51
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Cronk BD, Caserta LC, Laverack M, Gerdes RS, Hynes K, Hopf CR, Fadden MA, Nakagun S, Schuler KL, Buckles EL, Lejeune M, Diel DG. Infection and tissue distribution of highly pathogenic avian influenza A type H5N1 (clade 2.3.4.4b) in red fox kits ( Vulpes vulpes). Emerg Microbes Infect 2023; 12:2249554. [PMID: 37589241 PMCID: PMC10512766 DOI: 10.1080/22221751.2023.2249554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Avian influenza H5N1 is a highly pathogenic virus that primarily affects birds. However, it can also infect other animal species, including mammals. We report the infection of nine juvenile red foxes (Vulpes vulpes) with Highly Pathogenic Avian Influenza A type H5N1 (Clade 2.3.4.4b) in the spring of 2022 in the central, western, and northern regions of New York, USA. The foxes displayed neurologic signs, and examination of brain and lung tissue revealed lesions, with brain lesions ranging from moderate to severe meningoencephalitis. Analysis of tissue tropism using RT-PCR methods showed a comparatively lower Ct value in the brain, which was confirmed by in situ hybridization targeting Influenza A RNA. The viral RNA labelling was highly clustered and overlapped the brain lesions, observed in neurons, and grey matter. Whole viral genome sequences obtained from the affected foxes were subjected to phylogenetic and mutation analysis to determine influenza A clade, host specificity, and potential occurrence of viral reassortment. Infections in red foxes likely occurred due to preying on infected wild birds and are unlikely due to transmission between foxes or other mammals.
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Affiliation(s)
- Brittany D. Cronk
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa Laverack
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Rhea S. Gerdes
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Kevin Hynes
- New York State Department of Environmental Conservation, Wildlife Health Program, Albany, NY, USA
| | - Cynthia R. Hopf
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Melissa A. Fadden
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Shotaro Nakagun
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Krysten L. Schuler
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Elizabeth L. Buckles
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Manigandan Lejeune
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
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Simmons BC, Rhodes J, Rogers TR, Verweij PE, Abdolrasouli A, Schelenz S, Hemmings SJ, Talento AF, Griffin A, Mansfield M, Sheehan D, Bosch T, Fisher MC. Genomic Epidemiology Identifies Azole Resistance Due to TR 34/L98H in European Aspergillus fumigatus Causing COVID-19-Associated Pulmonary Aspergillosis. J Fungi (Basel) 2023; 9:1104. [PMID: 37998909 PMCID: PMC10672581 DOI: 10.3390/jof9111104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/31/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023] Open
Abstract
Aspergillus fumigatus has been found to coinfect patients with severe SARS-CoV-2 virus infection, leading to COVID-19-associated pulmonary aspergillosis (CAPA). The CAPA all-cause mortality rate is approximately 50% and may be complicated by azole resistance. Genomic epidemiology can help shed light on the genetics of A. fumigatus causing CAPA, including the prevalence of resistance-associated alleles. We present a population genomic analysis of 21 CAPA isolates from four European countries with these isolates compared against 240 non-CAPA A. fumigatus isolates from a wider population. Bioinformatic analysis and antifungal susceptibility testing were performed to quantify resistance and identify possible genetically encoded azole-resistant mechanisms. The phylogenetic analysis of the 21 CAPA isolates showed that they were representative of the wider A. fumigatus population with no obvious clustering. The prevalence of phenotypic azole resistance in CAPA was 14.3% (n = 3/21); all three CAPA isolates contained a known resistance-associated cyp51A polymorphism. The relatively high prevalence of azole resistance alleles that we document poses a probable threat to treatment success rates, warranting the enhanced surveillance of A. fumigatus genotypes in these patients. Furthermore, potential changes to antifungal first-line treatment guidelines may be needed to improve patient outcomes when CAPA is suspected.
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Affiliation(s)
- Benjamin C. Simmons
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
- UK Health Security Agency, London EP14 4PU, UK
| | - Johanna Rhodes
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
| | - Thomas R. Rogers
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands;
- Radboudumc-CWZ Center of Expertise for Mycology, Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands;
| | - Alireza Abdolrasouli
- Department of Infectious Diseases, Imperial College London, London W2 1NY, UK;
- Department of Infectious Diseases, King’s College Hospital, London SE5 9RS, UK
| | - Silke Schelenz
- Infection Sciences, King’s College Hospital, London SE5 9RS, UK;
- School of Immunology & Microbial Sciences, King’s College London, London WC2R 2LS, UK
| | - Samuel J. Hemmings
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
| | - Alida Fe Talento
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
- Department of Microbiology, Our Lady of Lourdes Hospital, A92 VW28 Drogheda, Ireland
- Department of Microbiology, Royal College of Surgeons, D02 YN77 Dublin, Ireland
| | - Auveen Griffin
- Department of Microbiology, St. James’ Hospital, D08 NHY1 Dublin, Ireland;
| | - Mary Mansfield
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
| | - David Sheehan
- Department of Clinical Microbiology, St. James’ Hospital Campus, Trinity College Dublin, D08 NHY1 Dublin, Ireland; (T.R.R.); (A.F.T.); (M.M.); (D.S.)
| | - Thijs Bosch
- Center for Infectious Disease Research, Diagnostics and Laboratory Surveillance, National for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA Bilthoven, The Netherlands;
| | - Matthew C. Fisher
- Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, UK; (J.R.); (S.J.H.); (M.C.F.)
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Rodriguez-Sanchez AC, Gónzalez-Salazar LA, Rodriguez-Orduña L, Cumsille Á, Undabarrena A, Camara B, Sélem-Mojica N, Licona-Cassani C. Phylogenetic classification of natural product biosynthetic gene clusters based on regulatory mechanisms. Front Microbiol 2023; 14:1290473. [PMID: 38029100 PMCID: PMC10663231 DOI: 10.3389/fmicb.2023.1290473] [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: 09/07/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The natural products (NPs) biosynthetic gene clusters (BGCs) represent the adapting biochemical toolkit for microorganisms to thrive different microenvironments. Despite their high diversity, particularly at the genomic level, detecting them in a shake-flask is challenging and remains the primary obstacle limiting our access to valuable chemicals. Studying the molecular mechanisms that regulate BGC expression is crucial to design of artificial conditions that derive on their expression. Here, we propose a phylogenetic analysis of regulatory elements linked to biosynthesis gene clusters, to classify BGCs to regulatory mechanisms based on protein domain information. We utilized Hidden Markov Models from the Pfam database to retrieve regulatory elements, such as histidine kinases and transcription factors, from BGCs in the MIBiG database, focusing on actinobacterial strains from three distinct environments: oligotrophic basins, rainforests, and marine environments. Despite the environmental variations, our isolated microorganisms share similar regulatory mechanisms, suggesting the potential to activate new BGCs using activators known to affect previously characterized BGCs.
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Affiliation(s)
| | - Luz A. Gónzalez-Salazar
- Centro de Biotecnologia FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
| | - Lorena Rodriguez-Orduña
- Centro de Biotecnologia FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
| | - Ándres Cumsille
- Centro de Biotecnología Daniel Alkalay, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Agustina Undabarrena
- Centro de Biotecnología Daniel Alkalay, Universidad Técnica Federico Santa María, Valparaíso, Chile
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Beatriz Camara
- Centro de Biotecnología Daniel Alkalay, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | | | - Cuauhtemoc Licona-Cassani
- Centro de Biotecnologia FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
- Integrative Biology Unit, The Institute for Obesity Research, Tecnológico de Monterrey, Monterrey, Mexico
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Arcari G, Cecilia F, Oliva A, Polani R, Raponi G, Sacco F, De Francesco A, Pugliese F, Carattoli A. Genotypic Evolution of Klebsiella pneumoniae Sequence Type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam, and Cefiderocol Treatment, Italy. Emerg Infect Dis 2023; 29:2266-2274. [PMID: 37877547 PMCID: PMC10617348 DOI: 10.3201/eid2911.230921] [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: 10/26/2023] Open
Abstract
In February 2022, a critically ill patient colonized with a carbapenem-resistant K. pneumoniae producing KPC-3 and VIM-1 carbapenemases was hospitalized for SARS-CoV-2 in the intensive care unit of Policlinico Umberto I hospital in Rome, Italy. During 95 days of hospitalization, ceftazidime/avibactam, meropenem/vaborbactam, and cefiderocol were administered consecutively to treat 3 respiratory tract infections sustained by different bacterial agents. Those therapies altered the resistome of K. pneumoniae sequence type 512 colonizing or infecting the patient during the hospitalization period. In vivo evolution of the K. pneumoniae sequence type 512 resistome occurred through plasmid loss, outer membrane porin alteration, and a nonsense mutation in the cirA siderophore gene, resulting in high levels of cefiderocol resistance. Cross-selection can occur between K. pneumoniae and treatments prescribed for other infective agents. K. pneumoniae can stably colonize a patient, and antimicrobial-selective pressure can promote progressive K. pneumoniae resistome evolution, indicating a substantial public health threat.
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55
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Lutgring JD, Kent AG, Bowers JR, Jasso-Selles DE, Albrecht V, Stevens VA, Pfeiffer A, Barnes R, Engelthaler DM, Johnson JK, Gargis AS, Rasheed JK, Limbago BM, Elkins CA, Karlsson M, Halpin AL. Comparison of carbapenem-susceptible and carbapenem-resistant Enterobacterales at nine sites in the USA, 2013-2016: a resource for antimicrobial resistance investigators. Microb Genom 2023; 9. [PMID: 37987646 DOI: 10.1099/mgen.0.001119] [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: 11/22/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) are an urgent public health threat. Genomic sequencing is an important tool for investigating CRE. Through the Division of Healthcare Quality Promotion Sentinel Surveillance system, we collected CRE and carbapenem-susceptible Enterobacterales (CSE) from nine clinical laboratories in the USA from 2013 to 2016 and analysed both phenotypic and genomic sequencing data for 680 isolates. We describe the molecular epidemiology and antimicrobial susceptibility testing (AST) data of this collection of isolates. We also performed a phenotype-genotype correlation for the carbapenems and evaluated the presence of virulence genes in Klebsiella pneumoniae complex isolates. These AST and genomic sequencing data can be used to compare and contrast CRE and CSE at these sites and serve as a resource for the antimicrobial resistance research community.
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Affiliation(s)
- Joseph D Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alyssa G Kent
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Jolene R Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Daniel E Jasso-Selles
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Valerie Albrecht
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of the Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Valerie A Stevens
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ashlyn Pfeiffer
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - Riley Barnes
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - David M Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute North, Flagstaff, Arizona, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amy S Gargis
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Kamile Rasheed
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brandi M Limbago
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Present address: Office of Science, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Karlsson
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Alison L Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Subramani P, Menichincheri G, Pirolo M, Arcari G, Kudirkiene E, Polani R, Carattoli A, Damborg P, Guardabassi L. Genetic background of neomycin resistance in clinical Escherichia coli isolated from Danish pig farms. Appl Environ Microbiol 2023; 89:e0055923. [PMID: 37787538 PMCID: PMC10617424 DOI: 10.1128/aem.00559-23] [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: 04/04/2023] [Accepted: 07/28/2023] [Indexed: 10/04/2023] Open
Abstract
Neomycin is the first-choice antibiotic for the treatment of porcine enteritis caused by enterotoxigenic Escherichia coli. Resistance to this aminoglycoside is on the rise after the increased use of neomycin due to the ban on zinc oxide. We identified the neomycin resistance determinants and plasmid contents in a historical collection of 128 neomycin-resistant clinical E. coli isolates from Danish pig farms. All isolates were characterized by whole-genome sequencing and antimicrobial susceptibility testing, followed by conjugation experiments and long-read sequencing of eight selected representative strains. We detected 35 sequence types (STs) with ST100 being the most prevalent lineage (38.3%). Neomycin resistance was associated with two resistance genes, namely aph(3')-Ia and aph(3')-Ib, which were identified in 93% and 7% of the isolates, respectively. The aph(3')-Ia was found on different large conjugative plasmids belonging to IncI1α, which was present in 67.2% of the strains, on IncHI1, IncHI2, and IncN, as well as on a multicopy ColRNAI plasmid. All these plasmids except ColRNAI carried genes encoding resistance to other antimicrobials or heavy metals, highlighting the risk of co-selection. The aph(3')-Ib gene occurred on a 19 kb chimeric, mobilizable plasmid that contained elements tracing back its origin to distantly related genera. While aph(3')-Ia was flanked by either Tn903 or Tn4352 derivatives, no clear association was observed between aph(3')-Ib and mobile genetic elements. In conclusion, the spread of neomycin resistance in porcine clinical E. coli is driven by two resistance determinants located on distinct plasmid scaffolds circulating within a highly diverse population dominated by ST100. IMPORTANCE Neomycin is the first-choice antibiotic for the management of Escherichia coli enteritis in pigs. This work shows that aph(3')-Ia and to a lesser extent aph(3')-Ib are responsible for the spread of neomycin resistance that has been recently observed among pig clinical isolates and elucidates the mechanisms of dissemination of these two resistance determinants. The aph(3')-Ia gene is located on different conjugative plasmid scaffolds and is associated with two distinct transposable elements (Tn903 and Tn4352) that contributed to its spread. The diffusion of aph(3')-Ib is mediated by a small non-conjugative, mobilizable chimeric plasmid that likely derived from distantly related members of the Pseudomonadota phylum and was not associated with any detectable mobile genetic element. Although the spread of neomycin resistance is largely attributable to horizontal transfer, both resistance determinants have been acquired by a predominant lineage (ST100) associated with enterotoxigenic E. coli, which accounted for approximately one-third of the strains.
