Antibiotic Susceptibility Profiles of Recent European Gram-Negative Anaerobes Schaumburg, IL 60173 USA P0679 M

Total Page:16

File Type:pdf, Size:1020Kb

Antibiotic Susceptibility Profiles of Recent European Gram-Negative Anaerobes Schaumburg, IL 60173 USA P0679 M IHMA, Inc. 2122 Palmer Drive Antibiotic Susceptibility Profiles of Recent European Gram-negative Anaerobes Schaumburg, IL 60173 USA P0679 M. Hackel1, M. Bailey-Person1, D. Sahm1, H. Leister-Tebbe2 1 Phone: +1.847.303.5003 International Health Management Associates, Inc., Schaumburg, IL, USA Fax: +1.847.303.5601 2 Pfizer Inc., Collegeville, PA, USA www.ihmainc.com Revised Abstract Results Conclusions Background: Anaerobic infections tend to be polymicrobial, and are often treated empirically with broad-spectrum therapies. Continual monitoring is required to provide clinicians with accurate and up-to-date data on which to base Figure 1. Distribution of Gram-negative Anaerobes by Country, TEST 2013-2015. Table 1. Bacteroides and Prevotella species Included in Study. • Tigecycline, meropenem and empiric treatment. The Tigecycline European Surveillance Trial (TEST) has monitored susceptibility patterns of metronidazole showed excellent in vitro Organism N Organism N anaerobic bacteria since 2004. In this study we evaluated tigecycline and five comparator compounds against recent Czech Republic activity against B. fragilis group European anaerobic isolates. Material/methods: 1,950 gram-negative anaerobic pathogens (1,276 Bacteroides fragilis Bacteroides fragilis group 1,276 Prevotella nigrescens 42 Sweden Italy organisms isolated from European group and 674 Prevotella spp.) were collected from 2013-2015 from 18 sites in 8 countries in Europe (Belgium, Czech 9% Bacteroides fragilis 647 Prevotella intermedia 31 Republic, France, Germany, Hungary, Italy, Spain, and Sweden). Organism identification was confirmed at a central 4% 0.1% hospitals, with >93% susceptible. laboratory (IHMA, Inc., Schaumburg, IL, US), and MIC values were determined using agar dilution following CLSI Hungary Bacteroides thetaiotaomicron 196 Prevotella oris 29 Clindamycin, piperacillin-tazobactam and guidelines. Percent susceptible was calculated using EUCAST (clindamycin, meropenem, metronidazole, and Bacteroides ovatus 141 Prevotella nanceinsis 18 cefoxitin exhibited lower activity, with only piperacillin-tazobactam), CLSI (cefoxitin) and FDA (tigecycline) breakpoints. Results: In vitro activity (MIC90 and 10% percent susceptible [%S]) is shown in the table. Belgium Bacteroides vulgatus 127 Prevotella, non-speciated 15 65% of B. fragilis group isolates 13% Parabacteroides distasonis 62 Prevotella oralis 14 susceptible to clindamycin. Antimicrobial B. fragilis group (1,276) Prevotella spp. (674) Germany Bacteroides uniformis 58 Prevotella bergensis 9 MIC90 % S MIC90 % S • Tigecycline, cefoxitin, meropenem, Tigecycline 4 93.3 0.5 99.4 Bacteroides caccae 29 Prevotella buccalis 9 30% metronidazole and piperacillin- Cefoxitin 32 80.2 4 99.0 Spain Bacteroides stercoris 14 Prevotella salivae 9 Clindamycin > 8 64.7 > 8 72.6 tazobactam each inhibited >99% of Meropenem 1 94.8 0.12 100 15% Bacteroides eggerthii 1 Prevotella baroniae 8 Prevotella spp. at their susceptible Metronidazole 1 99.9 2 100 Bacteroides fragilis Group 2 1 Prevotella corporis 7 Piperacillin Tazobactam 16 85.9 0.12 99.3 breakpoints, whereas clindamycin had France Prevotella species 674 Prevotella pallens 7 lower activity, with only 73% susceptible. Conclusions: Tigecycline, meropenem and metronidazole showed excellent in vitro activity against B. fragilis group 19% Prevotella bivia 190 Prevotella histicola 6 organisms isolated from European hospitals, with >93% susceptible. Clindamycin, piperacillin-tazobactam and • Differences in susceptibilities between cefoxitin exhibited lower activity, with only 65% of B. fragilis group isolates susceptible to clindamycin. Tigecycline, Prevotella buccae 94 Prevotella maculosa 2 genera highlight the need for continued cefoxitin, meropenem, metronidazole and