DOCSLIB.ORG

Microbiota Profiling with Long Amplicons Using Nanopore Sequencing: Full-Length 16S Rrna Gene and the 16S-ITS-23S of the Operon

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Microbiota Profiling with Long Amplicons Using Nanopore Sequencing: Full-Length 16S Rrna Gene and the 16S-ITS-23S of the Operon F1000Research 2019, 7:1755 Last updated: 03 AUG 2021 RESEARCH ARTICLE Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and the 16S- ITS-23S of the rrn operon [version 2; peer review: 2 approved, 3 approved with reservations] Anna Cuscó 1, Carlotta Catozzi 2,3, Joaquim Viñes1,3, Armand Sanchez3, Olga Francino3 1Vetgenomics, SL, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain 2Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italy 3Molecular Genetics Veterinary Service (SVGM), Universitat Autonoma of Barcelona, Bellaterra (Cerdanyola del Vallès), Barcelona, 08193, Spain v2 First published: 06 Nov 2018, 7:1755 Open Peer Review https://doi.org/10.12688/f1000research.16817.1 Latest published: 01 Aug 2019, 7:1755 https://doi.org/10.12688/f1000research.16817.2 Reviewer Status Invited Reviewers Abstract Background: Profiling the microbiome of low-biomass samples is 1 2 3 4 5 challenging for metagenomics since these samples are prone to contain DNA from other sources (e.g. host or environment). The usual version 2 approach is sequencing short regions of the 16S rRNA gene, which (revision) report fails to assign taxonomy to genus and species level. To achieve an 01 Aug 2019 increased taxonomic resolution, we aim to develop long-amplicon PCR-based approaches using Nanopore sequencing. We assessed two version 1 different genetic markers: the full-length 16S rRNA (~1,500 bp) and the 06 Nov 2018 report report report report report 16S-ITS-23S region from the rrn operon (4,300 bp). Methods: We sequenced a clinical isolate of Staphylococcus pseudintermedius, two mock communities and two pools of low- 1. Alfonso Benítez-Páez , Institute of biomass samples (dog skin). Nanopore sequencing was performed on Agrochemistry and Food Technology-Spanish MinION™ using the 1D PCR barcoding kit. Sequences were pre- National Research Council (IATA-CSIC), processed, and data were analyzed using EPI2ME or Minimap2 with rrn database. Consensus sequences of the 16S-ITS-23S genetic marker Valencia, Spain were obtained using canu. Results: The full-length 16S rRNA and the 16S-ITS-23S region of the 2. Rasmus H. Kirkegaard , Aalborg rrn operon were used to retrieve the microbiota composition of the University (AAU), Aalborg, Denmark samples at the genus and species level. For the Staphylococcus pseudintermedius isolate, the amplicons were assigned to the correct 3. Amanda Warr , University of Edinburgh, bacterial species in ~98% of the cases with the16S-ITS-23S genetic Edinburgh, UK marker, and in ~68%, with the 16S rRNA gene when using EPI2ME. Using mock communities, we found that the full-length 16S rRNA 4. Kon Chu, Seoul National University, Seoul, gene represented better the abundances of a microbial community; South Korea whereas, 16S-ITS-23S obtained better resolution at the species level. Page 1 of 29 F1000Research 2019, 7:1755 Last updated: 03 AUG 2021 Finally, we characterized low-biomass skin microbiota samples and detected species with an environmental origin. 