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Affiliation(s)
- Prabha Subramani
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | - Gaia Menichincheri
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | - Mattia Pirolo
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
| | - Gabriele Arcari
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | - Egle Kudirkiene
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
| | - Riccardo Polani
- Department of Molecular Medicine Sapienza, University of Rome, Rome, Italy
| | | | - Peter Damborg
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, Section for Veterinary Clinical Microbiology, University of Copenhagen, Frederiksberg C, Denmark
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Abrudan MI, Shamanna V, Prasanna A, Underwood A, Argimón S, Nagaraj G, Di Gregorio S, Govindan V, Vasanth A, Dharmavaram S, Kekre M, Aanensen DM, Ravikumar KL. Novel multidrug-resistant sublineages of Staphylococcus aureus clonal complex 22 discovered in India. mSphere 2023; 8:e0018523. [PMID: 37698417 PMCID: PMC10597471 DOI: 10.1128/msphere.00185-23] [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: 04/11/2023] [Accepted: 07/13/2023] [Indexed: 09/13/2023] Open
Abstract
Staphylococcus aureus is a major pathogen in India causing community and nosocomial infections, but little is known about its molecular epidemiology and mechanisms of resistance in hospital settings. Here, we use whole-genome sequencing (WGS) to characterize 478 S. aureus clinical isolates (393 methicillin-resistant Staphylococcus aureus (MRSA) and 85 methicilin-sensitive Staphylococcus aureus (MSSA) collected from 17 sentinel sites across India between 2014 and 2019. Sequencing results confirmed that sequence type 22 (ST22) (142 isolates, 29.7%), ST239 (74 isolates, 15.48%), and ST772 (67 isolates, 14%) were the most common clones. An in-depth analysis of 175 clonal complex (CC) 22 Indian isolates identified two novel ST22 MRSA lineages, both Panton-Valentine leukocidin+, both resistant to fluoroquinolones and aminoglycosides, and one harboring the the gene for toxic shock syndrome toxin 1 (tst). A temporal analysis of 1797 CC22 global isolates from 14 different studies showed that the two Indian ST22 lineages shared a common ancestor in 1984 (95% highest posterior density [HPD]: 1982-1986), as well as evidence of transmission to other parts of the world. Moreover, the study also gives a comprehensive view of ST2371, a sublineage of CC22, as a new emerging lineage in India and describes it in relationship with the other Indian ST22 isolates. In addition, the retrospective identification of a putative outbreak of multidrug-resistant (MDR) ST239 from a single hospital in Bangalore that persisted over a period of 3 years highlights the need for the implementation of routine surveillance and simple infection prevention and control measures to reduce these outbreaks. To our knowledge, this is the first WGS study that characterized CC22 in India and showed that the Indian clones are distinct from the EMRSA-15 clone. Thus, with the improved resolution afforded by WGS, this study substantially contributed to our understanding of the global population of MRSA. IMPORTANCE The study conducted in India between 2014 and 2019 presents novel insights into the prevalence of MRSA in the region. Previous studies have characterized two dominant clones of MRSA in India, ST772 and ST239, using whole-genome sequencing. However, this study is the first to describe the third dominant clone, ST22, using the same approach. The ST22 Indian isolates were analyzed in-depth, leading to the discovery of two new sublineages of hospital-acquired Staphylococcus aureus in India, both carrying antimicrobial resistance genes and mutations, which limit treatment options for patients. One of the newly characterized sublineages, second Indian cluster, carries the tsst-1 virulence gene, increasing the risk of severe infections. The geographic spread of the two novel lineages, both within India and internationally, could pose a global public health threat. The study also sheds light on ST2371 in India, a single-locus variant of ST22. The identification of a putative outbreak of MDR ST239 in a single hospital in Bangalore emphasizes the need for routine surveillance and simple infection prevention and control measures to reduce these outbreaks. Overall, this study significantly contributes to our understanding of the global population of MRSA, thanks to the improved resolution afforded by WGS.
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Affiliation(s)
- Monica I. Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
- Department of Biotechnology, NMAM Institute of Technology, Nitte (Deemed to be University), Mangalore, India
| | - Akshatha Prasanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Sabrina Di Gregorio
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Vandana Govindan
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Ashwini Vasanth
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Sravani Dharmavaram
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - K. L. Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
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Rodriguez EI, Tzeng YL, Stephens DS. Continuing genomic evolution of the Neisseria meningitidis cc11.2 urethritis clade, NmUC: a narrative review. Microb Genom 2023; 9:001113. [PMID: 37850987 PMCID: PMC10634446 DOI: 10.1099/mgen.0.001113] [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: 02/21/2023] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
Neisseria meningitidis (Nm) is a bacterial pathogen responsible for invasive meningococcal disease. Though typically colonizing the nasopharynx, multiple outbreaks of meningococcal urethritis were first reported in 2015-2016; outbreaks originally presumed to be caused by Neisseria gonorrhoeae (Ng). Genomic analysis revealed that the Nm isolates causing these outbreaks were a distinct clade, and had integrated gonococcal DNA at multiple genomic sites, including the gonococcal denitrification apparatus aniA-norB, a partial gonococcal operon of five genes containing ispD, and the acetylglutamate kinase gene argB with the adjacent gonococcal locus NGO0843. The urethritis isolates had also deleted the group C capsule biosynthesis genes cssA/B/C and csc, resulting in loss of capsule. Collectively, these isolates form the N. meningitidis urethritis clade (NmUC). Genomic analysis of recent (2016-2022) NmUC isolates revealed that the genomic features have been maintained in the clade, implying that they are important for NmUC's status as a urogenital pathogen. Furthermore, the analysis revealed the emergence of a sub-clade, designated NmUC-B, phylogenetically separated from the earlier NmUC-A. This sub-clade has integrated additional gonococcal alleles into the genome, including alleles associated with antimicrobial resistance. NmUC continues to adapt to a urethral niche and evolve as a urogenital pathogen.
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Affiliation(s)
- Emilio I. Rodriguez
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Yih-Ling Tzeng
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - David S. Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
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59
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Hamilton WL, Coscione S, Maes M, Warne B, Pike LJ, Khokhar FA, Blane B, Brown NM, Gouliouris T, Dougan G, Török ME, Baker S. The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom. Microb Genom 2023; 9:001122. [PMID: 37902454 PMCID: PMC10634454 DOI: 10.1099/mgen.0.001122] [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: 06/28/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023] Open
Abstract
Escherichia coli is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of E. coli BSI has increased over the last decade in the UK, and emerging antimicrobial resistance (AMR) profiles threaten treatment options. Here, we combined clinical, epidemiological, and whole genome sequencing data with high content imaging to characterise over 300 E. coli isolates associated with BSI in a large teaching hospital in the East of England. Overall, only a limited number of sequence types (ST) were responsible for the majority of organisms causing invasive disease. The most abundant (20 % of all isolates) was ST131, of which around 90 % comprised the pandemic O25b:H4 group. ST131-O25b:H4 isolates were frequently multi-drug resistant (MDR), with a high prevalence of extended spectrum β-lactamases (ESBL) and fluoroquinolone resistance. There was no association between AMR phenotypes and the source of E. coli bacteraemia or whether the infection was healthcare-associated. Several clusters of ST131 were genetically similar, potentially suggesting a shared transmission network. However, there was no clear epidemiological associations between these cases, and they included organisms from both healthcare-associated and non-healthcare-associated origins. The majority of ST131 isolates exhibited strong binding with an anti-O25b antibody, raising the possibility of developing rapid diagnostics targeting this pathogen. In summary, our data suggest that a restricted set of MDR E. coli populations can be maintained and spread across both community and healthcare settings in this location, contributing disproportionately to invasive disease and AMR.
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Affiliation(s)
- William L. Hamilton
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
| | - Suny Coscione
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Mailis Maes
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Ben Warne
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lindsay J. Pike
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1RQ, UK
| | - Fahad A. Khokhar
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- University of Cambridge, Department of Veterinary Medicine, Madingley Road, Cambridge, CB3 0ES, UK
| | - Beth Blane
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
| | - Nicholas M. Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
- Clinical Microbiology and Public Health Laboratory, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Gordon Dougan
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
| | - M. Estée Török
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0QQ, UK
| | - Stephen Baker
- University of Cambridge, Department of Medicine, Cambridge Biomedical Campus, Hills Road, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
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60
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Zang X, Pascoe B, Mourkas E, Kong K, Jiao X, Sheppard SK, Huang J. Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations. Microb Genom 2023; 9:001121. [PMID: 37877958 PMCID: PMC10634442 DOI: 10.1099/mgen.0.001121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
Non-human primates share recent common ancestry with humans and exhibit comparable disease symptoms. Here, we explored the transmission potential of enteric bacterial pathogens in monkeys exhibiting symptoms of recurrent diarrhoea in a biomedical research facility in China. The common zoonotic bacterium Campylobacter jejuni was isolated from macaques (Macaca mulatta and Macaca fascicularis) and compared to isolates from humans and agricultural animals in Asia. Among the monkeys sampled, 5 % (44/973) tested positive for C. jejuni, 11 % (5/44) of which displayed diarrhoeal symptoms. Genomic analysis of monkey isolates, and 1254 genomes from various sources in Asia, were used to identify the most likely source of human infection. Monkey and human isolates shared high average nucleotide identity, common MLST clonal complexes and clustered together on a phylogeny. Furthermore, the profiles of putative antimicrobial resistance genes were similar between monkeys and humans. Taken together these findings suggest that housed macaques became infected with C. jejuni either directly from humans or via a common contamination source.
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Affiliation(s)
- Xiaoqi Zang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Ben Pascoe
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, UK
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Ke Kong
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, UK
| | - Jinlin Huang
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou, PR China
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61
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Gulla S, Colquhoun DJ, Olsen AB, Spilsberg B, Lagesen K, Åkesson CP, Strøm S, Manji F, Birkbeck TH, Nilsen HK. Phylogeography and host specificity of Pasteurellaceae pathogenic to sea-farmed fish in the north-east Atlantic. Front Microbiol 2023; 14:1236290. [PMID: 37808299 PMCID: PMC10556747 DOI: 10.3389/fmicb.2023.1236290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/23/2023] [Indexed: 10/10/2023] Open
Abstract
The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon (Salmo salar) in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish (Cyclopterus lumpus) used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cultured from diseased salmon or lumpfish confirmed them all as bona fide members of the Pasteurellaceae family, with phylogenetic reconstruction dividing them into two distinct branches sharing <88% average nucleotide identity. These branches therefore constitute two separate species, namely Pasteurella skyensis and the as-yet invalidly named "Pasteurella atlantica". Both species further stratify into multiple discrete genomovars (gv.) and/or lineages, each being nearly or fully exclusive to a particular host, geographic region, and/or time period. Pasteurellosis in lumpfish is, irrespective of spatiotemporal origin, linked almost exclusively to the highly conserved "P. atlantica gv. cyclopteri" (Pac). In contrast, pasteurellosis in Norwegian sea-farmed salmon, dominated since the late-1980s by "P. atlantica gv. salmonicida" (Pas), first saw three specific lineages (Pas-1, -2, and -3) causing separate, geographically restricted, and short-lived outbreaks, before a fourth (Pas-4) emerged recently and became more widely disseminated. A similar situation involving P. skyensis (Ps) has apparently been unfolding in Scottish salmon farming since the mid-1990s, where two historic (Ps-1 and -2) and one contemporary (Ps-3) lineages have been recorded. While the epidemiology underlying all these outbreaks/epizootics remains unclear, repeated detection of 16S rRNA gene amplicons very closely related to P. skyensis and "P. atlantica" from at least five cetacean species worldwide raises the question as to whether marine mammals may play a part, possibly as reservoirs. In fact, the close relationship between the studied isolates and Phocoenobacter uteri associated with harbor porpoise (Phocoena phocoena), and their relatively distant relationship with other members of the genus Pasteurella, suggests that both P. skyensis and "P. atlantica" should be moved to the genus Phocoenobacter.
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Affiliation(s)
| | - Duncan J. Colquhoun
- Norwegian Veterinary Institute, Ås, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | | | | | | | - Sverri Strøm
- FoMAS – Fiskehelse og Miljø AS, Karmsund, Norway
| | | | - Thomas H. Birkbeck
- Division of Infection and Immunity, University of Glasgow, Glasgow, Scotland, United Kingdom
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Mentasti M, David S, Turton J, Morgan M, Turner L, Westlake J, Jenkins J, Williams C, Rey S, Watkins J, Daniel V, Mitchell S, Forbes G, Wootton M, Jones L. Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK. Microb Genom 2023; 9:001104. [PMID: 37668148 PMCID: PMC10569728 DOI: 10.1099/mgen.0.001104] [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: 05/20/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023] Open
Abstract
A multidrug-resistant strain of Klebsiella pneumoniae (Kp) sequence type (ST) 1788, an otherwise uncommon ST worldwide, was isolated from 65 patients at 11 hospitals and 11 general practices across South and West Wales, UK, between February 2019 and November 2021. A collection of 97 Kp ST1788 isolates (including 94 from Wales) was analysed to investigate the diversity and spread across Wales and to identify molecular marker(s) to aid development of a strain-specific real-time PCR. Whole genome sequencing (WGS) was performed with Illumina technology and the data were used to perform phylogenetic analyses. Pan-genome analysis of further Kp genome collections was used to identify an ST1788-specific gene target; a real-time PCR was then validated against a panel of 314 strains and 218 broth-enriched screening samples. Low genomic diversity was demonstrated amongst the 94 isolates from Wales. Evidence of spread within and across healthcare facilities was found. A yersiniabactin locus and the KL2 capsular locus were identified in 85/94 (90.4 %) and 94/94 (100 %) genomes respectively; bla SHV-232, bla TEM-1, bla CTX-M-15 and bla OXA-1 were simultaneously carried by 86/94 (91.5 %) isolates; 4/94 (4.3 %) isolates also carried bla OXA-48 carbapenemase. Aminoglycoside and fluoroquinolone resistance markers were found in 94/94 (100 %) and 86/94 (91.5 %) isolates respectively. The ST1788-specific real-time PCR was 100 % sensitive and specific. Our analyses demonstrated recent clonal expansion and spread of Kp ST1788 in the community and across healthcare facilities in South and West Wales with isolates carrying well-defined antimicrobial resistance and virulence markers. An ST1788-specific marker was also identified, enabling rapid and reliable preliminary characterization of isolates by real-time PCR. This study confirms the utility of WGS in investigating novel strains and in aiding proactive implementation of molecular tools to assist infection control specialists.