piperacillin-tazobactam each inhibited >99% of Prevotella spp. at their Prevotella melaninogenica 80 Prevotella heparinolytica 1 EUCAST susceptible breakpoints, whereas clindamycin had lower activity, with only 73% susceptible. Differences in evaluation of antimicrobial susceptibilities susceptibilities between genera highlight the need for continued evaluation of antimicrobial susceptibilities of gram- Prevotella denticola 59 Prevotella loescheii 1 of gram-negative anaerobic organisms to negative anaerobic organisms to aid in the selection of empiric therapy and monitor resistance trends. Prevotella disiens 42 Prevotella oulorum 1 aid in the selection of empiric therapy and Introduction monitor resistance trends. Anaerobic infections tend to be polymicrobial, and are often treated empirically with broad-spectrum therapies. Susceptibility to the most commonly used antimicrobials varies Figure 2. Distribution of Gram-negative Anaerobes by Specimen Source, TEST Table 2. In Vitro Activity of Tigecycline and Conparators Against Gram- among genera and even the species within a genus. Although there are many 2013-2015. negative Anaerobes from Europe. References and Acknowledgments: antimicrobial agents with activity against anaerobic bacteria, antimicrobial resistance 1. Nagy, E. (2010). Anaerobic infections. Drugs, 70(7), continues to rise [1]. Difficulty in isolating primary anaerobic pathogens and limited Organism (N) Antimicrobial MIC50 MIC90 %S %I %R Range 841-858. susceptibility testing by microbiology laboratories often results in the use of empirical Blood Other Genitourinary Respiratory B. fragilis group (1,276) Tigecycline 0.5 4 93.3 4.3 2.4 ≤ 0.06 - 32 2. Clinical and Laboratory Standards Institute. Methods treatment. For this reason, it is important to provide surveillance data to guide providers in 6% 2% the most effective choices for anti-anaerobic therapy. The Tigecycline European Gastro-intestinal 6% 6% Cefoxitin 8 32 80.2 14.8 5.0 ≤ 2 - > 32 for antimicrobial susceptibility testing of anaerobic Surveillance Trial (TEST), a longitudinal surveillance study, has been monitoring the bacteria; approved standard. 9th ed. M11–A9. Wayne, 6% PA: CLSI; 2012. activity of a number of antimicrobial agents against both gram-negative and gram-positive Bone Clindamycin 2 > 8 64.7 0 35.3 ≤ 0.25 - > 8 anaerobic organisms in Europe since 2007. This study reports the susceptibility data for 1% Meropenem 0.12 1 94.8 4.6 0.7 ≤ 0.06 - > 8 3. European Committee on Antimicrobial Susceptibility select gram-negative anaerobic bacteria from European hospitals from 2013 through Testing (EUCAST). 2016. Breakpoint tables for 2015. Metronidazole 0.5 1 99.9 0 0.1 ≤ 0.12 - 8 interpretation of MICs and zone diameters, version 3.0. http://www.eucast.org. Piperacillin Tazobactam 1 16 85.9 8.1 6.0 ≤ 0.06 - > 64 Materials & Methods 4. Clinical and Laboratory Standards Institute. Prevotella spp. (674) Tigecycline 0.12 0.5 99.4 0.6 0 ≤ 0.06 - 8 Performance Standards for Antimicrobial Susceptibility 1,950 gram-negative anaerobic pathogens (1,276 Bacteroides fragilis group and 674 Wound Testing; approved standard. 26th ed. M1100S–A26. Prevotella spp.) were collected over the years 2013-2015 from 18 sites in eight countries 23% Cefoxitin ≤ 2 4 99.0 0.9 0.2 ≤ 2 - > 32 Wayne, PA: CLSI; 2016. in Europe (Belgium, Czech Republic, France, Germany, Hungary, Italy, Spain, and Clindamycin ≤ 0.25 > 8 72.6 0 27.5 ≤ 0.25 - > 8 5. Tygacil®, 2010. Federal Drug Administration, Product Sweden). Only one isolate per patient was accepted. Sites were requested to send in a Information. Pfizer Inc., Collegeville, PA, USA. specific number of a select group of species. Isolates were identified to genus and Meropenem ≤ 0.06 0.12 100 0 0 ≤ 0.06 - 1 species by the local laboratory, and sent to the central laboratory (IHMA, Inc., Metronidazole 1 2 100 0 0 ≤ 0.12 - 4 We gratefully acknowledge the contributions of the Schaumburg, IL, US) for confirmation of identification and MIC testing. MIC values for investigators, laboratory personnel, and all members tigecycline and five comparators were determined by agar dilution following CLSI Piperacillin Tazobactam ≤ 0.06 0.12 99.3 0.6 0.2 ≤ 0.06 - 64 of the Tigecycline European and Surveillance Trial guidelines [2]. Percent susceptible (%S) was calculated using EUCAST (clindamycin, Body fluid group. This study was sponsored by Pfizer Inc. IHMA meropenem, metronidazole, and piperacillin-tazobactam) [3], CLSI (cefoxitin) [4] or FDA is a clinical research organization that has been 50% contracted by Pfizer Inc, to manage the TEST (tigecycline) [5] breakpoints. program..