5. Lee J. Kerkhof , Rutgers University, New Conclusions: Both full-length 16S rRNA and the 16S-ITS-23S of the rrn Brunswick, USA operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as Any reports and responses or comments on the dog skin. For an increased resolution at the species level, targeting article can be found at the end of the article. the 16S-ITS-23S of the rrn operon would be the best choice. Keywords microbiome, microbiota, 16S, rrn operon, nanopore, canine, low- biomass, skin, dog This article is included in the Nanopore Analysis gateway. Corresponding author: Anna Cuscó ([email protected]) Author roles: Cuscó A: Conceptualization, Formal Analysis, Investigation, Methodology, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing; Catozzi C: Investigation, Validation, Visualization, Writing – Review & Editing; Viñes J: Investigation, Visualization, Writing – Review & Editing; Sanchez A: Conceptualization, Funding Acquisition; Francino O: Conceptualization, Funding Acquisition, Methodology, Supervision, Writing – Review & Editing Competing interests: No competing interests were disclosed. Grant information: This work was supported by two grants awarded by Generalitat de Catalunya (Industrial Doctorate program, 2013 DI 011 and 2017 DI 037). Copyright: © 2019 Cuscó A et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite this article: Cuscó A, Catozzi C, Viñes J et al. Microbiota profiling with long amplicons using Nanopore sequencing: full- length 16S rRNA gene and the 16S-ITS-23S of the rrn operon [version 2; peer review: 2 approved, 3 approved with reservations] F1000Research 2019, 7:1755 https://doi.org/10.12688/f1000research.16817.2 First published: 06 Nov 2018, 7:1755 https://doi.org/10.12688/f1000research.16817.1 Page 2 of 29 F1000Research 2019, 7:1755 Last updated: 03 AUG 2021 dermatitis presented an overrepresentation of Staphylococcus REVISE D Amendments from Version 1 genus13,14, but the species was only confirmed when comple- We hereby present a revised version of our manuscript, based menting the studies using directed qPCRs for the species of 13 on the comments made by the referees and more results since interest or using a Staphylococcus-specific database and V1-V3 version 1 was published. region amplification14. The main changes of the manuscript when compared to version 1 are those stated here: With the launching of single-molecule technology sequencers - We have assessed the performance of the mapping approach (e.g. PacBio or Oxford Nanopore Technologies), these short- with the uncorrected long-amplicons strategy presented here. length associated issues can be overcome by sequencing the - We have expanded the results adding a section of the de novo assembly of the 16S-ITS-23S genetic marker. full-length 16S rRNA gene (~1,500 bp) or even the nearly- - We have provided more detail on the methodology used from complete rrn operon (~4,300 bp), which includes the 16S rRNA the lab bench to the bioinformatics part, with supplementary file 1 gene, ITS region, and 23S rRNA gene. providing the commands used for the mapping approach. - The mapping results have been updated since in version 1 Several studies assessing the full-length 16S rRNA gene have chimeras were computed differently for each amplicon and led already been performed using Nanopore sequencing to: i) char- to confusing results (more chimera for 16S rRNA than for 16S- 15–17 ITS-23S). Now for both amplicons, we have performed base-level acterize artificial bacterial communities (mock community) ; 18 alignment using Minimap2 as the first step before yacrd (detailed ii) complex microbiota samples, from the mouse gut , in Supplementary File 1). wastewater19, microalgae20 and dog skin21; and iii) the pathogenic - The figures and tables have been simplified, re-ordered and agent in a clinical sample22–24. Some studies have been performed completed to be more informative and clear. We got rid of the using the nearly-complete rrn operon to characterize mock graphic bars and kept the heatmaps. communities25 and complex natural communities26. Finally, we want to thank all the referees for their time to evaluate our work and their invaluable feedback. Here, we aim to assess these two long-amplicon approaches See referee reports using MinIONTM (Oxford Nanopore Technologies), a single- molecule sequencer that is portable, affordable with a small budget and offers long-read output. Its main limitation is a