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Taylor AJ, Yahara K, Pascoe B, Ko S, Mageiros L, Mourkas E, Calland JK, Puranen S, Hitchings MD, Jolley KA, Kobras CM, Bayliss S, Williams NJ, van Vliet AHM, Parkhill J, Maiden MCJ, Corander J, Hurst LD, Falush D, Keim P, Didelot X, Kelly DJ, Sheppard SK. Epistasis, core-genome disharmony, and adaptation in recombining bacteria. mBio 2024; 15:e0058124. [PMID: 38683013 PMCID: PMC11237541 DOI: 10.1128/mbio.00581-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and C. coli that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings, indirect evidence of negative epistasis. However, multiple HGT events enable recovery of the genome's co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred, and independently reinstated in a new genetic background-facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.IMPORTANCEGenetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox: 0n one hand, promoting adaptation by conferring novel functionality; on the other, potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyze natural populations of the enteric bacteria Campylobacter, an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in functional networks in a recipient genome. The positive impact of two-gene interactions appears to be adaptive by expanding metabolic capacity and facilitating niche shifts through interspecific hybridization. This challenges conventional ideas and highlights the possibility of multiple-step evolution of multi-gene traits by interspecific introgression.
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Affiliation(s)
- Aidan J Taylor
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ben Pascoe
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Seungwon Ko
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Leonardos Mageiros
- Swansea University Medical School, Institute of Life Science, Swansea, United Kingdom
- The Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | - Jessica K Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Santeri Puranen
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
| | - Matthew D Hitchings
- Swansea University Medical School, Institute of Life Science, Swansea, United Kingdom
| | - Keith A Jolley
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Carolin M Kobras
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sion Bayliss
- Bristol Veterinary School, University of Bristol, Bristol, United Kingdom
| | - Nicola J Williams
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Leahurst Campus, Wirral, United Kingdom
| | | | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Jukka Corander
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Laurence D Hurst
- The Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Daniel Falush
- The Centre for Microbes, Development and Health, Institut Pasteur of Shanghai, Shanghai, China
| | - Paul Keim
- Department of Biology, University of Oxford, Oxford, United Kingdom
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Xavier Didelot
- Department of Statistics, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David J Kelly
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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Michel C, Argudín MDLA, Wautier M, Echahidi F, Prevost B, Vandenberg O, Martiny D, Hallin M. Multiple interspecies recombination events documented by whole-genome sequencing in multidrug-resistant Haemophilus influenzae clinical isolates. Access Microbiol 2024; 6:000649.v3. [PMID: 38482359 PMCID: PMC10928409 DOI: 10.1099/acmi.0.000649.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/22/2023] [Indexed: 04/12/2024] Open
Abstract
Introduction Haemophilus influenzae (Hi) was long known as an easy-to-treat bacterium, but increasing resistance against beta-lactams and other critically important antibiotics is now a growing concern. We describe here the whole-genome sequencing (WGS) analysis of three non-typeable Hi isolates received in 2018-2019 by the Belgian National Reference Centre (NRC) for Haemophilus influenzae, as they presented an unusual multi-resistant profile. Methods All three isolates were sequenced by WGS and mapped to the reference isolate Hi Rd KW20. Shorten uptake signal sequences (USSs) known to be associated with homologous recombination were sought in ftsI, murE and murF genes, and inner partial sequences were compared against the blast nucleotide database to look for similarity with other Haemophilus species. Their antimicrobial resistance (AMR) genotype was studied. Core-genome multilocus sequence typing (MLST) was performed on the NTHi database pubMLST to place our isolates in the actual worldwide epidemiology. Results The isolates also harboured interspecies recombination patterns in the murF-murE-ftsI region involved in cell wall synthesis. The three isolates were multidrug resistant and two of them were also resistant to amoxicillin-clavulanic acid and showed a reduced susceptibility to meropenem. All three isolates belonged to the MLST clonal complex (CC) 422, and WGS revealed that the three were very similar. They harboured mobile genetic elements (carrying blaTEM-1B, mefA and msrD genes associated with resistance), mutations in gyrA and parC linked to fluoroquinolone resistance as well as remodelling events in ompP2 that might be related to lower carbapenem susceptibility. Conclusion The Hi evolution towards antimicrobial multiresistance (AMR) is a complex and poorly understood phenomenon, although probably linked to a large degree to the presence of USSs and exchange within the family Pasteurellaceae. To better understand the respective roles of clonal expansion, horizontal gene transfers, spontaneous mutations and interspecies genetic rearrangements in shaping Hi AMR, both analysis of Hi communities over time within individuals and worldwide monitoring of non-typeable Hi causing infections should be conducted.
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Affiliation(s)
- Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Maria De Los Angeles Argudín
- Department of Molecular Biology, Cliniques Universitaires Saint Luc (CUSL), Avenue Hippocrate 10, 1200, Brussels, Belgium
| | - Magali Wautier
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Pleinlaan 2, 1050 Brussels, Belgium
| | - Benoit Prevost
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Avenue Roosevelt 50, 1050 Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Faculty of Medicine and Pharmacy, Mons University, Chemin du Champ de Mars 37, 7000 Mons, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Belgian National Reference Centre for Haemophilus influenzae, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Rue Haute 322, 1000 Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, Gower Street, London, WC1E 6BT, UK
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Jabeen MF, Sanderson ND, Foster D, Crook DW, Cane JL, Borg C, Connolly C, Thulborn S, Pavord ID, Klenerman P, Street TL, Hinks TSC. Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies. Microbiol Spectr 2022; 10:e0227921. [PMID: 35323032 PMCID: PMC9045196 DOI: 10.1128/spectrum.02279-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
Previous metagenomic studies in asthma have been limited by inadequate sequencing depth for species-level bacterial identification and by heterogeneity in clinical phenotyping. We hypothesize that chronic bacterial airways infection is a key "treatable trait" whose prevalence, clinical phenotype and reliable biomarkers need definition. In this study, we have applied a method for Oxford Nanopore sequencing for the unbiased metagenomic characterization of severe asthma. We optimized methods to compare performance of Illumina MiSeq, Nanopore sequencing, and RT-qPCR on total sputum DNA extracts against culture/MALDI-TOF for analysis of induced sputum samples from highly phenotyped severe asthma during clinical stability. In participants with severe asthma (n = 23) H. influenzae was commonly cultured (n = 8) and identified as the dominant bacterial species by metagenomic sequencing using an optimized method for Illumina MiSeq and Oxford Nanopore. Alongside superior operational characteristics, Oxford Nanopore achieved near complete genome coverage of H. influenzae and demonstrated a high level of agreement with Illumina MiSeq data. Clinically significant infection was confirmed with validated H. influenzae plasmid-based quantitative PCR assay. H. influenzae positive patients were found to have sputum neutrophilia and lower FeNO. In conclusion, using an optimized method of direct sequencing of induced sputum samples, H. influenzae was identified as a clinically relevant pathogen in severe asthma and was identified reliably using metagenomic sequencing. Application of these protocols in ongoing analysis of large patient cohorts will allow full characterization of this clinical phenotype. IMPORTANCE The human airways were once thought sterile in health. Now metagenomic techniques suggest bacteria may be present, but their role in asthma is not understood. Traditional culture lacks sensitivity and current sequencing techniques are limited by operational problems and limited ability to identify pathogens at species level. We optimized a new sequencing technique-Oxford Nanopore technologies (ONT)-for use on human sputum samples and compared it with existing methods. We found ONT was effective for rapidly analyzing samples and could identify bacteria at the species level. We used this to show Haemophilus influenzae was a dominant bacterium in the airways in people with severe asthma. The presence of Haemophilus was associated with a "neutrophilic" form of asthma - a subgroup for which we currently lack specific treatments. Therefore, this technique could be used to target chronic antibiotic therapy and in research to characterize the full breadth of bacteria in the airways.