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Affiliation(s)
- Massimo Mentasti
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, OX3 7LF, UK
| | - Jane Turton
- HCAI, Fungal, AMR, AMU & Sepsis Division, UK Health Security Agency, London, NW9 5HT, UK
| | - Mari Morgan
- Healthcare Associated Infection, Antimicrobial Resistance Prescribing Programme, Public Health Wales Health Protection, Cardiff, CF10 4BZ, UK
| | - Luke Turner
- Bacteriology Department, Public Health Wales Microbiology, Swansea, SA2 8QA, UK
| | - Joseph Westlake
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Jonathan Jenkins
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Catie Williams
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Sara Rey
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Joanne Watkins
- Pathogen Genomics Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Victoria Daniel
- Bacteriology Department, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Shanine Mitchell
- Bacteriology Department, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Gavin Forbes
- Bacteriology Department, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Mandy Wootton
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
| | - Lim Jones
- Specialist Antimicrobial Chemotherapy Unit, Public Health Wales Microbiology, Cardiff, CF14 4XW, UK
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63
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Crestani C, Arcari G, Landier A, Passet V, Garnier D, Brémont S, Armatys N, Carmi-Leroy A, Toubiana J, Badell E, Brisse S. Corynebacterium ramonii sp. nov., a novel toxigenic member of the Corynebacterium diphtheriae species complex. Res Microbiol 2023; 174:104113. [PMID: 37572824 DOI: 10.1016/j.resmic.2023.104113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The Corynebacterium diphtheriae species complex comprises seven bacterial species, including Corynebacterium ulcerans, a zoonotic pathogen from multiple animal species. In this work, we characterise phenotypically and genotypically isolates belonging to two C. ulcerans lineages. Results from phylogenetic analyses, in silico DNA-DNA hybridization (DDH) and MALDI-TOF spectra differentiate lineage 2 from C. ulcerans lineage 1, which, together with their distinct transmission dynamics (probable human-to-human vs animal-to-human), indicates that lineage 2 is a separate Corynebacterium species, which we propose to name Corynebacterium ramonii. This species is of particular medical interest considering that its human-to-human transmission is likely, and that some C. ramonii isolates carry the diphtheria toxin gene.
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Affiliation(s)
- Chiara Crestani
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
| | - Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Annie Landier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Dorian Garnier
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvie Brémont
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Nathalie Armatys
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Annick Carmi-Leroy
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Julie Toubiana
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France; Necker-Enfants Malades University Hospital, Paris, France
| | - Edgar Badell
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France; Institut Pasteur, French National Reference Center for Corynebacteria of the Diphtheriae Complex, Paris, France.
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64
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Nuanmuang N, Leekitcharoenphon P, Njage PMK, Gmeiner A, Aarestrup FM. An Overview of Antimicrobial Resistance Profiles of Publicly Available Salmonella Genomes with Sufficient Quality and Metadata. Foodborne Pathog Dis 2023; 20:405-413. [PMID: 37540138 PMCID: PMC10510693 DOI: 10.1089/fpd.2022.0080] [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: 08/05/2023] Open
Abstract
Salmonella enterica (S. enterica) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns. A decade ago, it was estimated that the increased use of whole genome sequencing (WGS) combined with sharing of public data would drastically change and improve the surveillance and understanding of Salmonella epidemiology and AMR. This study aimed to evaluate the current usefulness of public WGS data for Salmonella surveillance and to investigate the associations between serovars, antibiotic resistance genes (ARGs), and metadata. Out of 191,306 Salmonella genomes deposited in European Nucleotide Archive and NCBI databases, 47,452 WGS with sufficient minimum metadata (country, year, and source) of S. enterica were retrieved from 116 countries and isolated between 1905 and 2020. For in silico analysis of the WGS data, KmerFinder, SISTR, and ResFinder were used for species, serovars, and AMR identification, respectively. The results showed that the five common isolation sources of S. enterica are human (29.10%), avian (22.50%), environment (11.89%), water (9.33%), and swine (6.62%). The most common ARG profiles for each class of antimicrobials are β-lactam (blaTEM-1B; 6.78%), fluoroquinolone [(parC[T57S], qnrB19); 0.87%], folate pathway antagonist (sul2; 8.35%), macrolide [mph(A); 0.39%], phenicol (floR; 5.94%), polymyxin B (mcr-1.1; 0.09%), and tetracycline [tet(A); 12.95%]. Our study reports the first overview of ARG profiles in publicly available Salmonella genomes from online databases. All data sets from this study can be searched at Microreact.
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Affiliation(s)
- Narong Nuanmuang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Murigu Kamau Njage
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Alexander Gmeiner
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Arcari G, Polani R, Santilli S, Capitani V, Sacco F, Bruno F, Garcia-Fernandez A, Raponi G, Villa L, Gentile G, Carattoli A. Multiplicity of blaKPC Genes and pKpQIL Plasmid Plasticity in the Development of Ceftazidime-Avibactam and Meropenem Coresistance in Klebsiella pneumoniae Sequence Type 307. Antimicrob Agents Chemother 2023; 67:e0036823. [PMID: 37428086 PMCID: PMC10433805 DOI: 10.1128/aac.00368-23] [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: 03/20/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
In 2021, Klebsiella pneumoniae sequence type 307 (ST307) strains causing pulmonary and bloodstream infections identified in a hospital in Rome, Italy, reached high levels of resistance to ceftazidime-avibactam (CZA). One of these strains reached high levels of resistance to both CZA and carbapenems and carried two copies of blaKPC-3 and one copy of blaKPC-31 located on plasmid pKpQIL. The genomes and plasmids of CZA-resistant ST307 strains were analyzed to identify the molecular mechanisms leading to the evolution of resistance and compared with ST307 genomes at local and global levels. A complex pattern of multiple plasmids in rearranged configurations, coresident within the CZA-carbapenem-resistant K. pneumoniae strain, was observed. Characterization of these plasmids revealed recombination and segregation events explaining why K. pneumoniae isolates from the same patient had different antibiotic resistance profiles. This study illustrates the intense genetic plasticity occurring in ST307, one of the most worldwide-diffused K. pneumoniae high-risk clones.
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Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Riccardo Polani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Stefania Santilli
- Complex Operating Unit of Microbiology and Virology, Policlinico Umberto I, Rome, Italy
| | - Valerio Capitani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Federica Sacco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Complex Operating Unit of Microbiology and Virology, Policlinico Umberto I, Rome, Italy
| | - Francesco Bruno
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Giammarco Raponi
- Complex Operating Unit of Microbiology and Virology, Policlinico Umberto I, Rome, Italy
- Department of Public Health, Sapienza University of Rome, Rome, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppe Gentile
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
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66
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Afolayan AO, Rigatou A, Grundmann H, Pantazatou A, Daikos G, Reuter S. Three Klebsiella pneumoniae lineages causing bloodstream infections variably dominated within a Greek hospital over a 15 year period. Microb Genom 2023; 9:mgen001082. [PMID: 37642647 PMCID: PMC10483420 DOI: 10.1099/mgen.0.001082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a major clinical and public health threat. The rapid dissemination of this pathogen is driven by several successful clones worldwide. We aimed to investigate the CRKP clonal lineages, their antibiotic resistance determinants and their potential transmissions in a tertiary care hospital located in Athens, Greece. Between 2003 and 2018, 392 CRKP isolates from bloodstream infections were recovered from hospitalized patients. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize 209 of these isolates. In total, 74 % (n=155) of 209 isolates belonged to three major clonal lineages: ST258 (n=108), ST147 (n=29) and ST11 (n=18). Acquired carbapenemase genes were the mechanisms of resistance in 205 isolates (bla KPC, n=123; bla VIM, n=56; bla NDM, n=20; bla OXA-48, n=6). Strong associations (P=0.0004) were observed between carbapenemase genes and clonal lineages. We first isolated bla VIM-1-carrying ST147 strains during the early sampling period in 2003, followed by the emergence of bla KPC-2-carrying ST258 in 2006 and bla NDM-1-carrying ST11 in 2013. Analysis of genetic distances between the isolates revealed six potential transmission events. When contextualizing the current collection with published data, ST147 reflected the global diversity, ST258 clustered with isolates representing the first introduction into Europe and ST11 formed a distinct geographically restricted lineage indicative of local spread. This study demonstrates the changing profile of bloodstream CRKP in a tertiary care hospital over a 15 year period and underlines the need for continued genomic surveys to develop strategies to contain further dissemination. This article contains data hosted by Microreact.
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Affiliation(s)
- Ayorinde O. Afolayan
- Institute for Infection Prevention and Control, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Hajo Grundmann
- Institute for Infection Prevention and Control, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - George Daikos
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sandra Reuter
- Institute for Infection Prevention and Control, Medical Center - University of Freiburg, Freiburg, Germany
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67
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Rodrigues JA, Blankenship HM, Cha W, Mukherjee S, Sloup RE, Rudrik JT, Soehnlen M, Manning SD. Pangenomic analyses of antibiotic-resistant Campylobacter jejuni reveal unique lineage distributions and epidemiological associations. Microb Genom 2023; 9:mgen001073. [PMID: 37526649 PMCID: PMC10483415 DOI: 10.1099/mgen.0.001073] [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: 10/06/2022] [Accepted: 06/29/2023] [Indexed: 08/02/2023] Open
Abstract
Application of whole-genome sequencing (WGS) to characterize foodborne pathogens has advanced our understanding of circulating genotypes and evolutionary relationships. Herein, we used WGS to investigate the genomic epidemiology of Campylobacter jejuni, a leading cause of foodborne disease. Among the 214 strains recovered from patients with gastroenteritis in Michigan, USA, 85 multilocus sequence types (STs) were represented and 135 (63.1 %) were phenotypically resistant to at least one antibiotic. Horizontally acquired antibiotic resistance genes were detected in 128 (59.8 %) strains and the genotypic resistance profiles were mostly consistent with the phenotypes. Core-gene phylogenetic reconstruction identified three sequence clusters that varied in frequency, while a neighbour-net tree detected significant recombination among the genotypes (pairwise homoplasy index P<0.01). Epidemiological analyses revealed that travel was a significant contributor to pangenomic and ST diversity of C. jejuni, while some lineages were unique to rural counties and more commonly possessed clinically important resistance determinants. Variation was also observed in the frequency of lineages over the 4 year period with chicken and cattle specialists predominating. Altogether, these findings highlight the importance of geographically specific factors, recombination and horizontal gene transfer in shaping the population structure of C. jejuni. They also illustrate the usefulness of WGS data for predicting antibiotic susceptibilities and surveillance, which are important for guiding treatment and prevention strategies.
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Affiliation(s)
- Jose A. Rodrigues
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Heather M. Blankenship
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Wonhee Cha
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Present address: National Veterinary Institute, Uppsala, Sweden
| | - Sanjana Mukherjee
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Present address: Center for Global Health Science and Security, Georgetown University, Washington, USA
| | - Rebekah E. Sloup
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - James T. Rudrik
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Marty Soehnlen
- Michigan Department of Health and Human Services, Bureau of Laboratories, Lansing, Michigan, USA
| | - Shannon D. Manning
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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Burgaya J, Marin J, Royer G, Condamine B, Gachet B, Clermont O, Jaureguy F, Burdet C, Lefort A, de Lastours V, Denamur E, Galardini M, Blanquart F. The bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans. PLoS Genet 2023; 19:e1010842. [PMID: 37531401 PMCID: PMC10395866 DOI: 10.1371/journal.pgen.1010842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023] Open
Abstract
Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.
