1
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Stammnitz MR, Gori K, Murchison EP. No evidence that a transmissible cancer has shifted from emergence to endemism in Tasmanian devils. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231875. [PMID: 38633353 PMCID: PMC11022658 DOI: 10.1098/rsos.231875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024]
Abstract
Tasmanian devils are endangered by a transmissible cancer known as Tasmanian devil facial tumour 1 (DFT1). A 2020 study by Patton et al. (Science 370, eabb9772 (doi:10.1126/science.abb9772)) used genome data from DFT1 tumours to produce a dated phylogenetic tree for this transmissible cancer lineage, and thence, using phylodynamics models, to estimate its epidemiological parameters and predict its future trajectory. It concluded that the effective reproduction number for DFT1 had declined to a value of one, and that the disease had shifted from emergence to endemism. We show that the study is based on erroneous mutation calls and flawed methodology, and that its conclusions cannot be substantiated.
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Affiliation(s)
- Maximilian R. Stammnitz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Elizabeth P. Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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2
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Sanderson H, White AP. Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella. Methods Mol Biol 2024; 2813:19-37. [PMID: 38888768 DOI: 10.1007/978-1-0716-3890-3_2] [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] [Indexed: 06/20/2024]
Abstract
Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.
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Affiliation(s)
- Haley Sanderson
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
- Biological Informatics Center of Excellence, Agriculture and Agri-Food Canada, Saskatoon, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
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3
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Li M, Li J, Kang L, Gong C, Luo M, Wang X, Guan X, Tong Y, Huang F. Genome sequencing reveals molecular epidemiological characteristics and new recombinations of adenovirus in Beijing, China, 2014-2019. J Med Virol 2023; 95:e29284. [PMID: 38087446 DOI: 10.1002/jmv.29284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/13/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023]
Abstract
To investigate the molecular epidemiological characteristics and genetic variations of human adenovirus (HAdV) in acute respiratory tract infections in Beijing. Whole-genome sequencing and phylogenetic analyses were performed for 83 strains of HAdV with different types in Beijing from 2014 to 2019. The clinical characteristics of HAdV infection were analyzed statistically. HAdV-B was divided into four genotypes, including B3 (n = 11), B7 (n = 13), B14 (n = 4), and B55 (n = 2). HAdV-C was divided into three genotypes, including C1 (n = 14), C2 (n = 13), and C5 (n = 10). In HAdV-C, nine recombinant adenovirus strains were identified in type 1, and seven recombinant strains were found in type 2. In type 1, we found three newly emerged intraspecific recombinant strains (A47, A48, and A52) collected in 2017, 2018, and 2019, respectively. In addition, the previously reported recombinant strains of HAdV-C1 showed more severe disease than other strains of HAdV-C, causing severe community-acquired pneumonia in both the elderly and children. Continuous population-wide molecular epidemiological surveillance of HAdV is essential for the prevention and control of respiratory infectious diseases.
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Affiliation(s)
- Maozhong Li
- Beijing Center for Disease Control and Prevention/Beijing Academy for Preventive Medicine/Beijing Institute of Tuberculosis Control Research and Prevention, Institute for immunization and prevention, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Jing Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lu Kang
- Beijing Center for Disease Control and Prevention/Beijing Academy for Preventive Medicine/Beijing Institute of Tuberculosis Control Research and Prevention, Institute for immunization and prevention, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Cheng Gong
- Beijing Center for Disease Control and Prevention/Beijing Academy for Preventive Medicine/Beijing Institute of Tuberculosis Control Research and Prevention, Institute for immunization and prevention, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
| | - Ming Luo
- Beijing Center for Disease Control and Prevention/Beijing Academy for Preventive Medicine/Beijing Institute of Tuberculosis Control Research and Prevention, Institute for immunization and prevention, Beijing, China
| | - Xue Wang
- Beijing Center for Disease Control and Prevention/Beijing Academy for Preventive Medicine/Beijing Institute of Tuberculosis Control Research and Prevention, Institute for immunization and prevention, Beijing, China
| | - Xuejiao Guan
- Beijing Center for Disease Control and Prevention/Beijing Academy for Preventive Medicine/Beijing Institute of Tuberculosis Control Research and Prevention, Institute for immunization and prevention, Beijing, China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Fang Huang
- Beijing Center for Disease Control and Prevention/Beijing Academy for Preventive Medicine/Beijing Institute of Tuberculosis Control Research and Prevention, Institute for immunization and prevention, Beijing, China
- Beijing Research Center for Respiratory Infectious Diseases, Beijing, China
- College of Public Health, Capital Medical University, Beijing, China
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4
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Jang H, Eshwar A, Lehner A, Gangiredla J, Patel IR, Beaubrun JJG, Chase HR, Negrete F, Finkelstein S, Weinstein LM, Ko K, Addy N, Ewing L, Woo J, Lee Y, Seo K, Jaradat Z, Srikumar S, Fanning S, Stephan R, Tall BD, Gopinath GR. Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. Microorganisms 2022; 10:microorganisms10071396. [PMID: 35889115 PMCID: PMC9319161 DOI: 10.3390/microorganisms10071396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.
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Affiliation(s)
- Hyein Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Athmanya Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Isha R. Patel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Junia Jean-Gilles Beaubrun
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Hannah R. Chase
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Flavia Negrete
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Samantha Finkelstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Leah M. Weinstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Katie Ko
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Nicole Addy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Laura Ewing
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Jungha Woo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Youyoung Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Kunho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Ziad Jaradat
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Shabarinath Srikumar
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
| | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
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5
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Perez-Sepulveda BM, Heavens D, Pulford CV, Predeus AV, Low R, Webster H, Dykes GF, Schudoma C, Rowe W, Lipscombe J, Watkins C, Kumwenda B, Shearer N, Costigan K, Baker KS, Feasey NA, Hinton JCD, Hall N. An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. Genome Biol 2021; 22:349. [PMID: 34930397 PMCID: PMC8690886 DOI: 10.1186/s13059-021-02536-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. Following the optimization of a logistics pipeline that involved shipping isolates as thermolysates in ambient conditions, the project assembled a diverse collection of 10,419 isolates from low- and middle-income countries. The genomes were sequenced using the LITE pipeline for library construction, with a total reagent cost of less than USD$10 per genome. Our method can be applied to other large bacterial collections to underpin global collaborations.
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Affiliation(s)
| | | | - Caisey V. Pulford
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Alexander V. Predeus
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Ross Low
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Hermione Webster
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Gregory F. Dykes
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - Will Rowe
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
- University of Birmingham, Birmingham, UK
| | | | - Chris Watkins
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Neil Shearer
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Karl Costigan
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kate S. Baker
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Nicholas A. Feasey
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK
- Malawi-Liverpool-Wellcome Programme, Blantyre, Malawi
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Neil Hall
- Earlham Institute, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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6
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Mortensen K, Lam TJ, Ye Y. Comparison of CRISPR-Cas Immune Systems in Healthcare-Related Pathogens. Front Microbiol 2021; 12:758782. [PMID: 34759910 PMCID: PMC8573248 DOI: 10.3389/fmicb.2021.758782] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and Clostridium difficile have been identified as the leading global cause of multidrug-resistant bacterial infections in hospitals. CRISPR-Cas systems are bacterial immune systems, empowering the bacteria with defense against invasive mobile genetic elements that may carry the antimicrobial resistance (AMR) genes, among others. On the other hand, the CRISPR-Cas systems are themselves mobile. In this study, we annotated and compared the CRISPR-Cas systems in these pathogens, utilizing their publicly available large numbers of sequenced genomes (e.g., there are more than 12 thousands of S. aureus genomes). The presence of CRISPR-Cas systems showed a very broad spectrum in these pathogens: S. aureus has the least tendency of obtaining the CRISPR-Cas systems with only 0.55% of its isolates containing CRISPR-Cas systems, whereas isolates of C. difficile we analyzed have CRISPR-Cas systems each having multiple CRISPRs. Statistical tests show that CRISPR-Cas containing isolates tend to have more AMRs for four of the pathogens (A. baumannii, E. faecium, P. aeruginosa, and S. aureus). We made available all the annotated CRISPR-Cas systems in these pathogens with visualization at a website (https://omics.informatics.indiana.edu/CRISPRone/pathogen), which we believe will be an important resource for studying the pathogens and their arms-race with invaders mediated through the CRISPR-Cas systems, and for developing potential clinical applications of the CRISPR-Cas systems for battles against the antibiotic resistant pathogens.