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Affiliation(s)
- Maisha F. Jabeen
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nicholas D. Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick W. Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jennifer L. Cane
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Catherine Borg
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Clare Connolly
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Samantha Thulborn
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ian D. Pavord
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Teresa L. Street
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Timothy S. C. Hinks
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
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Comparative pangenome analysis of capsulated Haemophilus influenzae serotype f highlights their high genomic stability. Sci Rep 2022; 12:3189. [PMID: 35210526 PMCID: PMC8873416 DOI: 10.1038/s41598-022-07185-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/11/2022] [Indexed: 11/20/2022] Open
Abstract
Haemophilus influenzae is an opportunistic pathogen adapted to the human respiratory tract. Non-typeable H. influenzae are highly heterogeneous, but few studies have analysed the genomic variability of capsulated strains. This study aims to examine the genetic diversity of 37 serotype f isolates from the Netherlands, Portugal, and Spain, and to compare all capsulated genomes available on public databases. Serotype f isolates belonged to CC124 and shared few single nucleotide polymorphisms (SNPs) (n = 10,999), but a high core genome (> 80%). Three main clades were identified by the presence of 75, 60 and 41 exclusive genes for each clade, respectively. Multi-locus sequence type analysis of all capsulated genomes revealed a reduced number of clonal complexes associated with each serotype. Pangenome analysis showed a large pool of genes (n = 6360), many of which were accessory genome (n = 5323). Phylogenetic analysis revealed that serotypes a, b, and f had greater diversity. The total number of SNPs in serotype f was significantly lower than in serotypes a, b, and e (p < 0.0001), indicating low variability within the serotype f clonal complexes. Capsulated H. influenzae are genetically homogeneous, with few lineages in each serotype. Serotype f has high genetic stability regardless of time and country of isolation.
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López-López N, Gil-Campillo C, Díez-Martínez R, Garmendia J. Learning from -omics strategies applied to uncover Haemophilus influenzae host-pathogen interactions: Current status and perspectives. Comput Struct Biotechnol J 2021; 19:3042-3050. [PMID: 34136102 PMCID: PMC8178019 DOI: 10.1016/j.csbj.2021.05.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/15/2022] Open
Abstract
Haemophilus influenzae has contributed to key bacterial genome sequencing hallmarks, as being not only the first bacterium to be genome-sequenced, but also starring the first genome-wide analysis of chromosomes directly transformed with DNA from a divergent genotype, and pioneering Tn-seq methodologies. Over the years, the phenomenal and constantly evolving development of -omic technologies applied to a whole range of biological questions of clinical relevance in the H. influenzae-host interplay, has greatly moved forward our understanding of this human-adapted pathogen, responsible for multiple acute and chronic infections of the respiratory tract. In this way, essential genes, virulence factors, pathoadaptive traits, and multi-layer gene expression regulatory networks with both genomic and epigenomic complexity levels are being elucidated. Likewise, the unstoppable increasing whole genome sequencing information underpinning H. influenzae great genomic plasticity, mainly when referring to non-capsulated strains, poses major challenges to understand the genomic basis of clinically relevant phenotypes and even more, to clearly highlight potential targets of clinical interest for diagnostic, therapeutic or vaccine development. We review here how genomic, transcriptomic, proteomic and metabolomic-based approaches are great contributors to our current understanding of the interactions between H. influenzae and the human airways, and point possible strategies to maximize their usefulness in the context of biomedical research and clinical needs on this human-adapted bacterial pathogen.
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Affiliation(s)
- Nahikari López-López
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | - Celia Gil-Campillo
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain
| | | | - Junkal Garmendia
- Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas (IdAB-CSIC)-Gobierno de Navarra, Mutilva, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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6
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Kc R, Leong KWC, Harkness NM, Lachowicz J, Gautam SS, Cooley LA, McEwan B, Petrovski S, Karupiah G, O'Toole RF. Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes. Microb Genom 2020; 6. [PMID: 32706329 PMCID: PMC7641420 DOI: 10.1099/mgen.0.000405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) colonizes human upper respiratory airways and plays a key role in the course and pathogenesis of acute exacerbations of chronic obstructive pulmonary disease (COPD). Currently, it is not possible to distinguish COPD isolates of NTHi from other clinical isolates of NTHi using conventional genotyping methods. Here, we analysed the core and accessory genome of 568 NTHi isolates, including 40 newly sequenced isolates, to look for genetic distinctions between NTHi isolates from COPD with respect to other illnesses, including otitis media, meningitis and pneumonia. Phylogenies based on polymorphic sites in the core-genome did not show discrimination between NTHi strains collected from different clinical phenotypes. However, pan-genome-wide association studies identified 79 unique NTHi accessory genes that were significantly associated with COPD. Furthermore, many of the COPD-related NTHi genes have known or predicted roles in virulence, transmembrane transport of metal ions and nutrients, cellular respiration and maintenance of redox homeostasis. This indicates that specific genes may be required by NTHi for its survival or virulence in the COPD lung. These results advance our understanding of the pathogenesis of NTHi infection in COPD lungs.