Recommended publications
  • The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio In
    microorganisms Review The Influence of Probiotics on the Firmicutes/Bacteroidetes Ratio in the Treatment of Obesity and Inflammatory Bowel disease Spase Stojanov 1,2, Aleš Berlec 1,2 and Borut Štrukelj 1,2,* 1 Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia; [email protected] (S.S.); [email protected] (A.B.) 2 Department of Biotechnology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia * Correspondence: borut.strukelj@ffa.uni-lj.si Received: 16 September 2020; Accepted: 31 October 2020; Published: 1 November 2020 Abstract: The two most important bacterial phyla in the gastrointestinal tract, Firmicutes and Bacteroidetes, have gained much attention in recent years. The Firmicutes/Bacteroidetes (F/B) ratio is widely accepted to have an important influence in maintaining normal intestinal homeostasis. Increased or decreased F/B ratio is regarded as dysbiosis, whereby the former is usually observed with obesity, and the latter with inflammatory bowel disease (IBD). Probiotics as live microorganisms can confer health benefits to the host when administered in adequate amounts. There is considerable evidence of their nutritional and immunosuppressive properties including reports that elucidate the association of probiotics with the F/B ratio, obesity, and IBD. Orally administered probiotics can contribute to the restoration of dysbiotic microbiota and to the prevention of obesity or IBD. However, as the effects of different probiotics on the F/B ratio differ, selecting the appropriate species or mixture is crucial. The most commonly tested probiotics for modifying the F/B ratio and treating obesity and IBD are from the genus Lactobacillus. In this paper, we review the effects of probiotics on the F/B ratio that lead to weight loss or immunosuppression.
    [Show full text]
  • Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis
    International Journal of Molecular Sciences Review Fatty Acid Diets: Regulation of Gut Microbiota Composition and Obesity and Its Related Metabolic Dysbiosis David Johane Machate 1, Priscila Silva Figueiredo 2 , Gabriela Marcelino 2 , Rita de Cássia Avellaneda Guimarães 2,*, Priscila Aiko Hiane 2 , Danielle Bogo 2, Verônica Assalin Zorgetto Pinheiro 2, Lincoln Carlos Silva de Oliveira 3 and Arnildo Pott 1 1 Graduate Program in Biotechnology and Biodiversity in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] (D.J.M.); [email protected] (A.P.) 2 Graduate Program in Health and Development in the Central-West Region of Brazil, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; pri.fi[email protected] (P.S.F.); [email protected] (G.M.); [email protected] (P.A.H.); [email protected] (D.B.); [email protected] (V.A.Z.P.) 3 Chemistry Institute, Federal University of Mato Grosso do Sul, Campo Grande 79079-900, Brazil; [email protected] * Correspondence: [email protected]; Tel.: +55-67-3345-7416 Received: 9 March 2020; Accepted: 27 March 2020; Published: 8 June 2020 Abstract: Long-term high-fat dietary intake plays a crucial role in the composition of gut microbiota in animal models and human subjects, which affect directly short-chain fatty acid (SCFA) production and host health. This review aims to highlight the interplay of fatty acid (FA) intake and gut microbiota composition and its interaction with hosts in health promotion and obesity prevention and its related metabolic dysbiosis.
