02/02/2023] Open
Abstract
Many women suffer from urinary tract infections (UTIs). In addition to pain and increased urgency to urinate, malodour is a significant issue for these patients. The specific factors causing this malodour are unclear, and there are no targeted treatment options to counteract it effectively. We used a metabolomics approach to compare the chemical composition of metabolites in the urine of women with E. coli UTIs (n = 15) and those who are healthy (n = 10). The biogenic amines trimethylamine and putrescine, which cause malodour in other urogenital conditions, were significantly increased in UTI patients. Conversely, the precursor of trimethylamine, trimethylamine N-oxide, was lower. To further confirm the source of the malodorous compounds, in vitro experiments were conducted by incubating strains of uropathogenic E. coli in sterilized urine from healthy women. All tested strains accumulated trimethylamine and putrescine. Notably, cadaverine was also produced by E. coli strains in vitro; however, it was not significantly different between both groups. We confirmed that the malodorous amines TMA and putrescine are found in higher concentrations in the urine of patients with an E.coli-caused UTI.
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18
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Santacruz L, Hurtado DX, Doohan R, Thomas OP, Puyana M, Tello E. Metabolomic study of soft corals from the Colombian Caribbean: PSYCHE and 1H-NMR comparative analysis. Sci Rep 2020; 10:5417. [PMID: 32214197 PMCID: PMC7096504 DOI: 10.1038/s41598-020-62413-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/24/2020] [Indexed: 12/12/2022] Open
Abstract
Marine organisms have evolved to survive against predators in complex marine ecosystems via the production of chemical compounds. Soft corals (Cnidaria, Anthozoa, Octocorallia) are an important source of chemically diverse metabolites with a broad spectrum of biological activities. Herein, we perform a comparative study between high-resolution proton nuclear magnetic resonance (1H-NMR) and pure shift yielded by chirp excitation (PSYCHE) experiments to analyze the metabolic profile of 24 soft corals from the Colombian Caribbean to correlate chemical fingerprints with their cytotoxic activity against three cancer cell lines (human cervical carcinoma (SiHa), human prostatic carcinoma (PC3) and human lung adenocarcinoma (A549)). All data obtained were explored using multivariate analysis using principal components analysis (PCA) and orthogonal partial least squares (OPLS) analysis. The results did not show a significant correlation between clusters using 1H-NMR data in the PCA and OPLS-DA models and therefore did not provide conclusive evidence; on the other hand, a metabolomic analysis of PSYCHE data obtained under the same parameters revealed that when a decoupled experiment is performed, it was possible to establish a statistically valid correlation between the chemical composition of soft corals and their cytotoxic activity against the PC3 cancer cell line, where the asperdiol and plexaurolone markers were putatively identified and related to the cytotoxic activity presented by extracts of Plexaurella sp. and Plexaura kukenthali, respectively. These results increase the speed, effectiveness and reliability of analyses for the study of this type of complex matrices.
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Affiliation(s)
- Liliana Santacruz
- Bioprospecting Research Group and Biosciences Doctoral Program, Faculty of Engineering, Campus Puente del Común, Universidad de la Sabana, 250001, Chía, Colombia
| | - Diana X Hurtado
- Bioprospecting Research Group and Biosciences Doctoral Program, Faculty of Engineering, Campus Puente del Común, Universidad de la Sabana, 250001, Chía, Colombia
| | - Roisin Doohan
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33, Galway, Ireland
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, National University of Ireland Galway (NUI Galway), University Road, H91 TK33, Galway, Ireland
| | - Mónica Puyana
- Departamento de Ciencias Biológicas y Ambientales, Universidad Jorge Tadeo Lozano, Carrera 4 # 22-61, 110311, Bogotá, Colombia
| | - Edisson Tello
- Bioprospecting Research Group and Biosciences Doctoral Program, Faculty of Engineering, Campus Puente del Común, Universidad de la Sabana, 250001, Chía, Colombia.
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19
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Rautureau GJP, Palama TL, Canard I, Mirande C, Chatellier S, van Belkum A, Elena-Herrmann B. Discrimination of Escherichia coli and Shigella spp. by Nuclear Magnetic Resonance Based Metabolomic Characterization of Culture Media. ACS Infect Dis 2019; 5:1879-1886. [PMID: 31545890 DOI: 10.1021/acsinfecdis.9b00199] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Dysentery is a major health threat that dramatically impacts childhood morbidity and mortality in developing countries. Various pathogenic agents cause dysentery, such as Shigella spp. and Escherichia coli, which are very closely related if not identical species. Sensitive and precise detection and identification of the infectious agent is important to target the best therapeutic strategy, but the differential diagnosis of these two groups remains a challenge using conventional methods. Here, we present a nuclear magnetic resonance (NMR) based multivariate classification model employing bacterial metabolic footprints in postculture growth media with remarkable segregation capability, including the discrimination of lactose negative E. coli and Shigella spp. Our results confirm the potential of metabolomic markers in the field of bacterial identification for the distinction of even very closely related species.
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Affiliation(s)
- Gilles J. P. Rautureau
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Tony L. Palama
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Isabelle Canard
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Caroline Mirande
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Sonia Chatellier
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Alex van Belkum
- bioMérieux, Innovation Unit—Microbiology Research, 38390 La Balme-les-Grottes, France
| | - Bénédicte Elena-Herrmann
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
- Université Grenoble Alpes, CNRS, INSERM, IAB, Allée des Alpes, 38000 Grenoble, France
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Rapid Growth and Metabolism of Uropathogenic Escherichia coli in Relation to Urine Composition. Clin Microbiol Rev 2019; 33:33/1/e00101-19. [PMID: 31619395 DOI: 10.1128/cmr.00101-19] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) strains cause a majority of urinary tract infections (UTIs). Since UPEC strains can become antibiotic resistant, adjunct or alternate therapies are urgently needed. UPEC strains grow extremely rapidly in patients with UTIs. Thus, this review focuses on the relation between urine composition and UPEC growth and metabolism. Compilation of urinary components from two major data sources suggests the presence of sufficient amino acids and carbohydrates as energy sources and abundant phosphorus, sulfur, and nitrogen sources. In a mouse UTI model, mutants lacking enzymes of the tricarboxylic acid cycle, gluconeogenesis, and the nonoxidative branch of the pentose cycle are less competitive than the corresponding parental strains, which is consistent with amino acids as major energy sources. Other evidence suggests that carbohydrates are required energy sources. UPEC strains in urine ex vivo and in vivo express transporters for peptides, amino acids, carbohydrates, and iron and genes associated with nitrogen limitation, amino acid synthesis, nucleotide synthesis, and nucleotide salvage. Mouse models confirm the requirement for many, but not all, of these genes. Laboratory evolution studies suggest that rapid nutrient uptake without metabolic rewiring is sufficient to account for rapid growth. Proteins and pathways required for rapid growth should be considered potential targets for alternate or adjunct therapies.
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