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Affiliation(s)
- Rajendra Kc
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Tasmania, Australia
| | - Kelvin W C Leong
- Department of Pharmacy and Biomedical Sciences, School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Victoria, Australia
| | - Nicholas M Harkness
- Department of Respiratory and Sleep Medicine, Royal Hobart Hospital, Tasmania, Australia
| | - Julia Lachowicz
- Department of Respiratory and Sleep Medicine, Royal Hobart Hospital, Tasmania, Australia
| | - Sanjay S Gautam
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Tasmania, Australia
| | - Louise A Cooley
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Tasmania, Australia
| | - Belinda McEwan
- Department of Microbiology and Infectious Diseases, Royal Hobart Hospital, Tasmania, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Victoria, Australia
| | - Gunasegaran Karupiah
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Tasmania, Australia
| | - Ronan F O'Toole
- Department of Pharmacy and Biomedical Sciences, School of Molecular Sciences, College of Science, Health and Engineering, La Trobe University, Victoria, Australia
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7
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Baddal B. Characterization of biofilm formation and induction of apoptotic DNA fragmentation by nontypeable Haemophilus influenzae on polarized human airway epithelial cells. Microb Pathog 2020; 141:103985. [PMID: 31968224 DOI: 10.1016/j.micpath.2020.103985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 10/25/2022]
Abstract
Nontypeable Haemophilus influenzae (NTHi) is a common airway commensal and opportunistic pathogen that persists within biofilm communities in vivo. Biofilm studies so far are mainly based on assays on plastic surfaces. The aim of this work was to investigate the capacity of clinical NTHi strains to form biofilm structures on polarized Calu-3 human airway epithelial cells and primary normal human bronchial epithelial cells and to characterize the biofilm architecture. Formation of adherent NTHi biofilms post colonization of host cells at multiple time-points was evaluated using confocal laser scanning microscopy and electron microscopy. NTHi biofilms were analyzed in terms of biofilm height and presence of extracellular matrix components, and their apoptotic effects on epithelial cells were measured by TUNEL assay. Strain Fi176 was observed to form robust biofilms on airway epithelia over time, while disrupting the integrity of Calu-3 monolayer by 72 h of co-culture. NTHi biofilms were observed to induce apoptotic DNA fragmentation in host cells at 24 h post infection. Biofilm formation on cell monolayers by Fi176ΔpilA strain was markedly reduced compared to WT strain. Biofilm inhibition and disruption assays by crystal violet staining indicated that DNA and proteins are part of NTHi biofilms in vitro. Our findings highlight critical stages of NTHi pathogenesis following host colonization and provide useful biofilm models for future antimicrobial drug discovery investigations.
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Affiliation(s)
- Buket Baddal
- Department of Medical Microbiology and Clinical Microbiology, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus; Microbial Pathogenesis Research Group, DESAM Institute, Near East University, Nicosia, Cyprus.
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8
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Kwun MJ, Oggioni MR, Bentley SD, Fraser C, Croucher NJ. Synergistic Activity of Mobile Genetic Element Defences in Streptococcus pneumoniae. Genes (Basel) 2019; 10:genes10090707. [PMID: 31540216 PMCID: PMC6771155 DOI: 10.3390/genes10090707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/01/2019] [Accepted: 09/06/2019] [Indexed: 01/02/2023] Open
Abstract
A diverse set of mobile genetic elements (MGEs) transmit between Streptococcus pneumoniae cells, but many isolates remain uninfected. The best-characterised defences against horizontal transmission of MGEs are restriction-modification systems (RMSs), of which there are two phase-variable examples in S. pneumoniae. Additionally, the transformation machinery has been proposed to limit vertical transmission of chromosomally integrated MGEs. This work describes how these mechanisms can act in concert. Experimental data demonstrate RMS phase variation occurs at a sub-maximal rate. Simulations suggest this may be optimal if MGEs are sometimes vertically inherited, as it reduces the probability that an infected cell will switch between RMS variants while the MGE is invading the population, and thereby undermine the restriction barrier. Such vertically inherited MGEs can be deleted by transformation. The lack of between-strain transformation hotspots at known prophage att sites suggests transformation cannot remove an MGE from a strain in which it is fixed. However, simulations confirmed that transformation was nevertheless effective at preventing the spread of MGEs into a previously uninfected cell population, if a recombination barrier existed between co-colonising strains. Further simulations combining these effects of phase variable RMSs and transformation found they synergistically inhibited MGEs spreading, through limiting both vertical and horizontal transmission.
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Affiliation(s)
- Min Jung Kwun
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London W2 1PG, UK.
| | - Marco R Oggioni
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
| | - Stephen D Bentley
- Pathogens and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, Old Road Campus, University of Oxford, Oxford OX3 7LF, UK.
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London W2 1PG, UK.
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9
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Aziz A, Sarovich DS, Nosworthy E, Beissbarth J, Chang AB, Smith-Vaughan H, Price EP, Harris TM. Molecular Signatures of Non-typeable Haemophilus influenzae Lung Adaptation in Pediatric Chronic Lung Disease. Front Microbiol 2019; 10:1622. [PMID: 31379777 PMCID: PMC6646836 DOI: 10.3389/fmicb.2019.01622] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/01/2019] [Indexed: 12/03/2022] Open
Abstract
Non-typeable Haemophilus influenzae (NTHi), an opportunistic pathogen of the upper airways of healthy children, can infect the lower airways, driving chronic lung disease. However, the molecular basis underpinning NTHi transition from a commensal to a pathogen is not clearly understood. Here, we performed comparative genomic and transcriptomic analyses of 12 paired, isogenic NTHi strains, isolated from the nasopharynx (NP) and bronchoalveolar lavage (BAL) of 11 children with chronic lung disease, to identify convergent molecular signatures associated with lung adaptation. Comparative genomic analyses of the 12 NP-BAL pairs demonstrated that five were genetically identical, with the remaining seven differing by only 1 to 3 mutations. Within-patient transcriptomic analyses identified between 2 and 58 differentially expressed genes in 8 of the 12 NP-BAL pairs, including pairs with no observable genomic changes. Whilst no convergence was observed at the gene level, functional enrichment analysis revealed significant under-representation of differentially expressed genes belonging to Coenzyme metabolism, Function unknown, Translation, ribosomal structure, and biogenesis Cluster of Orthologous Groups categories. In contrast, Carbohydrate transport and metabolism, Cell motility and secretion, Intracellular trafficking and secretion, and Energy production categories were over-represented. This observed trend amongst genetically unrelated NTHi strains provides evidence of convergent transcriptional adaptation of NTHi to pediatric airways that deserves further exploration. Understanding the pathoadaptative mechanisms that NTHi employs to infect and persist in the lower pediatric airways is essential for devising targeted diagnostics and treatments aimed at minimizing disease severity, and ultimately, preventing NTHi lung infections and subsequent chronic lung disease in children.
