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Deblais L, Jang H, Kauffman M, Gangiredla J, Sawyer M, Basa S, Poelstra JW, Babu US, Harrison LM, Hiett KL, Balan KV, Rajashekara G. Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio. Front Microbiol 2023; 14:1074548. [PMID: 37025625 PMCID: PMC10071015 DOI: 10.3389/fmicb.2023.1074548] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/30/2023] [Indexed: 04/08/2023] Open
Abstract
Introduction With more public interest in consuming locally grown produce, small specialty crop farms (SSCF) are a viable and growing segment of the food production chain in the United States. Methods The goal of this study was to investigate the genomic diversity of Campylobacter isolated from dairy manure (n = 69) collected from 10 SSCF in Northeast Ohio between 2018 and 2020. Results A total of 56 C. jejuni and 13 C. coli isolates were sequenced. Multi-locus sequence typing (MLST) identified 22 sequence types (STs), with ST-922 (18%) and ST-61 (13%) predominant in C. jejuni and ST-829 (62%) and ST-1068 (38%) predominant in C. coli. Interestingly, isolates with similar genomic and gene contents were detected within and between SSCF over time, suggesting that Campylobacter could be transmitted between farms and may persist in a given SSCF over time. Virulence-associated genes (n = 35) involved in the uptake and utilization of potassium and organic compounds (succinate, gluconate, oxoglutarate, and malate) were detected only in the C. jejuni isolates, while 45 genes associated with increased resistance to environmental stresses (capsule production, cell envelope integrity, and iron uptake) were detected only in the C. coli isolates. Campylobacter coli isolates were also sub-divided into two distinct clusters based on the presence of unique prophages (n = 21) or IncQ conjugative plasmid/type-IV secretion system genes (n = 15). Campylobacter coli isolates harbored genes associated with resistance to streptomycin (aadE-Cc; 54%) and quinolone (gyrA-T86I; 77%), while C. jejuni had resistance genes for kanamycin (aph3'-IIIa; 20%). Both species harbored resistance genes associated with β-lactam (especially, blaOXA-193; up to 100%) and tetracycline (tetO; up to 59%). Discussion/Conclusion Our study demonstrated that Campylobacter genome plasticity associated with conjugative transfer might provide resistance to certain antimicrobials and viral infections via the acquisition of protein-encoding genes involved in mechanisms such as ribosomal protection and capsule modification.
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Affiliation(s)
- Loic Deblais
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Hyein Jang
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Mike Kauffman
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Marianne Sawyer
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Saritha Basa
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jelmer W. Poelstra
- Molecular and Cellular Imaging Center, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Uma S. Babu
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Lisa M. Harrison
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Kelli L. Hiett
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Kannan V. Balan
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Gireesh Rajashekara
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
- *Correspondence: Gireesh Rajashekara,
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302
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Marasco R, Michoud G, Sefrji FO, Fusi M, Antony CP, Seferji KA, Barozzi A, Merlino G, Daffonchio D. The identification of the new species Nitratireductor thuwali sp. nov. reveals the untapped diversity of hydrocarbon-degrading culturable bacteria from the arid mangrove sediments of the Red Sea. Front Microbiol 2023; 14:1155381. [PMID: 37200916 PMCID: PMC10185800 DOI: 10.3389/fmicb.2023.1155381] [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: 01/31/2023] [Accepted: 04/04/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction The geological isolation, lack of freshwater inputs and specific internal water circulations make the Red Sea one of the most extreme-and unique-oceans on the planet. Its high temperature, salinity and oligotrophy, along with the consistent input of hydrocarbons due to its geology (e.g., deep-sea vents) and high oil tankers traffic, create the conditions that can drive and influence the assembly of unique marine (micro)biomes that evolved to cope with these multiple stressors. We hypothesize that mangrove sediments, as a model-specific marine environment of the Red Sea, act as microbial hotspots/reservoirs of such diversity not yet explored and described. Methods To test our hypothesis, we combined oligotrophic media to mimic the Red Sea conditions and hydrocarbons as C-source (i.e., crude oil) with long incubation time to allow the cultivation of slow-growing environmentally (rare or uncommon) relevant bacteria. Results and discussion This approach reveals the vast diversity of taxonomically novel microbial hydrocarbon degraders within a collection of a few hundred isolates. Among these isolates, we characterized a novel species, Nitratireductor thuwali sp. nov., namely, Nit1536T. It is an aerobic, heterotrophic, Gram-stain-negative bacterium with optimum growth at 37°C, 8 pH and 4% NaCl, whose genome and physiological analysis confirmed the adaptation to extreme and oligotrophic conditions of the Red Sea mangrove sediments. For instance, Nit1536T metabolizes different carbon substrates, including straight-chain alkanes and organic acids, and synthesizes compatible solutes to survive in salty mangrove sediments. Our results showed that the Red Sea represent a source of yet unknown novel hydrocarbon degraders adapted to extreme marine conditions, and their discovery and characterization deserve further effort to unlock their biotechnological potential.
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303
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Pottier M, Castagnet S, Gravey F, Leduc G, Sévin C, Petry S, Giard JC, Le Hello S, Léon A. Antimicrobial Resistance and Genetic Diversity of Pseudomonas aeruginosa Strains Isolated from Equine and Other Veterinary Samples. Pathogens 2022; 12:64. [PMID: 36678412 PMCID: PMC9867525 DOI: 10.3390/pathogens12010064] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections in humans. This bacterium is less represented in veterinary medicine, despite causing difficult-to-treat infections due to its capacity to acquire antimicrobial resistance, produce biofilms, and persist in the environment, along with its limited number of veterinary antibiotic therapies. Here, we explored susceptibility profiles to antibiotics and to didecyldimethylammonium chloride (DDAC), a quaternary ammonium widely used as a disinfectant, in 168 P. aeruginosa strains isolated from animals, mainly Equidae. A genomic study was performed on 41 of these strains to determine their serotype, sequence type (ST), relatedness, and resistome. Overall, 7.7% of animal strains were resistant to carbapenems, 10.1% presented a multidrug-resistant (MDR) profile, and 11.3% showed decreased susceptibility (DS) to DDAC. Genomic analyses revealed that the study population was diverse, and 4.9% were ST235, which is considered the most relevant human high-risk clone worldwide. This study found P. aeruginosa populations with carbapenem resistance, multidrug resistance, and DS to DDAC in equine and canine isolates. These strains, which are not susceptible to antibiotics used in veterinary and human medicine, warrant close the setting up of a clone monitoring, based on that already in place in human medicine, in a one-health approach.
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Affiliation(s)
- Marine Pottier
- Research Department, LABÉO, 14053 Caen, France
- Inserm UMR 1311, Dynamicure, Normandie University, UNICAEN, UNIROUEN, 14000 Caen, France
| | - Sophie Castagnet
- Research Department, LABÉO, 14053 Caen, France
- Inserm UMR 1311, Dynamicure, Normandie University, UNICAEN, UNIROUEN, 14000 Caen, France
| | - François Gravey
- Inserm UMR 1311, Dynamicure, Normandie University, UNICAEN, UNIROUEN, 14000 Caen, France
- CHU de Caen, Service de Microbiologie, Avenue de la Côte de Nacre, 14033 Caen, France
| | - Guillaume Leduc
- CHU de Caen, Service de Microbiologie, Avenue de la Côte de Nacre, 14033 Caen, France
| | - Corinne Sévin
- Anses, Normandy Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, 14430 Goustranville, France
| | - Sandrine Petry
- Anses, Normandy Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, 14430 Goustranville, France
| | - Jean-Christophe Giard
- Inserm UMR 1311, Dynamicure, Normandie University, UNICAEN, UNIROUEN, 14000 Caen, France
| | - Simon Le Hello
- Inserm UMR 1311, Dynamicure, Normandie University, UNICAEN, UNIROUEN, 14000 Caen, France
- CHU de Caen, Service de Microbiologie, Avenue de la Côte de Nacre, 14033 Caen, France
- CHU de Caen, Service d’Hygiène Hospitalière, Avenue de la Côte de Nacre, 14033 Caen, France
| | - Albertine Léon
- Research Department, LABÉO, 14053 Caen, France
- Inserm UMR 1311, Dynamicure, Normandie University, UNICAEN, UNIROUEN, 14000 Caen, France
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304
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Soundararajan M, Marincola G, Liong O, Marciniak T, Wencker FDR, Hofmann F, Schollenbruch H, Kobusch I, Linnemann S, Wolf SA, Helal M, Semmler T, Walther B, Schoen C, Nyasinga J, Revathi G, Boelhauve M, Ziebuhr W. Farming Practice Influences Antimicrobial Resistance Burden of Non-Aureus Staphylococci in Pig Husbandries. Microorganisms 2022; 11:microorganisms11010031. [PMID: 36677324 PMCID: PMC9865537 DOI: 10.3390/microorganisms11010031] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Non-aureus staphylococci (NAS) are ubiquitous bacteria in livestock-associated environments where they may act as reservoirs of antimicrobial resistance (AMR) genes for pathogens such as Staphylococcus aureus. Here, we tested whether housing conditions in pig farms could influence the overall AMR-NAS burden. Two hundred and forty porcine commensal and environmental NAS isolates from three different farm types (conventional, alternative, and organic) were tested for phenotypic antimicrobial susceptibility and subjected to whole genome sequencing. Genomic data were analysed regarding species identity and AMR gene carriage. Seventeen different NAS species were identified across all farm types. In contrast to conventional farms, no AMR genes were detectable towards methicillin, aminoglycosides, and phenicols in organic farms. Additionally, AMR genes to macrolides and tetracycline were rare among NAS in organic farms, while such genes were common in conventional husbandries. No differences in AMR detection existed between farm types regarding fosfomycin, lincosamides, fusidic acid, and heavy metal resistance gene presence. The combined data show that husbandry conditions influence the occurrence of resistant and multidrug-resistant bacteria in livestock, suggesting that changing husbandry practices may be an appropriate means of limiting the spread of AMR bacteria on farms.
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Affiliation(s)
| | - Gabriella Marincola
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Olivia Liong
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Tessa Marciniak
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Freya D. R. Wencker
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Franka Hofmann
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Hannah Schollenbruch
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Iris Kobusch
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Sabrina Linnemann
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Silver A. Wolf
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Mustafa Helal
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Torsten Semmler
- Genome Sequencing and Genomic Epidemiology, Robert Koch Institute, 13353 Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS4), Robert Koch Institute, 13353 Berlin, Germany
| | - Christoph Schoen
- Institute of Hygiene and Microbiology, University of Würzburg, 97080 Würzburg, Germany
| | - Justin Nyasinga
- Department of Pathology, Aga-Khan-University Hospital Nairobi, Nairobi, Kenya
- Department of Biomedical Sciences and Technology, The Technical University of Kenya, Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Aga-Khan-University Hospital Nairobi, Nairobi, Kenya
| | - Marc Boelhauve
- Department of Agriculture; South Westphalia University of Applied Sciences, 59494 Soest, Germany
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, University of Würzburg, 97080 Würzburg, Germany
- Correspondence: ; Tel.: +49-(0)931-31-2578
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305
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Chmiel JA, Carr C, Stuivenberg GA, Venema R, Chanyi RM, Al KF, Giguere D, Say H, Akouris PP, Domínguez Romero SA, Kwong A, Tai V, Koval SF, Razvi H, Bjazevic J, Burton JP. New perspectives on an old grouping: The genomic and phenotypic variability of Oxalobacter formigenes and the implications for calcium oxalate stone prevention. Front Microbiol 2022; 13:1011102. [PMID: 36620050 PMCID: PMC9812493 DOI: 10.3389/fmicb.2022.1011102] [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: 08/03/2022] [Accepted: 10/28/2022] [Indexed: 12/24/2022] Open
Abstract
Oxalobacter formigenes is a unique bacterium with the ability to metabolize oxalate as a primary carbon source. Most kidney stones in humans are composed of calcium and oxalate. Therefore, supplementation with an oxalate-degrading bacterium may reduce stone burden in patients suffering from recurrent calcium oxalate-based urolithiasis. Strains of O. formigenes are divided into two groups: group I and group II. However, the differences between strains from each group remain unclear and elucidating these distinctions will provide a better understanding of their physiology and potential clinical applications. Here, genomes from multiple O. formigenes strains underwent whole genome sequencing followed by phylogenetic and functional analyses. Genetic differences suggest that the O. formigenes taxon should be divided into an additional three species: Oxalobacter aliiformigenes sp. nov, Oxalobacter paeniformigenes sp. nov, and Oxalobacter paraformigenes sp. nov. Despite the similarities in the oxalyl-CoA gene (oxc), which is essential for oxalate degradation, these strains have multiple unique genetic features that may be potential exploited for clinical use. Further investigation into the growth of these strains in a simulated fecal environment revealed that O. aliiformigenes strains are capable of thriving within the human gut microbiota. O. aliiformigenes may be a better therapeutic candidate than current group I strains (retaining the name O. formigenes), which have been previously tested and shown to be ineffective as an oral supplement to mitigate stone disease. By performing genomic analyses and identifying these novel characteristics, Oxalobacter strains better suited to mitigation of calcium oxalate-based urolithiasis may be identified in the future.