higher error Introduction rate than massive sequencing. We will test our approaches by The microbiota profile of low-biomass samples such as skin is sequencing several samples with different degrees of complex- challenging for metagenomics. These samples are prone to contain ity: i) a clinical isolate of Staphylococcus pseudintermedius, DNA contamination from the host or exogenous sources, which ii) two bacterial mock communities; and iii) two complex skin can overcome the DNA of interest1,2. Thus, the usual approach microbiota samples. is amplifying and sequencing certain genetic markers that are ubiquitously found within the studied kingdom rather than per- Methods forming metagenomics. Ribosomal marker genes are a common Samples and DNA extraction choice: 16S rRNA and 23S rRNA genes to taxonomically We first sequenced a pure bacterial isolate of S. pseud- classify bacteria3,4; and ITS1 and ITS2 regions for fungi5,6. intermedius obtained from the ear of a dog affected by otitis. Until now, most studies of microbiota rely on massive paral- lel sequencing, and target a short fragment of the 16S rRNA Then, we used two DNA mock communities as simple and gene, which presents nine hypervariable regions (V1-V9) that well-defined microbiota samples: are used to infer taxonomy7,8. The most common choices for host-associated microbiota are V4 or V1-V2 regions, which • HM-783D, kindly donated by BEI resources, con- present different taxonomic coverage and resolution depending taining genomic DNA from 20 bacterial strains with on the taxa9,10. staggered ribosomal RNA operon counts (between 103 and 106 copies per organism per μl). Apart from the biases derived from the primer choice, short fragment strategies usually fail to assign taxonomy
Load more

Recommended publications
  • Prevalence of Colonization and Antimicrobial Resistance Among Coagulase Positive Staphylococci in Dogs, and the Relatedness of Canine and Human Staphylococcus Aureus
    PREVALENCE OF COLONIZATION AND ANTIMICROBIAL RESISTANCE AMONG COAGULASE POSITIVE STAPHYLOCOCCI IN DOGS, AND THE RELATEDNESS OF CANINE AND HUMAN STAPHYLOCOCCUS AUREUS A Thesis Submitted to the College of Graduate Studies and Research In Partial Fulfillment of the Requirements For the Degree of Doctor of Philosophy In the Department of Veterinary Microbiology In the College of Graduate Studies and Research University of Saskatchewan Saskatoon, Saskatchewan By Joseph Elliot Rubin © Copyright Joseph Elliot Rubin, May 2011. All rights reserved Permission to use Postgraduate Thesis In presenting this thesis in partial fulfillment of the requirement for a postgraduate degree from the University of Saskatchewan, I agree that the libraries of this university may make it free available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the following: Dr. Manuel Chirino-Trejo, DVM, MSc., PhD Department of Veterinary Microbiology University of Saskatchewan In his absence, permission may be granted from the head of the department of Veterinary Microbiology or the Dean of the Western College of Veterinary Medicine. It is understood that any copying, publication, or use of this thesis or part of it for financial gain shall not be allowed without with author’s written permission. It is also understood that due recognition shall be given to the author and to the University of Saskatchewan in any scholarly use which may be made of any material in this thesis. Requests for permission to copy or make other use of materials in this thesis in whole or in part should be addressed to: Head of the Department of Veterinary Microbiology Western College of Veterinary Medicine University of Saskatchewan 52 Campus Drive Saskatoon, Saskatchewan S7N 5B4 i Abstract Coagulase positive staphylococci, Staphylococcus aureus and Staphylococcus pseudintermedius, are important causes of infection in human beings and dogs respectively.