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Affiliation(s)
- Ammar Aziz
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Derek S. Sarovich
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Anne B. Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Respiratory and Sleep Medicine, Children’s Health Queensland, Queensland University of Technology, Brisbane, QLD, Australia
| | - Heidi Smith-Vaughan
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Erin P. Price
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Tegan M. Harris
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
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10
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Insights into the population structure and pan-genome of Haemophilus influenzae. INFECTION GENETICS AND EVOLUTION 2018; 67:126-135. [PMID: 30391557 DOI: 10.1016/j.meegid.2018.10.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/20/2018] [Accepted: 10/30/2018] [Indexed: 12/25/2022]
Abstract
The human-restricted bacterium Haemophilus influenzae is responsible for respiratory infections in both children and adults. While colonization begins in the upper airways, it can spread throughout the respiratory tract potentially leading to invasive infections. Although the spread of H. influenzae serotype b (Hib) has been prevented by vaccination, the emergence of infections by other serotypes as well as by non-typeable isolates (NTHi) have been observed, prompting the need for novel prevention strategies. Here, we aimed to study the population structure of H. influenzae and to get some insights into its pan-genome. We studied 305H. influenzae strains, enrolling 217 publicly available genomes, as well as 88 newly sequenced H. influenzae invasive strains isolated in Portugal, spanning a 24-year period. NTHi isolates presented a core-SNP-based genetic diversity about 10-fold higher than the one observed for Hib. The analysis of key factors involved in pathogenesis, such as lipooligosaccharides, hemagglutinating pili and High Molecular Weight-adhesins, suggests that NTHi shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion and persistence. Discreet NTHi subpopulations structures are proposed based on core-genome supported with 17 candidate genetic markers identified in the accessory genome. Additionally, this study provides two bioinformatics tools for in silico rapid identification of H. influenzae serotypes and NTHi clades previously proposed, obviating laboratory-based demanding procedures. The present study constitutes an important genomic framework that could lay way for future studies on the genetic determinants underlying invasiveness and disease and population structure of H. influenzae.
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11
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Osman KL, Jefferies JMC, Woelk CH, Devos N, Pascal TG, Mortier MC, Devaster JM, Wilkinson TMA, Cleary DW, Clarke SC. Patients with Chronic Obstructive Pulmonary Disease harbour a variation of Haemophilus species. Sci Rep 2018; 8:14734. [PMID: 30282975 PMCID: PMC6170463 DOI: 10.1038/s41598-018-32973-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/19/2018] [Indexed: 02/04/2023] Open
Abstract
H. haemolyticus is often misidentified as NTHi due to their close phylogenetic relationship. Differentiating between the two is important for correct identification and appropriate treatment of infective organism and to ensure any role of H. haemolyticus in disease is not being overlooked. Speciation however is not completely reliable by culture and PCR methods due to the loss of haemolysis by H. haemolyticus and the heterogeneity of NTHi. Haemophilus isolates from COPD as part of the AERIS study (ClinicalTrials - NCT01360398) were speciated by analysing sequence data for the presence of molecular markers. Further investigation into the genomic relationship was carried out using average nucleotide identity and phylogeny of allelic and genome alignments. Only 6.3% were identified as H. haemolyticus. Multiple in silico methods were able to distinguish H. haemolyticus from NTHi. However, no single gene target was found to be 100% accurate. A group of omp2 negative NTHi were observed to be phylogenetically divergent from H. haemolyticus and remaining NTHi. The presence of an atypical group from a geographically and disease limited set of isolates supports the theory that the heterogeneity of NTHi may provide a genetic continuum between NTHi and H. haemolyticus.
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Affiliation(s)
- Karen L Osman
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK
| | - Johanna M C Jefferies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK
| | - Christopher H Woelk
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK.,Merck Exploratory Science Center, Merck Research Laboratories, Cambridge, MA, USA
| | | | | | | | | | - Tom M A Wilkinson
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK.,NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom.,Wessex Investigational Sciences Hub, University of Southampton, Southampton, United Kingdom
| | - David W Cleary
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK.,NIHR Southampton Respiratory Biomedical Research Unit, Southampton, United Kingdom
| | - Stuart C Clarke
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants, SO16 6YD, UK. .,NIHR Biomedical Research Centre, University of Southampton, Southampton, United Kingdom. .,Wessex Investigational Sciences Hub, University of Southampton, Southampton, United Kingdom. .,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom. .,Global Health Research Institute, University of Southampton, Southampton, United Kingdom.
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12
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Heinz E. The return of Pfeiffer's bacillus: Rising incidence of ampicillin resistance in Haemophilus influenzae. Microb Genom 2018; 4:e000214. [PMID: 30207515 PMCID: PMC6202453 DOI: 10.1099/mgen.0.000214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
Haemophilus influenzae, originally named Pfeiffer's bacillus after its discoverer Richard Pfeiffer in 1892, was a major risk for global health at the beginning of the 20th century, causing childhood pneumonia and invasive disease as well as otitis media and other upper respiratory tract infections. The implementation of the Hib vaccine, targeting the major capsule type of H. influenzae, almost eradicated the disease in countries that adapted the vaccination scheme. However, a rising number of infections are caused by non-typeable H. influenzae (NTHi), which has no capsule and against which the vaccine therefore provides no protection, as well as other serotypes equally not recognised by the vaccine. The first line of treatment is ampicillin, but there is a steady rise in ampicillin resistance. This is both through acquired as well as intrinsic mechanisms, and is cause for serious concern and the need for more surveillance. There are also increasing reports of new modifications of the intrinsic ampicillin-resistance mechanism leading to resistance against cephalosporins and carbapenems, the last line of well-tolerated drugs, and ampicillin-resistant H. influenzae was included in the recently released priority list of antibiotic-resistant bacteria by the WHO. This review provides an overview of ampicillin resistance prevalence and mechanisms in the context of our current knowledge about population dynamics of H. influenzae.