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Affiliation(s)
- Kate Mortensen
- Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, United States
| | - Tony J Lam
- Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, United States
| | - Yuzhen Ye
- Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, United States
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7
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In vivo evolution of an emerging zoonotic bacterial pathogen in an immunocompromised human host. Nat Commun 2021; 12:4495. [PMID: 34301946 PMCID: PMC8302680 DOI: 10.1038/s41467-021-24668-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/24/2021] [Indexed: 11/08/2022] Open
Abstract
Zoonotic transfer of animal pathogens to human hosts can generate novel agents, but the genetic events following such host jumps are not well studied. Here we characterize the mechanisms driving adaptive evolution of the emerging zoonotic pathogen Bordetella hinzii in a patient with interleukin-12 receptor β1 deficiency. Genomic sequencing of 24 B. hinzii isolates cultured from blood and stool over 45 months revealed a clonal lineage that had undergone extensive within-host genetic and phenotypic diversification. Twenty of 24 isolates shared an E9G substitution in the DNA polymerase III ε-subunit active site, resulting in a proofreading deficiency. Within this proofreading-deficient clade, multiple lineages with mutations in DNA repair genes and altered mutational spectra emerged and dominated clinical cultures for more than 12 months. Multiple enzymes of the tricarboxylic acid cycle and gluconeogenesis pathways were repeatedly mutated, suggesting rapid metabolic adaptation to the human environment. Furthermore, an excess of G:C > T:A transversions suggested that oxidative stress shaped genetic diversification during adaptation. We propose that inactivation of DNA proofreading activity in combination with prolonged, but sub-lethal, oxidative attack resulting from the underlying host immunodeficiency facilitated rapid genomic adaptation. These findings suggest a fundamental role for host immune phenotype in shaping pathogen evolution following zoonotic infection. Bordetella hinzii is an emerging pathogen with zoonotic risk to humans, known to be able to cause respiratory tract infection, bacteremia and endocarditis. Here, applying whole genome sequencing to bacterial isolates, the authors characterize the mechanisms driving adaptive evolution in B. hinzii in a patient with interleukin-12 receptor β1 deficiency, suggesting a role for host immune phenotype in shaping within-host pathogen evolution following zoonotic infection.
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8
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Valiente-Mullor C, Beamud B, Ansari I, Francés-Cuesta C, García-González N, Mejía L, Ruiz-Hueso P, González-Candelas F. One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads. PLoS Comput Biol 2021; 17:e1008678. [PMID: 33503026 PMCID: PMC7870062 DOI: 10.1371/journal.pcbi.1008678] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 02/08/2021] [Accepted: 01/05/2021] [Indexed: 12/17/2022] Open
Abstract
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species were selected as reference sequences, and read alignment statistics, SNP calling, recombination rates, dN/dS ratios, and phylogenetic trees were evaluated depending on the mapping reference. The choice of different reference genomes proved to have an impact on almost all the parameters considered in the five species. In addition, these biases had potential epidemiological implications such as including/excluding isolates of particular clades and the estimation of genetic distances. These findings suggest that the single reference approach might introduce systematic errors during mapping that affect subsequent analyses, particularly for data sets with isolates from genetically diverse backgrounds. In any case, exploring the effects of different references on the final conclusions is highly recommended. Mapping consists in the alignment of reads (i.e., DNA fragments) obtained through high-throughput genome sequencing to a previously assembled reference sequence. It is a common practice in genomic studies to use a single reference for mapping, usually the ‘reference genome’ of a species—a high-quality assembly. However, the selection of an optimal reference is hindered by intrinsic intra-species genetic variability, particularly in bacteria. It is known that genetic differences between the reference genome and the read sequences may produce incorrect alignments during mapping. Eventually, these errors could lead to misidentification of variants and biased reconstruction of phylogenetic trees (which reflect ancestry between different bacterial lineages). To our knowledge, this is the first work to systematically examine the effect of different references for mapping on the inference of tree topology as well as the impact on recombination and natural selection inferences. Furthermore, the novelty of this work relies on a procedure that guarantees that we are evaluating only the effect of the reference. This effect has proved to be pervasive in the five bacterial species that we have studied and, in some cases, alterations in phylogenetic trees could lead to incorrect epidemiological inferences. Hence, the use of different reference genomes may be prescriptive to assess the potential biases of mapping.
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Affiliation(s)
- Carlos Valiente-Mullor
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Beatriz Beamud
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- * E-mail: (BB); (FG-C)
| | - Iván Ansari
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Carlos Francés-Cuesta
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Neris García-González
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Lorena Mejía
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Paula Ruiz-Hueso
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
| | - Fernando González-Candelas
- Joint Research Unit “Infection and Public Health” FISABIO-University of Valencia, Institute for Integrative Systems Biology (I2SysBio), Valencia, Spain
- CIBER in Epidemiology and Public Health, Valencia, Spain
- * E-mail: (BB); (FG-C)
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9
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Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap. BMJ Glob Health 2020; 5:e002244. [PMID: 33239336 PMCID: PMC7689591 DOI: 10.1136/bmjgh-2019-002244] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/26/2022] Open
Abstract
The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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11
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Vijayakumar S, Wattal C, J K O, Bhattacharya S, Vasudevan K, Anandan S, Walia K, Veeraraghavan B. Insights into the complete genomes of carbapenem-resistant Acinetobacter baumannii harbouring bla OXA-23, bla OXA-420 and bla NDM-1 genes using a hybrid-assembly approach. Access Microbiol 2020; 2:acmi000140. [PMID: 32974602 PMCID: PMC7497828 DOI: 10.1099/acmi.0.000140] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/10/2020] [Indexed: 12/20/2022] Open
Abstract
Carbapenem resistance in Acinetobacter baumannii is due to blaOXA-23, which is endemic in India. Recently, the sporadic presence of blaOXA-58 as well as the occurrence of dual carbapenemases were observed. The mobility as well as the dissemination of these resistance genes were mainly mediated by various mobile genetic elements. The present study was aimed at characterizing the genetic arrangement of blaOXA-23, blaNDM-1 and blaOXA-58 identified in two complete genomes of carbapenem-resistant A. baumannii (CRAB). Complete genomes obtained using a hybrid-assembly approach revealed the accurate arrangement of Tn2006 with blaOXA-23, ISAba125 with blaNDM and ISAba3 with blaOXA-58. In addition, the association of IntI1 integrase with the blaCARB-2 gene and several virulence factors required for type-IV pili assembly, motility and biofilm formation have been identified. The current study provided deeper insight into the complete characterization of insertion sequences and transposons associated with the carbapenem-resistant genes using short reads of IonTorrent PGM and long reads of MinIon in A. baumannii.
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Affiliation(s)
| | | | - Oberoi J K
- Sir Ganga Ram Hospital, New Delhi, India
| | | | | | | | - Kamini Walia
- Indian Council of Medical Research, New Delhi, India
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12
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Hurtado R, Maturrano L, Azevedo V, Aburjaile F. Pathogenomics insights for understanding Pasteurella multocida adaptation. Int J Med Microbiol 2020; 310:151417. [PMID: 32276876 DOI: 10.1016/j.ijmm.2020.151417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/01/2020] [Accepted: 03/19/2020] [Indexed: 12/16/2022] Open
Abstract
Pasteurella multocida is an important veterinary pathogen able to infect a wide range of animals in a broad spectrum of diseases. P. multocida is a complex microorganism in relation to its genomic flexibility, host adaptation and pathogenesis. Epidemiological analysis based on multilocus sequence typing, serotyping, genotyping, association with virulence genes and single nucleotide polymorphisms (SNPs), enables assessment of intraspecies diversity, phylogenetic and strain-specific relationships associated with host predilection or disease. A high number of sequenced genomes provides us a more accurate genomic and epidemiological interpretation to determine whether certain lineages can infect a host or produce disease. Comparative genomic analysis and pan-genomic approaches have revealed a flexible genome for hosting mobile genetic elements (MGEs) and therefore significant variation in gene content. Moreover, it was possible to find lineage-specific MGEs from the same niche, showing acquisition probably due to an evolutionary convergence event or to a genetic group with infective capacity. Furthermore, diversification selection analysis exhibits proteins exposed on the surface subject to selection pressures with an interstrain heterogeneity related to their ability to adapt. This article is the first review describing the genomic relationship to elucidate the diversity and evolution of P. multocida.