    [Show full text]
  • The Genera Staphylococcus and Macrococcus
    Prokaryotes (2006) 4:5–75 DOI: 10.1007/0-387-30744-3_1 CHAPTER 1.2.1 ehT areneG succocolyhpatS dna succocorcMa The Genera Staphylococcus and Macrococcus FRIEDRICH GÖTZ, TAMMY BANNERMAN AND KARL-HEINZ SCHLEIFER Introduction zolidone (Baker, 1984). Comparative immu- nochemical studies of catalases (Schleifer, 1986), The name Staphylococcus (staphyle, bunch of DNA-DNA hybridization studies, DNA-rRNA grapes) was introduced by Ogston (1883) for the hybridization studies (Schleifer et al., 1979; Kilp- group micrococci causing inflammation and per et al., 1980), and comparative oligonucle- suppuration. He was the first to differentiate otide cataloguing of 16S rRNA (Ludwig et al., two kinds of pyogenic cocci: one arranged in 1981) clearly demonstrated the epigenetic and groups or masses was called “Staphylococcus” genetic difference of staphylococci and micro- and another arranged in chains was named cocci. Members of the genus Staphylococcus “Billroth’s Streptococcus.” A formal description form a coherent and well-defined group of of the genus Staphylococcus was provided by related species that is widely divergent from Rosenbach (1884). He divided the genus into the those of the genus Micrococcus. Until the early two species Staphylococcus aureus and S. albus. 1970s, the genus Staphylococcus consisted of Zopf (1885) placed the mass-forming staphylo- three species: the coagulase-positive species S. cocci and tetrad-forming micrococci in the genus aureus and the coagulase-negative species S. epi- Micrococcus. In 1886, the genus Staphylococcus dermidis and S. saprophyticus, but a deeper look was separated from Micrococcus by Flügge into the chemotaxonomic and genotypic proper- (1886). He differentiated the two genera mainly ties of staphylococci led to the description of on the basis of their action on gelatin and on many new staphylococcal species.
    [Show full text]
  • A New Class of Quorum Quenching Molecules from Staphylococcus Species Affects Communication and Growth of Gram-Negative Bacteria
    A New Class of Quorum Quenching Molecules from Staphylococcus Species Affects Communication and Growth of Gram-Negative Bacteria Ya-Yun Chu1, Mulugeta Nega1, Martina Wo¨ lfle2, Laure Plener3, Stephanie Grond2, Kirsten Jung3, Friedrich Go¨ tz1* 1 Interfaculty Institute of Microbiology and Infectious Diseases Tu¨bingen (IMIT), Microbial Genetics, University of Tu¨bingen, Tu¨bingen, Germany, 2 Organic Chemistry, University of Tu¨bingen, Tu¨bingen, Germany, 3 Munich Center for Integrated Protein Science (CiPSM) at the Department of Microbiology, Ludwig-Maximilians-Universita¨t Mu¨nchen, Martinsried, Germany Abstract The knowledge that many pathogens rely on cell-to-cell communication mechanisms known as quorum sensing, opens a new disease control strategy: quorum quenching. Here we report on one of the rare examples where Gram-positive bacteria, the ‘Staphylococcus intermedius group’ of zoonotic pathogens, excrete two compounds in millimolar concentrations that suppress the quorum sensing signaling and inhibit the growth of a broad spectrum of Gram-negative beta- and gamma-proteobacteria. These compounds were isolated from Staphylococcus delphini. They represent a new class of quorum quenchers with the chemical formula N-[2-(1H-indol-3-yl)ethyl]-urea and N-(2-phenethyl)-urea, which we named yayurea A and B, respectively. In vitro studies with the N-acyl homoserine lactone (AHL) responding receptor LuxN of V. harveyi indicated that both compounds caused opposite effects on phosphorylation to those caused by AHL. This explains the quorum quenching activity. Staphylococcal strains producing yayurea A and B clearly benefit from an increased competitiveness in a mixed community. Citation: Chu Y-Y, Nega M, Wo¨lfle M, Plener L, Grond S, et al.