    [Show full text]
  • Gut Microbiota Differs in Composition and Functionality Between Children
    Diabetes Care Volume 41, November 2018 2385 Gut Microbiota Differs in Isabel Leiva-Gea,1 Lidia Sanchez-Alcoholado,´ 2 Composition and Functionality Beatriz Mart´ın-Tejedor,1 Daniel Castellano-Castillo,2,3 Between Children With Type 1 Isabel Moreno-Indias,2,3 Antonio Urda-Cardona,1 Diabetes and MODY2 and Healthy Francisco J. Tinahones,2,3 Jose´ Carlos Fernandez-Garc´ ´ıa,2,3 and Control Subjects: A Case-Control Mar´ıa Isabel Queipo-Ortuno~ 2,3 Study Diabetes Care 2018;41:2385–2395 | https://doi.org/10.2337/dc18-0253 OBJECTIVE Type 1 diabetes is associated with compositional differences in gut microbiota. To date, no microbiome studies have been performed in maturity-onset diabetes of the young 2 (MODY2), a monogenic cause of diabetes. Gut microbiota of type 1 diabetes, MODY2, and healthy control subjects was compared. PATHOPHYSIOLOGY/COMPLICATIONS RESEARCH DESIGN AND METHODS This was a case-control study in 15 children with type 1 diabetes, 15 children with MODY2, and 13 healthy children. Metabolic control and potential factors mod- ifying gut microbiota were controlled. Microbiome composition was determined by 16S rRNA pyrosequencing. 1Pediatric Endocrinology, Hospital Materno- Infantil, Malaga,´ Spain RESULTS 2Clinical Management Unit of Endocrinology and Compared with healthy control subjects, type 1 diabetes was associated with a Nutrition, Laboratory of the Biomedical Research significantly lower microbiota diversity, a significantly higher relative abundance of Institute of Malaga,´ Virgen de la Victoria Uni- Bacteroides Ruminococcus Veillonella Blautia Streptococcus versityHospital,Universidad de Malaga,M´ alaga,´ , , , , and genera, and a Spain lower relative abundance of Bifidobacterium, Roseburia, Faecalibacterium, and 3Centro de Investigacion´ BiomedicaenRed(CIBER)´ Lachnospira.
    [Show full text]
  • The Human Milk Microbiota Is Modulated by Maternal Diet
    microorganisms Article The Human Milk Microbiota is Modulated by Maternal Diet Marina Padilha 1,2,*, Niels Banhos Danneskiold-Samsøe 3, Asker Brejnrod 3, Christian Hoffmann 1,2, Vanessa Pereira Cabral 1,4, Julia de Melo Iaucci 1, Cristiane Hermes Sales 4 , Regina Mara Fisberg 4 , Ramon Vitor Cortez 1, Susanne Brix 5 , Carla Romano Taddei 1,6, Karsten Kristiansen 3 and Susana Marta Isay Saad 1,2,* 1 School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil; c.hoff[email protected] (C.H.); [email protected] (V.P.C.); [email protected] (J.d.M.I.); [email protected] (R.V.C.); [email protected] (C.R.T.) 2 Food Research Center (FoRC), University of São Paulo, São Paulo 05508-000, SP, Brazil 3 Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; [email protected] (N.B.D.-S.); [email protected] (A.B.); [email protected] (K.K.) 4 School of Public Health, University of São Paulo, São Paulo 01246-904, SP, Brazil; [email protected] (C.H.S.); regina.fi[email protected] (R.M.F.) 5 Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark; [email protected] 6 School of Arts, Sciences and Humanities, University of São Paulo, São Paulo 03828-000, SP, Brazil * Correspondence: [email protected] (M.P.); [email protected] (S.M.I.S.) Received: 17 September 2019; Accepted: 24 October 2019; Published: 29 October 2019 Abstract: Human milk microorganisms contribute not only to the healthy development of the immune system in infants, but also in shaping the gut microbiota.