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Affiliation(s)
- Raquel Hurtado
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil; Laboratory of Molecular Biology and Genetics, Veterinary Medicine Faculty, San Marcos University, Lima, Peru
| | - Lenin Maturrano
- Laboratory of Molecular Biology and Genetics, Veterinary Medicine Faculty, San Marcos University, Lima, Peru
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil
| | - Flávia Aburjaile
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Minas Gerais, Brazil; Laboratory of Plant Genetics and Biotechnology, Federal University of Pernambuco, Recife, 50670-901, Pernambuco, Brazil.
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13
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Goig GA, Blanco S, Garcia-Basteiro AL, Comas I. Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability. BMC Biol 2020; 18:24. [PMID: 32122347 PMCID: PMC7053099 DOI: 10.1186/s12915-020-0748-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/11/2020] [Indexed: 12/16/2022] Open
Abstract
Background Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data commonly do not account for errors potentially introduced by contamination, which could lead to the wrong assessment of allele frequency both in basic and clinical research. Results We used a taxonomic filter to remove contaminant reads from more than 4000 bacterial samples from 20 different studies and performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS. We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines. Conclusion As sequencing technologies consolidate as precision tools that are increasingly adopted in the research and clinical context, our results urge for the implementation of contamination-aware analysis pipelines. Taxonomic classifiers are a powerful tool to implement such pipelines.
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Affiliation(s)
- Galo A Goig
- Institute of Biomedicine of Valencia, IBV-CSIC, St. Jaume Roig 11, 46010, Valencia, Spain.
| | - Silvia Blanco
- Centro de Investigaçao em Saúde de Manhiça (CISM), Bairro Cambeve, Rua 12, Distrito da Manhiça, 1929, Maputo, Mozambique
| | - Alberto L Garcia-Basteiro
- Centro de Investigaçao em Saúde de Manhiça (CISM), Bairro Cambeve, Rua 12, Distrito da Manhiça, 1929, Maputo, Mozambique.,ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Iñaki Comas
- Institute of Biomedicine of Valencia, IBV-CSIC, St. Jaume Roig 11, 46010, Valencia, Spain.,CIBER in Epidemiology and Public Health, Madrid, Spain
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Rubio-Gómez JM, Santiago CM, Udaondo Z, Garitaonaindia MT, Krell T, Ramos JL, Daddaoua A. Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide. Front Microbiol 2020; 11:202. [PMID: 32153524 PMCID: PMC7044273 DOI: 10.3389/fmicb.2020.00202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 01/28/2020] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas aeruginosa is an ubiquitous gram-negative opportunistic human pathogen which is not considered part of the human commensal gut microbiota. However, depletion of the intestinal microbiota (Dysbiosis) following antibiotic treatment facilitates the colonization of the intestinal tract by Multidrug-Resistant P. aeruginosa. One possible strategy is based on the use of functional foods with prebiotic activity. The bifidogenic effect of the prebiotic inulin and its hydrolyzed form (fructooligosaccharide: FOS) is well established since they promote the growth of specific beneficial (probiotic) gut bacteria such as bifidobacteria. Previous studies of the opportunistic nosocomial pathogen Pseudomonas aeruginosa PAO1 have shown that inulin and to a greater extent FOS reduce growth and biofilm formation, which was found to be due to a decrease in motility and exotoxin secretion. However, the transcriptional basis for these phenotypic alterations remains unclear. To address this question we conducted RNA-sequence analysis. Changes in the transcript level induced by inulin and FOS were similar, but a set of transcript levels were increased in response to inulin and reduced in the presence of FOS. In the presence of inulin or FOS, 260 and 217 transcript levels, respectively, were altered compared to the control to which no polysaccharide was added. Importantly, changes in transcript levels of 57 and 83 genes were found to be specific for either inulin or FOS, respectively, indicating that both compounds trigger different changes. Gene pathway analyses of differentially expressed genes (DEG) revealed a specific FOS-mediated reduction in transcript levels of genes that participate in several canonical pathways involved in metabolism and growth, motility, biofilm formation, β-lactamase resistance, and in the modulation of type III and VI secretion systems; results that have been partially verified by real time quantitative PCR measurements. Moreover, we have identified a genomic island formed by a cluster of 15 genes, encoding uncharacterized proteins, which were repressed in the presence of FOS. The analysis of isogenic mutants has shown that genes of this genomic island encode proteins involved in growth, biofilm formation and motility. These results indicate that FOS selectively modulates bacterial pathogenicity by interfering with different signaling pathways.
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Affiliation(s)
- José Manuel Rubio-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Department of Pharmacology, School of Pharmacy, University of Granada, Granada, Spain
| | - Carlos Molina Santiago
- Department of Microbiology, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", University of Málaga, Málaga, Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Mireia Tena Garitaonaindia
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Juan-Luis Ramos
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Abdelali Daddaoua
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
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Thongratsakul S, Usui M, Higuchi H, Takahashi T, Sato T, Poolkhet C, Tamura Y. Prevalence and characterization of Staphylococcus aureus isolated in raw milk from cows in Hokkaido, Japan. Trop Anim Health Prod 2019; 52:1631-1637. [PMID: 31845117 DOI: 10.1007/s11250-019-02169-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/01/2019] [Indexed: 11/28/2022]
Abstract
The aim of this study was to characterize the phenotypes and genotypes of Staphylococcus aureus isolated from raw bovine milk in Hokkaido, Japan. S. aureus isolates were identified in 135 of 436 milk samples from cows with and without signs of mastitis from three farms in Hokkaido. These clinical isolates were characterized for antimicrobial susceptibility patterns, molecular typing using phage-open-reading frame typing (POT), coagulase gene type, virulence genes, and biofilm-associated genes and were evaluated for biofilm-forming ability. Most isolates were susceptible to the antimicrobial agents tested. The highest rate of resistance was to ampicillin. Molecular typing of all S. aureus isolates indicated a predominance of coagulase type VI and 0-17-34 POT type, and virulence genes were highly prevalent in the isolates from all farms. Moreover, a high percentage of the 0-17-34 POT type isolates showed extensive formation of biofilm. These findings will help veterinarians and farmers to understand the epidemiology of S. aureus so that they can monitor the transmission and spread of this pathogen and control it more effectively.
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Affiliation(s)
- Sukanya Thongratsakul
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand.
| | - Masaru Usui
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Hidetoshi Higuchi
- Laboratory of Animal Health, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Toshihiko Takahashi
- Livestock Hygiene, Department of Sustainable Agriculture, College of Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Tomomi Sato
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Chaithep Poolkhet
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Yutaka Tamura
- Laboratory of Food Microbiology and Food Safety, Department of Health and Environmental Sciences, School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
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Bouso JM, Planet PJ. Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing. BMC Genomics 2019; 20:793. [PMID: 31666009 PMCID: PMC6822416 DOI: 10.1186/s12864-019-6134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques provide new opportunities to sequence and construct complete bacterial genomes faster and at a lower cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to its slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps. Results Our DNA extraction method was compared to 6 other methods with variations in timing of mechanical disruption and enzymatic digestion of the cell wall, quantity of matrix material, and reagents used in extraction and precipitation. We tested our optimized method on 38 clinical isolates from the M. avium and M. abscessus complexes, which yielded optimal quality and quantity measurements for Oxford Nanopore Technologies sequencing. We also present the efficient completion of circularized M. avium subspecies hominissuis genomes using our extraction technique and the long-read sequencing MinION platform, including the identification of a novel plasmid. Conclusions Our optimized extraction protocol and assembly pipeline was both sufficient and efficient for genome closure. We expect that our finely-tuned extraction method will prove to be a valuable tool in long-read sequencing and completion of mycobacterial genomes going forward. Utilization of comprehensive, long-read based approaches will advance the understanding evolution and pathogenicity of NTM infections.