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Affiliation(s)
- Judit Burgaya
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - Julie Marin
- Université Sorbonne Paris Nord, INSERM, IAME, Bobigny, France
| | - Guilhem Royer
- Université Paris Cité, INSERM, IAME, Paris, France
- Département de Prévention, Diagnostic et Traitement des Infections, Hôpital Henri Mondor, Créteil, France
- Unité Ecologie et Evolution de la Résistance aux Antibiotiques, Institut Pasteur, UMR CNRS 6047, Université Paris-Cité, Paris, France
| | | | | | | | | | | | - Agnès Lefort
- Université Paris Cité, INSERM, IAME, Paris, France
| | | | - Erick Denamur
- Université Paris Cité, INSERM, IAME, Paris, France
- Laboratoire de Génétique Moléculaire, Hôpital Bichat, AP-HP, Paris, France
| | - Marco Galardini
- Institute for Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School (MHH), Hannover, Germany
| | - François Blanquart
- Center for Interdisciplinary Research in Biology, Collège de France, CNRS UMR7241 / INSERM U1050, PSL Research University, Paris, France
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Coyle NM, O'Toole C, Thomas JCL, Ryder D, Feil EJ, Geary M, Bean TP, Joseph AW, Waine A, Cheslett D, Verner-Jeffreys DW. Vibrio aestuarianus clade A and clade B isolates are associated with Pacific oyster ( Magallana gigas) disease outbreaks across Ireland. Microb Genom 2023; 9:mgen001078. [PMID: 37540224 PMCID: PMC10483421 DOI: 10.1099/mgen.0.001078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023] Open
Abstract
Bacteria from the family Vibrionaceae have been implicated in mass mortalities of farmed Pacific oysters (Magallana gigas) in multiple countries, leading to substantial impairment of growth in the sector. In Ireland there has been concern that Vibrio have been involved in serious summer outbreaks. There is evidence that Vibrio aestuarianus is increasingly becoming the main pathogen of concern for the Pacific oyster industry in Ireland. While bacteria belonging to the Vibrio splendidus clade are also detected frequently in mortality episodes, their role in the outbreaks of summer mortality is not well understood. To identify and characterize strains involved in these outbreaks, 43 Vibrio isolates were recovered from Pacific oyster summer mass mortality episodes in Ireland from 2008 to 2015 and these were whole-genome sequenced. Among these, 25 were found to be V. aestuarianus (implicated in disease) and 18 were members of the V. splendidus species complex (role in disease undetermined). Two distinct clades of V. aestuarianus - clade A and clade B - were found that had previously been described as circulating within French oyster culture. The high degree of similarity between the Irish and French V. aestuarianus isolates points to translocation of the pathogen between Europe's two major oyster-producing countries, probably via trade in spat and other age classes. V. splendidus isolates were more diverse, but the data reveal a single clone of this species that has spread across oyster farms in Ireland. This underscores that Vibrio could be transmitted readily across oyster farms. The presence of V. aestuarianus clades A and B in not only France but also Ireland adds weight to growing concern that this pathogen is spreading and impacting Pacific oyster production within Europe.
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Affiliation(s)
- Nicola M. Coyle
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Ciar O'Toole
- Marine Institute, Oranmore, Co. Galway H91 R673, Ireland
| | - Jennifer C. L. Thomas
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - David Ryder
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
| | - Edward J. Feil
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Michelle Geary
- Marine Institute, Oranmore, Co. Galway H91 R673, Ireland
| | - Timothy P. Bean
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | | | - Ava Waine
- Centre for Environment Fisheries and Aquaculture, Weymouth DT4 8UB, UK
- Newcastle University, School of Natural and Environmental Sciences, Newcastle Upon Tyne, NE1 7RU, UK
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Jimenez-Silva C, Rivero R, Douglas J, Bouckaert R, Villabona-Arenas CJ, Atkins KE, Gastelbondo B, Calderon A, Guzman C, Echeverri-De la Hoz D, Muñoz M, Ballesteros N, Castañeda S, Patiño LH, Ramirez A, Luna N, Paniz-Mondolfi A, Serrano-Coll H, Ramirez JD, Mattar S, Drummond AJ. Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia. COMMUNICATIONS MEDICINE 2023; 3:97. [PMID: 37443390 DOI: 10.1038/s43856-023-00328-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. METHODS To better understand the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia. We performed Bayesian phylodynamic analyses to estimate the time of variants' introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. RESULTS Here, we detect a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the pandemic's start. We show that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). CONCLUSIONS Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions toward the emergence and circulation of novel SARS-CoV-2 variants.
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Affiliation(s)
- Cinthy Jimenez-Silva
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
| | - Ricardo Rivero
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia.
- Paul G. Allen School for Global Health, Washington State University, Pullman, Washington, USA.
| | - Jordan Douglas
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- Department of Physics, University of Auckland, Auckland, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
| | - Ch Julian Villabona-Arenas
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katherine E Atkins
- Centre for Mathematical Modelling of Infectious Diseases and Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
- Centre for Global Health, Usher Institute, Edinburgh Medical School, University of Edinburgh, Edinburgh, UK
| | - Bertha Gastelbondo
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
- Grupo de Investigaciones Microbiológicas y Biomédicas de Córdoba-GIMBIC, Universidad de Córdoba, Monteria, Colombia
- Grupo de Salud Pública y Auditoría en Salud, Corporación Universitaria del Caribe- CECAR, Sincelejo, Colombia
| | - Alfonso Calderon
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
| | - Camilo Guzman
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
- Grupo de Investigación, Evaluación y Desarrollo de Farmacos y Afines - IDEFARMA, Universidad de Córdoba, Montería, Colombia
| | - Daniel Echeverri-De la Hoz
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz H Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Hector Serrano-Coll
- Instituto Colombiano de Medicina Tropical-Universidad CES, Medellín, Colombia
| | - Juan David Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - Salim Mattar
- Instituto de Investigaciones Biológicas del Trópico (IIBT), Facultad de Medicina Veterinaria y Zootecnia, Universidad de Córdoba, Montería, Colombia.
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
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71
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Rhoads DD, Pummil J, Ekesi NS, Alrubaye AAK. Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis. PLoS One 2023; 18:e0283914. [PMID: 37406030 DOI: 10.1371/journal.pone.0283914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.
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Affiliation(s)
- Douglas D Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
| | - Jeff Pummil
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Arkansas High Performance Computing Center, University of Arkansas, Fayetteville, AR, United States of America
| | - Nnamdi S Ekesi
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK, United States of America
| | - Adnan A K Alrubaye
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, United States of America
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Ljungquist O, Haldorsen B, Pöntinen AK, Janice J, Josefsen EH, Elstrøm P, Kacelnik O, Sundsfjord A, Samuelsen Ø. Nationwide, population-based observational study of the molecular epidemiology and temporal trend of carbapenemase-producing Enterobacterales in Norway, 2015 to 2021. Euro Surveill 2023; 28:2200774. [PMID: 37410381 PMCID: PMC10370044 DOI: 10.2807/1560-7917.es.2023.28.27.2200774] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/29/2023] [Indexed: 07/07/2023] Open
Abstract
IntroductionNational and regional carbapenemase-producing Enterobacterales (CPE) surveillance is essential to understand the burden of antimicrobial resistance, elucidate outbreaks, and develop infection-control or antimicrobial-treatment recommendations.AimThis study aimed to describe CPE and their epidemiology in Norway from 2015 to 2021.MethodsA nationwide, population-based observational study of all verified clinical and carriage CPE isolates submitted to the national reference laboratory was conducted. Isolates were characterised by antimicrobial susceptibility testing, whole genome sequencing (WGS) and basic metadata. Annual CPE incidences were also estimated.ResultsA total of 389 CPE isolates were identified from 332 patients of 63 years median age (range: 0-98). These corresponded to 341 cases, 184 (54%) being male. Between 2015 and 2021, the annual incidence of CPE cases increased from 0.6 to 1.1 per 100,000 person-years. For CPE-isolates with available data on colonisation/infection, 58% (226/389) were associated with colonisation and 38% (149/389) with clinical infections. WGS revealed a predominance of OXA-48-like (51%; 198/389) and NDM (34%; 134/389) carbapenemases in a diversified population of Escherichia coli and Klebsiella pneumoniae, including high-risk clones also detected globally. Most CPE isolates were travel-related (63%; 245/389). Although local outbreaks and healthcare-associated transmission occurred, no interregional spread was detected. Nevertheless, 18% (70/389) of isolates not directly related to import points towards potentially unidentified transmission routes. A decline in travel-associated cases was observed during the COVID-19 pandemic.ConclusionsThe close-to-doubling of CPE case incidence between 2015 and 2021 was associated with foreign travel and genomic diversity. To limit further transmission and outbreaks, continued screening and monitoring is essential.
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Affiliation(s)
- Oskar Ljungquist
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Bjørg Haldorsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Jessin Janice
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Ellen Haldis Josefsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Petter Elstrøm
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Oliver Kacelnik
- Department of Antibiotic Resistance and Infection Prevention, Norwegian Institute of Public Health, Oslo, Norway
| | - Arnfinn Sundsfjord
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group on Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Microbial Pharmacology and Population Biology Research Group, Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
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Rutanga JP, de Block T, Cuypers WL, Cafmeyer J, Peeters M, Umumararungu E, Ngabonziza JCS, Rucogoza A, Vandenberg O, Martiny D, Dusabe A, Nkubana T, Dougan G, Muvunyi CM, Mwikarago IE, Jacobs J, Deborggraeve S, Van Puyvelde S. Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58. PLoS Negl Trop Dis 2023; 17:e0011285. [PMID: 37327220 DOI: 10.1371/journal.pntd.0011285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/04/2023] [Indexed: 06/18/2023] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. Typhi haplotype in endemic areas of Asia and East sub-Saharan Africa. The situation in Rwanda is currently unknown and therefore to reveal the genetic diversity and AMR of S. Typhi in Rwanda, 25 historical (1984-1985) and 26 recent (2010-2018) isolates from Rwanda were analysed using whole genome sequencing (WGS). WGS was locally implemented using Illumina MiniSeq and web-based analysis tools, thereafter complemented with bioinformatic approaches for more in-depth analyses. Whereas historical S. Typhi isolates were found to be fully susceptible to antimicrobials and show a diversity of genotypes, i.e 2.2.2, 2.5, 3.3.1 and 4.1; the recent isolates showed high AMR rates and were predominantly associated with genotype 4.3.1.2 (H58, 22/26; 84,6%), possibly resulting from a single introduction in Rwanda from South Asia before 2010. We identified practical challenges for the use of WGS in endemic regions, including a high cost for shipment of molecular reagents and lack of high-end computational infrastructure for the analyses, but also identified WGS to be feasible in the studied setting and giving opportunity for synergy with other programs.
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Affiliation(s)
- Jean Pierre Rutanga
- College of Science and Technology, University of Rwanda, Kigali, Rwanda
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | | | - Wim L Cuypers
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Jean Claude S Ngabonziza
- Rwanda Biomedical Centre, Kigali, Rwanda
- Department of Clinical Biology, University of Rwanda, Kigali, Rwanda
| | | | - Olivier Vandenberg
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), Hôpital Erasme-Cliniques universitaires de Bruxelles, Université Libre de Bruxelles, Brussels, Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB), Brussels, Belgium
- National Reference Centre for Campylobacter, CHU Saint-Pierre, Brussels, Belgium
- Faculté de Médecine et Pharmacie, Université de Mons (UMONS), Mons, Belgium
| | - Angélique Dusabe
- Centre Hospitalier Universtaire de Kigali (CHUK), Kigali, Rwanda
| | | | - Gordon Dougan
- Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | | | - Sandra Van Puyvelde
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Medicine, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Gupta P, Liao S, Ezekiel M, Novak N, Rossi A, LaCross N, Oakeson K, Rohrwasser A. Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah. Microbiol Spectr 2023; 11:e0039123. [PMID: 37154725 PMCID: PMC10269515 DOI: 10.1128/spectrum.00391-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations detected in wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 and March 2022. Wastewater sequencing confirmed the presence of Omicron (B.1.1.529) in Utah in samples collected on November 19, 2021, up to 10 days before its corresponding detection via clinical sequencing. Analysis of diversity of SARS-CoV-2 lineages revealed Delta as the most frequently detected lineage during November 2021 (67.71%), but it started declining in December 2021 with the onset of Omicron (B.1.1529) and its sublineage BA.1 (6.79%). The proportion of Omicron increased to ~58% by January 4, 2022, and completely displaced Delta by February 7, 2022. Wastewater genomic surveillance revealed the presence of Omicron sublineage BA.3, a lineage that was not identified from Utah's clinical surveillance. Interestingly, several Omicron-defining mutations began to appear in early November 2021 and increased in prevalence across sewersheds from December to January, aligning with the surge in clinical cases. Our study highlights the importance of tracking epidemiologically relevant mutations in detecting emerging lineages in the early stages of an outbreak. Wastewater genomic epidemiology provides an unbiased representation of community-wide infection dynamics and is an excellent complementary tool to SARS-CoV-2 clinical surveillance, with the potential of guiding public health action and policy decisions. IMPORTANCE SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has had a significant impact on public health. Global emergence of novel SARS-CoV-2 variants, shift to at-home tests, and reduction in clinical tests demonstrate the need for a reliable and effective surveillance strategy to contain COVID-19 spread. Monitoring of SARS-CoV-2 viruses in wastewater is an effective way to trace new outbreaks, establish baseline levels of infection, and complement clinical surveillance efforts. Wastewater genomic surveillance, in particular, can provide valuable insights into the evolution and spread of SARS-CoV-2 variants. We characterized the diversity of SARS-CoV-2 mutations and lineages using whole-genome sequencing to trace the introduction of lineage B.1.1.519 (Omicron) in Utah. Our data showed that Omicron appeared in Utah on November 19, 2021, up to 10 days prior to its detection in patient samples, indicating that wastewater surveillance provides an early warning signal. Our findings are important from a public health perspective as timely identification of communities with high COVID-19 transmission could help guide public health interventions.
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Affiliation(s)
- Pooja Gupta
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Stefan Liao
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Maleea Ezekiel
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nicolle Novak
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Alessandro Rossi
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Nathan LaCross
- Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Kelly Oakeson
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
| | - Andreas Rohrwasser
- Utah Public Health Laboratory, Utah Department of Health and Human Services, Salt Lake City, Utah, USA
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Arredondo-Alonso S, Blundell-Hunter G, Fu Z, Gladstone RA, Fillol-Salom A, Loraine J, Cloutman-Green E, Johnsen PJ, Samuelsen Ø, Pöntinen AK, Cléon F, Chavez-Bueno S, De la Cruz MA, Ares MA, Vongsouvath M, Chmielarczyk A, Horner C, Klein N, McNally A, Reis JN, Penadés JR, Thomson NR, Corander J, Taylor PW, McCarthy AJ. Evolutionary and functional history of the Escherichia coli K1 capsule. Nat Commun 2023; 14:3294. [PMID: 37322051 PMCID: PMC10272209 DOI: 10.1038/s41467-023-39052-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasive E. coli isolates, we show that the K1-cps locus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenic E. coli (ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhances E. coli survival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizes E. coli from distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage.