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Affiliation(s)
- Eva Heinz
- Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
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13
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Pettigrew MM, Ahearn CP, Gent JF, Kong Y, Gallo MC, Munro JB, D'Mello A, Sethi S, Tettelin H, Murphy TF. Haemophilus influenzae genome evolution during persistence in the human airways in chronic obstructive pulmonary disease. Proc Natl Acad Sci U S A 2018; 115:E3256-E3265. [PMID: 29555745 PMCID: PMC5889651 DOI: 10.1073/pnas.1719654115] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nontypeable Haemophilus influenzae (NTHi) exclusively colonize and infect humans and are critical to the pathogenesis of chronic obstructive pulmonary disease (COPD). In vitro and animal models do not accurately capture the complex environments encountered by NTHi during human infection. We conducted whole-genome sequencing of 269 longitudinally collected cleared and persistent NTHi from a 15-y prospective study of adults with COPD. Genome sequences were used to elucidate the phylogeny of NTHi isolates, identify genomic changes that occur with persistence in the human airways, and evaluate the effect of selective pressure on 12 candidate vaccine antigens. Strains persisted in individuals with COPD for as long as 1,422 d. Slipped-strand mispairing, mediated by changes in simple sequence repeats in multiple genes during persistence, regulates expression of critical virulence functions, including adherence, nutrient uptake, and modification of surface molecules, and is a major mechanism for survival in the hostile environment of the human airways. A subset of strains underwent a large 400-kb inversion during persistence. NTHi does not undergo significant gene gain or loss during persistence, in contrast to other persistent respiratory tract pathogens. Amino acid sequence changes occurred in 8 of 12 candidate vaccine antigens during persistence, an observation with important implications for vaccine development. These results indicate that NTHi alters its genome during persistence by regulation of critical virulence functions primarily by slipped-strand mispairing, advancing our understanding of how a bacterial pathogen that plays a critical role in COPD adapts to survival in the human respiratory tract.
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Affiliation(s)
- Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510
| | - Christian P Ahearn
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
| | - Janneane F Gent
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06510
| | - Yong Kong
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06510
- W.M. Keck Foundation Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT 06510
| | - Mary C Gallo
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
| | - James B Munro
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Adonis D'Mello
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Sanjay Sethi
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Department of Medicine, Veterans Affairs Western New York Healthcare System, Buffalo, NY 14215
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Timothy F Murphy
- Department of Microbiology and Immunology, University at Buffalo, The State University of New York, Buffalo, NY 14203;
- Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo, NY 14203
- Division of Infectious Diseases, Department of Medicine, University at Buffalo, The State University of New York, Buffalo, NY 14203
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14
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Osman KL, Jefferies JM, Woelk CH, Cleary DW, Clarke SC. The adhesins of non-typeable Haemophilus influenzae. Expert Rev Anti Infect Ther 2018; 16:187-196. [PMID: 29415569 DOI: 10.1080/14787210.2018.1438263] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen of the respiratory tract and the greatest contributor to invasive Haemophilus disease. Additionally, in children, NTHi is responsible for the majority of otitis media (OM) which can lead to chronic infection and hearing loss. In adults, NTHi infection in the lungs is responsible for the onset of acute exacerbations in chronic obstructive pulmonary disease (COPD). Unfortunately, there is currently no vaccine available to protect against NTHi infections. Areas covered: NTHi uses an arsenal of adhesins to colonise the respiratory epithelium. The adhesins also have secondary roles that aid in the virulence of NTHi, including mechanisms that avoid immune clearance, adjust pore size to avoid antimicrobial destruction, form micro-colonies and invoke phase variation for protein mediation. Bacterial adhesins can also be ideal antigens for subunit vaccine design due to surface exposure and immunogenic capabilities. Expert commentary: The host-pathogen interactions of the NTHi adhesins are not fully investigated. The relationship between adhesins and the extracellular matrix (ECM) play a part in the success of NTHi colonisation and virulence by immune evasion, migration and biofilm development. Further research into these immunogenic proteins would further our understanding and enable a basis for better combatting NTHi disease.
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Affiliation(s)
- Karen L Osman
- a Faulty of Medicine , University of Southampton , Southampton , UK
| | | | - Christopher H Woelk
- a Faulty of Medicine , University of Southampton , Southampton , UK.,b Merck Exploratory Science Center , Merck Research Laboratories , Cambridge , MA , USA
| | - David W Cleary
- a Faulty of Medicine , University of Southampton , Southampton , UK.,c Faculty of Medicine and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK.,d NIHR Southampton Biomedical Research Centre , University Hospital Southampton Foundation NHS Trust , Southampton SO16 6YD , UK
| | - Stuart C Clarke
- a Faulty of Medicine , University of Southampton , Southampton , UK.,c Faculty of Medicine and Institute for Life Sciences , University of Southampton , Southampton SO17 1BJ , UK.,d NIHR Southampton Biomedical Research Centre , University Hospital Southampton Foundation NHS Trust , Southampton SO16 6YD , UK.,e Global Health Research Institute , University of Southampton , Southampton SO17 1BJ , UK
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15
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Price EP, Harris TM, Spargo J, Nosworthy E, Beissbarth J, Chang AB, Smith-Vaughan HC, Sarovich DS. Simultaneous identification of Haemophilus influenzae and Haemophilus haemolyticus using real-time PCR. Future Microbiol 2017; 12:585-593. [PMID: 28604066 DOI: 10.2217/fmb-2016-0215] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
AIM To design a highly specific and sensitive multiplex real-time PCR assay for the differentiation of the pathogen Haemophilus influenzae from its nonpathogenic near-neighbor Haemophilus haemolyticus. MATERIALS & METHODS A comparison of 380 Haemophilus spp. genomes was used to identify loci specific for each species. Novel PCR assays targeting H. haemolyticus (hypD) and H. influenzae (siaT) were designed. RESULTS & DISCUSSION PCR screening across 143 isolates demonstrated 100% specificity for hypD and siaT. These two assays were multiplexed with the recently described fucP assay for further differentiation among H. influenzae. CONCLUSION The triplex assay provides rapid, unambiguous, sensitive and highly specific genotyping results for the simultaneous detection of hypD and siaT, including fucose-positive H. influenzae (fucP), in a single PCR.