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Affiliation(s)
- Jennifer M Bouso
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Planet
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
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17
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Molecular Epidemiology of Xanthomonas perforans Outbreaks in Tomato Plants from Transplant to Field as Determined by Single-Nucleotide Polymorphism Analysis. Appl Environ Microbiol 2019; 85:AEM.01220-19. [PMID: 31253682 DOI: 10.1128/aem.01220-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/25/2019] [Indexed: 01/15/2023] Open
Abstract
Outbreaks of bacterial spot on tomato (BST) caused by Xanthomonas perforans are a major concern for sustainable crop production. BST is a common occurrence in tomato transplants grown for field production. We hypothesized that BST outbreaks in commercial fields originate from X. perforans strains inadvertently introduced from commercial transplant facilities. To test this hypothesis, we used a genome-wide single-nucleotide polymorphism (SNP) analysis to characterize X. perforans strains recovered from tomato transplant facilities and fields in commercial production areas. X. perforans strains were isolated from symptomatic transplants prior to roguing at two commercial transplant growers. Then, the same groups of transplants were tracked to commercial fields to recover X. perforans strains from diseased plants prior to harvest. Whole-genome sequencing was carried out on 84 strains isolated from transplant and field plants from Florida and South Carolina. SNPs were called using three reference strains that represented the genetic variation of the sampled strains. Field strains showing genetic similarity to transplant strains had a difference of 2 to 210 SNPs. Transplant and field strains clustered together by grower within each phylogenomic group, consistent with expectations. The range of genetic divergence among strains isolated from field plants was similar to the range obtained from strains on transplants. Using the range of genetic variation observed in transplants, we estimate that 60% to 100% of field strains were an extension of the transplant strain population. Our results stress the importance of BST management to reduce X. perforans movement from transplant to field and to minimize subsequent disease outbreaks.IMPORTANCE Current management of Xanthomonas perforans on tomato plants mainly relies on the frequent application of pesticides. However, the lack of effective pesticides and the development of strain tolerance to certain bactericides limit the ability to control outbreaks in production fields. Better knowledge of probable sources of X. perforans inoculum during tomato production is required to refine management strategies. Tomato plants are typically established in the field using transplants. This study aimed to determine if strains from field epidemics were coming from transplant facilities or resulted from local field outbreaks. The overall goal was to identify potential sources of inoculum and subsequently develop strategies to reduce carryover from transplant production to the field. Our results indicate that tomato producers should shift disease management efforts to transplant facilities to reduce disease in the field. Improved transplant health should reduce the likelihood of bacterial spot outbreaks and subsequently reduce pesticide usage in the field.
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Manolio TA, Rowley R, Williams MS, Roden D, Ginsburg GS, Bult C, Chisholm RL, Deverka PA, McLeod HL, Mensah GA, Relling MV, Rodriguez LL, Tamburro C, Green ED. Opportunities, resources, and techniques for implementing genomics in clinical care. Lancet 2019; 394:511-520. [PMID: 31395439 PMCID: PMC6699751 DOI: 10.1016/s0140-6736(19)31140-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/09/2019] [Accepted: 05/03/2019] [Indexed: 12/19/2022]
Abstract
Advances in technologies for assessing genomic variation and an increasing understanding of the effects of genomic variants on health and disease are driving the transition of genomics from the research laboratory into clinical care. Genomic medicine, or the use of an individual's genomic information as part of their clinical care, is increasingly gaining acceptance in routine practice, including in assessing disease risk in individuals and their families, diagnosing rare and undiagnosed diseases, and improving drug safety and efficacy. We describe the major types and measurement tools of genomic variation that are currently of clinical importance, review approaches to interpreting genomic sequence variants, identify publicly available tools and resources for genomic test interpretation, and discuss several key barriers in using genomic information in routine clinical practice.
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Affiliation(s)
- Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Dan Roden
- Department of Medicine, Department of Pharmacology, and Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomic and Precision Medicine, Duke University, Durham, NC, USA
| | - Carol Bult
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Rex L Chisholm
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary V Relling
- Pharmaceutical Sciences Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laura Lyman Rodriguez
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cecelia Tamburro
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eric D Green
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Mottram L, Chakraborty S, Cox E, Fleckenstein J. How genomics can be used to understand host susceptibility to enteric infection, aiding in the development of vaccines and immunotherapeutic interventions. Vaccine 2019; 37:4805-4810. [PMID: 30709726 PMCID: PMC6663652 DOI: 10.1016/j.vaccine.2019.01.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/26/2018] [Accepted: 01/10/2019] [Indexed: 12/27/2022]
Abstract
Thanks to the modern sequencing era, the extent to which infectious disease imposes selective pressures on the worldwide human population is being revealed. This is aiding our understanding of the underlying immunological and host mechanistic defenses against these pathogens, as well as potentially assisting in the development of vaccines and therapeutics to control them. As a consequence, the workshop "How genomics can be used to understand host susceptibility to enteric infection, aiding in the development of vaccines and immunotherapeutic interventions" at the VASE 2018 meeting, aimed to discuss how genomics and related tools could be used to assist Shigella and ETEC vaccine development. The workshop featured four short presentations which highlighted how genomic applications can be used to assist in the identification of genetic patterns related to the virulence of disease, or host genetic factors that could contribute to immunity or successful vaccine responses. Following the presentations, there was an open debate with workshop attendees to discuss the best ways to utilise such genomic studies, to improve or accelerate the process of both Shigella and ETEC vaccine development. The workshop concluded by making specific recommendations on how genomic research methods could be strengthened and harmonised within the ETEC and Shigella research communities.
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Affiliation(s)
- Lynda Mottram
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Eric Cox
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - James Fleckenstein
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, United States; Medicine Service, Veterans Affairs Medical Center, St. Louis, MO, United States
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Microbial evolutionary medicine: from theory to clinical practice. THE LANCET. INFECTIOUS DISEASES 2019; 19:e273-e283. [PMID: 31053492 DOI: 10.1016/s1473-3099(19)30045-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 11/21/2018] [Accepted: 02/04/2019] [Indexed: 12/15/2022]
Abstract
Medicine and clinical microbiology have traditionally attempted to identify and eliminate the agents that cause disease. However, this traditional approach is becoming inadequate for dealing with a changing disease landscape. Major challenges to human health are non-communicable chronic diseases, often driven by altered immunity and inflammation, and communicable infections from agents which harbour antibiotic resistance. This Review focuses on the so-called evolutionary medicine framework, to study how microbial communities influence human health. The evolutionary medicine framework aims to predict and manipulate microbial effects on human health by integrating ecology, evolutionary biology, microbiology, bioinformatics, and clinical expertise. We focus on the potential of evolutionary medicine to address three key challenges: detecting microbial transmission, predicting antimicrobial resistance, and understanding microbe-microbe and human-microbe interactions in health and disease, in the context of the microbiome.
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In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World. mSphere 2019; 4:4/2/e00040-19. [PMID: 30944210 PMCID: PMC6449604 DOI: 10.1128/msphere.00040-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE. Elizabethkingia anophelis is an emerging global multidrug-resistant opportunistic pathogen. We assessed the diversity among 13 complete genomes and 23 draft genomes of E. anophelis strains derived from various environmental settings and human infections from different geographic regions around the world from 1950s to the present. Putative integrative and conjugative elements (ICEs) were identified in 31/36 (86.1%) strains in the study. A total of 52 putative ICEs (including eight degenerated elements lacking integrases) were identified and categorized into three types based on the architecture of the conjugation module and the phylogeny of the relaxase, coupling protein, TraG, and TraJ protein sequences. The type II and III ICEs were found to integrate adjacent to tRNA genes, while type I ICEs integrate into intergenic regions or into a gene. The ICEs carry various cargo genes, including transcription regulator genes and genes conferring antibiotic resistance. The adaptive immune CRISPR-Cas system was found in nine strains, including five strains in which CRISPR-Cas machinery and ICEs coexist at different locations on the same chromosome. One ICE-derived spacer was present in the CRISPR locus in one strain. ICE distribution in the strains showed no geographic or temporal patterns. The ICEs in E. anophelis differ in architecture and sequence from CTnDOT, a well-studied ICE prevalent in Bacteroides spp. The categorization of ICEs will facilitate further investigations of the impact of ICE on virulence, genome epidemiology, and adaptive genomics of E. anophelis. IMPORTANCEElizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a large E. anophelis outbreak in Wisconsin in the United States; this ICE has integrated into the mutY gene of the outbreak strain, creating a mutator phenotype. Similar to ICEs found in many bacterial species, ICEs in E. anophelis carry various cargo genes that enable recipients to resist antibiotics and adapt to various ecological niches. The adaptive immune CRISPR-Cas system is present in nine of 36 strains. An ICE-derived spacer was found in the CRISPR locus in a strain that has no ICE, suggesting a past encounter and effective defense against ICE.