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Affiliation(s)
- Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | - Zuyi Fu
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Rebecca A Gladstone
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Alfred Fillol-Salom
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | | | - Elaine Cloutman-Green
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - François Cléon
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Susana Chavez-Bueno
- University of Missouri Kansas City, Kansas City, USA
- Division of Infectious Diseases, Children's Mercy Hospital Kansas City, UMKC School of Medicine, Kansas City, USA
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Agnieszka Chmielarczyk
- Faculty of Medicine, Chair of Microbiology, Jagiellonian University Medical College, Czysta str. 18, 31-121, Kraków, Poland
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, UK
| | - Nigel Klein
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joice N Reis
- Laboratory of Pathology and Molecular Biology (LPBM), Gonçalo Moniz Research Institute, Oswaldo Cruz Foundation, Salvador, Brazil
- Faculdade de Farmácia, Universidade Federal da Bahia, Salvador, Brazil
| | - José R Penadés
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
| | - Peter W Taylor
- School of Pharmacy, University College London, London, UK.
| | - Alex J McCarthy
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
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Mixão V, Pinto M, Sobral D, Di Pasquale A, Gomes JP, Borges V. ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data. Genome Med 2023; 15:43. [PMID: 37322495 PMCID: PMC10273728 DOI: 10.1186/s13073-023-01196-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time-consuming and difficult to reproduce. RESULTS We developed ReporTree, a flexible bioinformatics pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance threshold(s) or cluster stability regions and to generate surveillance-oriented reports based on the available metadata, such as timespan, geography, or vaccination/clinical status. ReporTree is able to maintain cluster nomenclature in subsequent analyses and to generate a nomenclature code combining cluster information at different hierarchical levels, thus facilitating the active surveillance of clusters of interest. By handling several input formats and clustering methods, ReporTree is applicable to multiple pathogens, constituting a flexible resource that can be smoothly deployed in routine surveillance bioinformatics workflows with negligible computational and time costs. This is demonstrated through a comprehensive benchmarking of (i) the cg/wgMLST workflow with large datasets of four foodborne bacterial pathogens and (ii) the alignment-based SNP workflow with a large dataset of Mycobacterium tuberculosis. To further validate this tool, we reproduced a previous large-scale study on Neisseria gonorrhoeae, demonstrating how ReporTree is able to rapidly identify the main species genogroups and characterize them with key surveillance metadata, such as antibiotic resistance data. By providing examples for SARS-CoV-2 and the foodborne bacterial pathogen Listeria monocytogenes, we show how this tool is currently a useful asset in genomics-informed routine surveillance and outbreak detection of a wide variety of species. CONCLUSIONS In summary, ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters that contributes to a sustainable and efficient public health genomics-informed pathogen surveillance. ReporTree is implemented in python 3.8 and is freely available at https://github.com/insapathogenomics/ReporTree .
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Affiliation(s)
- Verónica Mixão
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Daniel Sobral
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Adriano Di Pasquale
- National Reference Centre (NRC) for Whole Genome Sequencing of Microbial Pathogens: Database and Bioinformatics analysis (GENPAT), Istituto Zooprofilattico Sperimentale Dell'Abruzzo E del Molise "Giuseppe Caporale" (IZSAM), Teramo, Italy
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal.
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Chindelevitch L, van Dongen M, Graz H, Pedrotta A, Suresh A, Uplekar S, Jauneikaite E, Wheeler N. Ten simple rules for the sharing of bacterial genotype-Phenotype data on antimicrobial resistance. PLoS Comput Biol 2023; 19:e1011129. [PMID: 37347768 PMCID: PMC10286994 DOI: 10.1371/journal.pcbi.1011129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
The increasing availability of high-throughput sequencing (frequently termed next-generation sequencing (NGS)) data has created opportunities to gain deeper insights into the mechanisms of a number of diseases and is already impacting many areas of medicine and public health. The area of infectious diseases stands somewhat apart from other human diseases insofar as the relevant genomic data comes from the microbes rather than their human hosts. A particular concern about the threat of antimicrobial resistance (AMR) has driven the collection and reporting of large-scale datasets containing information from microbial genomes together with antimicrobial susceptibility test (AST) results. Unfortunately, the lack of clear standards or guiding principles for the reporting of such data is hampering the field's advancement. We therefore present our recommendations for the publication and sharing of genotype and phenotype data on AMR, in the form of 10 simple rules. The adoption of these recommendations will enhance AMR data interoperability and help enable its large-scale analyses using computational biology tools, including mathematical modelling and machine learning. We hope that these rules can shed light on often overlooked but nonetheless very necessary aspects of AMR data sharing and enhance the field's ability to address the problems of understanding AMR mechanisms, tracking their emergence and spread in populations, and predicting microbial susceptibility to antimicrobials for diagnostic purposes.
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Affiliation(s)
- Leonid Chindelevitch
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, United Kingdom
| | | | | | | | - Anita Suresh
- FIND, the global alliance for diagnostics, Geneva, Switzerland
| | - Swapna Uplekar
- FIND, the global alliance for diagnostics, Geneva, Switzerland
| | - Elita Jauneikaite
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, England, United Kingdom
- NIHR HPRU in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College, London, England, United Kingdom
| | - Nicole Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, England, United Kingdom
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78
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Fauzia KA, Aftab H, Miftahussurur M, Waskito LA, Tuan VP, Alfaray RI, Matsumoto T, Yurugi M, Subsomwong P, Kabamba ET, Akada J, Yamaoka Y. Genetic determinants of Biofilm formation of Helicobacter pylori using whole-genome sequencing. BMC Microbiol 2023; 23:159. [PMID: 37264297 PMCID: PMC10234030 DOI: 10.1186/s12866-023-02889-8] [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: 02/02/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Infection with Helicobacter pylori as the cause of gastric cancer is a global public health concern. In addition to protecting germs from antibiotics, biofilms reduce the efficacy of H. pylori eradication therapy. The nucleotide polymorphisms (SNPs) related with the biofilm forming phenotype of Helicobacter pylori were studied. RESULTS Fifty-six H. pylori isolate from Bangladeshi patients were included in this cross-sectional study. Crystal violet assay was used to quantify biofilm amount, and the strains were classified into high- and low-biofilm formers As a result, strains were classified as 19.6% high- and 81.4% low-biofilm formers. These phenotypes were not related to specific clades in the phylogenetic analysis. The accessories genes associated with biofilm from whole-genome sequences were extracted and analysed, and SNPs among the previously reported biofilm-related genes were analysed. Biofilm formation was significantly associated with SNPs of alpA, alpB, cagE, cgt, csd4, csd5, futB, gluP, homD, and murF (P < 0.05). Among the SNPs reported in alpB, strains encoding the N156K, G160S, and A223V mutations were high-biofilm formers. CONCLUSIONS This study revealed the potential role of SNPs in biofilm formation and proposed a method to detect mutation in biofilm from whole-genome sequences.
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Affiliation(s)
- Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Hafeza Aftab
- Department of Gastroenterology, Dhaka Medical College and Hospital, Dhaka, 1000, Bangladesh
| | - Muhammad Miftahussurur
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Langgeng Agung Waskito
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
- Department of Physiology and Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, 749000, Vietnam
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Michiyuki Yurugi
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Phawinee Subsomwong
- Department of Microbiology and Immunology, Hirosaki University Graduate School of Medicine, Hirosaki, 036-8562, Aomori, Japan
| | - Evariste Tshibangu Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
- Research Center for Infectious Sciences, Department of Parasitology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, 879-5593, Japan.
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60115, Indonesia.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, 77030, USA.
- Borneo Medical and Health Research Centre, University Malaysia Sabah, Kota Kinabalu, Sabah, 88400, Malaysia.
- The Research Center for GLOBAL and LOCAL Infectious Diseases (RCGLID), Oita University, Yufu, 879-5593, Oita, Japan.
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79
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Mhango C, Banda A, Chinyama E, Mandolo JJ, Kumwenda O, Malamba-Banda C, Barnes KG, Kumwenda B, Jambo KC, Donato CM, Esona MD, Mwangi PN, Steele AD, Iturriza-Gomara M, Cunliffe NA, Ndze VN, Kamng’ona AW, Dennis FE, Nyaga MM, Chaguza C, Jere KC. Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi. Virus Evol 2023; 9:vead030. [PMID: 37305707 PMCID: PMC10256189 DOI: 10.1093/ve/vead030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 04/12/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, 5 years after the introduction of the Rotarix rotavirus vaccine. Here, we analysed representative twenty-seven whole genome sequences (G3P[4], n = 20; G3P[6], n = 1; and G3P[8], n = 6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each ribonucleic acid (RNA) segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1, and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease-burden settings to inform disease prevention and control.
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Affiliation(s)
- Chimwemwe Mhango
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Akuzike Banda
- Department of Computer Science, Faculty of Science, University of Malawi, Zomba 305205, Malawi
| | - End Chinyama
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Jonathan J Mandolo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Orpha Kumwenda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Chikondi Malamba-Banda
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- Department of Biological Sciences, Academy of Medical Sciences, Malawi University of Science and Technology, Thyolo 310105, Malawi
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Benjamin Kumwenda
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Kondwani C Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Celeste M Donato
- Enteric Diseases Group, Murdoch Children’s Research Institute, 50 Flemington Road, Parkville, Melbourne 3052, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mathew D Esona
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa
| | - Peter N Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of Free State, Bloemfontein 9300, South Africa
| | - A Duncan Steele
- Diarrhoeal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa, Pretoria 0204, South Africa
| | - Miren Iturriza-Gomara
- Centre for Vaccine Innovation and Access, Program for Appropriate Technology in Health (PATH), Geneva 1218, Switzerland
| | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool L69 7BE, UK
| | - Valentine N Ndze
- Faculty of Health Sciences, University of Buea, PO Box 63, Buea, Cameroon
| | - Arox W Kamng’ona
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Department of Biomedical Sciences, School of Life Sciences and Allied Health Professions, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
| | - Francis E Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, P. O. Box LG 581, Legon, Ghana
| | | | - Chrispin Chaguza
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut 06510, USA
- NIHR Mucosal Pathogens Research Unit, Division of Infection and Immunity, University College London, London WC1E 6BT, UK
- Yale Institute for Global Health, Yale University, New Haven, Connecticut 06510, USA
| | - Khuzwayo C Jere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7BE, UK
- Department of Medical Laboratory Sciences, Faculty of Biomedical Sciences and Health Profession, Kamuzu University of Health Sciences, Blantyre 312225, Malawi
- NIHR Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool, Liverpool L69 7BE, UK
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of Free State, Bloemfontein 9300, South Africa
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Jung A, Droit L, Febles B, Fronick C, Cook L, Handley SA, Parikh BA, Wang D. Tracking the prevalence and emergence of SARS CoV2 variants of concern using a regional genomic surveillance program. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.08.23289687. [PMID: 37214888 PMCID: PMC10197817 DOI: 10.1101/2023.05.08.23289687] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
SARS-CoV-2 molecular testing coupled with whole genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOC) as well as novel variant discovery. Since the beginning of the pandemic millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of efforts of both national and regional diagnostic laboratories. Here we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the USA. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of VOC. Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories.
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Affiliation(s)
- Ana Jung
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Lindsay Droit
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Binita Febles
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Catarina Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Lisa Cook
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Scott A. Handley
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Bijal A Parikh
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - David Wang
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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81
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Sørgaard M, Sveinsson K, Patel S, Nilsen HK, Olsen AB, Vaagnes Ø, Colquhoun DJ, Gulla S. MLVA genotyping of Moritella viscosa reveals serial emergence of novel, host-specific clonal complexes in Norwegian salmon farming. JOURNAL OF FISH DISEASES 2023; 46:535-543. [PMID: 36787245 DOI: 10.1111/jfd.13766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
A Multi-Locus Variable number of tandem repeat Analysis (MLVA) genotyping scheme was developed for the epidemiological study of Moritella viscosa, which causes 'winter ulcer' predominantly in sea-reared Atlantic salmon (Salmo salar L.). The assay involves multiplex PCR amplification of six Variable Number of Tandem Repeat (VNTR) loci, followed by capillary electrophoresis and data interpretation. A collection of 747 spatiotemporally diverse M. viscosa isolates from nine fish species was analysed, the majority from farmed Norwegian salmon. MLVA distributed 76% of the isolates across three major clonal complexes (CC1, CC2 and CC3), with the remaining forming minor clusters and singletons. While 90% of the salmon isolates belong to either CC1, CC2 or CC3, only 20% of the isolates recovered from other fish species do so, indicating a considerable degree of host specificity. We further highlight a series of 'clonal shifts' amongst Norwegian salmon isolates over the 35-year sampling period, with CC1 showing exclusive predominance prior to the emergence of CC2, which was later supplanted by CC3, before the recent re-emergence of CC1. Apparently, these shifts have rapidly swept the entire Norwegian coastline and conceivably, as suggested by typing of a small number of non-Norwegian isolates, the Northeast Atlantic region as a whole.