    [Show full text]
  • Prevotella Biva Poster.Pptx
    Novel Infection Status Post Electrocution Requiring a 4th Ray Amputation WilliamJudson IV, D.O.1, John Murphy, D.O.1, Phillip Sussman, D.O.1, John Harker D.O.1 HCA Healthcare/USF Morsani College of Medicine GME Programs/Largo Medical Center Background Treatment • Prevotella bivia is an anaerobic, non-pigmented, Gram-negative bacillus species that is known to inhabit the human female vaginal tract and oral flora. It is most commonly associated with endometritis and pelvic inflammatory disease.1, 2 • Rarely, P. bivia has been found in the nail bed, chest wall, intervertebral discs, and hip and knee joints.1 The bacteria has been linked to necrotizing fasciitis, osteomyelitis, or septic arthritis.3, 4 • Only 3 other reports have described P. bivia infections in the upper Figure 1: Dorsum of the right hand on Figure 2: Ulnar aspect of right 4th and 5th Figures 13 and 14: Most recent images of patients hand in March, 2020. 2 presentation fingers Wound over the dorsum of the hand completely healed. Patient with flexion extremity with one patient requiring amputation , and one with deep soft contractures of remaining digits. tissue infection requiring multiple debridements and extensive tenosynovectomy.5 Discussion • Delays in diagnosis are common due to P. bivia’s long incubation period • P. bivia infections, although rare in orthopedic practice, can lead to and association with aerobic organisms that more commonly cause soft extensive debridements and possible amputation leading to great tissue infections leading to inappropriate antibiotic coverage. morbidity when affecting the upper extremities.1, 2, 5 • Here we present a case on P.
    [Show full text]
  • Research Article Enterotype Bacteroides Is Associated with a High Risk in Patients with Diabetes: a Pilot Study
    Hindawi Journal of Diabetes Research Volume 2020, Article ID 6047145, 11 pages https://doi.org/10.1155/2020/6047145 Research Article Enterotype Bacteroides Is Associated with a High Risk in Patients with Diabetes: A Pilot Study Jiajia Wang,1,2,3 Wenjuan Li,1,2,3 Chuan Wang,1,2,3 Lingshu Wang,1,2,3 Tianyi He,1,2,3 Huiqing Hu,1,2,3 Jia Song,1,2,3 Chen Cui,1,2,3 Jingting Qiao,1,2,3 Li Qing,1,2,3 Lili Li,1,2,3 Nan Zang,1,2,3 Kewei Wang,1,2,3 Chuanlong Wu,1,2,3 Lin Qi,1,2,3 Aixia Ma ,1,2,3 Huizhen Zheng,1,2,3 Xinguo Hou ,1,2,3 Fuqiang Liu ,1,2,3 and Li Chen 1,2,3 1Department of Endocrinology, Qilu Hospital of Shandong University, Jinan, Shandong, China 250012 2Institute of Endocrine and Metabolic Diseases of Shandong University, Jinan, Shandong, China 250012 3Key Laboratory of Endocrine and Metabolic Diseases, Shandong Province Medicine & Health, Jinan, Shandong, China 250012 Correspondence should be addressed to Fuqiang Liu; [email protected] and Li Chen; [email protected] Received 28 July 2019; Revised 14 November 2019; Accepted 19 November 2019; Published 22 January 2020 Academic Editor: Jonathan M. Peterson Copyright © 2020 Jiajia Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. More and more studies focus on the relationship between the gastrointestinal microbiome and type 2 diabetes, but few of them have actually explored the relationship between enterotypes and type 2 diabetes.