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Guglielmini J, Bourhy P, Schiettekatte O, Zinini F, Brisse S, Picardeau M. Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance. PLoS Negl Trop Dis 2019; 13:e0007374. [PMID: 31026256 PMCID: PMC6513109 DOI: 10.1371/journal.pntd.0007374] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 05/13/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus. The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.
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Affiliation(s)
- Julien Guglielmini
- Institut Pasteur, Bioinformatics and Biostatistics Hub, C3BI, USR 3756 IP CNRS, Paris, France
| | - Pascale Bourhy
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Olivier Schiettekatte
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
- Université Paris Diderot, Ecole Doctorale BioSPC, Paris, France
| | - Farida Zinini
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Mathieu Picardeau
- Institut Pasteur, Biology of Spirochetes unit, National Reference Center for Leptospirosis, Paris, France
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Abstract
Inspection of the genomes of bacterial pathogens indicates that their pathogenic potential relies, at least in part, on the activity of different elements that have been acquired by horizontal gene transfer from other (usually unknown) microorganisms. Similarly, in the case of resistance to antibiotics, besides mutation-driven resistance, the incorporation of novel resistance genes is a widespread evolutionary procedure for the acquisition of this phenotype. Current information in the field supports the idea that most (if not all) genes acquired by horizontal gene transfer by bacterial pathogens and contributing to their virulence potential or to antibiotic resistance originate in environmental, not human-pathogenic, microorganisms. Herein I discuss the potential functions that the genes that are dubbed virulence or antibiotic resistance genes may have in their original hosts in nonclinical, natural ecosystems. In addition, I discuss the potential bottlenecks modulating the transfer of virulence and antibiotic resistance determinants and the consequences in terms of speciation of acquiring one or another of both categories of genes. Finally, I propose that exaptation, a process by which a change of function is achieved by a change of habitat and not by changes in the element with the new functionality, is the basis of the evolution of virulence determinants and of antibiotic resistance genes.
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Branchu P, Bawn M, Kingsley RA. Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants. Infect Immun 2018; 86:e00079-18. [PMID: 29784861 PMCID: PMC6056856 DOI: 10.1128/iai.00079-18] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of nontyphoidal Salmonella (NTS) infections, accounting for a quarter of infections, second only to S. enterica serovar Enteritidis in incidence. S Typhimurium was once considered the archetypal broad-host-range Salmonella serovar due to its wide distribution in livestock and wild animals, and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, and ATCC 14028). But it has become clear that these strains do not reflect the genotypic or phenotypic diversity of S Typhimurium. Here, we review the epidemiological record of S Typhimurium and studies of the host-pathogen interactions of diverse strains of S Typhimurium. We present the concept of distinct pathovariants of S Typhimurium that exhibit diversity of host range, distribution in the environment, pathogenicity, and risk to food safety. We review recent evidence from whole-genome sequencing that has revealed the extent of genomic diversity of S Typhimurium pathovariants, the genomic basis of differences in the level of risk to human and animal health, and the molecular epidemiology of prominent strains. An improved understanding of the impact of genome variation of bacterial pathogens on pathogen-host and pathogen-environment interactions has the potential to improve quantitative risk assessment and reveal how new pathogens evolve.
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Affiliation(s)
- Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
- Earlham Institute, Norwich Research Park, Colney, Norwich, United Kingdom
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Colney, Norwich, United Kingdom
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Human Genomic Loci Important in Common Infectious Diseases: Role of High-Throughput Sequencing and Genome-Wide Association Studies. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2018; 2018:1875217. [PMID: 29755620 PMCID: PMC5884297 DOI: 10.1155/2018/1875217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 03/07/2018] [Indexed: 12/27/2022]
Abstract
HIV/AIDS, tuberculosis (TB), and malaria are 3 major global public health threats that undermine development in many resource-poor settings. Recently, the notion that positive selection during epidemics or longer periods of exposure to common infectious diseases may have had a major effect in modifying the constitution of the human genome is being interrogated at a large scale in many populations around the world. This positive selection from infectious diseases increases power to detect associations in genome-wide association studies (GWASs). High-throughput sequencing (HTS) has transformed both the management of infectious diseases and continues to enable large-scale functional characterization of host resistance/susceptibility alleles and loci; a paradigm shift from single candidate gene studies. Application of genome sequencing technologies and genomics has enabled us to interrogate the host-pathogen interface for improving human health. Human populations are constantly locked in evolutionary arms races with pathogens; therefore, identification of common infectious disease-associated genomic variants/markers is important in therapeutic, vaccine development, and screening susceptible individuals in a population. This review describes a range of host-pathogen genomic loci that have been associated with disease susceptibility and resistant patterns in the era of HTS. We further highlight potential opportunities for these genetic markers.
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Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis. mBio 2018. [PMID: 29535201 PMCID: PMC5850319 DOI: 10.1128/mbio.02061-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis, the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury were also lost by D. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing. Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome “dark matter,” cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.
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Kulsum U, Kapil A, Singh H, Kaur P. NGSPanPipe: A Pipeline for Pan-genome Identification in Microbial Strains from Experimental Reads. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1052:39-49. [DOI: 10.1007/978-981-10-7572-8_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Nunvar J, Capek V, Fiser K, Fila L, Drevinek P. What matters in chronic Burkholderia cenocepacia infection in cystic fibrosis: Insights from comparative genomics. PLoS Pathog 2017; 13:e1006762. [PMID: 29228063 PMCID: PMC5739508 DOI: 10.1371/journal.ppat.1006762] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/21/2017] [Accepted: 11/19/2017] [Indexed: 01/29/2023] Open
Abstract
Burkholderia cenocepacia causes severe pulmonary infections in cystic fibrosis (CF) patients. Since the bacterium is virtually untreatable by antibiotics, chronic infections persist for years and might develop into fatal septic pneumonia (cepacia syndrome, CS). To devise new strategies to combat chronic B. cenocepacia infections, it is essential to obtain comprehensive knowledge about their pathogenesis. We conducted a comparative genomic analysis of 32 Czech isolates of epidemic clone B. cenocepacia ST32 isolated from various stages of chronic infection in 8 CF patients. High numbers of large-scale deletions were found to occur during chronic infection, affecting preferentially genomic islands and nonessential replicons. Recombination between insertion sequences (IS) was inferred as the mechanism behind deletion formation; the most numerous IS group was specific for the ST32 clone and has undergone transposition burst since its divergence. Genes functionally related to transition metal metabolism were identified as hotspots for deletions and IS insertions. This functional category was also represented among genes where nonsynonymous point mutations and indels occurred parallelly among patients. Another category exhibiting parallel mutations was oxidative stress protection; mutations in catalase KatG resulted in impaired detoxification of hydrogen peroxide. Deep sequencing revealed substantial polymorphism in genes of both categories within the sputum B. cenocepacia ST32 populations, indicating extensive adaptive evolution. Neither oxidative stress response nor transition metal metabolism genes were previously reported to undergo parallel evolution during chronic CF infection. Mutations in katG and copper metabolism genes were overrepresented in patients where chronic infection developed into CS. Among professional phagocytes, macrophages use both hydrogen peroxide and copper for their bactericidal activity; our results thus tentatively point to macrophages as suspects in pathogenesis towards the fatal CS. The large Burkholderia cenocepacia populations which persist in cystic fibrosis lungs during many years of chronic infections have an inherent potential for adaptive evolution. The results provided by comparative genomics are key in understanding the processes involved. Mutational events which have taken place allow us to deductively reconstruct the history of chronic infection and to identify driving forces acting upon the bacteria. Beyond the conventional point mutation analysis of next generation sequencing data, we observed interesting phenomena such as large deletions and transposable element movement which represent another facet of adaptive evolution of B. cenocepacia during chronic infection. We also found, unexpectedly, that adaptive evolution in B. cenocepacia strain ST32 affects a set of genes conspicuously different from related species B. dolosa; these appear to be linked to host immune response. Our study provides clues to the complex puzzle of chronic B. cenocepacia infection establishment, persistence and outcome in cystic fibrosis.