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Affiliation(s)
| | | | - Sonal Patel
- Norwegian Veterinary Institute, Ås, Norway
- Vaxxinova Norway AS, Bergen, Norway
| | | | | | - Øyvind Vaagnes
- Vaxxinova Norway AS, Bergen, Norway
- Blue Analytics AS, Bergen, Norway
| | - Duncan J Colquhoun
- Norwegian Veterinary Institute, Ås, Norway
- University of Bergen, Bergen, Norway
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82
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Alastruey-Izquierdo A, Martín-Galiano AJ. The challenges of the genome-based identification of antifungal resistance in the clinical routine. Front Microbiol 2023; 14:1134755. [PMID: 37152754 PMCID: PMC10157239 DOI: 10.3389/fmicb.2023.1134755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
The increasing number of chronic and life-threatening infections caused by antimicrobial resistant fungal isolates is of critical concern. Low DNA sequencing cost may facilitate the identification of the genomic profile leading to resistance, the resistome, to rationally optimize the design of antifungal therapies. However, compared to bacteria, initiatives for resistome detection in eukaryotic pathogens are underdeveloped. Firstly, reported mutations in antifungal targets leading to reduced susceptibility must be extensively collected from the literature to generate comprehensive databases. This information should be complemented with specific laboratory screenings to detect the highest number possible of relevant genetic changes in primary targets and associations between resistance and other genomic markers. Strikingly, some drug resistant strains experience high-level genetic changes such as ploidy variation as much as duplications and reorganizations of specific chromosomes. Such variations involve allelic dominance, gene dosage increments and target expression regime effects that should be explicitly parameterized in antifungal resistome prediction algorithms. Clinical data indicate that predictors need to consider the precise pathogen species and drug levels of detail, instead of just genus and drug class. The concomitant needs for mutation accuracy and assembly quality assurance suggest hybrid sequencing approaches involving third-generation methods will be utilized. Moreover, fatal fast infections, like fungemia and meningitis, will further require both sequencing and analysis facilities are available in-house. Altogether, the complex nature of antifungal resistance demands extensive sequencing, data acquisition and processing, bioinformatic analysis pipelines, and standard protocols to be accomplished prior to genome-based protocols are applied in the clinical setting.
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Affiliation(s)
- Ana Alastruey-Izquierdo
- Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- Center for Biomedical Research in Network in Infectious Diseases (CIBERINFEC-CB21/13/00105), Instituto de Salud Carlos III, Madrid, Spain
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83
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Bayliss SC, Locke RK, Jenkins C, Chattaway MA, Dallman TJ, Cowley LA. Rapid geographical source attribution of Salmonella enterica serovar Enteritidis genomes using hierarchical machine learning. eLife 2023; 12:e84167. [PMID: 37042517 PMCID: PMC10147375 DOI: 10.7554/elife.84167] [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: 10/13/2022] [Accepted: 04/02/2023] [Indexed: 04/13/2023] Open
Abstract
Salmonella enterica serovar Enteritidis is one of the most frequent causes of Salmonellosis globally and is commonly transmitted from animals to humans by the consumption of contaminated foodstuffs. In the UK and many other countries in the Global North, a significant proportion of cases are caused by the consumption of imported food products or contracted during foreign travel, therefore, making the rapid identification of the geographical source of new infections a requirement for robust public health outbreak investigations. Herein, we detail the development and application of a hierarchical machine learning model to rapidly identify and trace the geographical source of S. Enteritidis infections from whole genome sequencing data. 2313 S. Enteritidis genomes, collected by the UKHSA between 2014-2019, were used to train a 'local classifier per node' hierarchical classifier to attribute isolates to four continents, 11 sub-regions, and 38 countries (53 classes). The highest classification accuracy was achieved at the continental level followed by the sub-regional and country levels (macro F1: 0.954, 0.718, 0.661, respectively). A number of countries commonly visited by UK travelers were predicted with high accuracy (hF1: >0.9). Longitudinal analysis and validation with publicly accessible international samples indicated that predictions were robust to prospective external datasets. The hierarchical machine learning framework provided granular geographical source prediction directly from sequencing reads in <4 min per sample, facilitating rapid outbreak resolution and real-time genomic epidemiology. The results suggest additional application to a broader range of pathogens and other geographically structured problems, such as antimicrobial resistance prediction, is warranted.
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Affiliation(s)
- Sion C Bayliss
- Bristol Veterinary School, University of BristolBristolUnited Kingdom
| | - Rebecca K Locke
- Milner Centre for Evolution, Life Sciences Department, University of BathBathUnited Kingdom
- Genomic Laboratory Hub (GLH), Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation TrustCambridgeUnited Kingdom
| | - Claire Jenkins
- Gastrointestinal Reference Services, UK Health Security AgencyLondonUnited Kingdom
| | - Marie Anne Chattaway
- Gastrointestinal Reference Services, UK Health Security AgencyLondonUnited Kingdom
| | - Timothy J Dallman
- Institute for Risk Assessment Sciences, Utrecht UniversityUtrechtNetherlands
| | - Lauren A Cowley
- Milner Centre for Evolution, Life Sciences Department, University of BathBathUnited Kingdom
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84
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Tiwari SK, van der Putten BCL, Fuchs TM, Vinh TN, Bootsma M, Oldenkamp R, La Ragione R, Matamoros S, Hoa NT, Berens C, Leng J, Álvarez J, Ferrandis-Vila M, Ritchie JM, Fruth A, Schwarz S, Domínguez L, Ugarte-Ruiz M, Bethe A, Huber C, Johanns V, Stamm I, Wieler LH, Ewers C, Fivian-Hughes A, Schmidt H, Menge C, Semmler T, Schultsz C. Genome-wide association reveals host-specific genomic traits in Escherichia coli. BMC Biol 2023; 21:76. [PMID: 37038177 PMCID: PMC10088187 DOI: 10.1186/s12915-023-01562-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/10/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Escherichia coli is an opportunistic pathogen which colonizes various host species. However, to what extent genetic lineages of E. coli are adapted or restricted to specific hosts and the genomic determinants of such adaptation or restriction is poorly understood. RESULTS We randomly sampled E. coli isolates from four countries (Germany, UK, Spain, and Vietnam), obtained from five host species (human, pig, cattle, chicken, and wild boar) over 16 years, from both healthy and diseased hosts, to construct a collection of 1198 whole-genome sequenced E. coli isolates. We identified associations between specific E. coli lineages and the host from which they were isolated. A genome-wide association study (GWAS) identified several E. coli genes that were associated with human, cattle, or chicken hosts, whereas no genes associated with the pig host could be found. In silico characterization of nine contiguous genes (collectively designated as nan-9) associated with the human host indicated that these genes are involved in the metabolism of sialic acids (Sia). In contrast, the previously described sialic acid regulon known as sialoregulon (i.e. nanRATEK-yhcH, nanXY, and nanCMS) was not associated with any host species. In vitro growth experiments with a Δnan-9 E. coli mutant strain, using the sialic acids 5-N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) as sole carbon source, showed impaired growth behaviour compared to the wild-type. CONCLUSIONS This study provides an extensive analysis of genetic determinants which may contribute to host specificity in E. coli. Our findings should inform risk analysis and epidemiological monitoring of (antimicrobial resistant) E. coli.
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Affiliation(s)
- Sumeet K Tiwari
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Program, Norwich Research Park, Norwich, UK
| | - Boas C L van der Putten
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Thilo M Fuchs
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Trung N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho, Vietnam
| | | | - Rik Oldenkamp
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Amsterdam Institute for Life and Environment, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Roberto La Ragione
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Sebastien Matamoros
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Ngo T Hoa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - Christian Berens
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Joy Leng
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Julio Álvarez
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
- Department of Animal Health, Faculty of Veterinary Medicine, Complutense University of Madrid, Madrid, Spain
| | | | - Jenny M Ritchie
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Angelika Fruth
- Robert Koch Institute, Enteropathogenic Bacteria and Legionella, Wernigerode, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Lucas Domínguez
- Tropical medicine and global health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK
- Microbiology- Parasitology Unit, Biomedical Research Center and Microbiology Department, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
| | - María Ugarte-Ruiz
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Astrid Bethe
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Charlotte Huber
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany
| | - Vanessa Johanns
- Robert Koch Institute, Advanced Light and Electron Microscopy, Berlin, Germany
| | - Ivonne Stamm
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Kornwestheim, Germany
| | | | - Christa Ewers
- Institute of Hygiene and Infectious Diseases of Animals, Giessen, Germany
| | - Amanda Fivian-Hughes
- Department of Microbial Sciences, School of Biosciences, University of Surrey, Guildford, UK
| | - Herbert Schmidt
- Institute of Food Science and Biotechnology, Department of Food Microbiology and Hygiene, University of Hohenheim, Stuttgart, Germany
| | - Christian Menge
- Friedrich-Loeffler-Institut, Institute of Molecular Pathogenesis, Jena, Germany
| | - Torsten Semmler
- Robert Koch Institute, Genome Sequencing and Genomic Epidemiology, Berlin, Germany.
| | - Constance Schultsz
- Department of Global Health, Amsterdam Institute for Global Health and Development, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.
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85
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Hawkins PA, Chochua S, Lo SW, Belman S, Antonio M, Kwambana-Adams B, von Gottberg A, du Plessis M, Cornick J, Beall B, Breiman RF, Bentley SD, McGee L. A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction. Microb Genom 2023; 9. [PMID: 37083600 DOI: 10.1099/mgen.0.000998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The introduction of pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) around the world has proved successful in preventing invasive pneumococcal disease. However, immunization against Streptococcus pneumoniae has led to serotype replacement by non-vaccine serotypes, including serotype 15A. Clonal complex 63 (CC63) is associated with many serotypes and has been reported in association with 15A after introduction of PCVs. A total of 865 CC63 isolates were included in this study, from the USA (n=391) and a global collection (n=474) from 1998-2019 and 1995-2018, respectively. We analysed the genomic sequences to identify serotypes and penicillin-binding protein (PBP) genes 1A, 2B and 2X, and other resistance determinants, to predict minimum inhibitory concentrations (MICs) against penicillin, erythromycin, clindamycin, co-trimoxazole and tetracycline. We conducted phylogenetic and spatiotemporal analyses to understand the evolutionary history of the 15A-CC63 sub-lineage. Overall, most (89.5 %, n=247) pre-PCV isolates in the CC63 cluster belonged to serotype 14, with 15A representing 6.5 % of isolates. Conversely, serotype 14 isolates represented 28.2 % of post-PCV CC63 isolates (n=618), whilst serotype 15A isolates represented 65.4 %. Dating of the CC63 lineage determined the most recent common ancestor emerged in the 1980s, suggesting the 15A-CC63 sub-lineage emerged from its closest serotype 14 ancestor prior to the development of pneumococcal vaccines. This sub-lineage was predominant in the USA, Israel and China. Multidrug resistance (to three or more drug classes) was widespread among isolates in this sub-lineage. We show that the CC63 lineage is globally distributed and most of the isolates are penicillin non-susceptible, and thus should be monitored.
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Affiliation(s)
- Paulina A Hawkins
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sopio Chochua
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stephanie W Lo
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Sophie Belman
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Martin Antonio
- MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Brenda Kwambana-Adams
- MRC Unit The Gambia, London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Anne von Gottberg
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Mignon du Plessis
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Jen Cornick
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Bernard Beall
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert F Breiman
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Lesley McGee
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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86
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Kumar R, Yadav G, Kuddus M, Ashraf GM, Singh R. Unlocking the microbial studies through computational approaches: how far have we reached? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:48929-48947. [PMID: 36920617 PMCID: PMC10016191 DOI: 10.1007/s11356-023-26220-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 02/24/2023] [Indexed: 04/16/2023]
Abstract
The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking between proteins and phyto/biochemicals for drug design, and modeling of the 3D structure of proteins. These in silico approaches provided insight into analyzing pathogenic and nonpathogenic strains that helped in the identification of probable genes for vaccines and antimicrobial agents and comparing whole-genome sequences to microbial evolution. Artificial intelligence, more precisely machine learning (ML) and deep learning (DL), has proven to be a promising approach in the field of microbiology to handle, analyze, and utilize large data that are generated through nucleic acid sequencing and proteomics. This enabled the understanding of the functional and taxonomic diversity of microorganisms. ML and DL have been used in the prediction and forecasting of diseases and applied to trace environmental contaminants and environmental quality. This review presents an in-depth analysis of the recent application of silico approaches in microbial genomics, proteomics, functional diversity, vaccine development, and drug design.
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Affiliation(s)
- Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Garima Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Saudi Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Sharjah Institute for Medical Research, University of Sharjah, Sharjah , 27272, United Arab Emirates
| | - Rachana Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh Lucknow Campus, Lucknow, Uttar Pradesh, India.
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87
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Meinersmann RJ, Berrang ME, Shariat NW, Richards A, Miller WG. Despite Shared Geography, Campylobacter Isolated from Surface Water Are Genetically Distinct from Campylobacter Isolated from Chickens. Microbiol Spectr 2023; 11:e0414722. [PMID: 36861983 PMCID: PMC10100874 DOI: 10.1128/spectrum.04147-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/31/2023] [Indexed: 03/03/2023] Open
Abstract
We tested the hypothesis that Campylobacter isolated from chicken ceca and river water in an overlapping geographic area would share genetic information. Isolates of C. jejuni from chicken ceca were collected from a commercial slaughter plant and isolates of C. jejuni were also collected from rivers and creeks in the same watershed. Isolates were subjected to whole-genome sequencing and the data were used for core genome multilocus sequence typing (cgMLST). Cluster analysis showed that there were four distinct subpopulations, two from chickens and two from water. Calculation of fixation statistic (Fst) showed that all four subpopulations were significantly distinct. Greater than 90% of the loci were differentiated by subpopulation. Only two genes showed clear differentiation of both chicken subpopulations from both water subpopulations. Sequence fragments of the CJIE4 bacteriophage family were found frequently in the main chicken subpopulation and the water outgroup subpopulation but were sparsely found in the main water population and not at all in the chicken outgroup. CRISPR spacers that targeted the phage sequences were common in the main water subpopulation, only once in the main chicken subpopulation, and not at all in the chicken or water outgroups. Restriction enzyme genes also showed a biased distribution. These data suggest that there is little transfer of C. jejuni genetic material between chickens and nearby river water. Campylobacter differentiation according to these two sources does not show clear evidence of evolutionary selection; the differentiation is probably due to geospatial isolation, genetic drift, and the action of CRISPRs and restriction enzymes. IMPORTANCE Campylobacter jejuni causes gastroenteritis in humans, and chickens and environmental water are leading sources of infection. We tested the hypothesis that Campylobacter isolated from chicken ceca and river water in an overlapping geographic area would share genetic information. Isolates of Campylobacter were collected from water and chicken sources in the same watershed and their genomes were sequenced and analyzed. Four distinct subpopulations were found. There was no evidence of sharing genetic material between the subpopulations. Phage profiles, CRISPR profiles and restriction systems differed by subpopulation.