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Affiliation(s)
- Erin P Price
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.,Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Tegan M Harris
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Jessie Spargo
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Elizabeth Nosworthy
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Jemima Beissbarth
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | - Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia
| | | | - Derek S Sarovich
- Child Health Division, Menzies School of Health Research, Darwin, NT, Australia.,Centre for Animal Health Innovation, Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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16
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Waseem H, Williams MR, Stedtfeld T, Chai B, Stedtfeld RD, Cole JR, Tiedje JM, Hashsham SA. Virulence factor activity relationships (VFARs): a bioinformatics perspective. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:247-260. [PMID: 28261716 PMCID: PMC5897045 DOI: 10.1039/c6em00689b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Virulence factor activity relationships (VFARs) - a concept loosely based on quantitative structure-activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety. A rapid increase in sequencing capabilities and bioinformatics tools has significantly increased the potential for VFAR-based analyses. This review summarizes more than 20 bioinformatics databases and tools, developed over the last decade, along with their virulence and antimicrobial resistance prediction capabilities. With the number of bacterial whole genome sequences exceeding 241 000 and metagenomic analysis projects exceeding 13 000 and the ability to add additional genome sequences for few hundred dollars, it is evident that further development of VFARs is not limited by the availability of information at least at the genomic level. However, additional information related to co-occurrence, treatment response, modulation of virulence due to environmental and other factors, and economic impact must be gathered and incorporated in a manner that also addresses the associated uncertainties. Of the bioinformatics tools, a majority are either designed exclusively for virulence/resistance determination or equipped with a dedicated module. The remaining have the potential to be employed for evaluating virulence. This review focusing broadly on omics technologies and tools supports the notion that these tools are now sufficiently developed to allow the application of VFAR approaches combined with additional engineering and economic analyses to rank and prioritize organisms important to a given niche. Knowledge gaps do exist but can be filled with focused experimental and theoretical analyses that were unimaginable a decade ago. Further developments should consider the integration of the measurement of activity, risk, and uncertainty to improve the current capabilities.
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Affiliation(s)
- Hassan Waseem
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
| | - Tiffany Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA.
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA and Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA. and Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA and Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
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17
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Ali R, Blackburn RM, Kozlakidis Z. Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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18
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Marrazzo P, Maccari S, Taddei A, Bevan L, Telford J, Soriani M, Pezzicoli A. 3D Reconstruction of the Human Airway Mucosa In Vitro as an Experimental Model to Study NTHi Infections. PLoS One 2016; 11:e0153985. [PMID: 27101006 PMCID: PMC4839639 DOI: 10.1371/journal.pone.0153985] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/06/2016] [Indexed: 12/04/2022] Open
Abstract
We have established an in vitro 3D system which recapitulates the human tracheo-bronchial mucosa comprehensive of the pseudostratified epithelium and the underlying stromal tissue. In particular, we reported that the mature model, entirely constituted of primary cells of human origin, develops key markers proper of the native tissue such as the mucociliary differentiation of the epithelial sheet and the formation of the basement membrane. The infection of the pseudo-tissue with a strain of NonTypeable Haemophilus influenzae results in bacteria association and crossing of the mucus layer leading to an apparent targeting of the stromal space where they release large amounts of vesicles and form macro-structures. In summary, we propose our in vitro model as a reliable and potentially customizable system to study mid/long term host-pathogen processes.
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Affiliation(s)
| | - Silvia Maccari
- GSK Vaccines S.r.l., via Fiorentina 1, 53100, Siena, Italy
| | - Annarita Taddei
- Interdepartmental Centre for Electron Microscopy, Tuscia University, Viterbo, Italy
| | - Luke Bevan
- Respiratory Disease Area, Novartis Institutes for BioMedical Research, Horsham, RH12 5AB, United Kingdom
| | - John Telford
- GSK Vaccines S.r.l., via Fiorentina 1, 53100, Siena, Italy
| | - Marco Soriani
- GSK Vaccines S.r.l., via Fiorentina 1, 53100, Siena, Italy
- * E-mail: (AP); (MS)
| | - Alfredo Pezzicoli
- GSK Vaccines S.r.l., via Fiorentina 1, 53100, Siena, Italy
- * E-mail: (AP); (MS)
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19
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Gregory MT, Bertout JA, Ericson NG, Taylor SD, Mukherjee R, Robins HS, Drescher CW, Bielas JH. Targeted single molecule mutation detection with massively parallel sequencing. Nucleic Acids Res 2015; 44:e22. [PMID: 26384417 PMCID: PMC4756847 DOI: 10.1093/nar/gkv915] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/02/2015] [Indexed: 11/14/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have transformed genomic research and have the potential to revolutionize clinical medicine. However, the background error rates of sequencing instruments and limitations in targeted read coverage have precluded the detection of rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding error correction and rolling circle amplification (RCA)-based target enrichment to vastly improve NGS-based rare variant detection. The CypherSeq methodology involves the ligation of sample DNA into circular vectors, which contain double-stranded barcodes for computational error correction and adapters for library preparation and sequencing. CypherSeq is capable of detecting rare mutations genome-wide as well as those within specific target genes via RCA-based enrichment. We demonstrate that CypherSeq is capable of correcting errors incurred during library preparation and sequencing to reproducibly detect mutations down to a frequency of 2.4 × 10−7 per base pair, and report the frequency and spectra of spontaneous and ethyl methanesulfonate-induced mutations across the Saccharomycescerevisiae genome.
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Affiliation(s)
- Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica A Bertout
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sean D Taylor
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rithun Mukherjee
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Harlan S Robins
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Charles W Drescher
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Department of Pathology, University of Washington, Seattle, WA 98195, USA
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20
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Murphy TF, Kirkham C, Jones MM, Sethi S, Kong Y, Pettigrew MM. Expression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease. J Infect Dis 2015; 212:1798-805. [PMID: 25995193 DOI: 10.1093/infdis/jiv299] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/13/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Immunoglobulin (Ig)A proteases of Haemophilus influenzae are highly specific endopeptidases that cleave the hinge region of human IgA1 and also mediate invasion and trafficking in human respiratory epithelial cells, facilitating persistence of H. influenzae. Little is known about the expression of IgA proteases in clinical settings of H. influenzae infection. METHODS We identified and characterized IgA protease genes in H. influenzae and studied their expression and proteolytic specificity, in vitro and in vivo in 169 independent strains of H. influenzae collected longitudinally over 10 years from adults with chronic obstructive pulmonary disease. RESULTS The H. influenzae pangenome has 2 alleles of IgA protease genes; all strains have igaA, and 40% of strains have igaB. Each allele has 2 variants with differing proteolytic specificities for human IgA1. A total of 88% of 169 strains express IgA protease activity. Expression of the 4 forms of IgA protease varies among strains. Based on the presence of IgA1 fragments in sputum samples, each of the different forms of IgA protease is selectively expressed in the human airways during infection. CONCLUSIONS Four variants of IgA proteases are variably expressed by H. influenzae during infection of the human airways.