    [Show full text]
  • Draft Genome Sequence of Staphylococcus Agnetis 3682, the Producing
    Journal of Global Antimicrobial Resistance 19 (2019) 50–52 Contents lists available at ScienceDirect Journal of Global Antimicrobial Resistance journal homepage: www.elsevier.com/locate/jgar Genome Note Draft genome sequence of Staphylococcus agnetis 3682, the producing strain of the broad-spectrum lantibiotic agneticin 3682 a a a Patrícia Carlin Fagundes , Márcia Silva Francisco , Ilana Nascimento Sousa Santos , a a Selda Loase Salustiano Marques-Bastos , Juliana Aparecida Souza Paz , b a, Rodolpho Mattos Albano , Maria do Carmo de Freire Bastos * a Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil b Departamento de Bioquímica, Instituto de Biologia Roberto Alcântara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil A R T I C L E I N F O A B S T R A C T Article history: Objectives: Here we report the draft genome sequence of Staphylococcus agnetis 3682, a strain producing Received 15 July 2019 agneticin 3682, a broad-spectrum lantibiotic with potential medical applications. The inhibitory activity Received in revised form 15 August 2019 of S. agnetis 3682 against multidrug-resistant methicillin-resistant Staphylococcus aureus (MRSA) isolates Accepted 17 August 2019 involved in human infections was also investigated. Available online 24 August 2019 Methods: A sequencing library was constructed using a Nextera XT DNA Library Preparation Kit. An Illumina MiSeq system was used to perform whole-genome shotgun sequencing. De novo genome Keywords: assembly was performed using the A5-miseq pipeline. Staphylococcus agnetis 3628 genome annotation Staphylococcus agnetis was performed by the RAST server, and BAGEL4 and antiSMASH v.4.0 platforms were used for mining Agneticin 3682 bacteriocin gene clusters.
    [Show full text]
  • Genome Analysis of Staphylococcus Agnetis, an Agent of Lameness in Broiler Chickens
    RESEARCH ARTICLE Genome Analysis of Staphylococcus agnetis, an Agent of Lameness in Broiler Chickens Adnan A. K. Al-Rubaye1,2☯, M. Brian Couger3☯, Sohita Ojha1,2, Jeff F. Pummill4, Joseph A. Koon II5, Robert F. Wideman, Jr.1,6‡, Douglas D. Rhoads1,2‡* 1 Interdisciplinary Graduate Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America, 2 Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States of America, 3 Department of Microbiology, Oklahoma State University, Stillwater, OK, United States of America, 4 Arkansas High Performance Computing Center, University of Arkansas, Fayetteville, AR, United States of America, 5 Department of Biology, Ouachita Baptist University, Arkadelphia, AR, United States of America, 6 Department of Poultry Sciences, University of Arkansas, Fayetteville, AR, United States of America ☯ These authors contributed equally to this work. ‡ These authors also contributed equally to this work. * [email protected] OPEN ACCESS Abstract Citation: Al-Rubaye AAK, Couger MB, Ojha S, Pummill JF, Koon JA, II, Wideman RF, Jr., et al. Lameness in broiler chickens is a significant animal welfare and financial issue. Lameness (2015) Genome Analysis of Staphylococcus agnetis, can be enhanced by rearing young broilers on wire flooring. We have identified Staphylo- an Agent of Lameness in Broiler Chickens. PLoS coccus agnetis as significantly involved in bacterial chondronecrosis with osteomyelitis ONE 10(11): e0143336. doi:10.1371/journal. pone.0143336 (BCO) in proximal tibia and femorae, leading to lameness in broiler chickens in the wire floor system. Administration of S. agnetis in water induces lameness. Previously reported in Editor: Gabriel Moreno-Hagelsieb, Wilfrid Laurier University, CANADA some cases of cattle mastitis, this is the first report of this poorly described pathogen in chickens.