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Affiliation(s)
- Jaroslav Nunvar
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Vaclav Capek
- Bioinformatics Centre, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Karel Fiser
- Department of Paediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Libor Fila
- Department of Pneumology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Pavel Drevinek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
- * E-mail:
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29
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Gao X, Deng L, Stack G, Yu H, Chen X, Naito-Matsui Y, Varki A, Galán JE. Evolution of host adaptation in the Salmonella typhoid toxin. Nat Microbiol 2017; 2:1592-1599. [PMID: 28993610 PMCID: PMC5705260 DOI: 10.1038/s41564-017-0033-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 08/23/2017] [Indexed: 12/03/2022]
Abstract
The evolution of virulence traits is central for the emergence or re-emergence of microbial pathogens and for their adaptation to a specific host 1-5 . Typhoid toxin is an essential virulence factor of the human-adapted bacterial pathogen Salmonella Typhi 6,7 , the cause of typhoid fever in humans 8-12 . Typhoid toxin has a unique A2B5 architecture with two covalently linked enzymatic 'A' subunits, PltA and CdtB, associated with a homopentameric 'B' subunit made up of PltB, which has binding specificity for the N-acetylneuraminic acid (Neu5Ac) sialoglycans 6,13 prominently present in humans 14 . Here, we examine the functional and structural relationship between typhoid toxin and ArtAB, an evolutionarily related AB5 toxin encoded by the broad-host Salmonella Typhimurium 15 . We find that ArtA and ArtB, homologues of PltA and PltB, can form a functional complex with the typhoid toxin CdtB subunit after substitution of a single amino acid in ArtA, while ArtB can form a functional complex with wild-type PltA and CdtB. We also found that, after addition of a single-terminal Cys residue, a CdtB homologue from cytolethal distending toxin can form a functional complex with ArtA and ArtB. In line with the broad host specificity of S. Typhimurium, we found that ArtB binds human glycans, terminated in N-acetylneuraminic acid, as well as glycans terminated in N-glycolylneuraminic acid (Neu5Gc), which are expressed in most other mammals 14 . The atomic structure of ArtB bound to its receptor shows the presence of an additional glycan-binding site, which broadens its binding specificity. Despite equivalent toxicity in vitro, we found that the ArtB/PltA/CdtB chimaeric toxin exhibits reduced lethality in an animal model, indicating that the host specialization of typhoid toxin has optimized its targeting mechanisms to the human host. This is a remarkable example of a toxin evolving to broaden its enzymatic activities and adapt to a specific host.
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Affiliation(s)
- Xiang Gao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Lingquan Deng
- Glycobiology Research and Training Center, Departments of Medicine, Pathology and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
- GlycoMimetics, Inc., 9708 Medical Center Drive, Rockville, MD, 20850, USA
| | - Gabrielle Stack
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
| | - Hai Yu
- Department of Chemistry, University of California Davis, Davis, CA, 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California Davis, Davis, CA, 95616, USA
| | - Yuko Naito-Matsui
- Glycobiology Research and Training Center, Departments of Medicine, Pathology and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ajit Varki
- Glycobiology Research and Training Center, Departments of Medicine, Pathology and Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA.
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Nübel U. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics. Curr Top Microbiol Immunol 2017; 398:35-53. [PMID: 27738914 DOI: 10.1007/82_2016_505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.
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Affiliation(s)
- Ulrich Nübel
- DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ, Braunschweig, Germany. .,Technical University Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
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31
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Steglich M, Nübel U. The challenge of detecting indels in bacterial genomes from short-read sequencing data. J Biotechnol 2017; 250:11-15. [PMID: 28267569 DOI: 10.1016/j.jbiotec.2017.02.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/24/2017] [Accepted: 02/26/2017] [Indexed: 10/20/2022]
Abstract
We tested the capabilities of four different software tools to detect insertions and deletions (indels) in a bacterial genome on the basis of short sequencing reads. We included tools applying the gapped-alignment (VarScan, FreeBayes) or split-read (Pindel) methods, respectively, and a combinatorial approach with local de-novo assembly (ScanIndel). Tests were performed with 151-basepair, paired-end sequencing reads simulated from a bacterial (Clostridioides difficile R20291) genome sequence with predefined indels (indel length, 1-2321bp). Results achieved with the different tools varied widely, and the specific sensitivity and false-discovery rates strongly depended on indel size. All tools tested were able to detect short indels (≤29 basepairs) at sensitivities close to 100%, albeit Pindel reported up to 20% false calls. In contrast, gapped-alignment and split-read tools failed to recover large proportions of long indels (>29bp) even at 120-fold coverage, and again, Pindel produced significant numbers of false-positive calls. Outstandingly, ScanIndel detected and reconstructed 97% of long indels on average (95% confidence intervals, 88%-99%) and, at the same time, produced negligible amounts of false calls. Hence, the combinatorial approach implemented in ScanIndel was able to recover the positions, types and sequences of indels with excellent sensitivity and false-discovery rate, by encompassing the full indel length spectrum present in the datasets.
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Affiliation(s)
| | - Ulrich Nübel
- Leibniz Institute DSMZ, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site, Hannover-Braunschweig, Germany
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Genomic changes associated with the evolutionary transition of an insect gut symbiont into a blood-borne pathogen. ISME JOURNAL 2017; 11:1232-1244. [PMID: 28234349 PMCID: PMC5437933 DOI: 10.1038/ismej.2016.201] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/25/2016] [Accepted: 11/30/2016] [Indexed: 12/25/2022]
Abstract
The genus Bartonella comprises facultative intracellular bacteria with a unique lifestyle. After transmission by blood-sucking arthropods they colonize the erythrocytes of mammalian hosts causing acute and chronic infectious diseases. Although the pathogen–host interaction is well understood, little is known about the evolutionary origin of the infection strategy manifested by Bartonella species. Here we analyzed six genomes of Bartonella apis, a honey bee gut symbiont that to date represents the closest relative of pathogenic Bartonella species. Comparative genomics revealed that B. apis encodes a large set of vertically inherited genes for amino acid and cofactor biosynthesis and nitrogen metabolism. Most pathogenic bartonellae have lost these ancestral functions, but acquired specific virulence factors and expanded a vertically inherited gene family for harvesting cofactors from the blood. However, the deeply rooted pathogen Bartonella tamiae has retained many of the ancestral genome characteristics reflecting an evolutionary intermediate state toward a host-restricted intraerythrocytic lifestyle. Our findings suggest that the ancestor of the pathogen Bartonella was a gut symbiont of insects and that the adaptation to blood-feeding insects facilitated colonization of the mammalian bloodstream. This study highlights the importance of comparative genomics among pathogens and non-pathogenic relatives to understand disease emergence within an evolutionary-ecological framework.
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Baltrus DA, McCann HC, Guttman DS. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:152-168. [PMID: 27798954 PMCID: PMC6638251 DOI: 10.1111/mpp.12506] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 05/12/2023]
Abstract
A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
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Affiliation(s)
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey UniversityAuckland 0632New Zealand
| | - David S. Guttman
- Department of Cell and Systems BiologyUniversity of TorontoTorontoON M5S 3B2Canada
- Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoON M5S 3B2Canada
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Guthrie JL, Gardy JL. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis. Ann N Y Acad Sci 2016; 1388:59-77. [PMID: 28009051 DOI: 10.1111/nyas.13273] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/13/2022]
Abstract
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission.