    [Show full text]
  • Prevotella Intermedia
    The principles of identification of oral anaerobic pathogens Dr. Edit Urbán © by author Department of Clinical Microbiology, Faculty of Medicine ESCMID Online University of Lecture Szeged, Hungary Library Oral Microbiological Ecology Portrait of Antonie van Leeuwenhoek (1632–1723) by Jan Verkolje Leeuwenhook in 1683-realized, that the film accumulated on the surface of the teeth contained diverse structural elements: bacteria Several hundred of different© bacteria,by author fungi and protozoans can live in the oral cavity When these organisms adhere to some surface they form an organizedESCMID mass called Online dental plaque Lecture or biofilm Library © by author ESCMID Online Lecture Library Gram-negative anaerobes Non-motile rods: Motile rods: Bacteriodaceae Selenomonas Prevotella Wolinella/Campylobacter Porphyromonas Treponema Bacteroides Mitsuokella Cocci: Veillonella Fusobacterium Leptotrichia © byCapnophyles: author Haemophilus A. actinomycetemcomitans ESCMID Online C. hominis, Lecture Eikenella Library Capnocytophaga Gram-positive anaerobes Rods: Cocci: Actinomyces Stomatococcus Propionibacterium Gemella Lactobacillus Peptostreptococcus Bifidobacterium Eubacterium Clostridium © by author Facultative: Streptococcus Rothia dentocariosa Micrococcus ESCMIDCorynebacterium Online LectureStaphylococcus Library © by author ESCMID Online Lecture Library Microbiology of periodontal disease The periodontium consist of gingiva, periodontial ligament, root cementerum and alveolar bone Bacteria cause virtually all forms of inflammatory
    [Show full text]
  • A Review of the Source and Function of Microbiota in Breast Milk
    68 A Review of the Source and Function of Microbiota in Breast Milk M. Susan LaTuga, MD, MSPH1 Alison Stuebe, MD, MSc2,3 Patrick C. Seed, MD, PhD4 1 Department of Pediatrics, Division of Neonatology, Albert Einstein Address for correspondence M. Susan LaTuga, MD, MSPH, Albert College of Medicine, Bronx, New York Einstein College of Medicine, 1601 Tenbroeck Ave, 2nd floor, Bronx, NY 2 Department of Obstetrics and Gynecology, University of North 10461 (e-mail: mlatuga@montefiore.org). Carolina School of Medicine 3 Department of Maternal and Child Health, Gillings School of Global Public Health, Chapel Hill, North Carolina 4 Department of Pediatrics, Division of Infectious Diseases, Duke University, Durham, North Carolina Semin Reprod Med 2014;32:68–73 Abstract Breast milk contains a rich microbiota composed of viable skin and non-skin bacteria. The extent of the breast milk microbiota diversity has been revealed through new culture-independent studies using microbial DNA signatures. However, the extent to which the breast milk microbiota are transferred from mother to infant and the function of these breast milk microbiota for the infant are only partially understood. Here, we appraise hypotheses regarding the formation of breast milk microbiota, including retrograde infant-to-mother transfer and enteromammary trafficking, and we review current knowledge of mechanisms determining the extent of breast milk microbiota transfer from mother to infant. We highlight known functions of constituents in the breast milk microbiota—to enhance immunity, liberate nutrients, synergize with breast Keywords milk oligosaccharides to enhance intestinal barrier function, and strengthen a functional ► enteromammary gut–brain axis. We also consider the pathophysiology of maternal mastitis with respect trafficking to a dysbiosis or abnormal shift in the breast milk microbiota.
    [Show full text]
  • Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals
    fmicb-12-673969 August 14, 2021 Time: 15:47 # 1 ORIGINAL RESEARCH published: 19 August 2021 doi: 10.3389/fmicb.2021.673969 Characterization of the Genitourinary Microbiome of 1,165 Middle-Aged and Elderly Healthy Individuals Junjie Qin1,2,3†, Xulian Shi1†, Junming Xu1,2,3†, Simin Yuan1†, Bo Zheng2, Enpu Zhang1, Guixiao Huang1, Guo Li1, Ganggang Jiang1, Shan Gao1, Cheng Tian3, Ruochun Guo3, Zhicong Fu3, Qingru Huang3, Rentao Yang3, Wenyong Zhang4, Shenghui Li3 and Song Wu1,5,6* 1 Department of Urology, The Third Affiliated Hospital of Shenzhen University (Luohu Hospital Group), Shenzhen, China, 2 State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Shenzhen, China, 3 Department of Human Microbiome, Promegene Institute, Shenzhen, China, 4 School of Medicine, Southern University of Science and Technology, Shenzhen, China, 5 Teaching Center of Shenzhen Luohu Hospital, Shantou University Medical College, Shantou, China, 6 Department of Urology and Guangdong Key Laboratory of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China Edited by: Accumulated evidence shows that complex microbial communities resides in the David W. Ussery, healthy human urinary tract and can change in urological disorders. However, University of Arkansas for Medical Sciences, United States there lacks a comprehensive profiling of the genitourinary microbiota in healthy Reviewed by: cohort. Here, we performed 16S rRNA gene sequencing of midstream urine Ruijin Guo, specimens from 1,172 middle-aged and elderly healthy individuals. The core microbiota Beijing Genomics Institute (BGI), included 6 dominant genera (mean relative abundance >5%), including Prevotella, China Mingbang Wang, Streptococcus, Lactobacillus, Gardnerella, Escherichia-Shigella, and Veillonella, and Fudan University, China 131 low-abundance genera (0.01–5%), displaying a distinct microbiome profiles to *Correspondence: that of host-matched gut microbiota.