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Affiliation(s)
- John A. Chmiel
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | - Charles Carr
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Gerrit A. Stuivenberg
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | - Robertson Venema
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Ryan M. Chanyi
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Kait F. Al
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | - Daniel Giguere
- Department of Biology, Western University, London, ON, Canada
| | - Henry Say
- Department of Biology, Western University, London, ON, Canada
| | - Polycronis P. Akouris
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada
| | | | - Aaron Kwong
- Department of Medicine, Western University, London, ON, Canada
| | - Vera Tai
- Department of Biology, Western University, London, ON, Canada
| | - Susan F. Koval
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Hassan Razvi
- Division of Urology, Department of Surgery, Western University, London, ON, Canada
| | - Jennifer Bjazevic
- Division of Urology, Department of Surgery, Western University, London, ON, Canada
| | - Jeremy P. Burton
- Department of Microbiology and Immunology, Western University, London, ON, Canada,Canadian Centre for Human Microbiome and Probiotics Research, London, ON, Canada,Division of Urology, Department of Surgery, Western University, London, ON, Canada,*Correspondence: Jeremy P. Burton,
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306
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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307
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Cunningham SA, Eberly AR, Beisken S, Posch AE, Schuetz AN, Patel R. Core Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates. Microbiol Spectr 2022; 10:e0392022. [PMID: 36350158 PMCID: PMC9769729 DOI: 10.1128/spectrum.03920-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Over the past decade, whole-genome sequencing (WGS) has overtaken traditional bacterial typing methods for studies of genetic relatedness. Further, WGS data generated during epidemiologic studies can be used in other clinically relevant bioinformatic applications, such as antibiotic resistance prediction. Using commercially available software tools, the relatedness of 38 clinical isolates of multidrug-resistant Pseudomonas aeruginosa was defined by two core genome multilocus sequence typing (cgMLST) methods, and the WGS data of each isolate was analyzed to predict antibiotic susceptibility to nine antibacterial agents. The WGS typing and resistance prediction data were compared with pulsed-field gel electrophoresis (PFGE) and phenotypic antibiotic susceptibility results, respectively. Simpson's Diversity Index and adjusted Wallace pairwise assessments of the three typing methods showed nearly identical discriminatory power. Antibiotic resistance prediction using a trained analytical pipeline examined 342 bacterial-drug combinations with an overall categorical agreement of 92.4% and very major, major, and minor error rates of 3.6, 4.1, and 4.1%, respectively. IMPORTANCE Multidrug-resistant Pseudomonas aeruginosa isolates are a serious public health concern due to their resistance to nearly all or all of the available antibiotics, including carbapenems. Utilizing molecular approaches in conjunction with antibiotic susceptibility prediction software warrants investigation for use in the clinical laboratory workflow. These molecular tools coupled with antibiotic resistance prediction tools offer the opportunity to overcome the extended turnaround time and technical challenges of phenotypic susceptibility testing.
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Affiliation(s)
- Scott A. Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Allison R. Eberly
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Audrey N. Schuetz
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, Minnesota, USA
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308
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dessouky YE, Elsayed SW, Abdelsalam NA, Saif NA, Álvarez-Ordóñez A, Elhadidy M. Genomic insights into zoonotic transmission and antimicrobial resistance in Campylobacter jejuni from farm to fork: a one health perspective. Gut Pathog 2022; 14:44. [PMID: 36471447 PMCID: PMC9721040 DOI: 10.1186/s13099-022-00517-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/08/2022] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Campylobacteriosis represents a global public health threat with various socio-economic impacts. Among different Campylobacter species, Campylobacter jejuni (C. jejuni) is considered to be the foremost Campylobacter species responsible for most of gastrointestinal-related infections. Although these species are reported to primarily inhabit birds, its high genetic and phenotypic diversity allowed their adaptation to other animal reservoirs and to the environment that may impact on human infection. MAIN BODY A stringent and consistent surveillance program based on high resolution subtyping is crucial. Recently, different epidemiological investigations have implemented high-throughput sequencing technologies and analytical pipelines for higher resolution subtyping, accurate source attribution, and detection of antimicrobial resistance determinants among these species. In this review, we aim to present a comprehensive overview on the epidemiology, clinical presentation, antibiotic resistance, and transmission dynamics of Campylobacter, with specific focus on C. jejuni. This review also summarizes recent attempts of applying whole-genome sequencing (WGS) coupled with bioinformatic algorithms to identify and provide deeper insights into evolutionary and epidemiological dynamics of C. jejuni precisely along the farm-to-fork continuum. CONCLUSION WGS is a valuable addition to traditional surveillance methods for Campylobacter. It enables accurate typing of this pathogen and allows tracking of its transmission sources. It is also advantageous for in silico characterization of antibiotic resistance and virulence determinants, and hence implementation of control measures for containment of infection.
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Affiliation(s)
- Yara El dessouky
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Salma W. Elsayed
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.7269.a0000 0004 0621 1570Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nehal Adel Abdelsalam
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.7776.10000 0004 0639 9286Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Nehal A. Saif
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Avelino Álvarez-Ordóñez
- grid.4807.b0000 0001 2187 3167Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mohamed Elhadidy
- grid.440881.10000 0004 0576 5483Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt ,grid.440881.10000 0004 0576 5483Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt ,grid.10251.370000000103426662Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt
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309
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Phylogenomic analysis of a metagenome-assembled genome indicates a new taxon of an anoxygenic phototroph bacterium in the family Chromatiaceae and the proposal of “Candidatus Thioaporhodococcus” gen. nov. Arch Microbiol 2022; 204:688. [DOI: 10.1007/s00203-022-03298-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
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310
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Mäklin T, Thorpe HA, Pöntinen AK, Gladstone RA, Shao Y, Pesonen M, McNally A, Johnsen PJ, Samuelsen Ø, Lawley TD, Honkela A, Corander J. Strong pathogen competition in neonatal gut colonisation. Nat Commun 2022; 13:7417. [PMID: 36456554 PMCID: PMC9715557 DOI: 10.1038/s41467-022-35178-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.
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Affiliation(s)
- Tommi Mäklin
- grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Harry A. Thorpe
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Anna K. Pöntinen
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.412244.50000 0004 4689 5540Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Rebecca A. Gladstone
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Yan Shao
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK
| | - Maiju Pesonen
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Alan McNally
- grid.6572.60000 0004 1936 7486Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Pål J. Johnsen
- grid.10919.300000000122595234Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- grid.412244.50000 0004 4689 5540Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway ,grid.10919.300000000122595234Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Trevor D. Lawley
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK
| | - Antti Honkela
- grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland
| | - Jukka Corander
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Hinxton, Cambridgeshire UK ,grid.7737.40000 0004 0410 2071Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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311
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Ares-Arroyo M, Coluzzi C, P.C. Rocha E. Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation. Nucleic Acids Res 2022; 51:3001-3016. [PMID: 36442505 PMCID: PMC10123127 DOI: 10.1093/nar/gkac1079] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/30/2022] Open
Abstract
Abstract
Plasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their co-occurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmid-encoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation.
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Affiliation(s)
- Manuel Ares-Arroyo
- Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France
| | - Charles Coluzzi
- Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France
| | - Eduardo P.C. Rocha
- Institut Pasteur, Université de Paris Cité , CNRS UMR3525, Microbial Evolutionary Genomics, Paris , France
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312
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A Comprehensive Genomic Analysis of the Emergent Klebsiella pneumoniae ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain. Pathogens 2022; 11:pathogens11121394. [PMID: 36558729 PMCID: PMC9781218 DOI: 10.3390/pathogens11121394] [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: 10/13/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/24/2022] Open
Abstract
Klebsiella pneumoniae is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of K. pneumoniae is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitating the emergence of new threatening clones. In the last years, ST16 has been described as an emergent, clinically relevant strain, increasingly associated with outbreaks, and carrying virulence factors (such as ICEKp, iuc, rmpADC/2) and a diversity of resistance genes. However, a far-reaching phylogenetic study of ST16, including geographically, clinically and temporally distributed isolates is not available. In this work, we analyzed all publicly available ST16 K. pneumoniae genomes in terms of virulence factors, including capsular lipopolysaccharide and polysaccharide diversity, plasmids and antimicrobial resistance genes. A core genome SNP analysis shows that less than 1% of studied sites were variant sites, with a median pairwise single nucleotide polymorphism difference of 87 SNPs. The number and diversity of antimicrobial resistance genes, but not of virulence-related genes, increased consistently in ST16 strains during the studied period. A genomic comparison between ST16 and the high-risk clone ST11 K. pneumoniae, showed great similarities in their capacity to acquire resistance and virulence markers, differing mostly in the great diversity of capsular lipopolysaccharide and polysaccharide types in ST11, in comparison with ST16. While virulence and antimicrobial resistance scores indicated that ST11 might still constitute a more difficult-to-manage strain, results presented here demonstrate the great potential of the ST16 clone becoming critical in public health.
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313
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Draft Genome Sequences of Four Methicillin-Resistant Staphylococcus aureus Strains (M080_2017, M106_2017, M181_2017, and M191_2017), Isolated from a Malaysian Teaching Hospital. Microbiol Resour Announc 2022; 11:e0086722. [DOI: 10.1128/mra.00867-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Draft genome sequences were obtained for four methicillin-resistant
Staphylococcus aureus
(MRSA) strains isolated from various wards of the Hospital Canselor Tuanku Muhriz (HCTM), Kuala Lumpur, Malaysia, in 2017. Using different bioinformatics tools, we annotated the draft genomes and identified multiple antimicrobial resistance genes.