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Affiliation(s)
- Jennifer L Guthrie
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada.,Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
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Tan A, Atack JM, Jennings MP, Seib KL. The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development. Front Immunol 2016; 7:586. [PMID: 28018352 PMCID: PMC5149525 DOI: 10.3389/fimmu.2016.00586] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 11/28/2016] [Indexed: 12/11/2022] Open
Abstract
Infectious diseases are a leading cause of morbidity and mortality worldwide, and vaccines are one of the most successful and cost-effective tools for disease prevention. One of the key considerations for rational vaccine development is the selection of appropriate antigens. Antigens must induce a protective immune response, and this response should be directed to stably expressed antigens so the target microbe can always be recognized by the immune system. Antigens with variable expression, due to environmental signals or phase variation (i.e., high frequency, random switching of expression), are not ideal vaccine candidates because variable expression could lead to immune evasion. Phase variation is often mediated by the presence of highly mutagenic simple tandem DNA repeats, and genes containing such sequences can be easily identified, and their use as vaccine antigens reconsidered. Recent research has identified phase variably expressed DNA methyltransferases that act as global epigenetic regulators. These phase-variable regulons, known as phasevarions, are associated with altered virulence phenotypes and/or expression of vaccine candidates. As such, genes encoding candidate vaccine antigens that have no obvious mechanism of phase variation may be subject to indirect, epigenetic control as part of a phasevarion. Bioinformatic and experimental studies are required to elucidate the distribution and mechanism of action of these DNA methyltransferases, and most importantly, whether they mediate epigenetic regulation of potential and current vaccine candidates. This process is essential to define the stably expressed antigen target profile of bacterial pathogens and thereby facilitate efficient, rational selection of vaccine antigens.
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Affiliation(s)
- Aimee Tan
- Institute for Glycomics, Griffith University , Gold Coast, QLD , Australia
| | - John M Atack
- Institute for Glycomics, Griffith University , Gold Coast, QLD , Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University , Gold Coast, QLD , Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University , Gold Coast, QLD , Australia
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Herfst S, Böhringer M, Karo B, Lawrence P, Lewis NS, Mina MJ, Russell CJ, Steel J, de Swart RL, Menge C. Drivers of airborne human-to-human pathogen transmission. Curr Opin Virol 2016; 22:22-29. [PMID: 27918958 PMCID: PMC7102691 DOI: 10.1016/j.coviro.2016.11.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/11/2016] [Accepted: 11/19/2016] [Indexed: 12/02/2022]
Abstract
Chain of pathogen transmission between individual donor and recipient is modeled. Related pairs of efficient and inefficient ‘airborne’ pathogens are contrasted. Drivers operate on tissue, individual, community, country, and global levels. Pandemic risk is heightened by pathogen evolution and changes in host interaction. Ultimate drivers include socio-economic developments and climate changes.
Airborne pathogens — either transmitted via aerosol or droplets — include a wide variety of highly infectious and dangerous microbes such as variola virus, measles virus, influenza A viruses, Mycobacterium tuberculosis, Streptococcus pneumoniae, and Bordetella pertussis. Emerging zoonotic pathogens, for example, MERS coronavirus, avian influenza viruses, Coxiella, and Francisella, would have pandemic potential were they to acquire efficient human-to-human transmissibility. Here, we synthesize insights from microbiological, medical, social, and economic sciences to provide known mechanisms of aerosolized transmissibility and identify knowledge gaps that limit emergency preparedness plans. In particular, we propose a framework of drivers facilitating human-to-human transmission with the airspace between individuals as an intermediate stage. The model is expected to enhance identification and risk assessment of novel pathogens.
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Affiliation(s)
- Sander Herfst
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands.
| | - Michael Böhringer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany
| | - Basel Karo
- Robert Koch Institut, Department for Infectious Disease Epidemiology, Seestr. 10, 13353 Berlin, Germany; PhD Programme "Epidemiology", Braunschweig-Hannover, Germany
| | - Philip Lawrence
- Université de Lyon, UMRS 449, Laboratoire de Biologie Générale, Université Catholique de Lyon - EPHE, Lyon 69288, France; Molecular Basis of Viral Pathogenicity, International Centre for Research in Infectiology (CIRI), INSERM U1111 - CNRS UMR5308, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon 69007, France
| | - Nicola S Lewis
- Centre for Pathogen Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Michael J Mina
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Charles J Russell
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - John Steel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rik L de Swart
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Christian Menge
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Naumburger Str. 96a, 07743 Jena, Germany
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Point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone of Campylobacter jejuni. Proc Natl Acad Sci U S A 2016; 113:10690-5. [PMID: 27601641 DOI: 10.1073/pnas.1605869113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Infections due to clonal expansion of highly virulent bacterial strains are clear and present threats to human and animal health. Association of genetic changes with disease is now a routine, but identification of causative mutations that enable disease remains difficult. Campylobacter jejuni is an important zoonotic pathogen transmitted to humans mainly via the foodborne route. C. jejuni typically colonizes the gut, but a hypervirulent and rapidly expanding clone of C. jejuni recently emerged, which is able to translocate across the intestinal tract, causing systemic infection and abortion in pregnant animals. The genetic basis responsible for this hypervirulence is unknown. Here, we developed a strategy, termed "directed genome evolution," by using hybridization between abortifacient and nonabortifacient strains followed by selection in an animal disease model and whole-genome sequence analysis. This strategy successfully identified SNPs in porA, encoding the major outer membrane protein, are responsible for the hypervirulence. Defined mutagenesis verified that these mutations were both necessary and sufficient for causing abortion. Furthermore, sequence analysis identified porA as the gene with the top genome-wide signal of adaptive evolution using Fu's Fs, a population genetic metric for recent population size changes, which is consistent with the recent expansion of clone "sheep abortion." These results identify a key virulence factor in Campylobacter and a potential target for the control of this zoonotic pathogen. Furthermore, this study provides general, unbiased experimental and computational approaches that are broadly applicable for efficient elucidation of disease-causing mutations in bacterial pathogens.
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Zhang Y, Wang S, Hu B, Zhao F, Xiang P, Ji D, Chen F, Liu X, Yang F, Wu Y, Kong M, Nan L, Miao Y, Jiang W, Fang Y, Zhang J, Bao Z, Olszewski MA, Zhao H. Direct detection of Helicobacter pylori in biopsy specimens using a high-throughput multiple genetic detection system. Future Microbiol 2016; 11:1521-1534. [PMID: 27599152 DOI: 10.2217/fmb-2016-0149] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM We evaluated the direct high-throughput multiple genetic detection system (dHMGS) for Helicobacter pylori in gastric biopsies. MATERIALS & METHODS One hundred and thirty-three specimens were concurrently analyzed by dHMGS, rapid urease test, culture and sequencing. RESULTS dHMGS was highly sensitive and specific for H. pylori identification compared with culture and rapid urease test. The correlation coefficient of the quantitative standard curve was R2 = 0.983. A significant difference in the relative H. pylori DNA abundance was found in different gastroduodenal diseases. Concordance rates between dHMGS and sequencing for resistance mutations were 97.1, 100.0, 85.3 and 97.1%, respectively. Finally, dHMGS could efficiently distinguish mixed infection in biopsy specimens. CONCLUSION The dHMGS could efficiently diagnose and quantify H. pylori burden in biopsies, simultaneously screening for virulence, antibiotic resistance and presence of the multistrain infections.