    [Show full text]
  • Db20-0503.Full.Pdf
    Page 1 of 32 Diabetes Analysis of the Composition and Functions of the Microbiome in Diabetic Foot Osteomyelitis based on 16S rRNA and Metagenome Sequencing Technology Zou Mengchen1*; Cai Yulan2*; Hu Ping3*; Cao Yin1; Luo Xiangrong1; Fan Xinzhao1; Zhang Bao4; Wu Xianbo4; Jiang Nan5; Lin Qingrong5; Zhou Hao6; Xue Yaoming1; Gao Fang1# 1Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China 2Department of Endocrinology, Affiliated Hospital of Zunyi Medical College, Zunyi, China 3Department of Geriatric Medicine, Xiaogan Central Hospital, Xiaogan, China 4School of Public Health and Tropic Medicine, Southern Medical University, Guangzhou, China 5Department of Orthopaedics & Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, China 6Department of Hospital Infection Management of Nanfang Hospital, Southern Medical University, Guangzhou, China *Zou mengchen, Cai yulan and Hu ping contributed equally to this work. Running title: Microbiome of Diabetic Foot Osteomyelitis Word count: 3915 Figures/Tables Count: 4Figures / 3 Tables References: 26 Diabetes Publish Ahead of Print, published online August 14, 2020 Diabetes Page 2 of 32 Keywords: diabetic foot osteomyelitis; microbiome; 16S rRNA sequencing; metagenome sequencing #Corresponding author: Gao Fang, E-mail: [email protected], Tel: 13006871226 Page 3 of 32 Diabetes ABSTRACT Metagenome sequencing has not been used in infected bone specimens. This study aimed to analyze the microbiome and its functions. This prospective observational study explored the microbiome and its functions of DFO (group DM) and posttraumatic foot osteomyelitis (PFO) (group NDM) based on 16S rRNA sequencing and metagenome sequencing technologies. Spearman analysis was used to explore the correlation between dominant species and clinical indicators of patients with DFO.
    [Show full text]
  • Prevotella in Pigs: the Positive and Negative Associations with Production and Health
    microorganisms Review Prevotella in Pigs: The Positive and Negative Associations with Production and Health Samat Amat 1,2, Hannah Lantz 1, Peris M. Munyaka 1 and Benjamin P. Willing 1,* 1 Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; [email protected] (S.A.); [email protected] (H.L.); [email protected] (P.M.M.) 2 Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108-6050, USA * Correspondence: [email protected]; Tel.: +1-780-492-8908 Received: 1 September 2020; Accepted: 11 October 2020; Published: 14 October 2020 Abstract: A diverse and dynamic microbial community (known as microbiota) resides within the pig gastrointestinal tract (GIT). The microbiota contributes to host health and performance by mediating nutrient metabolism, stimulating the immune system, and providing colonization resistance against pathogens. Manipulation of gut microbiota to enhance growth performance and disease resilience in pigs has recently become an active area of research in an era defined by increasing scrutiny of antimicrobial use in swine production. In order to develop microbiota-targeted strategies, or to identify potential next-generation probiotic strains originating from the endogenous members of GIT microbiota in pigs, it is necessary to understand the role of key commensal members in host health. Many, though not all, correlative studies have associated members of the genus Prevotella with positive outcomes in pig production, including growth performance and immune response; therefore, a comprehensive review of the genus in the context of pig production is needed. In the present review, we summarize the current state of knowledge about the genus Prevotella in the intestinal microbial community of pigs, including relevant information from other animal species that provide mechanistic insights, and identify gaps in knowledge that must be addressed before development of Prevotella species as next-generation probiotics can be supported.