    [Show full text]
  • Advancements in the Understanding of Staphylococcal
    ADVANCEMENTS IN THE UNDERSTANDING OF STAPHYLOCOCCAL MASTITIS THROUGH THE USE OF MOLECULAR TOOLS __________________________________________ A Dissertation presented to the Faculty of the Graduate School at the University of Missouri-Columbia __________________________________________ In partial fulfillment of the requirements for the degree Doctor of Philosophy __________________________________________ By PAMELA RAE FRY ADKINS Dr. John Middleton, Dissertation Supervisor May 2017 The undersigned, appointed by the dean of the Graduate School, have examined the dissertation entitled ADVANCEMENTS IN THE UNDERSTANDING OF STAPHYLOCOCCAL MASTITIS THROUGH THE USE OF MOLECULAR TOOLS presented by Pamela R. F. Adkins, a candidate for the degree of Doctor of Philosophy, and hereby certify that, in their opinion, it is worthy of acceptance. Professor John R. Middleton Professor James N. Spain Professor Michael J. Calcutt Professor George C. Stewart Professor Thomas J. Reilly DEDICATION I dedicate this to my husband, Eric Adkins, and my mother, Denice Condon. I am forever grateful for their eternal love and support. ACKNOWLEDGEMENTS I thank John R. Middleton, committee chair, for this support and guidance. I sincerely appreciate his mentorship in the areas of research, scientific writing, and life in academia. I also thank all the other members of my committee, including Michael Calcutt, George Stewart, James Spain, and Thomas Reilly. I am grateful for their guidance and expertise, which has helped me through many aspects of this research. I thank Simon Dufour (University of Montreal), Larry Fox (Washington State University) and Suvi Taponen (University of Helsinki) for their contribution to this research. I acknowledge Julie Holle for her technical assistance, for always being willing to help, and for being so supportive.
    [Show full text]
  • Gatunki Koagulazododatnie Rodzaju Staphylococcus – Taksonomia, Chorobotwórczość 235
    POST. MIKROBIOL., GATUNKI KOAGULAZODODATNIE 2017, 56, 2, 233–244 http://www.pm.microbiology.pl RODZAJU STAPHYLOCOCCUS – TAKSONOMIA, CHOROBOTWÓRCZOŚĆ Wioletta Kmieciak1*, Eligia Maria Szewczyk1 1 Zakład Mikrobiologii Farmaceutycznej i Diagnostyki Mikrobiologicznej, Uniwersytet Medyczny w Łodzi Wpłynęło w grudniu 2016 r. Zaakceptowano w lutym 2017 r. 1. Wstęp. 2. Koagulaza gronkowcowa. 3. Staphylococcus aureus. 4. Gronkowce grupy SIG. 4.1. Staphylococcus intermedius. 4.2. Staphylococcus pseudintermedius. 4.3. Staphylococcus delphini. 5. Staphylococcus hyicus. 6. Staphylococcus schleiferi subsp. coagulans. 7. Staphylococcus lutrae. 8. Staphylococcus agnetis. 9. Podsumowanie Coagulase-positive species of the genus Staphylococcus – taxonomy, pathogenicity Abstract: Staphylococci constitute an important component of the human microbiome. Most of them are coagulase-negative species, whose importance in the pathogenesis of human infections has been widely recognized and is being documented on a regular basis. Until recently, the only well-known coagulase-positive staphylococcus species recognized as human pathogen was Staphylococcus aureus. Previously, the ability to produce coagulase was used as its basic diagnostic feature, because other coagulase-positive species were associated with animal hosts. Progress in the laboratory medicine, in which automatic or semi-automatic systems identify the staphylococci species, revealed a phenomenon of spreading of the coagulase positive staphylococci to new niches and hosts, as they are being isolated from human clinical materials with increasing frequency. As a result, many reaserchers and laboratories have turned their attention to the phenomenon, which caused an inflow of new data on these species. An increasingly expansive pathogenic potential of coagulase-positive staphylococci against humans has been documented. In the presented study, recent data on both S.