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Affiliation(s)
| | | | - Nikki W. Shariat
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Amber Richards
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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Amaro C, Carmona-Salido H. Vibrio vulnificus, an Underestimated Zoonotic Pathogen. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:175-194. [PMID: 36792876 DOI: 10.1007/978-3-031-22997-8_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
V. vulnificus, continues being an underestimated yet lethal zoonotic pathogen. In this chapter, we provide a comprehensive review of numerous aspects of the biology, epidemiology, and virulence mechanisms of this poorly understood pathogen. We will emphasize the widespread role of horizontal gene transfer in V. vulnificus specifically virulence plasmids and draw parallels from aquaculture farms to human health. By placing current findings in the context of climate change, we will also contend that fish farms act as evolutionary drivers that accelerate species evolution and the emergence of new virulent groups. Overall, we suggest that on-farm control measures should be adopted both to protect animals from Vibriosis, and also as a public health measure to prevent the emergence of new zoonotic groups.
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Affiliation(s)
- Carmen Amaro
- Departamento de Microbiología y Ecología, & Instituto Universitario de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain.
| | - Héctor Carmona-Salido
- Departamento de Microbiología y Ecología, & Instituto Universitario de Biotecnologia i Biomedicina (BIOTECMED), Universitat de València, Burjassot, Valencia, Spain
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89
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Genomic Epidemiology and Multilevel Genome Typing of Australian Salmonella enterica Serovar Enteritidis. Microbiol Spectr 2023; 11:e0301422. [PMID: 36625638 PMCID: PMC9927265 DOI: 10.1128/spectrum.03014-22] [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] [Indexed: 01/11/2023] Open
Abstract
Salmonella enterica serovar Enteritidis is one of the leading causes of salmonellosis in Australia. In this study, a total of 568 S. Enteritidis isolates from two Australian states across two consecutive years were analyzed and compared to international strains, using the S. Enteritidis multilevel genome typing (MGT) database, which contained 40,390 publicly available genomes from 99 countries. The Australian S. Enteritidis isolates were divided into three phylogenetic clades (A, B, and C). Clades A and C represented 16.4% and 3.5% of the total isolates, respectively, and were of local origin. Clade B accounted for 80.1% of the isolates which belonged to seven previously defined lineages but was dominated by the global epidemic lineage. At the MGT5 level, three out of five top sequence types (STs) in Australia were also top STs in Asia, suggesting that a fair proportion of Australian S. Enteritidis cases may be epidemiologically linked with Asian strains. In 2018, a large egg-associated local outbreak was caused by a recently defined clade B lineage prevalent in Europe and was closely related, but not directly linked, to three European isolates. Additionally, over half (54.8%) of predicted multidrug resistance (MDR) isolates belonged to 10 MDR-associated MGT-STs, which were also frequent in Asian S. Enteritidis . Overall, this study investigated the genomic epidemiology of S. Enteritidis in Australia, including the first large local outbreak, using MGT. The open MGT platform enables a standardized and sharable nomenclature that can be effectively applied to public health for unified surveillance of S. Enteritidis nationally and globally. IMPORTANCE Salmonella enterica serovar Enteritidis is a leading cause of foodborne infections. We previously developed a genomic typing database (MGTdb) for S. Enteritidis to facilitate global surveillance of this pathogen. In this study, we examined the genomic features of Australian S. Enteritidis using the MGTdb and found that Australian S. Enteritidis is mainly epidemiologically linked with Asian strains (especially strains carrying antimicrobial resistance genes), followed by European strains. The first large-scale egg-associated local outbreak in Australia was caused by a recently defined lineage prevalent in Europe, and three European isolates in the MGTdb were closely related but not directly linked to this outbreak. In summary, the S. Enteritidis MGTdb open platform is shown to be a potentially powerful tool for national and global public health surveillance of this pathogen.
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Suzuki M, Hashimoto Y, Hirabayashi A, Yahara K, Yoshida M, Fukano H, Hoshino Y, Shibayama K, Tomita H. Genomic Epidemiological Analysis of Antimicrobial-Resistant Bacteria with Nanopore Sequencing. Methods Mol Biol 2023; 2632:227-246. [PMID: 36781732 DOI: 10.1007/978-1-0716-2996-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Antimicrobial-resistant (AMR) bacterial infections caused by clinically important bacteria, including ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) and mycobacteria (Mycobacterium tuberculosis and nontuberculous mycobacteria), have become a global public health threat. Their epidemic and pandemic clones often accumulate useful accessory genes in their genomes, such as AMR genes (ARGs) and virulence factor genes (VFGs). This process is facilitated by horizontal gene transfer among microbial communities via mobile genetic elements (MGEs), such as plasmids and phages. Nanopore long-read sequencing allows easy and inexpensive analysis of complex bacterial genome structures, although some aspects of sequencing data calculation and genome analysis methods are not systematically understood. Here we describe the latest and most recommended experimental and bioinformatics methods available for the construction of complete bacterial genomes from nanopore sequencing data and the detection and classification of genotypes of bacterial chromosomes, ARGs, VFGs, plasmids, and other MGEs based on their genomic sequences for genomic epidemiological analysis of AMR bacteria.
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Affiliation(s)
- Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
| | - Yusuke Hashimoto
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Aki Hirabayashi
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keigo Shibayama
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haruyoshi Tomita
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Japan.,Laboratory of Bacterial Drug Resistance, Gunma University Graduate School of Medicine, Maebashi, Japan
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91
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White-tailed deer ( Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern. Proc Natl Acad Sci U S A 2023; 120:e2215067120. [PMID: 36719912 PMCID: PMC9963525 DOI: 10.1073/pnas.2215067120] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to white-tailed deer (WTD) and its ability to transmit from deer to deer raised concerns about the role of WTD in the epidemiology and ecology of the virus. Here, we present a comprehensive cross-sectional study assessing the prevalence, genetic diversity, and evolution of SARS-CoV-2 in WTD in the State of New York (NY). A total of 5,462 retropharyngeal lymph node samples collected from free-ranging hunter-harvested WTD during the hunting seasons of 2020 (Season 1, September to December 2020, n = 2,700) and 2021 (Season 2, September to December 2021, n = 2,762) were tested by SARS-CoV-2 real-time RT-PCR (rRT-PCR). SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 samples (21.1%) from Season 2. Hotspots of infection were identified in multiple confined geographic areas of NY. Sequence analysis of SARS-CoV-2 genomes from 164 samples demonstrated the presence of multiple SARS-CoV-2 lineages and the cocirculation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD. Our analysis suggests the occurrence of multiple spillover events (human to deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission and adaptation of the viruses. Detection of Alpha and Gamma variants in WTD long after their broad circulation in humans in NY suggests that WTD may serve as a wildlife reservoir for VOCs no longer circulating in humans. Thus, implementation of continuous surveillance programs to monitor SARS-CoV-2 dynamics in WTD is warranted, and measures to minimize virus transmission between humans and animals are urgently needed.
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92
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Arcari G, Polani R, Bruno F, Capitani V, Sacco F, Menichincheri G, Raponi G, Carattoli A. Ceftazidime-avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution. Microb Genom 2023; 9:mgen000931. [PMID: 36752778 PMCID: PMC9997735 DOI: 10.1099/mgen.0.000931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
The first reports of carbapenem-resistant Enterobacterales in our hospital date back to 2006. In that period, few ertapenem-resistant but meropenem-susceptible Klebsiella pneumoniae isolates belonging to sequence type (ST) 37 were retrieved from clinical samples. These strains produced the CTX-M-15 extended spectrum β-lactamase, OmpK35 was depleted due to a nonsense mutation, and a novel OmpK36 variant was identified. Yet, starting from 2010, Klebsiella pneumoniae carbapenemase (KPC)-producing ST512 isolates started prevailing and ST37 vanished from sight. Since 2018 the clinical use of the combination of ceftazidime-avibactam (CZA) has been introduced in clinical practice for the treatment of bacteria producing serine-β-lactamases, but KPC-producing, CZA-resistant K. pneumoniae are emerging. In 2021, four CZA-resistant ST37 isolates producing KPC variants were isolated from the same number of patients. blaKPC gene cloning in Escherichia coli was used to define the role of those KPC variants on CZA resistance, and whole genome sequencing was performed on these isolates and on three ST37 historical isolates from 2011. CZA resistance was due to mutations in the blaKPC genes carried on related pKpQIL-type plasmids, and three variants of the KPC enzyme have been identified in the four ST37 strains. The four ST37 isolates were closely related to each other and to the historical isolates, suggesting that ST37 survived without notice in our hospital for 10 years, waiting to re-emerge as a CZA-resistant K. pneumoniae clone. The ancestor of these contemporary isolates derives from ST37 wild-type porin strains, with no other mutations in chromosomal genes involved in conferring antibiotic resistance (parC, gyrA, ramR, mgrB, pmrB).
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Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Riccardo Polani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Francesco Bruno
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Valerio Capitani
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Federica Sacco
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Gaia Menichincheri
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giammarco Raponi
- Department of Public Health, Sapienza University of Rome, Rome, Italy
| | - Alessandra Carattoli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
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93
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Soldan S, Su C, Monaco MC, Brown N, Clauze A, Andrada F, Feder A, Planet P, Kossenkov A, Schäffer D, Ohayon J, Auslander N, Jacobson S, Lieberman P. Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells. RESEARCH SQUARE 2023:rs.3.rs-2398872. [PMID: 36778367 PMCID: PMC9915775 DOI: 10.21203/rs.3.rs-2398872/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Epidemiological studies have demonstrated that Epstein-Barr virus (EBV) is a known etiologic risk factor, and perhaps prerequisite, for the development of MS. EBV establishes life-long latent infection in a subpopulation of memory B cells. Although the role of memory B cells in the pathobiology of MS is well established, studies characterizing EBV-associated mechanisms of B cell inflammation and disease pathogenesis in EBV (+) B cells from MS patients are limited. Accordingly, we analyzed spontaneous lymphoblastoid cell lines (SLCLs) from multiple sclerosis patients and healthy controls to study host-virus interactions in B cells, in the context of an individual's endogenous EBV. We identify differences in EBV gene expression and regulation of both viral and cellular genes in SLCLs. Our data suggest that EBV latency is dysregulated in MS SLCLs with increased lytic gene expression observed in MS patient B cells, especially those generated from samples obtained during "active" disease. Moreover, we show increased inflammatory gene expression and cytokine production in MS patient SLCLs and demonstrate that tenofovir alafenamide, an antiviral that targets EBV replication, decreases EBV viral loads, EBV lytic gene expression, and EBV-mediated inflammation in both SLCLs and in a mixed lymphocyte assay. Collectively, these data suggest that dysregulation of EBV latency in MS drives a pro-inflammatory, pathogenic phenotype in memory B cells and that this response can be attenuated by suppressing EBV lytic activation. This study provides further support for the development of antiviral agents that target EBV-infection for use in MS.
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Affiliation(s)
| | | | - Maria Chiara Monaco
- National Institutes of Health - National Institute of Neurological Disorders and Stroke
| | | | | | | | | | | | | | - Daniel Schäffer
- Computational Biology Department, Carnegie Mellon University
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94
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Ahrens AK, Selinka HC, Wylezich C, Wonnemann H, Sindt O, Hellmer HH, Pfaff F, Höper D, Mettenleiter TC, Beer M, Harder TC. Investigating Environmental Matrices for Use in Avian Influenza Virus Surveillance-Surface Water, Sediments, and Avian Fecal Samples. Microbiol Spectr 2023; 11:e0266422. [PMID: 36700688 PMCID: PMC10100768 DOI: 10.1128/spectrum.02664-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023] Open
Abstract
Surveillance of avian influenza viruses (AIV) in wild water bird populations is important for early warning to protect poultry from incursions of high-pathogenicity (HP) AIV. Access to individual water birds is difficult and restricted and limits sampling depth. Here, we focused on environmental samples such as surface water, sediments, and environmentally deposited fresh avian feces as matrices for AIV detection. Enrichment of viral particles by ultrafiltration of 10-L surface water samples using Rexeed-25-A devices was validated using a bacteriophage ϕ6 internal control system, and AIV detection was attempted using real-time RT-PCR and virus isolation. While validation runs suggested an average enrichment of about 60-fold, lower values of 10 to 15 were observed for field water samples. In total 25/36 (60%) of water samples and 18/36 (50%) of corresponding sediment samples tested AIV positive. Samples were obtained from shallow water bodies in habitats with large numbers of waterfowl during an HPAIV epizootic. Although AIV RNA was detected in a substantial percentage of samples virus isolation failed. Virus loads in samples often were too low to allow further sub- and pathotyping. Similar results were obtained with environmentally deposited avian feces. Moreover, the spectrum of viruses detected by these active surveillance methods did not fully mirror an ongoing HPAIV epizootic among waterfowl as detected by passive surveillance, which, in terms of sensitivity, remains unsurpassed. IMPORTANCE Avian influenza viruses (AIV) have a wide host range in the avian metapopulation and, occasionally, transmission to humans also occurs. Surface water plays a particularly important role in the epidemiology of AIV, as the natural virus reservoir is found in aquatic wild birds. Environmental matrices comprising surface water, sediments, and avian fecal matter deposited in the environment were examined for their usefulness in AIV surveillance. Despite virus enrichment efforts, environmental samples regularly revealed very low virus loads, which hampered further sub- and pathotyping. Passive surveillance based on oral and cloacal swabs of diseased and dead wild birds remained unsurpassed with respect to sensitivity.