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314
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Li X, Yang Z, Zhang G, Si S, Wu X, Cai L. Plasmid Genomes Reveal the Distribution, Abundance, and Organization of Mercury-Related Genes and Their Co-Distribution with Antibiotic Resistant Genes in Gammaproteobacteria. Genes (Basel) 2022; 13:2149. [PMID: 36421823 PMCID: PMC9690531 DOI: 10.3390/genes13112149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/13/2022] [Accepted: 11/13/2022] [Indexed: 09/29/2023] Open
Abstract
Mercury (Hg) pollution poses human health and environmental risks worldwide, as it can have toxic effects and causes selective pressure that facilitates the spread of antibiotic resistant genes (ARGs) among microbes. More and more studies have revealed that numerous Hg-related genes (HRGs) can help to resist and transform Hg. In the present study, we systematically analyzed the HRG distribution, abundance, organization, and their co-distribution with ARGs, using 18,731 publicly available plasmid genomes isolated from a Gammaproteobacteria host. Our results revealed that there were many Hg-resistant (mer) operon genes but they were not extensively distributed across plasmids, with only 9.20% of plasmids harboring HRGs. Additionally, no hgcAB genes (which methylate Hg to create methylmercury) were identified in any of the analyzed plasmids. The host source significantly influenced the number of HRGs harbored by plasmids; plasmids isolated from humans and animals harbored a significantly smaller number of HRGs than plasmids isolated from the wastewater and sludge. HRG clusters displayed an extremely high organizational diversity (88 HRG cluster types), though incidences of more than half of the HRG cluster types was <5. This indicates the frequent rearrangement among HRGs in plasmids. The 1368 plasmids harboring both HRGs and ARGs, were dominated by Klebsiella, followed by Escherichia, Salmonella, and Enterobacter. The tightness of the HRG and ARG co-distribution in plasmids was affected by the host sources but not by pathogenicity. HRGs were more likely to co-occur with specific ARG classes (sulfonamide, macrolide-lincosamide-streptogramin, and aminoglycoside resistance genes). Collectively, our results reveal the distribution characteristics of HRGs in plasmids, and they have important implications for further understanding the environmental risks caused by the spread of ARGs through the plasmid-mediated co-transfer of ARGs and HRGs.
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Affiliation(s)
- Xiangyang Li
- School of Life and Health Science, Kaili University, Kaili 556011, China
- Bacterial Genome Data Mining & Bioinformatic Analysis Center, Kaili University, Kaili 556011, China
| | - Zilin Yang
- School of Sciences, Kaili University, Kaili 556018, China
| | - Guohui Zhang
- School of Life and Health Science, Kaili University, Kaili 556011, China
| | - Shengli Si
- School of Life and Health Science, Kaili University, Kaili 556011, China
| | - Xianzhi Wu
- School of Life and Health Science, Kaili University, Kaili 556011, China
| | - Lin Cai
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China
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315
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A Broad-Host-Range Plasmid Outbreak: Dynamics of IncL/M Plasmids Transferring Carbapenemase Genes. Antibiotics (Basel) 2022; 11:antibiotics11111641. [DOI: 10.3390/antibiotics11111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022] Open
Abstract
IncL/M broad-host-range conjugative plasmids are involved in the global spread of blaOXA-48 and the emergence of blaNDM-1. The aim of this study was to evaluate the transmission potential of plasmids encoding the emergent NDM-1 carbapenemase compared to the pandemic OXA-48. The conjugation rate and fitness cost of IncM2 and IncL plasmids encoding these carbapenemase genes were tested using a variety of host bacteria. Genomic analysis of uropathogenic Escherichia coli SAP1756 revealed that blaNDM-1 was encoded on an IncM2 plasmid, which also harboured blaTEM-1, bleMBL and sul1 and was highly similar to plasmids isolated from the same geographical area. Conjugation experiments demonstrated that NDM-1 and OXA-48-carrying plasmids transfer successfully between different Enterobacterales species, both in vitro and in vivo. Interestingly, E. coli isolates tested as recipients belonging to phylogroups A, B1, D and F were able to receive IncM2 plasmid pSAP1756, while phylogroups B2, C, E and G were not permissive to its acquisition. In general, the IncL OXA-48-carrying plasmids tested transferred at higher rates than IncM2 harbouring NDM-1 and imposed a lower burden to their host, possibly due to the inactivation of the tir fertility inhibition gene and reflecting their worldwide dissemination. IncM2 plasmids carrying blaNDM-1 are considered emergent threats that need continuous monitoring. In addition to sequencing efforts, phenotypic analysis of conjugation rates and fitness cost are effective methods for estimating the pandemic potential of antimicrobial resistance plasmids.
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316
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Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis J, Dempsey D, Dickerman A, Dietrich E, Kenyon R, Kuscuoglu M, Lefkowitz E, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen G, Overbeek J, Parrello B, Parrello V, Porter J, Pusch G, Shukla M, Singh I, Stewart L, Tan G, Thomas C, VanOeffelen M, Vonstein V, Wallace Z, Warren A, Wattam A, Xia F, Yoo H, Zhang Y, Zmasek C, Scheuermann R, Stevens R. Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res 2022; 51:D678-D689. [PMID: 36350631 PMCID: PMC9825582 DOI: 10.1093/nar/gkac1003] [Citation(s) in RCA: 248] [Impact Index Per Article: 124.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.
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Affiliation(s)
- Robert D Olson
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Rida Assaf
- Department of Computer Science, American University of Beirut, Beirut, Lebanon
| | - Thomas Brettin
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Neal Conrad
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Clark Cucinell
- University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA
| | - James J Davis
- To whom correspondence should be addressed. Tel: +1 630 252 1190;
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Allan Dickerman
- University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA
| | - Emily M Dietrich
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Ronald W Kenyon
- University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA
| | - Mehmet Kuscuoglu
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Jian Lu
- J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Dustin Machi
- University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA
| | - Catherine Macken
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Chunhong Mao
- University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA
| | - Anna Niewiadomska
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Marcus Nguyen
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gary J Olsen
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - Jamie C Overbeek
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Bruce Parrello
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
| | | | - Jacob S Porter
- Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gordon D Pusch
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA
| | - Maulik Shukla
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | | | - Lucy Stewart
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Gene Tan
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Chris Thomas
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | | | | | - Zachary S Wallace
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA,Department of Computer Science and Engineering, University of California, San Diego, CA 92039, USA
| | - Andrew S Warren
- University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA
| | - Alice R Wattam
- University of Virginia Biocomplexity Institute, Charlottesville, VA 22904, USA
| | - Fangfang Xia
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Hyunseung Yoo
- Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60637, USA,Division of Data Science and Learning, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Christian M Zmasek
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA 92037, USA,Department of Pathology, University of California, San Diego, CA 92093, USA,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037, USA,Global Virus Network, Baltimore, MD 21201, USA
| | - Rick L Stevens
- Computing Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA,Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
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317
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Kittiwan N, Calland JK, Mourkas E, Hitchings MD, Murray S, Tadee P, Tadee P, Duangsonk K, Meric G, Sheppard SK, Patchanee P, Pascoe B. Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs. Microb Genom 2022; 8:mgen000882. [PMID: 36326658 PMCID: PMC9836093 DOI: 10.1099/mgen.0.000882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Streptococcus suis is a leading cause of bacterial meningitis in South-East Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry, causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. Gene flow between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome characterization identified extensive genetic diversity and frequent AMR carriage in isolates from healthy pigs. Multiple AMR genes were identified, conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptible to three or more different antimicrobial classes, and 75 % of non-serotype 2 isolates were non-susceptible to six or more classes (compared to 37.5 % of serotype 2 isolates). AMR genes were found on integrative and conjugative elements previously observed in other species, suggesting a mobile gene pool that can be accessed by invasive disease isolates. This article contains data hosted by Microreact.
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Affiliation(s)
- Nattinee Kittiwan
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Veterinary Research and Development Center (Upper Northern Region), Hang Chat, Lampang 52190, Thailand
| | - Jessica K. Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | - Evangelos Mourkas
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK
| | - Matthew D. Hitchings
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK
| | - Susan Murray
- Swansea University Medical School, Swansea University, Singleton Park, Swansea, UK,Present address: Pathogen Genomics Unit, Public Health Wales, Cardiff, Wales, UK
| | - Pakpoom Tadee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Phacharaporn Tadee
- Faculty of Animal Science and Technology, Maejo University, Chiang Mai 50290, Thailand
| | - Kwanjit Duangsonk
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Guillaume Meric
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Present address: Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Samuel K. Sheppard
- Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Faculty of Allied Medical Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Prapas Patchanee
- Department of Food Animal Clinics, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,*Correspondence: Prapas Patchanee,
| | - Ben Pascoe
- Integrative Research Centre for Veterinary Preventive Medicine, Faculty of Veterinary Medicine, Chiang Mai University, Chiang Mai 50100, Thailand,Ineos Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, South Parks Road, Oxford, UK,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, UK,Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK,*Correspondence: Ben Pascoe,
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318
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Optimized Method for Bacterial Nucleic Acid Extraction from Positive Blood Culture Broth for Whole-Genome Sequencing, Resistance Phenotype Prediction, and Downstream Molecular Applications. J Clin Microbiol 2022; 60:e0101222. [PMID: 36314799 PMCID: PMC9667764 DOI: 10.1128/jcm.01012-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The application of direct metagenomic sequencing from positive blood culture broth may solve the challenges of sequencing from low-bacterial-load blood samples in patients with sepsis. Forty prospectively collected blood culture broth samples growing Gram-negative bacteria were extracted using commercially available kits to achieve high-quality DNA.
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319
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Teo JQM, Tang CY, Tan SH, Chang HY, Ong SM, Lee SJY, Koh TH, Sim JHC, Kwa ALH, Ong RTH. Genomic Surveillance of Carbapenem-Resistant Klebsiella pneumoniae from a Major Public Health Hospital in Singapore. Microbiol Spectr 2022; 10:e0095722. [PMID: 36066252 PMCID: PMC9602435 DOI: 10.1128/spectrum.00957-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/04/2022] [Indexed: 12/30/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global public health threat. In this study, we employed whole-genome sequencing (WGS) to determine the genomic epidemiology of a longitudinal collection of clinical CRKP isolates recovered from a large public acute care hospital in Singapore. Phylogenetic analyses, a characterization of resistance and virulence determinants, and plasmid profiling were performed for 575 unique CRKP isolates collected between 2009 and 2020. The phylogenetic analyses identified the presence of global high-risk clones among the CRKP population (clonal group [CG] 14/15, CG17/20, CG147, CG258, and sequence type [ST] 231), and these clones constituted 50% of the isolates. Carbapenemase production was common (n = 497, 86.4%), and KPC was the predominant carbapenemase (n = 235, 40.9%), followed by OXA-48-like (n = 128, 22.3%) and NDM (n = 93, 16.2%). Hypervirulence was detected in 59 (10.3%) isolates and was most common in the ST231 carbapenemase-producing isolates (21/59, 35.6%). Carbapenemase genes were associated with diverse plasmid replicons; however, there was an association of blaOXA-181/232 with ColKP3 plasmids. This study presents the complex and diverse epidemiology of the CRKP strains circulating in Singapore. Our study highlights the utility of WGS-based genomic surveillance in tracking the population dynamics of CRKP. IMPORTANCE In this study, we characterized carbapenem-resistant Klebsiella pneumoniae clinical isolates collected over a 12-year period in the largest public acute-care hospital in Singapore using whole-genome sequencing. The results of this study demonstrate significant genomic diversity with the presence of well-known epidemic, multidrug-resistant clones amid a diverse pool of nonepidemic lineages. Genomic surveillance involving comprehensive resistance, virulence, and plasmid gene content profiling provided critical information for antimicrobial resistance monitoring and highlighted future surveillance priorities, such as the emergence of ST231 K. pneumoniae strains bearing multidrug resistance, virulence elements, and the potential plasmid-mediated transmission of the blaOXA-48-like gene. The findings here also reinforce the necessity of unique infection control and prevention strategies that take the genomic diversity of local circulating strains into consideration.