    [Show full text]
  • The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus Aureus Isolate from a Malaysian Hospital
    Standards in Genomic Sciences (2014) 9: 933-939 DOI:10.4056/sigs.3887716 The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus aureus Isolate from a Malaysian Hospital LS Lee1,2, LK Teh1, ZF Zainuddin2 and MZ Salleh1* 1Integrative Pharmacogenomics Centre, Faculty of Pharmacy, Universiti Teknologi MARA Malaysia, 42300 Bandar Puncak Alam, Selangor, Malaysia. 2School of Health Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Ma- laysia * Corresponding author: MZ Salleh ([email protected]) Keywords: Staphylococcus aureus, MRSA, Malaysia, Genomics We report the genome sequence of a healthcare-associated MRSA type ST239 clone isolated from a patient with septicemia in Malaysia. This clone typifies the characteristics of ST239 lineage, including resistance to multiple antibiotics and antiseptics. Introduction cin, ciprofloxacin and co-trimoxazole. Antibiotic resistance in S. aureus is a major con- Genome sequencing information cern, as an increasing number of infections are caused by methicillin-resistant S. aureus (MRSA). Genome project history Figure 1 shows the phylogenetic position of S. This organism was selected for sequencing as a aureus in relation to other staphylococci. In Ma- representative of MRSA infection in a local Malay- laysia, the incidence of MRSA-related infections is sian hospital. The genome sequences of this or- a cause of concern in hospitals country-wide. ganism were deposited in GenBank (WGS data- Health-associated MRSA (HA-MRSA) has been base). Sequencing, finishing and annotation were dominated by a few lineages in Southeast Asia, performed at the Pharmacogenomics Centre particularly ST239. Sequence type 239 is an inter- (PROMISE), UiTM. Table 2 presents the project in- national healthcare-associated (HA) MRSA lineage formation and its association with MIGS version prevalent in Asia, South America and Eastern Eu- 2.0 compliance [14].
    [Show full text]
  • Whole Genome Comparisons of Staphylococcus Agnetis Isolates from Cattle and Chickens
    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896779; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Whole genome comparisons of Staphylococcus agnetis isolates from cattle and chickens. 2 3 Abdulkarim Shwani,a Pamela R. F. Adkins,b Nnamdi S. Ekesi,a Adnan Alrubaye,a Michael J. 4 Calcutt,c John R. Middleton,b Douglas D. Rhoadsa,# 5 aCell and Molecular Biology program, University of Arkansas, Fayetteville, Arkansas, USA 6 bDept. of Veterinary Medicine and Surgery, University of Missouri, Columbia, Missouri, USA 7 cDept. of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA 8 9 Running Head: S. agnetis phylogenomics 10 11 #Address correspondence to Douglas Rhoads, [email protected] 12 Keywords: Staphlococcus, Broiler, Mastitis, Lameness, Phylogeny 13 14 Abstract 15 S. agnetis has been previously associated with subclinical or clinically mild cases of mastitis in 16 dairy cattle and is one of several Staphylococcal species that have been isolated from the bone 17 and blood of lame broilers. We were the first to report that S. agnetis could be obtained 18 frequently from bacterial chondronecrosis with osteomyelitis (BCO) lesions of lame broilers. 19 Further, we showed that a particular isolate of S. agnetis, chicken isolate 908, can induce 20 lameness in over 50% of exposed chickens, far exceeding normal BCO incidences in broiler 21 operations. We have previously reported the assembly and annotation of the genome of isolate 22 908. To better understand the relationship between dairy cattle and broiler isolates, we 23 assembled 11 additional genomes for S.
    [Show full text]
  • Understanding Biological Factors Associated with Pelvic Organ Prolapse in Late Gestation Sows
    Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2021 Understanding biological factors associated with pelvic organ prolapse in late gestation sows Zoe E. Kiefer Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Recommended Citation Kiefer, Zoe E., "Understanding biological factors associated with pelvic organ prolapse in late gestation sows" (2021). Graduate Theses and Dissertations. 18526. https://lib.dr.iastate.edu/etd/18526 This Thesis is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Understanding biological factors associated with pelvic organ prolapse in late gestation sows by Zoë Elizabeth Kiefer A thesis submitted to the graduate faculty in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE Major: Animal Physiology (Reproductive Physiology) Program of Study Committee: Jason W. Ross, Major Professor Aileen F. Keating Stephan Schmitz-Esser The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this thesis. The Graduate College will ensure this thesis is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2021 Copyright © Zoë Elizabeth Kiefer, 2021. All rights reserved. ii DEDICATION I dedicate this thesis to everyone who has encouraged and supported me throughout this journey.