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Affiliation(s)
- Timothy F Murphy
- Division of Infectious Diseases Department of Microbiology and Immunology Clinical and Translational Research Center, University at Buffalo, State University of New York
| | - Charmaine Kirkham
- Division of Infectious Diseases Clinical and Translational Research Center, University at Buffalo, State University of New York
| | - Megan M Jones
- Department of Microbiology and Immunology Clinical and Translational Research Center, University at Buffalo, State University of New York
| | - Sanjay Sethi
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine Veterans Affairs Western New York Healthcare System, Buffalo, New York
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, W.M. Keck Biotechnology Resource Laboratory
| | - Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
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21
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Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K, Chauhan DS, Sivasubbu S, Scaria V. Comparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome. PLoS One 2015; 10:e0122979. [PMID: 25853708 PMCID: PMC4390332 DOI: 10.1371/journal.pone.0122979] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 02/26/2015] [Indexed: 11/18/2022] Open
Abstract
The tubercle complex consists of closely related mycobacterium species which appear to be variants of a single species. Comparative genome analysis of different strains could provide useful clues and insights into the genetic diversity of the species. We integrated genome assemblies of 96 strains from Mycobacterium tuberculosis complex (MTBC), which included 8 Indian clinical isolates sequenced and assembled in this study, to understand its pangenome architecture. We predicted genes for all the 96 strains and clustered their respective CDSs into homologous gene clusters (HGCs) to reveal a hard-core, soft-core and accessory genome component of MTBC. The hard-core (HGCs shared amongst 100% of the strains) was comprised of 2,066 gene clusters whereas the soft-core (HGCs shared amongst at least 95% of the strains) comprised of 3,374 gene clusters. The change in the core and accessory genome components when observed as a function of their size revealed that MTBC has an open pangenome. We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates. We report PCR validation on 9 candidate genes depicting 7 genes completely absent from H37Rv and H37Ra whereas 2 genes shared partial homology with them accounting to probable insertion and deletion events. The pangenome approach is a promising tool for studying strain specific genetic differences occurring within species. We also suggest that since selecting appropriate target genes for typing purposes requires the expected target gene be present in all isolates being typed, therefore estimating the core-component of the species becomes a subject of prime importance.
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Affiliation(s)
- Vinita Periwal
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India
| | - Ashok Patowary
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India
| | - Anju Gupta
- Open Source Drug Discovery Unit, Council of Scientific and Industrial Research (CSIR), Anusandhan Bhavan, 2 Rafi Marg, New Delhi 110001, India
| | - Meghna Singh
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- Academy of Scientific & Innovative Research (AcSIR), 2, Rafi Marg, Anusandhan Bhawan, New Delhi 110001, India
| | - Ashish Mittal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Shamini Jeyapaul
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Rajendra Kumar Chauhan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
| | - Ajay Vir Singh
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Pravin Kumar Singh
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Parul Garg
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Viswa Mohan Katoch
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Kiran Katoch
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Devendra Singh Chauhan
- National JALMA Institute of Leprosy and other Mycobacterial Diseases, Post Box No.101,Tajganj, Agra-282001, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- * E-mail: (VS); (SS)
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi—110007, India
- * E-mail: (VS); (SS)
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Choi J, Nix EB, Gaultier GN, Cox AD, McCready W, Ulanova M. Naturally occurring bactericidal antibodies specific for Haemophilus influenzae Lipooligosaccharide are present in healthy adult individuals. Vaccine 2015; 33:1941-7. [DOI: 10.1016/j.vaccine.2015.02.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/03/2015] [Accepted: 02/22/2015] [Indexed: 11/30/2022]
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Vaccines for Nontypeable Haemophilus influenzae: the Future Is Now. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2015; 22:459-66. [PMID: 25787137 DOI: 10.1128/cvi.00089-15] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Infections due to nontypeable Haemophilus influenzae result in enormous global morbidity in two clinical settings: otitis media in children and respiratory tract infections in adults with chronic obstructive pulmonary disease (COPD). Recurrent otitis media affects up to 20% of children and results in hearing loss, delays in speech and language development and, in developing countries, chronic suppurative otitis media. Infections in people with COPD result in clinic and emergency room visits, hospital admissions, and respiratory failure. An effective vaccine would prevent morbidity, help control health care costs, and reduce antibiotic use, a major contributor to the global crisis in bacterial antibiotic resistance. The widespread use of the pneumococcal conjugate vaccines is causing a relative increase in H. influenzae otitis media. The partial protection against H. influenzae otitis media induced by the pneumococcal H. influenzae protein D conjugate vaccine represents a proof of principle of the feasibility of a vaccine for nontypeable H. influenzae. An ideal vaccine antigen should be conserved among strains, have abundant epitopes on the bacterial surface, be immunogenic, and induce protective immune responses. Several surface proteins of H. influenzae have been identified as potential vaccine candidates and are in various stages of development. With continued research, progress toward a broadly effective vaccine to prevent infections caused by nontypeable H. influenzae is expected over the next several years.
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Haemophilus influenzae: recent advances in the understanding of molecular pathogenesis and polymicrobial infections. Curr Opin Infect Dis 2015; 27:268-74. [PMID: 24699388 DOI: 10.1097/qco.0000000000000056] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW Non-typeable Haemophilus influenzae (NTHi) is a human-specific mucosal pathogen and one of the most common causes of bacterial infections in children and patients with chronic obstructive pulmonary disease. It is also frequently found in polymicrobial superinfections. Great strides have recently been made in the understanding of the molecular mechanisms underlying NTHi pathogenesis. RECENT FINDINGS By using new methodology, such as experimental human colonization models and whole-genome approaches, investigators have shed light upon the various strategies of NTHi that are involved in pathogenesis. These include the escape of the mucociliary elevator, evasion of host immunity, survival in environments with scarce nutrients, and finally participation in polymicrobial infections. Lipooligosaccharide branching, proteinous adhesins, metabolic adaption to nutrient availability and many scavenging systems are implicated in these processes. Interestingly, genome-based studies comparing virulent and commensal strains have identified many hypothetical proteins as virulence determinants, suggesting that much regarding the molecular pathogenesis of NTHi remains to be solved. SUMMARY NTHi is an opportunistic pathogen and highly specialized colonizer of the human respiratory tract that has developed intricate mechanisms to establish growth and survival in the human host. Continued research is needed to further elucidate NTHi host-pathogen and pathogen-pathogen interactions.