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Affiliation(s)
- Jocelyn Qi-Min Teo
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Cheng Yee Tang
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Si Hui Tan
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Hong Yi Chang
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Sze Min Ong
- Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | | | - Tse-Hsien Koh
- Department of Microbiology, Singapore General Hospital, Singapore, Singapore
| | | | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
- Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
- Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
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320
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Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya A, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, Baker SJC, Dave M, McCarthy M, Mukiri KM, Nasir JA, Golbon B, Imtiaz H, Jiang X, Kaur K, Kwong M, Liang ZC, Niu KC, Shan P, Yang JYJ, Gray K, Hoad GR, Jia B, Bhando T, Carfrae L, Farha M, French S, Gordzevich R, Rachwalski K, Tu M, Bordeleau E, Dooley D, Griffiths E, Zubyk HL, Brown ED, Maguire F, Beiko R, Hsiao WWL, Brinkman FSL, Van Domselaar G, McArthur AG. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 2022; 51:D690-D699. [PMID: 36263822 PMCID: PMC9825576 DOI: 10.1093/nar/gkac920] [Citation(s) in RCA: 280] [Impact Index Per Article: 140.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 01/30/2023] Open
Abstract
The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.
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Affiliation(s)
- Brian P Alcock
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - William Huynh
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Romeo Chalil
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keaton W Smith
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Amogelang R Raphenya
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mateusz A Wlodarski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Aaron Petkau
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Sohaib A Syed
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kara K Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sheridan J C Baker
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Mugdha Dave
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Madeline C McCarthy
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Karyn M Mukiri
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jalees A Nasir
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Bahar Golbon
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Hamna Imtiaz
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Xingjian Jiang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Komal Kaur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan Kwong
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Zi Cheng Liang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Keyu C Niu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Prabakar Shan
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Jasmine Y J Yang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kristen L Gray
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gemma R Hoad
- Research Computing Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Baofeng Jia
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Timsy Bhando
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Lindsey A Carfrae
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Maya A Farha
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Shawn French
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Rodion Gordzevich
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kenneth Rachwalski
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Megan M Tu
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Emily Bordeleau
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Damion Dooley
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Emma Griffiths
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Haley L Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada,Department of Community Health & Epidemiology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada,Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - William W L Hsiao
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada,Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada,Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew G McArthur
- To whom correspondence should be addressed. Tel: +1 905 525 9140 (Ext 21663);
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321
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Souza SSR, Turcotte MR, Li J, Zhang X, Wolfe KL, Gao F, Benton CS, Andam CP. Population analysis of heavy metal and biocide resistance genes in Salmonella enterica from human clinical cases in New Hampshire, United States. Front Microbiol 2022; 13:983083. [PMID: 36338064 PMCID: PMC9626534 DOI: 10.3389/fmicb.2022.983083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
Microbes frequently encounter heavy metals and other toxic compounds generated from natural biogeochemical processes and anthropogenic activities. Here, we analyzed the prevalence and association of genes conferring resistance to heavy metals, biocides, and antimicrobial compounds in 394 genome sequences of clinical human-derived S. enterica from New Hampshire, USA. The most prevalent was the gold operon (gesABC-golTSB), which was present in 99.2% of the genomes. In contrast, the other five heavy metal operons (arsenic, copper, mercury, silver, tellurite) were present in 0.76% (3/394)–5.58% (22/394) of the total population. The heavy metal operons and three biocide resistance genes were differentially distributed across 15 sequence types (STs) and 16 serotypes. The number of heavy metal operons and biocide resistance genes per genome was significantly associated with high number of antimicrobial resistance (AMR) genes per genome. Notable is the mercury operon which exhibited significant association with genes conferring resistance to aminoglycosides, cephalosporins, diaminopyrimidine, sulfonamide, and fosfomycin. The mercury operon was co-located with the AMR genes aac(3)-IV, ant(3”)-IIa, aph(3’)-Ia, and aph(4)-Ia, CTX-M-65, dfrA14, sul1, and fosA3 genes within the same plasmid types. Lastly, we found evidence for negative selection of individual genes of each heavy metal operon and the biocide resistance genes (dN/dS < 1). Our study highlights the need for continued surveillance of S. enterica serotypes that carry those genes that confer resistance to heavy metals and biocides that are often associated with mobile AMR genes. The selective pressures imposed by heavy metals and biocides on S. enterica may contribute to the co-selection and spread of AMR in human infections.
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Affiliation(s)
- Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- *Correspondence: Stephanie S. R. Souza, ; orcid.org/0000-0002-4207-8231
| | - Madison R. Turcotte
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
| | - Jinfeng Li
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Xinglu Zhang
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Kristin L. Wolfe
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | - Fengxiang Gao
- New Hampshire Department of Health and Human Services, Concord, NH, United States
| | | | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, United States
- Cheryl P. Andam, ; orcid.org/0000-0003-4428-0924
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322
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Shapovalova V, Shaidullina E, Azizov I, Sheck E, Martinovich A, Dyachkova M, Matsvay A, Savochkina Y, Khafizov K, Kozlov R, Shipulin G, Edelstein M. Molecular Epidemiology of mcr-1-Positive Escherichia coli and Klebsiella pneumoniae Isolates: Results from Russian Sentinel Surveillance (2013-2018). Microorganisms 2022; 10:microorganisms10102034. [PMID: 36296310 PMCID: PMC9607333 DOI: 10.3390/microorganisms10102034] [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: 09/27/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The dissemination of mobile colistin resistance (mcr) genes is a serious healthcare threat because polymyxins represent "last-line" therapeutics for multi-drug-resistant Gram-negative pathogens. This study aimed to assess the prevalence of colistin resistance and mcr genes and characteristics of clinical Escherichia coli (Eco) and Klebsiella pneumoniae (Kpn) isolates and plasmids carrying these genes in Russia. METHODS A total of 4324 Eco and 4530 Kpn collected in the frame of sentinel surveillance in 2013-2018 were tested for susceptibility to colistin and other antibiotics using the broth microdilution method. mcr genes were screened by real-time PCR. Phylogeny, genomic features and plasmids of mcr-positive isolates were assessed using whole-genome sequencing and subsequent bioinformatic analysis. RESULTS Colistin resistance was detected in 2.24% Eco and 9.3% Kpn. Twenty-two (0.51%) Eco and two (0.04%) Kpn from distant sites carried mcr-1.1. Most mcr-positive isolates co-harbored ESBLs and other resistance determinants to various antibiotic classes. The mcr-positive Eco belonged to 16 MLST types, with ST359 being most common; Kpn belonged to ST307 and ST23. mcr-1.1 was carried mainly in IncI2 (n = 18) and IncX4 (n = 5) plasmids highly similar to those identified previously in human, animal and environmental isolates. CONCLUSION This study demonstrated a dissemination of "typical" mcr-bearing plasmids among diverse Eco and Kpn genotypes and across a wide geographic area in Russia. Given the frequent association of mcr with other resistance determinants and potential clinical impact, the continual surveillance of this threat is warranted.
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Affiliation(s)
- Valeria Shapovalova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
- Correspondence:
| | - Elvira Shaidullina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Alexey Martinovich
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Alina Matsvay
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Yulia Savochkina
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Kamil Khafizov
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Roman Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - German Shipulin
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Mikhail Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
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323
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Karthik K, Anbazhagan S, Chitra MA, Sridhar R. First report of the whole genome of Moraxella bovoculi genotype 1 from India and comparative genomics of Moraxella bovoculi to identify genotype-specific markers. Arch Microbiol 2022; 204:663. [PMID: 36201053 DOI: 10.1007/s00203-022-03276-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/02/2022]
Abstract
Moraxella bovoculi has been isolated frequently from cattle with Infectious bovine keratoconjunctivitis (IBK). Two diverse genotypes of M. bovoculi, 1 and 2 were identified based on whole genome sequence analysis. It is essential to discriminate between the two genotypes to frame prevention and control measures. The whole genome of M. bovoculi TN7 was sequenced and compared to other M. bovoculi strains available in the NCBI database. M. bovoculi TN7 was found to be genotype 1, had an RTX toxin operon and pilA gene that are the known virulence factors in related Moraxella sp., but lacked antimicrobial resistance genes. M. bovoculi was found to have an open pangenome with 4051 (75.31%) accessory genes, and the addition of each new genome adds 18 genes to the pangenome. Comparison of pilin protein amino acid sequences revealed three new sequence types. Furthermore, the presence of linx, nagL, swrC and mdtA genes was found to be genotype 1 specific, whereas hyaD, garR, gbsA, yhdG, gabT, iclR, higB2, hmuU, hmuT and hemS were found only in genotype 2. Polymerase Chain Reaction (PCR) primers were designed and evaluated on strain TN7 plus seven additional strains accessible to us that had not been whole genome sequenced. This initial evaluation of the designed primers for the linX and hyaD genes produced the expected banding patterns on PCR gels for genotypes 1 and 2, respectively, among the 8 strains. The genotype-specific genes identified in this study can be used as markers for accurate diagnosis of genotype 1 isolates and this can aid in the development of autogenous or other molecular vaccines for treatment of infectious bovine keratoconjunctivitis (IBK) in resource-limited research settings.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India. .,Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, Tamil Nadu, India.
| | - Subbaiyan Anbazhagan
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, 500078, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
| | - Ramaswamy Sridhar
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
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324
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Biggel M, Horlbog J, Nüesch-Inderbinen M, Chattaway MA, Stephan R. Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland. Microb Genom 2022; 8:mgen000877. [PMID: 36301086 PMCID: PMC9676052 DOI: 10.1099/mgen.0.000877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/15/2022] [Indexed: 07/20/2023] Open
Abstract
Salmonella is a leading cause of foodborne outbreaks and systemic infections worldwide. Emerging multi-drug resistant Salmonella lineages such as a ciprofloxacin-resistant subclade (CIPR) within Salmonella enterica serovar Kentucky ST198 threaten the effective prevention and treatment of infections. To understand the genomic diversity and antimicrobial resistance gene content associated with S. Kentucky in Switzerland, we whole-genome sequenced 70 human clinical isolates obtained between 2010 and 2020. Most isolates belonged to ST198-CIPR. High- and low-level ciprofloxacin resistance among CIPR isolates was associated with variable mutations in ramR and acrB in combination with stable mutations in quinolone-resistance determining regions (QRDRs). Analysis of isolates from patients with prolonged ST198 colonization indicated subclonal adaptions with the ramR locus as a mutational hotspot. SNP analyses identified multiple clusters of near-identical isolates, which were often associated with travel but included spatiotemporally linked isolates from Switzerland. The largest SNP cluster was associated with travellers returning from Indonesia, and investigation of global data linked >60 additional ST198 salmonellosis isolates to this cluster. Our results emphasize the urgent need for implementing whole-genome sequencing as a routine tool for Salmonella surveillance and outbreak detection.
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Affiliation(s)
- Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
| | - Jule Horlbog
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
- National Reference Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty University of Zürich, Zürich, Switzerland
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325
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Zhang Y, Zhang H, Zhang Z, Qian Q, Zhang Z, Xiao J. ProPan: a comprehensive database for profiling prokaryotic pan-genome dynamics. Nucleic Acids Res 2022; 51:D767-D776. [PMID: 36169225 PMCID: PMC9825599 DOI: 10.1093/nar/gkac832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 01/30/2023] Open
Abstract
Compared with conventional comparative genomics, the recent studies in pan-genomics have provided further insights into species genomic dynamics, taxonomy and identification, pathogenicity and environmental adaptation. To better understand genome characteristics of species of interest and to fully excavate key metabolic and resistant genes and their conservations and variations, here we present ProPan (https://ngdc.cncb.ac.cn/propan), a public database covering 23 archaeal species and 1,481 bacterial species (in a total of 51,882 strains) for comprehensively profiling prokaryotic pan-genome dynamics. By analyzing and integrating these massive datasets, ProPan offers three major aspects for the pan-genome dynamics of the species of interest: 1) the evaluations of various species' characteristics and composition in pan-genome dynamics; 2) the visualization of map association, the functional annotation and presence/absence variation for all contained species' gene clusters; 3) the typical characteristics of the environmental adaptation, including resistance genes prediction of 126 substances (biocide, antimicrobial drug and metal) and evaluation of 31 metabolic cycle processes. Besides, ProPan develops a very user-friendly interface, flexible retrieval and multi-level real-time statistical visualization. Taken together, ProPan will serve as a weighty resource for the studies of prokaryotic pan-genome dynamics, taxonomy and identification as well as environmental adaptation.