    [Show full text]
  • Whole Genome Comparisons of Staphylococcus Agnetis Isolates from Cattle and Chickens
    bioRxiv preprint doi: https://doi.org/10.1101/2020.01.06.896779; this version posted January 7, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 Whole genome comparisons of Staphylococcus agnetis isolates from cattle and chickens. 2 3 Abdulkarim Shwani,a Pamela R. F. Adkins,b Nnamdi S. Ekesi,a Adnan Alrubaye,a Michael J. 4 Calcutt,c John R. Middleton,b Douglas D. Rhoadsa,# 5 aCell and Molecular Biology program, University of Arkansas, Fayetteville, Arkansas, USA 6 bDept. of Veterinary Medicine and Surgery, University of Missouri, Columbia, Missouri, USA 7 cDept. of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA 8 9 Running Head: S. agnetis phylogenomics 10 11 #Address correspondence to Douglas Rhoads, [email protected] 12 Keywords: Staphlococcus, Broiler, Mastitis, Lameness, Phylogeny 13 14 Abstract 15 We report the comparisons of genomes of eleven isolates of Staphylococcus agnetis obtained 16 from dairy cattle and chickens. S. agnetis has been previously associated with subclinical or 17 clinically mild cases of mastitis in dairy cattle and is one of several Staphylococcal species 18 isolated from the bone and blood of lame broilers. We have previously shown that a chicken 19 isolate 908 can induce bacterial chondronecrosis with osteomyelitis (BCO) in chickens with 20 incidences of lameness over 50%. We have also assembled and analyzed the genome of isolate 21 908. To better understand the relationship between dairy cattle and broiler isolates, we 22 assembled genomes for S.
    [Show full text]
  • Review Memorandum
    510(k) SUBSTANTIAL EQUIVALENCE DETERMINATION DECISION SUMMARY A. 510(k) Number: K181663 B. Purpose for Submission: To obtain clearance for the ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel C. Measurand: Bacillus cereus group, Bacillus subtilis group, Corynebacterium, Cutibacterium acnes (P. acnes), Enterococcus, Enterococcus faecalis, Enterococcus faecium, Lactobacillus, Listeria, Listeria monocytogenes, Micrococcus, Staphylococcus, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Streptococcus, Streptococcus agalactiae (GBS), Streptococcus anginosus group, Streptococcus pneumoniae, Streptococcus pyogenes (GAS), mecA, mecC, vanA and vanB. D. Type of Test: A multiplexed nucleic acid-based test intended for use with the GenMark’s ePlex instrument for the qualitative in vitro detection and identification of multiple bacterial and yeast nucleic acids and select genetic determinants of antimicrobial resistance. The BCID-GP assay is performed directly on positive blood culture samples that demonstrate the presence of organisms as determined by Gram stain. E. Applicant: GenMark Diagnostics, Incorporated F. Proprietary and Established Names: ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel G. Regulatory Information: 1. Regulation section: 21 CFR 866.3365 - Multiplex Nucleic Acid Assay for Identification of Microorganisms and Resistance Markers from Positive Blood Cultures 2. Classification: Class II 3. Product codes: PAM, PEN, PEO 4. Panel: 83 (Microbiology) H. Intended Use: 1. Intended use(s): The GenMark ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a qualitative nucleic acid multiplex in vitro diagnostic test intended for use on GenMark’s ePlex Instrument for simultaneous qualitative detection and identification of multiple potentially pathogenic gram-positive bacterial organisms and select determinants associated with antimicrobial resistance in positive blood culture.
    [Show full text]