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Affiliation(s)
- Yanmei Zhang
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China.,Key Laboratory of Clinical Geriatric Medicine, Shanghai 200040, China.,Research Center on Aging & Medicine, Fudan University, Shanghai 200040, China
| | - Shiwen Wang
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Binjie Hu
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Fuju Zhao
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Ping Xiang
- Department of Endoscopy, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Danian Ji
- Department of Endoscopy, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Fei Chen
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Xiaoli Liu
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Feng Yang
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Yong Wu
- Ningbo HEALTH Gene Technologies Co., Ltd, Ningbo 315000, PR China
| | - Mimi Kong
- Ningbo HEALTH Gene Technologies Co., Ltd, Ningbo 315000, PR China
| | - Li Nan
- Ningbo HEALTH Gene Technologies Co., Ltd, Ningbo 315000, PR China
| | - Yingxin Miao
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Wenrong Jiang
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Yi Fang
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Jinghao Zhang
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Zhijun Bao
- Department of Gastroenterology, Gerontology Institute of Shanghai affiliated to Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China
| | - Michal A Olszewski
- Department of Internal Medicine, Division of Pulmonary & Critical Care Medicine, University of Michigan Medical School & Veterans' Affairs Ann Arbor Health System, Ann Arbor, MI 48105, USA
| | - Hu Zhao
- Department of Laboratory Medicine, Huadong Hospital affiliated to Fudan University, No. 221 Yanan West Road, Shanghai 200040, China.,Key Laboratory of Clinical Geriatric Medicine, Shanghai 200040, China.,Research Center on Aging & Medicine, Fudan University, Shanghai 200040, China
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Narciso-da-Rocha C, Manaia CM. Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 563-564:1-9. [PMID: 27131885 DOI: 10.1016/j.scitotenv.2016.04.062] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/08/2016] [Accepted: 04/08/2016] [Indexed: 06/05/2023]
Abstract
The environment is the original and most ancient source of the antibiotic resistance determinants that threat the human health nowadays. In the environment, water is a privileged habitat and mode of dissemination of bacteria of different origins. Freshwater bodies that cross urban areas are supposed to hold a complex mixture of both human/animal origin and strictly environmental bacteria. In this study, we were interested in unveiling the bacterial diversity in urban river transects and, simultaneously, investigate the occurrence of antibiotic resistant bacteria, in particular the multidrug resistant (MDR). With this aim, water and sediments of two rivers were sampled from an urban transect and the bacterial diversity was assessed based on 16S rRNA gene-based community analysis and, simultaneously, total heterotrophic bacteria were isolated in the presence and in the absence of antibiotics. The three predominant phyla were Proteobacteria, Bacteroidetes and Actinobacteria, in water, or Acidobacteria, in sediments. MDR bacteria were observed to belong to the predominant phyla observed in water, mostly of the classes Gamma- and Betaproteobacteria (Proteobacteria) and Sphingobacteriia and Flavobacteriia (Bacteroidetes) and belonged to genera of ubiquitous (Pseudomonas, Acinetobacter, Stenotrophomonas) or mainly environmental (Chitinophaga, Chryseobacterium) bacteria. The observation that MDR bacteria are widespread in the environment and over distinct phylogenetic lineages has two relevant implications: i) the potential of environmental bacteria as source or facilitators for antibiotic resistance acquisition; ii) the need to complement culture-independent methods with culture-based approaches in order to identify major sources of MDR profiles.
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Affiliation(s)
- Carlos Narciso-da-Rocha
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401, Porto, Portugal
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401, Porto, Portugal.
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40
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Anaplasma marginale: Diversity, Virulence, and Vaccine Landscape through a Genomics Approach. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9032085. [PMID: 27610385 PMCID: PMC5005611 DOI: 10.1155/2016/9032085] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/26/2016] [Indexed: 12/23/2022]
Abstract
In order to understand the genetic diversity of A. marginale, several efforts have been made around the world. This rickettsia affects a significant number of ruminants, causing bovine anaplasmosis, so the interest in its virulence and how it is transmitted have drawn interest not only from a molecular point of view but also, recently, some genomics research have been performed to elucidate genes and proteins with potential as antigens. Unfortunately, so far, we still do not have a recombinant anaplasmosis vaccine. In this review, we present a landscape of the multiple approaches carried out from the genomic perspective to generate valuable information that could be used in a holistic way to finally develop an anaplasmosis vaccine. These approaches include the analysis of the genetic diversity of A. marginale and how this affects control measures for the disease. Anaplasmosis vaccine development is also reviewed from the conventional vaccinomics to genome-base vaccinology approach based on proteomics, metabolomics, and transcriptomics analyses reported. The use of these new omics approaches will undoubtedly reveal new targets of interest in the near future, comprising information of potential antigens and the immunogenic effect of A. marginale proteins.
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41
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Rusconi B, Sanjar F, Koenig SSK, Mammel MK, Tarr PI, Eppinger M. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. Front Microbiol 2016; 7:985. [PMID: 27446025 PMCID: PMC4928038 DOI: 10.3389/fmicb.2016.00985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 06/08/2016] [Indexed: 01/29/2023] Open
Abstract
Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.
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Affiliation(s)
- Brigida Rusconi
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Fatemeh Sanjar
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Sara S K Koenig
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
| | - Mark K Mammel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration Laurel, MD, USA
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine St. Louis, MO, USA
| | - Mark Eppinger
- South Texas Center for Emerging Infectious Diseases, University of Texas at San AntonioSan Antonio, TX, USA; Department of Biology, University of Texas at San AntonioSan Antonio, TX, USA
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Aussel L, Beuzón CR, Cascales E. Meeting report: Adaptation and communication of bacterial pathogens. Virulence 2016; 7:481-90. [PMID: 26890494 DOI: 10.1080/21505594.2016.1152441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacteria usually live in complex environments, sharing niche and resources with other bacterial species, unicellular eukaryotic cells or complex organisms. Thus, they have evolved mechanisms to communicate, to compete and to adapt to changing environment as diverse as human tissues, animals or plants. Understanding the molecular mechanisms underlying these adaptation processes is therefore of primary importance for epidemiology and human health protection, and was the focus of a Current Trends in Biomedicine workshop organized by the International University of Andalucia in late October 2015 in Baeza (Spain). The topic was covered by complementary sessions: (i) interbacterial communication and competition that enable a better access to nutrients or a more efficient colonization of the ecological niche, (ii) adaptation of intracellular pathogens to their host, focusing on metabolic pathways, adaptive mechanisms and populational heterogeneity, and (iii) adaptation of animal and plant pathogens as well as plant-associated bacteria to a plant niche. This workshop emphasized the broad repertoire of mechanisms and factors bacteria have evolved to become efficient pathogens.
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Affiliation(s)
- Laurent Aussel
- a Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université , CNRS - UMR 7257, Marseille Cedex , France
| | - Carmen R Beuzón
- b Departamento de Biología Celular , Genética y Fisiología, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC) , Málaga , Spain
| | - Eric Cascales
- c Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université , CNRS - UMR 7255, Marseille Cedex , France
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Ugolotti E, Larghero P, Vanni I, Bandettini R, Tripodi G, Melioli G, Di Marco E, Raso A, Biassoni R. Whole-genome sequencing as standard practice for the analysis of clonality in outbreaks of meticillin-resistant Staphylococcus aureus in a paediatric setting. J Hosp Infect 2016; 93:375-81. [PMID: 27184087 DOI: 10.1016/j.jhin.2016.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/01/2016] [Indexed: 10/21/2022]
Abstract
Meticillin-resistant Staphylococcus aureus (MRSA) is one of the leading causes of hospital-associated infections. This study investigated the potential use of whole-genome sequencing (WGS) for surveillance purposes by re-examining MRSA strains related to past outbreaks among hospitalized paediatric patients. WGS data ameliorated the genotypic profile previously obtained with Sanger sequencing and pulsed-field gel electrophoresis typing, and discriminated between strains that were related and unrelated to the outbreaks. This allowed strain clonality to be defined with a higher level of resolution than achieved previously. This study demonstrates the potential of WGS to trace hospital outbreaks, which may lead to WGS becoming standard practice in outbreak investigations.
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Affiliation(s)
- E Ugolotti
- Istituto Giannina Gaslini, Genova, Italy
| | - P Larghero
- Istituto Giannina Gaslini, Genova, Italy
| | - I Vanni
- Istituto Giannina Gaslini, Genova, Italy; Lung Cancer Unit, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | | | - G Tripodi
- Istituto Giannina Gaslini, Genova, Italy
| | - G Melioli
- Istituto Giannina Gaslini, Genova, Italy
| | - E Di Marco
- Istituto Giannina Gaslini, Genova, Italy
| | - A Raso
- Istituto Giannina Gaslini, Genova, Italy
| | - R Biassoni
- Istituto Giannina Gaslini, Genova, Italy.
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Molecular Phylogenetics: Concepts for a Newcomer. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:185-196. [DOI: 10.1007/10_2016_49] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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45
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Spratt BG, Anderson RM. Special feature on evolution and genetics in medicine. Proc Biol Sci 2015; 282:20152811. [PMID: 26702049 PMCID: PMC4707767 DOI: 10.1098/rspb.2015.2811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Brian G Spratt
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Roy M Anderson
- Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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