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Skaare D, Anthonisen IL, Caugant DA, Jenkins A, Steinbakk M, Strand L, Sundsfjord A, Tveten Y, Kristiansen BE. Multilocus sequence typing and ftsI sequencing: a powerful tool for surveillance of penicillin-binding protein 3-mediated beta-lactam resistance in nontypeable Haemophilus influenzae. BMC Microbiol 2014; 14:131. [PMID: 24884375 PMCID: PMC4039647 DOI: 10.1186/1471-2180-14-131] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/14/2014] [Indexed: 12/26/2022] Open
Abstract
Background Beta-lactam resistance in Haemophilus influenzae due to ftsI mutations causing altered penicillin-binding protein 3 (PBP3) is increasing worldwide. Low-level resistant isolates with the N526K substitution (group II low-rPBP3) predominate in most geographical regions, while high-level resistant isolates with the additional S385T substitution (group III high-rPBP3) are common in Japan and South Korea. Knowledge about the molecular epidemiology of rPBP3 strains is limited. We combined multilocus sequence typing (MLST) and ftsI/PBP3 typing to study the emergence and spread of rPBP3 in nontypeable H. influenzae (NTHi) in Norway. Results The prevalence of rPBP3 in a population of 795 eye, ear and respiratory isolates (99% NTHi) from 2007 was 15%. The prevalence of clinical PBP3-mediated resistance to ampicillin was 9%, compared to 2.5% three years earlier. Group II low-rPBP3 predominated (96%), with significant proportions of isolates non-susceptible to cefotaxime (6%) and meropenem (20%). Group III high-rPBP3 was identified for the first time in Northern Europe. Four MLST sequence types (ST) with characteristic, highly diverging ftsI alleles accounted for 61% of the rPBP3 isolates. The most prevalent substitution pattern (PBP3 type A) was present in 41% of rPBP3 isolates, mainly carried by ST367 and ST14. Several unrelated STs possessed identical copies of the ftsI allele encoding PBP3 type A. Infection sites, age groups, hospitalization rates and rPBP3 frequencies differed between STs and phylogenetic groups. Conclusions This study is the first to link ftsI alleles to STs in H. influenzae. The results indicate that horizontal gene transfer contributes to the emergence of rPBP3 by phylogeny restricted transformation. Clonally related virulent rPBP3 strains are widely disseminated and high-level resistant isolates emerge in new geographical regions, threatening current empiric antibiotic treatment. The need of continuous monitoring of beta-lactam susceptibility and a global system for molecular surveillance of rPBP3 strains is underlined. Combining MLST and ftsI/PBP3 typing is a powerful tool for this purpose.
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Affiliation(s)
- Dagfinn Skaare
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway.
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26
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Extensive cotransformation of natural variation into chromosomes of naturally competent Haemophilus influenzae. G3-GENES GENOMES GENETICS 2014; 4:717-31. [PMID: 24569039 PMCID: PMC4059242 DOI: 10.1534/g3.113.009597] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Naturally competent bacterial species actively take up environmental DNA and can incorporate it into their chromosomes by homologous recombination. This can bring genetic variation from environmental DNA to recipient chromosomes, often in multiple long “donor” segments. Here, we report the results of genome sequencing 96 colonies of a laboratory Haemophilus influenzae strain, which had been experimentally transformed by DNA from a diverged clinical isolate. Donor segments averaged 6.9 kb (spanning several genes) and were clustered into recombination tracts of ~19.5 kb. Individual colonies had replaced from 0.1 to 3.2% of their chromosomes, and ~1/3 of all donor-specific single-nucleotide variants were present in at least one recombinant. We found that nucleotide divergence did not obviously limit the locations of recombination tracts, although there were small but significant reductions in divergence at recombination breakpoints. Although indels occasionally transformed as parts of longer recombination tracts, they were common at breakpoints, suggesting that indels typically block progression of strand exchange. Some colonies had recombination tracts in which variant positions contained mixtures of both donor and recipient alleles. These tracts were clustered around the origin of replication and were interpreted as the result of heteroduplex segregation in the original transformed cell. Finally, a pilot experiment demonstrated the utility of natural transformation for genetically dissecting natural phenotypic variation. We discuss our results in the context of the potential to merge experimental and population genetic approaches, giving a more holistic understanding of bacterial gene transfer.
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Genome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure. Proc Natl Acad Sci U S A 2014; 111:5439-44. [PMID: 24706866 DOI: 10.1073/pnas.1403353111] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen.
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Su YC, Resman F, Hörhold F, Riesbeck K. Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f. BMC Genomics 2014; 15:38. [PMID: 24438474 PMCID: PMC3928620 DOI: 10.1186/1471-2164-15-38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif. RESULTS The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments. Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi. CONCLUSIONS The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.
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Affiliation(s)
| | | | | | - Kristian Riesbeck
- Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Jan Waldenströms gata 59, SE-205 02 Malmö, Sweden.
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Haemophilus parainfluenzae expresses diverse lipopolysaccharide O-antigens using ABC transporter and Wzy polymerase-dependent mechanisms. Int J Med Microbiol 2013; 303:603-17. [PMID: 24035104 PMCID: PMC3989065 DOI: 10.1016/j.ijmm.2013.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/09/2013] [Accepted: 08/18/2013] [Indexed: 12/11/2022] Open
Abstract
Lipopolysaccharide O-antigens are the basis of serotyping schemes for Gram negative bacteria and help to determine the nature of host–bacterial interactions. Haemophilus parainfluenzae is a normal commensal of humans but is also an occasional pathogen. The prevalence, diversity and biosynthesis of O-antigens were investigated in this species for the first time. 18/18 commensal H. parainfluenzae isolates contain a O-antigen biosynthesis gene cluster flanked by glnA and pepB, the same position as the hmg locus for tetrasaccharide biosynthesis in Haemophilus influenzae. The O-antigen loci show diverse restriction digest patterns but fall into two main groups: (1) those encoding enzymes for the synthesis and transfer of FucNAc4N in addition to the Wzy-dependent mechanism of O-antigen synthesis and transport and (2) those encoding galactofuranose synthesis/transfer enzymes and an ABC transporter. The other glycosyltransferase genes differ between isolates. Three H. parainfluenzae isolates fell outside these groups and are predicted to synthesise O-antigens containing ribitol phosphate or deoxytalose. Isolates using the ABC transporter system encode a putative O-antigen ligase, required for the synthesis of O-antigen-containing LPS glycoforms, at a separate genomic location. The presence of an O-antigen contributes significantly to H. parainfluenzae resistance to the killing effect of human serum in vitro. The discovery of O-antigens in H. parainfluenzae is striking, as its close relative H. influenzae lacks this cell surface component.
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