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Affiliation(s)
- Ann Kathrin Ahrens
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Ole Sindt
- State Laboratory of Schleswig-Holstein, Neumuenster, Germany
| | - Hartmut H. Hellmer
- Climate Sciences, Physical Oceanography of the Polar Seas, Alfred Wegener Institute, Bremerhaven, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | | | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
| | - Timm C. Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Isle of Riems, Germany
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95
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Novel Multilocus Sequence Typing and Global Sequence Clustering Schemes for Characterizing the Population Diversity of Streptococcus mitis. J Clin Microbiol 2023; 61:e0080222. [PMID: 36515506 PMCID: PMC9879099 DOI: 10.1128/jcm.00802-22] [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] [Indexed: 12/15/2022] Open
Abstract
Streptococcus mitis is a common oral commensal and an opportunistic pathogen that causes bacteremia and infective endocarditis; however, the species has received little attention compared to other pathogenic streptococcal species. Effective and easy-to-use molecular typing tools are essential for understanding bacterial population diversity and biology, but schemes specific for S. mitis are not currently available. We therefore developed a multilocus sequence typing (MLST) scheme and defined sequence clusters or lineages of S. mitis using a comprehensive global data set of 322 genomes (148 publicly available and 174 newly sequenced). We used internal 450-bp sequence fragments of seven housekeeping genes (accA, gki, hom, oppC, patB, rlmN, and tsf) to define the MLST scheme and derived the global S. mitis sequence clusters using the PopPUNK clustering algorithm. We identified an initial set of 259 sequence types (STs) and 258 global sequence clusters. The schemes showed high concordance (100%), capturing extensive S. mitis diversity with strains assigned to multiple unique STs and global sequence clusters. The tools also identified extensive within- and between-host S. mitis genetic diversity among isolates sampled from a cohort of healthy individuals, together with potential transmission events, supported by both phylogeny and pairwise single nucleotide polymorphism (SNP) distances. Our novel molecular typing and strain clustering schemes for S. mitis allow for the integration of new strain data, are electronically portable at the PubMLST database (https://pubmlst.org/smitis), and offer a standardized approach to understanding the population structure of S. mitis. These robust tools will enable new insights into the epidemiology of S. mitis colonization, disease and transmission.
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96
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Chaillon A, Bojorquez I, Sepúlveda J, Harvey-Vera AY, Rangel MG, Skaathun B, Mehta SR, Ignacio C, Porrachia M, Smith DM, Strathdee SA. Cocirculation and replacement of SARS-CoV-2 variants in crowded settings and marginalized populations along the US-Mexico border. SALUD PUBLICA DE MEXICO 2023; 65:10-18. [PMID: 36750073 PMCID: PMC10291843 DOI: 10.21149/13980] [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: 06/20/2022] [Accepted: 10/13/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To interrogate the circulating SARS-CoV-2 lin-eages and recombinant variants in persons living in migrant shelters and persons who inject drugs (PWID). MATERIALS AND METHODS We combined data from two studies with marginalized populations (migrants in shelters and persons who inject drugs) in Tijuana, Mexico. SARS-CoV-2 variants were identified on nasal swabs specimens and compared to publicly available genomes sampled in Mexico and California. RESULTS All but 2 of the 10 lineages identified were predomi-nantly detected in North and Central America. Discrepan-cies between migrants and PWID can be explained by the temporal emergence and short time span of most of these lineages in the region. CONCLUSION The results illustrate the temporo-spatial structure for SARS-CoV-2 lineage dispersal and the potential co-circulation of multiple lineages in high-risk populations with close social contacts. These conditions create the potential for recombination to take place in the California-Baja California border.
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Affiliation(s)
- Antoine Chaillon
- Division of Infectious Diseases and Global Public Health, University of California San Diego. San Diego, United States.
| | - Ietza Bojorquez
- Departamento de Estudios de Población, El Colegio de la Frontera Norte. Tijuana, Mexico.
| | - Jaime Sepúlveda
- Institute for Global Health Sciences, University of California. San Francisco, United States.
| | - Alicia Yolanda Harvey-Vera
- Division of Infectious Diseases and Global Public Health, University of California San Diego. San Diego, United States/Facultad de Medicina, Universidad de Xochicalco. Tijuana, Mexico/United States-Mexico Border Health Commission. Tijuana, Mexico.
| | - M Gudelia Rangel
- Departamento de Estudios de Población, El Colegio de la Frontera Norte/United States-Mexico Border Health Commission. Tijuana, Mexico.
| | - Britt Skaathun
- Division of Infectious Diseases and Global Public Health, University of California San Diego. San Diego, United States.
| | - Sanjay R Mehta
- Division of Infectious Diseases and Global Public Health, University of California San Diego/Veterans Affairs Health System. San Diego, United States.
| | - Caroline Ignacio
- Division of Infectious Diseases and Global Public Health, University of California San Diego. San Diego, United States.
| | - Magali Porrachia
- Division of Infectious Diseases and Global Public Health, University of California San Diego/Veterans Affairs Health System. San Diego, United States.
| | - Davey M Smith
- Division of Infectious Diseases and Global Public Health, University of California San Diego/Veterans Affairs Health System. San Diego, United States.
| | - Steffanie A Strathdee
- Division of Infectious Diseases and Global Public Health, University of California San Diego. San Diego, United States.
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97
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Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study. J Immunol Res 2023; 2023:2274415. [PMID: 36874624 PMCID: PMC9977553 DOI: 10.1155/2023/2274415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/07/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Background Although the monkeypox virus-associated illness was previously confined to Africa, recently, it has started to spread across the globe and become a significant threat to human lives. Hence, this study was designed to identify the B and T cell epitopes and develop an epitope-based peptide vaccine against this virus's cell surface binding protein through an in silico approach to combat monkeypox-associated diseases. Results The analysis revealed that the cell surface binding protein of the monkeypox virus contains 30 B cell and 19 T cell epitopes within the given parameter. Among the T cell epitopes, epitope "ILFLMSQRY" was found to be one of the most potential peptide vaccine candidates. The docking analysis revealed an excellent binding affinity of this epitope with the human receptor HLA-B∗15:01 with a very low binding energy (-7.5 kcal/mol). Conclusion The outcome of this research will aid the development of a T cell epitope-based peptide vaccine, and the discovered B and T cell epitopes will facilitate the creation of other epitope and multi-epitope-based vaccines in the future. This research will also serve as a basis for further in vitro and in vivo analysis to develop a vaccine that is effective against the monkeypox virus.
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98
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Maes M, Khokhar F, Wilkinson SAJ, Smith AD, Kovalenko G, Dougan G, Quick J, Loman NJ, Baker S, Curran MD, Skittrall JP, Houldcroft CJ. Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era. Microb Genom 2023; 9:mgen000920. [PMID: 36748435 PMCID: PMC9973849 DOI: 10.1099/mgen.0.000920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/01/2022] [Indexed: 01/09/2023] Open
Abstract
Human adenovirus F41 causes acute gastroenteritis in children, and has recently been associated with an apparent increase in paediatric hepatitis of unknown aetiology in the UK, with further cases reported in multiple countries. Relatively little is known about the genetic diversity of adenovirus F41 in UK children; and it is unclear what, if any, impact the COVID-19 pandemic has had on viral diversity in the UK. Methods that allow F41 to be sequenced from clinical samples without the need for viral culture are required to provide the genomic data to address these questions. Therefore, we evaluated an overlapping-amplicon method of sequencing adenovirus genomes from clinical samples using Oxford Nanopore technology. We applied this method to a small sample of adenovirus-species-F-positive extracts collected as part of standard care in the East of England region in January-May 2022. This method produced genomes with >75 % coverage in 13/22 samples and >50 % coverage in 19/22 samples. We identified two F41 lineages present in paediatric patients in the East of England in 2022. Where F41 genomes from paediatric hepatitis cases were available (n=2), these genomes fell within the diversity of F41 from the UK and continental Europe sequenced before and after the 2020-2021 phase of the COVID-19 pandemic. Our analyses suggest that overlapping amplicon sequencing is an appropriate method for generating F41 genomic data from high-virus-load clinical samples, and currently circulating F41 viral lineages were present in the UK and Europe before the COVID-19 pandemic.
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Affiliation(s)
- Mailis Maes
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke’s Hospital, Cambridge, UK
| | - Fahad Khokhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Sam A. J. Wilkinson
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Andrew D. Smith
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Ganna Kovalenko
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Martin D. Curran
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jordan P. Skittrall
- Clinical Microbiology and Public Health Laboratory, UK Health Security Agency, Addenbrooke’s Hospital, Cambridge, UK
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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99
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Delaye L. CurSa: scripts to curate metadata and sample genomes from GISAID for analysis and display in nextstrain and microreact. Biol Methods Protoc 2023; 8:bpad007. [PMID: 37180471 PMCID: PMC10174701 DOI: 10.1093/biomethods/bpad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/26/2023] [Accepted: 04/11/2023] [Indexed: 05/16/2023] Open
Abstract
The coronavirus SARS-CoV-2 is the most sequenced pathogen ever, with several million genome copies deposited in the GISAID database. This large amount of genomic information poses non-trivial bioinformatic challenges for those interested in studying the evolution of SARS-CoV-2. One common problem when studying the phylogeny of the coronavirus in its geographical context is to count with accurate information of the location of the samples. However, this information is filled by hand by research groups all over the world and sometimes typos and inconsistencies are introduced in the metadata when submitting the sequences to GISAID. Correcting these errors is laborious and time-consuming. Here, we provide a suite of Perl scripts designated to facilitate the curation of this vital information and perform a random sampling of genome sequences if necessary. The scripts provided here can be used to curate geographic information in the metadata and sample the sequences from any country of interest to ease the preparation of files for Nextstrain and Microreact, thus accelerating evolutionary studies of this important pathogen. CurSa scripts are accessible via: https://github.com/luisdelaye/CurSa/.
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Affiliation(s)
- Luis Delaye
- Correspondence address. Tel: +52 (462) 623 9600; E-mail:
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100
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Frosth S, Morris ERA, Wilson H, Frykberg L, Jacobsson K, Parkhill J, Flock JI, Wood T, Guss B, Aanensen DM, Boyle AG, Riihimäki M, Cohen ND, Waller AS. Conservation of vaccine antigen sequences encoded by sequenced strains of Streptococcus equi subsp. equi. Equine Vet J 2023; 55:92-101. [PMID: 35000217 PMCID: PMC10078666 DOI: 10.1111/evj.13552] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/08/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Streptococcus equi subspecies equi (S equi) is the cause of Strangles, one of the most prevalent diseases of horses worldwide. Variation within the immunodominant SeM protein has been documented, but a new eight-component fusion protein vaccine, Strangvac, does not contain live S equi or SeM and conservation of the antigens it contains have not been reported. OBJECTIVE To define the diversity of the eight Strangvac antigens across a diverse S equi population. STUDY DESIGN Genomic description. METHODS Antigen sequences from the genomes of 759 S equi isolates from 19 countries, recovered between 1955 and 2018, were analysed. Predicted amino acid sequences in the antigen fragments of SEQ0256(Eq5), SEQ0402(Eq8), SEQ0721(EAG), SEQ0855(SclF), SEQ0935(CNE), SEQ0999(IdeE), SEQ1817(SclI) and SEQ2101(SclC) in Strangvac and SeM were extracted from the 759 assembled genomes and compared. RESULTS The predicted amino acid sequences of SclC, SclI and IdeE were identical across all 759 genomes. CNE was truncated in the genome of five (0.7%) isolates. SclF was absent from one genome and another encoded a single amino acid substitution. EAG was truncated in two genomes. Eq5 was truncated in four genomes and 123 genomes encoded a single amino acid substitution. Eq8 was truncated in three genomes, one genome encoded four amino acid substitutions and 398 genomes encoded a single amino acid substitution at the final amino acid of the Eq8 antigen fragment. Therefore, at least 1579 (99.9%) of 1580 amino acids in Strangvac were identical in 743 (97.9%) genomes, and all genomes encoded identical amino acid sequences for at least six of the eight Strangvac antigens. MAIN LIMITATIONS Three hundred and seven (40.4%) isolates in this study were recovered from horses in the UK. CONCLUSIONS The predicted amino acid sequences of antigens in Strangvac were highly conserved across this collection of S equi.
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Affiliation(s)
- Sara Frosth
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ellen Ruth A Morris
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, Texas, USA
| | | | - Lars Frykberg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karin Jacobsson
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Jan-Ingmar Flock
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Intervacc AB, Stockholm, Sweden
| | | | - Bengt Guss
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - David M Aanensen
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ashley G Boyle
- Department of Clinical Studies New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Miia Riihimäki
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Noah D Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, Texas, USA
| | - Andrew S Waller
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Intervacc AB, Stockholm, Sweden
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