    [Show full text]
  • Tenebrio Molitor Larvae Meal Affects the Cecal Microbiota of Growing Pigs
    Tenebrio Molitor Larvae Meal Affects the Cecal Microbiota of Growing Pigs Sandra Meyer, Denise K. Gessner, Garima Maheshwari, Julia Röhrig, Theresa Friedhoff, Erika Most, Holger Zorn, Robert Ringseis and Klaus Eder Table S1. Characteristics of gene-specific primers used for qPCR analysis in small intestinal mucosa. Annealing PCR Forward (5` to 3`) NCBI GeneBank Gene Temperature Product Slope R2 E Reverse (5` to 3`) Accession No. (°C) Size (bp) Reference genes CAGTCACCTTGAGCCGGGCGA ATP5MC1 64 94 NM_001025218 -3.55 0.999 1.91 TAGCGCCCCGGTGGTTTGC AGGGGCTCTCCAGAACATCATCC GAPDH 60 446 NM_001206359 -3.33 1.000 2.00 TCGCGTGCTCTTGCTGGGGTTGG GTCGCAAGACTTATGTGACC RPS9 62 325 XM_021094878 -3.28 0.999 2.02 AGCTTAAAGACCTGGGTCTG CTACGCCCCCGTCGCAAAGG SDHA 64 380 XM_021076930 -3.32 1.000 2.00 AGTTTGCCCCCAGGCGGTTG Target genes GATCGGCTCCATCGTCAGCA CLDN1 60 115 NM_001244539 -3.54 0.994 1.92 CGACACGCAGGACATCCACA ACTTCCAAACTGGCTGTTGC CXCL8 59 120 NM_213867 -3.59 0.994 1.90 GGAATGCGTATTTATGCACTGG GTTCTCTGAGAAATGGGAGC IL1B 58 143 NM_214055 -3.51 0.997 1.93 CTGGTCATCATCACAGAAGG AAGGTGATGCCACCTCAGAC IL6 60 151 NM_001252429 -3.54 0.994 1.92 TCTGCCAGTACCTCCTTGCT MUC1 CGGGCTTCTGGGACTCTTTT 58 312 XM_021089728 -3.63 0.999 1.89 1 TTCTTTCGTCGGCACTGACA TGTGTTTTGCTTTGGGTCCAG MUC13 58 171 NM_001105293 -3.58 1.000 1.90 CACAGCCAACTCCACTGTAGC CTTCCAACCATCCTCCCACC MUC2 58 174 XM_021082584 -3.53 0.996 1.92 GCCGTCTTGAAATCATCGCC GCCTACTCGTCCAACGGGAA OCLN 60 246 NM_001163647 -3.60 0.999 1.90 GCCCGTCGTGTAGTCTGTCT CAGACTTCGACCACAACGGA SLC15A1 58 99 NM_214347 -3.52 0.998 1.93 TTATCCCGCCAGTACCCAGA CGCAACCATTGGAGTTGGCGC SLC2A2 63 122 NM_001097417 -3.37 0.997 1.98 TGGCACAAACAAACATCCCACTCA CTGACACTGGTGCTTGCTTT SLC2A5 57 156 XM_021095282 -3.45 0.989 1.95 TTCGCTCATGTATTCCCCGA GTGGCGGACAGTAGTGAACA SLC5A1 57 89 NM_001164021 -3.31 1.000 1.92 AGAAGGCAGGATTTCAGGCA GTCGTCCTGATCCTGACCCG TJP1 60 207 XM_021098827 -3.26 0.996 2.03 TGGTGGGTTTGGTGGGTTGA CCAAGGACTCAGATCATCGT TNF 58 146 NM_214022 -3.36 1.000 1.99 GCTGGTTGTCTTTCAGCTTC Table S2.
    [Show full text]