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Affiliation(s)
| | | | - Zaichao Zhang
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Qiheng Qian
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhewen Zhang
- Correspondence may also be addressed to Zhewen Zhang.
| | - Jingfa Xiao
- To whom correspondence should be addressed. Tel: +86 10 8409 7443; Fax: +86 10 8409 7720;
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326
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Abstract
Antibiotic resistance is rapidly spreading via the horizontal transfer of resistance genes in mobile genetic elements. While plasmids are key drivers of this process, few integrative phages encode antibiotic resistance genes. Here, we find that phage-plasmids, elements that are both phages and plasmids, often carry antibiotic resistance genes. We found 60 phage-plasmids with 184 antibiotic resistance genes, providing resistance for broad-spectrum-cephalosporins, carbapenems, aminoglycosides, fluoroquinolones, and colistin. These genes are in a few hot spots, seem to have been cotranslocated with transposable elements, and are often in class I integrons, which had not been previously found in phages. We tried to induce six phage-plasmids with resistance genes (including four with resistance integrons) and succeeded in five cases. Other phage-plasmids and integrative prophages were coinduced in these experiments. As a proof of concept, we focused on a P1-like element encoding an extended spectrum β-lactamase, blaCTX-M-55. After induction, we confirmed that it is capable of infecting and converting four other E. coli strains. Its reinduction led to the further conversion of a sensitive strain, confirming that it is a fully functional phage. This study shows that phage-plasmids carry a large diversity of clinically relevant antibiotic resistance genes that they can transfer across bacteria. As plasmids, these elements seem plastic and capable of acquiring genes from other plasmids. As phages, they may provide novel paths of transfer for resistance genes because they can infect bacteria that are distant in time and space from the original host. As a matter of alarm, they may also mediate transfer to other types of phages.
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327
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da Silva S, Guedes FADF, Amaral JRV, Ribeiro JRDA, de Souza YPA, de Freitas-Almeida ÂC, Thompson FL, Ramos RTJ, Whiteley AS, Macrae A, de Oliveira SS. Aeromonas allosaccharophila Strain AE59-TE2 Is Highly Antagonistic towards Multidrug-Resistant Human Pathogens, What Does Its Genome Tell Us? Life (Basel) 2022; 12:1492. [PMID: 36294926 PMCID: PMC9605075 DOI: 10.3390/life12101492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of the solution. This work reports on 57 antagonistic Aeromonas strains, of which 38 strains were antagonistic towards problematic human pathogens. The genome of the most antagonistic strain was sequenced and identified as Aeromonas allosaccharophila. Its genome was fully annotated and mined for genes that might explain that activity. Strain AE59-TE was antagonistic toward clinically relevant gram-negative and gram-positive multidrug-resistant bacteria, including Klebsiella pneumoniae KPC, Escherichia coli ESBL, Salmonella typhimurium, and Staphylococcus aureus MRSA. Strain AE59-TE2 was identified by multilocus sequence analysis. Genome mining identified four genes homologous to the bacteriocin, zoocin A from Streptococcus equi and a gene 98% similar to cvpA linked to colicin V production. A. allosaccharophila strain AE59-TE2 produced antimicrobial activity against a broad range of bacteria, including important gram-negative bacteria, not typically targeted by bacteriocins. Herewere described novel zoocin genes that are promising for industrial applications in the food and health sectors. Interesting and important antagonistic activity is described combined with the first detailed genomic analysis of the species Aeromonas allosaccharophila.
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Affiliation(s)
- Sheila da Silva
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - Fernanda Alves de Freitas Guedes
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - João Ricardo Vidal Amaral
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | - José Roberto de Assis Ribeiro
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
| | | | - Ângela Correa de Freitas-Almeida
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro Biomédico, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Av. 28 de Setembro, 87, 3° Andar, Fundos, Vila Isabel, Rio de Janeiro 20550-170, Brazil
| | - Fabiano Lopes Thompson
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Instituto de Biologia, 2° Andar-Sala 93, Rio de Janeiro 219410-970, Brazil
| | - Rommel Thiago Jucá Ramos
- Instituto de Ciências Biológicas, Centro de Genômica e Biologia de Sistemas da Universidade Federal do Pará (UFPA), Rua Augusto Corrêa, 01 Guamá, Belém 66075-970, Brazil
| | - Andrew Steven Whiteley
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Canberra, ACT 2601, Australia
| | - Andrew Macrae
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco I, 1° Andar-Sala 047, Rio de Janeiro 21941-902, Brazil
| | - Selma Soares de Oliveira
- Programa Pós-Graduação de Biotecnologia Vegetal e Bioprocessos da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco K, 2° Andar-Sala 032, Rio de Janeiro 21941-902, Brazil
- Instituto de Microbiologia Paulo de Góes da Universidade Federal do Rio de Janeiro, Av. Prof. Rodolpho Paulo Rocco, s/n-Prédio do CCS-Bloco I, 1° Andar-Sala 047, Rio de Janeiro 21941-902, Brazil
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328
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Genome Sequencing of Methicillin-Resistant and Methicillin-Susceptible
Mammaliicoccus sciuri
from Diseased Animals. Microbiol Resour Announc 2022; 11:e0071422. [PMID: 36125295 PMCID: PMC9583799 DOI: 10.1128/mra.00714-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mammaliicoccus sciuri
(previously
Staphylococcus sciuri
) is a frequent colonizer of mammals. We report the draft genomes of a methicillin-resistant strain (2254A) isolated from an armadillo and a methicillin-susceptible strain (6942A) from a cow. Genomes were sequenced using long-read Nanopore sequencing.
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329
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Ruegsegger L, Xiao J, Naziripour A, Kanumuambidi T, Brown D, Williams F, Marshall SH, Rudin SD, Yen K, Chu T, Chen L, Sozzi E, Bartelt L, Kreiswirth B, Bonomo RA, van Duin D. Multidrug-Resistant Gram-Negative Bacteria in Burn Patients. Antimicrob Agents Chemother 2022; 66:e0068822. [PMID: 36066237 PMCID: PMC9487463 DOI: 10.1128/aac.00688-22] [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: 05/11/2022] [Accepted: 08/15/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with burn injuries are at high risk for infectious complications, and infections are the most common cause of death after the first 72 h of hospitalization. Hospital-acquired infections caused by multidrug resistant (MDR) Gram-negative bacteria (GNB) in this population are concerning. Here, we evaluated carriage with MDR GNB in patients in a large tertiary-care burn intensive care unit. Twenty-nine patients in the burn unit were screened for intestinal carriage. Samples were cultured on selective media. Median time from admission to the burn unit to first sample collection was 9 days (IQR 5 - 17 days). In 21 (72%) patients, MDR GNB were recovered; the most common bacterial species isolated was Pseudomonas aeruginosa, which was found in 11/29 (38%) of patients. Two of these patients later developed bloodstream infections with P. aeruginosa. Transmission of KPC-31-producing ST22 Citrobacter freundii was detected. Samples from two patients grew genetically similar C. freundii isolates that were resistant to ceftazidime-avibactam. On analysis of whole-genome sequencing, blaKPC-31 was part of a Tn4401b transposon that was present on two different plasmids in each C. freundii isolate. Plasmid curing experiments showed that removal of both copies of blaKPC-31 was required to restore susceptibility to ceftazidime-avibactam. In summary, MDR GNB colonization is common in burn patients and patient-to-patient transmission of highly resistant GNB occurs. These results emphasize the ongoing need for infection prevention and antimicrobial stewardship efforts in this highly vulnerable population.
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Affiliation(s)
- Laura Ruegsegger
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jamie Xiao
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Arash Naziripour
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Trey Kanumuambidi
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dylan Brown
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Felicia Williams
- Department of Surgery, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Steven H. Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Susan D. Rudin
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Kelly Yen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Tingyu Chu
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Emanuele Sozzi
- Department of Environmental Science and Engineering, UNC Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Luther Bartelt
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Barry Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Robert A. Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
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330
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Miral A, Kautsky A, Alves-Carvalho S, Cottret L, Guillerm-Erckelboudt AY, Buguet M, Rouaud I, Tranchimand S, Tomasi S, Bartoli C. Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance. Microorganisms 2022; 10:1859. [PMID: 36144461 PMCID: PMC9503503 DOI: 10.3390/microorganisms10091859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/06/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.
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Affiliation(s)
- Alice Miral
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Adam Kautsky
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
| | - Susete Alves-Carvalho
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
| | - Ludovic Cottret
- CNRS, Université de Toulouse, 31320 Castanet-Tolosan, France
| | | | - Manon Buguet
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Isabelle Rouaud
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Sylvain Tranchimand
- Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Sophie Tomasi
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)—UMR 6226, University of Rennes 1, 35000 Rennes, France
| | - Claudia Bartoli
- IGEPP, INRAE, Institut Agro, University of Rennes 1, LIPME, INRAE, 35653 Le Rheu, France
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331
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Lear L, Padfield D, Dowsett T, Jones M, Kay S, Hayward A, Vos M. Bacterial colonisation dynamics of household plastics in a coastal environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156199. [PMID: 35636543 DOI: 10.1016/j.scitotenv.2022.156199] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 05/25/2023]
Abstract
Accumulation of plastics in the marine environment has widespread detrimental consequences for ecosystems and wildlife. Marine plastics are rapidly colonised by a wide diversity of bacteria, including human pathogens, posing potential risks to health. Here, we investigate the effect of polymer type, residence time and estuarine location on bacterial colonisation of common household plastics, including pathogenic bacteria. We submerged five main household plastic types: low-density PE (LDPE), high-density PE (HDPE), polypropylene (PP), polyvinyl chloride (PVC) and polyethylene terephthalate (PET) at an estuarine site in Cornwall (U.K.) and tracked bacterial colonisation dynamics. Using both culture-dependent and culture-independent approaches, we found that bacteria rapidly colonised plastics irrespective of polymer type, reaching culturable densities of up to 1000 cells cm3 after 7 weeks. Community composition of the biofilms changed over time, but not among polymer types. The presence of pathogenic bacteria, quantified using the insect model Galleria mellonella, increased dramatically over a five-week period, with Galleria mortality increasing from 4% in week one to 65% in week five. No consistent differences in virulence were observed between polymer types. Pathogens isolated from plastic biofilms using Galleria enrichment included Serratia and Enterococcus species and they harboured a wide range of antimicrobial resistance genes. Our findings show that plastics in coastal waters are rapidly colonised by a wide diversity of bacteria independent of polymer type. Further, our results show that marine plastic biofilms become increasingly associated with virulent bacteria over time.
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Affiliation(s)
- Luke Lear
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Daniel Padfield
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom.
| | - Tirion Dowsett
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Maia Jones
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Suzanne Kay
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
| | - Alex Hayward
- Department of Biosciences, University of Exeter, Penryn Campus, TR10 9FE, United Kingdom
| | - Michiel Vos
- European Centre for Environment and Human Health, University of Exeter Medical School, Environment and Sustainability Institute, Penryn Campus, TR10 9FE, United Kingdom
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332
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A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome. PLoS Biol 2022; 20:e3001792. [PMID: 36067158 PMCID: PMC9447899 DOI: 10.1371/journal.pbio.3001792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings. However, only a limited number of research groups globally have the computational resources to analyze such data. We retrieved 442 Tbp of sequencing reads from 214,095 metagenomic samples from the European Nucleotide Archive (ENA) and aligned them using a uniform approach against ARGs and 16S/18S rRNA genes. Here, we present the results of this extensive computational analysis and share the counts of reads aligned. Over 6.76∙108 read fragments were assigned to ARGs and 3.21∙109 to rRNA genes, where we observed distinct differences in both the abundance of ARGs and the link between microbiome and resistome compositions across various sampling types. This collection is another step towards establishing global surveillance of AMR and can serve as a resource for further research into the environmental spread and dynamic changes of ARGs. The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods and a deeper understanding of how resistance genes are transmitted around the world. This study presents a large-scale remapping of sequencing reads of publicly available metagenomic datasets that can be used to monitor the global prevalence of AMR genes.
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333
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Rosenbergová Z, Oftedal TF, Ovchinnikov KV, Thiyagarajah T, Rebroš M, Diep DB. Identification of a Novel Two-Peptide Lantibiotic from Vagococcus fluvialis. Microbiol Spectr 2022; 10:e0095422. [PMID: 35730941 PMCID: PMC9431498 DOI: 10.1128/spectrum.00954-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/24/2022] [Indexed: 11/20/2022] Open
Abstract
Infections caused by multiresistant pathogens have become a major problem in both human and veterinary medicine. Due to the declining efficacy of many antibiotics, new antimicrobials are needed. Promising alternatives or additions to antibiotics are bacteriocins, antimicrobial peptides of bacterial origin with activity against many pathogens, including antibiotic-resistant strains. From a sample of fermented maize, we isolated a Vagococcus fluvialis strain producing a bacteriocin with antimicrobial activity against multiresistant Enterococcus faecium. Whole-genome sequencing revealed the genes for a novel two-peptide lantibiotic. The production of the lantibiotic by the isolate was confirmed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, which revealed distinct peaks at 4,009.4 m/z and 3,181.7 m/z in separate fractions from reversed-phase chromatography. The combination of the two peptides resulted in a 1,200-fold increase in potency, confirming the two-peptide nature of the bacteriocin, named vagococcin T. The bacteriocin was demonstrated to kill sensitive cells by the formation of pores in the cell membrane, and its inhibition spectrum covers most Gram-positive bacteria, including multiresistant pathogens. To our knowledge, this is the first bacteriocin characterized from Vagococcus. IMPORTANCE Enterococci are common commensals in the intestines of humans and animals, but in recent years, they have been identified as one of the major causes of hospital-acquired infections due to their ability to quickly acquire virulence and antibiotic resistance determinants. Many hospital isolates are multiresistant, thereby making current therapeutic options critically limited. Novel antimicrobials or alternative therapeutic approaches are needed to overcome this global problem. Bacteriocins, natural ribosomally synthesized peptides produced by bacteria to eliminate other bacterial species living in a competitive environment, provide such an alternative. In this work, we purified and characterized a novel two-peptide lantibiotic produced by Vagococcus fluvialis LMGT 4216 isolated from fermented maize. The novel lantibiotic showed a broad spectrum of inhibition of Gram-positive strains, including vancomycin-resistant Enterococcus faecium, demonstrating its therapeutic potential.
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Affiliation(s)
- Zuzana Rosenbergová
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovakia
| | - Thomas F. Oftedal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Thasanth Thiyagarajah
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Martin Rebroš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Bratislava, Slovakia
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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334
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Babiker A, Bower C, Lutgring JD, Petit RA, Howard-Anderson J, Ansari U, McAllister G, Adamczyk M, Breaker E, Satola SW, Jacob JT, Woodworth MH. Clinical and Genomic Epidemiology of mcr-9-Carrying Carbapenem-Resistant Enterobacterales Isolates in Metropolitan Atlanta, 2012 to 2017. Microbiol Spectr 2022; 10:e0252221. [PMID: 35856667 PMCID: PMC9431279 DOI: 10.1128/spectrum.02522-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. Recently, the ninth allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, was reported. However, its clinical and public health significance remains unclear. We queried genomes of carbapenem-resistant Enterobacterales (CRE) for mcr-9 from a convenience sample of clinical isolates collected between 2012 and 2017 through the Georgia Emerging Infections Program, a population- and laboratory-based surveillance program. Isolates underwent phenotypic characterization and whole-genome sequencing. Phenotypic characteristics, genomic features, and clinical outcomes of mcr-9-positive and -negative CRE cases were then compared. Among 235 sequenced CRE genomes, 13 (6%) were found to harbor mcr-9, all of which were Enterobacter cloacae complex. The median MIC and rates of heteroresistance and inducible resistance to colistin were similar between mcr-9-positive and -negative isolates. However, rates of resistance were higher among mcr-9-positive isolates across most antibiotic classes. All cases had significant health care exposures. The 90-day mortality was similarly high in both mcr-9-positive (31%) and -negative (7%) CRE cases. Nucleotide identity and phylogenetic analysis did not reveal geotemporal clustering. mcr-9-positive isolates had a significantly higher number of median [range] antimicrobial resistance (AMR) genes (16 [4 to 22] versus 6 [2 to 15]; P < 0.001) than did mcr-9-negative isolates. Pangenome tests confirmed a significant association of mcr-9 detection with mobile genetic element and heavy metal resistance genes. Overall, the presence of mcr-9 was not associated with significant changes in colistin resistance or clinical outcomes, but continued genomic surveillance to monitor for emergence of AMR genes is warranted. IMPORTANCE Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. A recently described allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, has been widely reported among Enterobacterales species. However, its clinical and public health significance remains unclear. We compared characteristics and outcomes of mcr-9-positive and -negative CRE cases. All cases were acquired in the health care setting and associated with a high rate of mortality. The presence of mcr-9 was not associated with significant changes in colistin resistance, heteroresistance, or inducible resistance but was associated with resistance to other antimicrobials and antimicrobial resistance (AMR), virulence, and heavy metal resistance (HMR) genes. Overall, the presence of mcr-9 was not associated with significant phenotypic changes or clinical outcomes. However, given the increase in AMR and HMR gene content and potential clinical impact, continued genomic surveillance of multidrug-resistant organisms to monitor for emergence of AMR genes is warranted.
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Affiliation(s)
- Ahmed Babiker
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Chris Bower
- Georgia Emerging Infections Program, Decatur, Georgia, USA
- Atlanta VA Medical Center, Decatur, Georgia, USA
- Foundation for Atlanta Veterans Education and Research, Decatur, Georgia, USA
| | - Joseph D. Lutgring
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Jessica Howard-Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Uzma Ansari
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michelle Adamczyk
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Erin Breaker
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sarah W. Satola
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Georgia Emerging Infections Program, Decatur, Georgia, USA
| | - Jesse T. Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Georgia Emerging Infections Program, Decatur, Georgia, USA
| | - Michael H. Woodworth
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Georgia Emerging Infections Program, Decatur, Georgia, USA
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335
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Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates from Two Romanian Hospitals Co-Presenting Resistance and Heteroresistance to Colistin. Antibiotics (Basel) 2022; 11:antibiotics11091171. [PMID: 36139950 PMCID: PMC9495256 DOI: 10.3390/antibiotics11091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/12/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae is a notorious human pathogen involved in healthcare-associated infections. The worldwide expansion of infections induced by colistin-resistant and carbapenemase-producing Enterobacterales (CPE) isolates has been increasingly reported. This study aims to analyze the phenotypic and molecular profiles of 10 colistin-resistant (CR) isolates and 2 pairs of colistin-heteroresistant (ChR) (parental and the corresponding resistant mutants) isolates of K. pneumoniae CPE sourced from two hospitals. The phenotypes of strains in the selected collection had been previously characterized. Antimicrobial susceptibility testing was performed using a Vitek 2 Compact system (BioMérieux SA, Marcy l’Etoile, France), the disc diffusion method, and broth microdilution (BMD) for colistin. Whole-genome sequencing (WGS) did not uncover evidence of any mobile colistin resistance (mcr) genes, although the mgrB gene of seven isolates appeared to be disrupted by insertion sequences (ISKpn25 or ISKpn26). Possible deleterious missense mutations were found in phoP (L4F), phoQ (Q426L, L26Q, L224Q, Q317K), pmrB (R256G, P95L, T157P, V352E), and crrB (P151S) genes. The identified isolates belonged to the following clonal lineages: ST101 (n = 6), ST147 (n = 5), ST258 (n = 2), and ST307 (n = 1). All strains harbored IncF plasmids. OXA-48 producers carried IncL and IncR plasmids, while one blaNDM-1 genome was found to harbor IncC plasmids. Ceftazidime–avibactam remains a therapeutic option for KPC-2 and OXA-48 producers. Resistance to meropenem–vaborbactam has emerged in some blakPC-2-carrying isolates. Our study demonstrates that the results of WGS can provide essential evidence for the surveillance of antimicrobial resistance.
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336
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WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000-2017 in Peru. Antibiotics (Basel) 2022; 11:antibiotics11091170. [PMID: 36139949 PMCID: PMC9495214 DOI: 10.3390/antibiotics11091170] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Salmonella Typhimurium is associated with foodborne diseases worldwide, including in Peru, and its emerging antibiotic resistance (AMR) is now a global public health problem. Therefore, country-specific monitoring of the AMR emergence is vital to control this pathogen, and in these aspects, whole genome sequence (WGS)—based approaches are better than gene-based analyses. Here, we performed the antimicrobial susceptibility test for ten widely used antibiotics and WGS-based various analyses of 90 S. Typhimurium isolates (human, animal, and environment) from 14 cities of Peru isolated from 2000 to 2017 to understand the lineage and antimicrobial resistance pattern of this pathogen in Peru. Our results suggest that the Peruvian isolates are of Typhimurium serovar and predominantly belong to sequence type ST19. Genomic diversity analyses indicate an open pan-genome, and at least ten lineages are circulating in Peru. A total of 48.8% and 31.0% of isolates are phenotypically and genotypically resistant to at least one antibiotic, while 12.0% are multi-drug resistant (MDR). Genotype−phenotype correlations for ten tested drugs show >80% accuracy, and >90% specificity. Sensitivity above 90% was only achieved for ciprofloxacin and ceftazidime. Two lineages exhibit the majority of the MDR isolates. A total of 63 different AMR genes are detected, of which 30 are found in 17 different plasmids. Transmissible plasmids such as lncI-gamma/k, IncI1-I(Alpha), Col(pHAD28), IncFIB, IncHI2, and lncI2 that carry AMR genes associated with third-generation antibiotics are also identified. Finally, three new non-synonymous single nucleotide variations (SNVs) for nalidixic acid and eight new SNVs for nitrofurantoin resistance are predicted using genome-wide association studies, comparative genomics, and functional annotation. Our analysis provides for the first time the WGS-based details of the circulating S. Typhimurium lineages and their antimicrobial resistance pattern in Peru.
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337
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Tønnessen R, García I, Debech N, Lindstrøm JC, Wester AL, Skaare D. Molecular epidemiology and antibiotic resistance profiles of invasive Haemophilus influenzae from Norway 2017–2021. Front Microbiol 2022; 13:973257. [PMID: 36106084 PMCID: PMC9467436 DOI: 10.3389/fmicb.2022.973257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Invasive Haemophilus influenzae (Hi) disease has decreased in countries that included Hi type b (Hib) vaccination in their childhood immunization programs in the 1990s. Non-typeable (NT) and non-b strains are now the leading causes of invasive Hi disease in Europe, with most cases reported in young children and the elderly. Concerningly, no vaccines toward such strains are available and beta-lactam resistance is increasing. We describe the epidemiology of invasive Hi disease reported to the Norwegian Surveillance System for Communicable Diseases (MSIS) (2017–2021, n = 407). Whole-genome sequencing (WGS) was performed on 245 isolates. We investigated the molecular epidemiology (core genome phylogeny) and the presence of antibiotic resistance markers (including chromosomal mutations associated with beta-lactam or quinolone resistance). For isolates characterized with both WGS and phenotypic antibiotic susceptibility testing (AST) (n = 113) we assessed correlation between resistance markers and susceptibility categorization by calculation of sensitivity, specificity, and predictive values. Incidence rates of invasive Hi disease in Norway ranged from 0.7 to 2.3 per 100,000 inhabitants/year (mean 1.5 per 100,000) and declined during the COVID-19 pandemic. The bacterial population consisted of two major phylogenetic groups with subclustering by serotype and multi-locus sequence type (ST). NTHi accounted for 71.8% (176). The distribution of STs was in line with previous European reports. We identified 13 clusters, including four encapsulated and three previously described international NTHi clones with blaTEM–1 (ST103) or altered PBP3 (rPBP3) (ST14/IIA and ST367/IIA). Resistance markers were detected in 25.3% (62/245) of the isolates, with blaTEM–1 (31, 50.0%) and rPBP3 (28, 45.2%) being the most frequent. All isolates categorized as resistant to aminopenicillins, tetracycline or chloramphenicol possessed relevant resistance markers, and the absence of relevant substitutions in PBP3 and GyrA/ParC predicted susceptibility to cefotaxime, ceftriaxone, meropenem and quinolones. Among the 132 WGS-only isolates, one isolate had PBP3 substitutions associated with resistance to third-generation cephalosporins, and one isolate had GyrA/ParC alterations associated with quinolone resistance. The detection of international virulent and resistant NTHi clones underlines the need for a global molecular surveillance system. WGS is a useful supplement to AST and should be performed on all invasive isolates.
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Affiliation(s)
- Ragnhild Tønnessen
- Department of Infection Control and Vaccines, Norwegian Institute of Public Health, Oslo, Norway
- European Public Health Microbiology Training Program (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- *Correspondence: Ragnhild Tønnessen,
| | - Ignacio García
- Department of Bacteriology, Norwegian Institute of Public Health, Oslo, Norway
| | - Nadia Debech
- Department of Bacteriology, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Dagfinn Skaare
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
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338
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Complete Genome Sequence of a Salmonella enterica subsp.
enterica
Serovar Tennessee Strain from Tahini. Microbiol Resour Announc 2022; 11:e0040722. [PMID: 35894624 PMCID: PMC9387254 DOI: 10.1128/mra.00407-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Salmonella sp. infections are associated with contaminated low-moisture foods (with high fat content) with increasing frequency. Here, we report the complete genome sequence of Salmonella enterica subsp. enterica serovar Tennessee, which was isolated from tahini (a paste made from ground sesame seeds) purchased at a local retailer in Berlin, Germany.
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339
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Draft Genome Sequence of
Helicobacter
sp. Strain CaF467b, Isolated from a Pig Manure Storage Tank. Microbiol Resour Announc 2022; 11:e0025522. [PMID: 35867526 PMCID: PMC9387212 DOI: 10.1128/mra.00255-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this report, we present the draft genome sequence of an unclassified Helicobacter strain, CaF467b. This bacterial isolate was recovered from a pig manure storage tank. The draft genome sequence is 1,655,514 bp in length with 1,709 predicted genes and a G+C content of 34.07%.
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340
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Abbasi BA, Dharan A, Mishra A, Saraf D, Ahamad I, Suravajhala P, Valadi J. In Silico Characterization of Uncharacterized Proteins From Multiple Strains of Clostridium Difficile. Front Genet 2022; 13:878012. [PMID: 36035185 PMCID: PMC9403866 DOI: 10.3389/fgene.2022.878012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Clostridium difficile (C. difficile) is a multi-strain, spore-forming, Gram-positive, opportunistic enteropathogen bacteria, majorly associated with nosocomial infections, resulting in severe diarrhoea and colon inflammation. Several antibiotics including penicillin, tetracycline, and clindamycin have been employed to control C. difficile infection, but studies have suggested that injudicious use of antibiotics has led to the development of resistance in C. difficile strains. However, many proteins from its genome are still considered uncharacterized proteins that might serve crucial functions and assist in the biological understanding of the organism. In this study, we aimed to annotate and characterise the 6 C. difficile strains using in silico approaches. We first analysed the complete genome of 6 C. difficile strains using standardised approaches and analysed hypothetical proteins (HPs) employing various bioinformatics approaches coalescing, including identifying contigs, coding sequences, phage sequences, CRISPR-Cas9 systems, antimicrobial resistance determination, membrane helices, instability index, secretory nature, conserved domain, and vaccine target properties like comparative homology analysis, allergenicity, antigenicity determination along with structure prediction and binding-site analysis. This study provides crucial supporting information about the functional characterization of the HPs involved in the pathophysiology of the disease. Moreover, this information also aims to assist in mechanisms associated with bacterial pathogenesis and further design candidate inhibitors and bona fide pharmaceutical targets.
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Affiliation(s)
| | | | | | | | | | - Prashanth Suravajhala
- Bioclues.org, Hyderabad, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
| | - Jayaraman Valadi
- Bioclues.org, Hyderabad, India
- School of Computational and Data Sciences, Vidyashilp University, Bengaluru, India
- Department of Computer Science, FLAME University, Pune, India
- *Correspondence: Prashanth Suravajhala, ; Jayaraman Valadi,
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341
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Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation. Cell 2022; 185:2879-2898.e24. [PMID: 35931020 DOI: 10.1016/j.cell.2022.07.003] [Citation(s) in RCA: 174] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/17/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
Abstract
Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n = 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation. Stepwise generation of a lytic five-phage combination, targeting sensitive and resistant IBD-associated Kp clade members through distinct mechanisms, enables effective Kp suppression in colitis-prone mice, driving an attenuated inflammation and disease severity. Proof-of-concept assessment of Kp-targeting phages in an artificial human gut and in healthy volunteers demonstrates gastric acid-dependent phage resilience, safety, and viability in the lower gut. Collectively, we demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance, while effectively inhibiting non-communicable disease-contributing pathobionts.
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342
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Damas MSF, Ferreira RL, Campanini EB, Soares GG, Campos LC, Laprega PM, Soares da Costa A, Freire CCDM, Pitondo-Silva A, Cerdeira LT, da Cunha AF, Pranchevicius MCDS. Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil. Front Med (Lausanne) 2022; 9:931379. [PMID: 35966843 PMCID: PMC9366087 DOI: 10.3389/fmed.2022.931379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (blaIND–13, blaCIA–3, blaTEM–116, blaOXA–209, blaVEB–15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.
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Affiliation(s)
| | - Roumayne Lopes Ferreira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Emeline Boni Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | | | - Pedro Mendes Laprega
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Andrea Soares da Costa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | | | - André Pitondo-Silva
- Programa de Pós-graduação em Odontologia e Tecnologia Ambiental, Universidade de Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical - BIOTROP, Universidade Federal de São Carlos, São Carlos, Brazil
- *Correspondence: Maria-Cristina da Silva Pranchevicius,
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343
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Highly Virulent and Multidrug-Resistant Escherichia coli Sequence Type 58 from a Sausage in Germany. Antibiotics (Basel) 2022; 11:antibiotics11081006. [PMID: 35892394 PMCID: PMC9331442 DOI: 10.3390/antibiotics11081006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 11/16/2022] Open
Abstract
Studies have previously described the occurrence of multidrug-resistant (MDR) Escherichia coli in human and veterinary medical settings, livestock, and, to a lesser extent, in the environment and food. While they mostly analyzed foodborne E. coli regarding phenotypic and sometimes genotypic antibiotic resistance and basic phylogenetic classification, we have limited understanding of the in vitro and in vivo virulence characteristics and global phylogenetic contexts of these bacteria. Here, we investigated in-depth an E. coli strain (PBIO3502) isolated from a pork sausage in Germany in 2021. Whole-genome sequence analysis revealed sequence type (ST)58, which has an internationally emerging high-risk clonal lineage. In addition to its MDR phenotype that mostly matched the genotype, PBIO3502 demonstrated pronounced virulence features, including in vitro biofilm formation, siderophore secretion, serum resilience, and in vivo mortality in Galleria mellonella larvae. Along with the genomic analysis indicating close phylogenetic relatedness of our strain with publicly available, clinically relevant representatives of the same ST, these results suggest the zoonotic and pathogenic character of PBIO3502 with the potential to cause infection in humans and animals. Additionally, our study highlights the necessity of the One Health approach while integrating human, animal, and environmental health, as well as the role of meat products and food chains in the putative transmission of MDR pathogens.
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344
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Colon VA, Lugsomya K, Lam HK, Wahl LC, Parkes RSV, Cormack CA, Horlbog JA, Stevens M, Stephan R, Magouras I. Serotype Diversity and Antimicrobial Resistance Profile of Salmonella enterica Isolates From Freshwater Turtles Sold for Human Consumption in Wet Markets in Hong Kong. Front Vet Sci 2022; 9:912693. [PMID: 35937281 PMCID: PMC9353134 DOI: 10.3389/fvets.2022.912693] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Chelonians are recognized as a source of human salmonellosis through direct contact or consumption of their meat. Freshwater turtles sold for food are widely available in wet markets in Asia. In this pilot study, 50 turtles belonging to three species were randomly sampled from wet markets throughout Hong Kong. The turtles were humanely euthanised and their feces or the colon were sampled for Salmonella culture. The Salmonella isolates obtained were serotyped and examined for phenotypic antimicrobial resistance and the presence of antimicrobial resistance genes. The study reports a high prevalence (42%, 95% CI: 29.4–55.8) and considerable serotype diversity of Salmonella among turtles sold in wet markets. The most common among the 11 serotypes isolated were S. Oranienburg and S. Thompson, which have been reported in turtles previously. The serotype S. Manhattan is reported in chelonians for the first time. Resistance to streptomycin and chloramphenicol was common, despite the latter being banned from aquaculture in mainland China since 2002. Resistance against fluoroquinolones and third-generation cephalosporins which represent first-line treatment options for salmonellosis was also observed. The multidrug-resistance gene cfr is identified for the first time in Salmonella. This is a worrying finding as it indicates an expansion of the cfr reservoir and potential horizontal spread to other bacteria. The results of this study emphasize the need for close surveillance of Salmonella from turtles sold as food and better regulation of turtle farming to safeguard public health and improve animal welfare.
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Affiliation(s)
- Violaine Albane Colon
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Kittitat Lugsomya
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Hoi Kiu Lam
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Lloyd Christian Wahl
- Centre for Applied One Health Research and Policy Advice, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Rebecca Sarah Victoria Parkes
- Department of Veterinary Clinical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Centre for Animal Health and Welfare, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Catherine Anne Cormack
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Jule Anna Horlbog
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zürich, Switzerland
- Vetsuisse Faculty, National Reference Center for Enteropathogenic Bacteria and Listeria (NENT), Institute for Food Safety and Hygiene, University of Zurich, Zürich, Switzerland
| | - Marc Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zürich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zürich, Switzerland
| | - Ioannis Magouras
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Centre for Applied One Health Research and Policy Advice, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- *Correspondence: Ioannis Magouras
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345
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Colonization of White-Tailed Deer (Odocoileus virginianus) from Urban and Suburban Environments with Cephalosporinase- and Carbapenemase-Producing Enterobacterales. Appl Environ Microbiol 2022; 88:e0046522. [PMID: 35736227 PMCID: PMC9275232 DOI: 10.1128/aem.00465-22] [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: 02/03/2023] Open
Abstract
Wildlife play a role in the acquisition, maintenance, and dissemination of antimicrobial resistance (AMR). This is especially true at the human-domestic animal-wildlife interface, like urbanized areas, where interactions occur that can promote the cross-over of AMR bacteria and genes. We conducted a 2-year fecal surveillance (n = 783) of a white-tailed deer (WTD) herd from an urban park system in Ohio to identify and characterize cephalosporin-resistant and carbapenemase-producing bacteria using selective enrichment. Using generalized linear mixed models we found that older (OR = 2.3, P < 0.001), male (OR = 1.8, P = 0.001) deer from urbanized habitats (OR = 1.4, P = 0.001) were more likely to harbor extended-spectrum cephalosporin-resistant Enterobacterales. In addition, we isolated two carbapenemase-producing Enterobacterales (CPE), a Klebsiella quasipneumoniae harboring blaKPC-2 and an Escherichia coli harboring blaNDM-5, from two deer from urban habitats. The genetic landscape of the plasmid carrying blaKPC-2 was unique, not clustering with other reported plasmids encoding KPC-2, and only sharing 78% of its sequence with its nearest match. While the plasmid carrying blaNDM-5 shared sequence similarity with other reported plasmids encoding NDM-5, the intact IS26 mobile genetic elements surrounding multiple drug resistant regions, including the blaNDM-5, has been reported infrequently. Both carbapenemase genes were successfully conjugated to a J53 recipient conferring a carbapenem-resistant phenotype. Our findings highlight that urban environments play a significant role on the transmission of AMR bacteria and genes to wildlife and suggest WTD may play a role in the dissemination of clinically and epidemiologically relevant antimicrobial resistant bacteria. IMPORTANCE The role of wildlife in the spread of antimicrobial resistance is not fully characterized. Some wildlife, including white-tailed deer (WTD), can thrive in suburban and urban environments. This may result in the exchange of antimicrobial resistant bacteria and resistance genes between humans and wildlife, and lead to their spread in the environment. We found that WTD living in an urban park system carried antimicrobial resistant bacteria that were important to human health and resistant to antibiotics used to treat serious bacterial infections. This included two deer that carried bacteria resistant to carbapenem antibiotics which are critically important for treatment of life-threatening infections. These two bacteria had the ability to transfer their AMR resistance genes to other bacteria, making them a threat to public health. Our results suggest that WTD may contribute to the spread of antimicrobial resistant bacteria in the environment.
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346
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Jang H, Eshwar A, Lehner A, Gangiredla J, Patel IR, Beaubrun JJG, Chase HR, Negrete F, Finkelstein S, Weinstein LM, Ko K, Addy N, Ewing L, Woo J, Lee Y, Seo K, Jaradat Z, Srikumar S, Fanning S, Stephan R, Tall BD, Gopinath GR. Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies. Microorganisms 2022; 10:microorganisms10071396. [PMID: 35889115 PMCID: PMC9319161 DOI: 10.3390/microorganisms10071396] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.
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Affiliation(s)
- Hyein Jang
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Athmanya Eshwar
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Angelika Lehner
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Isha R. Patel
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Junia Jean-Gilles Beaubrun
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Hannah R. Chase
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Flavia Negrete
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Samantha Finkelstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Leah M. Weinstein
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Katie Ko
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Nicole Addy
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Laura Ewing
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Jungha Woo
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Youyoung Lee
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
| | - Kunho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea;
| | - Ziad Jaradat
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Shabarinath Srikumar
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin & WHO Collaborating Centre for Cronobacter, Belfield, D04 N2E5 Dublin, Ireland; (S.S.); (S.F.)
| | - Roger Stephan
- Institute for Food Safety and Hygiene, University of Zurich, CH-8057 Zurich, Switzerland; (A.E.); (A.L.); (R.S.)
| | - Ben D. Tall
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
| | - Gopal R. Gopinath
- Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA; (H.J.); (J.G.); (I.R.P.); (J.J.-G.B.); (H.R.C.); (F.N.); (S.F.); (L.M.W.); (K.K.); (N.A.); (L.E.); (J.W.); (Y.L.)
- Correspondence: (B.D.T.); (G.R.G.)
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347
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Vezina B, Rosa MN, Canu A, Tola S. Genomic surveillance reveals antibiotic resistance gene transmission via phage recombinases within sheep mastitis-associated Streptococcus uberis. BMC Vet Res 2022; 18:264. [PMID: 35799261 PMCID: PMC9261030 DOI: 10.1186/s12917-022-03341-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022] Open
Abstract
Background Streptococcus uberis is one of the main causative agents of ovine mastitis, however little is known about this global, environmental pathogen and its genomic mechanisms of disease. In this study, we performed genomic analysis on 46 S. uberis isolates collected from mastitis-infected sheep in Sardinia (Italy). Results Genomes were assigned into lineage clusters using PopPUNK, which found 27 distinct isolate clusters, indicating considerable genetic variability consistent with environmental isolates. Geographic trends were identified including regional linkage of several isolate clusters. Multi-locus Sequence Typing (MLST) performed poorly and provided no new insights. Genomes were then screened for antimicrobial resistance genes, which were compared to phenotypic resistance profiles. Isolates showed consistent phenotypic resistance to aminoglycosides with variable resistance to novobiocin and tetracycline. In general, identification of antimicrobial resistance genes did not correlate with phenotypic resistance profiles, indicating unknown genetic determinants. A multi-antimicrobial resistance cassette (aminoglycoside, lincosamide and streptogramin) was identified in the chromosome of three genomes, flanked by vestigial phage recombinases. This locus appears to have spread horizontally within discrete S. uberis populations within a 40 km radius (Sassari region). Genomes were screened for putative virulence factors, which identified 16 genes conserved between sheep and cow isolates, with no host-specific genes shared uniformly across all host-specific isolates. Pangenomic analysis was then performed to identify core genes which were putatively surface-exposed, for identification of potential vaccine targets. As all genomes encoded sortase, core genes were screened for the sortase cleavage motif. Of the 1445 core S. uberis genes, 64 were putative sortase substrates and were predominantly adhesins, permeases and peptidases, consistent with compounds found within ruminant milk such as xanthine, fibronectin and lactoferrin. Conclusions This study demonstrated the importance of whole genome sequencing for surveillance of S. uberis and tracking horizontal acquisition of antimicrobial resistance genes, as well as providing insight into genetic determinants of disease, which cannot be inferred from the MLST schemes. Future mastitis surveillance should be informed by genomic analysis. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03341-1.
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Affiliation(s)
- Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Maria Nives Rosa
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Via Duca degli Abruzzi 8, 07100, Sassari, Italy
| | - Antonella Canu
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Via Duca degli Abruzzi 8, 07100, Sassari, Italy
| | - Sebastiana Tola
- Istituto Zooprofilattico Sperimentale della Sardegna "G. Pegreffi", Via Duca degli Abruzzi 8, 07100, Sassari, Italy.
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348
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Comparative analysis of multiplexed PCR and short- and long-read whole genome sequencing to investigate a large Klebsiella pneumoniae outbreak in New York State. Diagn Microbiol Infect Dis 2022; 104:115765. [DOI: 10.1016/j.diagmicrobio.2022.115765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022]
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349
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Diorio-Toth L, Irum S, Potter RF, Wallace MA, Arslan M, Munir T, Andleeb S, Burnham CAD, Dantas G. Genomic Surveillance of Clinical Pseudomonas aeruginosa Isolates Reveals an Additive Effect of Carbapenemase Production on Carbapenem Resistance. Microbiol Spectr 2022; 10:e0076622. [PMID: 35638817 PMCID: PMC9241860 DOI: 10.1128/spectrum.00766-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 01/15/2023] Open
Abstract
Carbapenem resistance in Pseudomonas aeruginosa is increasing globally, and surveillance to define the mechanisms of such resistance in low- and middle-income countries is limited. This study establishes the genotypic mechanisms of β-lactam resistance by whole-genome sequencing (WGS) in 142 P. aeruginosa clinical isolates recovered from three hospitals in Islamabad and Rawalpindi, Pakistan between 2016 and 2017. Isolates were subjected to antimicrobial susceptibility testing (AST) by Kirby-Bauer disk diffusion, and their genomes were assembled from Illumina sequencing data. β-lactam resistance was high, with 46% of isolates resistant to piperacillin-tazobactam, 42% to cefepime, 48% to ceftolozane-tazobactam, and 65% to at least one carbapenem. Twenty-two percent of isolates were resistant to all β-lactams tested. WGS revealed that carbapenem resistance was associated with the acquisition of metallo-β-lactamases (MBLs) or extended-spectrum β-lactamases (ESBLs) in the blaGES, blaVIM, and blaNDM families, and mutations in the porin gene oprD. These resistance determinants were found in globally distributed lineages, including ST235 and ST664, as well as multiple novel STs which have been described in a separate investigation. Analysis of AST results revealed that acquisition of MBLs/ESBLs on top of porin mutations had an additive effect on imipenem resistance, suggesting that there is a selective benefit for clinical isolates to encode multiple resistance determinants to the same drugs. The strong association of these resistance determinants with phylogenetic background displays the utility of WGS for monitoring carbapenem resistance in P. aeruginosa, while the presence of these determinants throughout the phylogenetic tree shows that knowledge of the local epidemiology is crucial for guiding potential treatment of multidrug-resistant P. aeruginosa infections. IMPORTANCE Pseudomonas aeruginosa is associated with serious infections, and treatment can be challenging. Because of this, carbapenems and β-lactam/β-lactamase inhibitor combinations have become critical tools in treating multidrug-resistant (MDR) P. aeruginosa infections, but increasing resistance threatens their efficacy. Here, we used WGS to study the genotypic and phylogenomic patterns of 142 P. aeruginosa isolates from the Potohar region of Pakistan. We sequenced both MDR and antimicrobial susceptible isolates and found that while genotypic and phenotypic patterns of antibiotic resistance correlated with phylogenomic background, populations of MDR P. aeruginosa were found in all major phylogroups. We also found that isolates possessing multiple resistance mechanisms had significantly higher levels of imipenem resistance compared to the isolates with a single resistance mechanism. This study demonstrates the utility of WGS for monitoring patterns of antibiotic resistance in P. aeruginosa and potentially guiding treatment choices based on the local spread of β-lactamase genes.
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Affiliation(s)
- Luke Diorio-Toth
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sidra Irum
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Robert F. Potter
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Muhammad Arslan
- Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | - Tehmina Munir
- Department of Microbiology, Army Medical College, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Saadia Andleeb
- Atta ur Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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350
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Fuesslin V, Krautwurst S, Srivastava A, Winter D, Liedigk B, Thye T, Herrera-León S, Wohl S, May J, Fobil JN, Eibach D, Marz M, Schuldt K. Prediction of Antibiotic Susceptibility Profiles of Vibrio cholerae Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon. Front Microbiol 2022; 13:909692. [PMID: 35814690 PMCID: PMC9257098 DOI: 10.3389/fmicb.2022.909692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 12/01/2022] Open
Abstract
During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform-especially in light of an upcoming less error-prone technology for the platform-appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.
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Affiliation(s)
- Valeria Fuesslin
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sebastian Krautwurst
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Akash Srivastava
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Doris Winter
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Britta Liedigk
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Thorsten Thye
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Silvia Herrera-León
- National Center of Microbiology, Institute of Health Carlos III, Madrid, Spain
| | - Shirlee Wohl
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jürgen May
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- Tropical Medicine II, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Julius N. Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Accra, Ghana
| | - Daniel Eibach
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
| | - Kathrin Schuldt
- Infectious Disease Epidemiology Department, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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