1
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Stege PB, Schokker D, Harders F, Kar SK, Stockhofe N, Perricone V, Rebel JMJ, de Jong IC, Bossers A. Diet-induced changes in the jejunal microbiota of developing broilers reduce the abundance of Enterococcus hirae and Enterococcus faecium. BMC Genomics 2024; 25:627. [PMID: 38910254 PMCID: PMC11193906 DOI: 10.1186/s12864-024-10496-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/05/2024] [Indexed: 06/25/2024] Open
Abstract
Modern broiler breeds allow for high feed efficiency and rapid growth, which come at a cost of increased susceptibility to pathogens and disease. Broiler growth rate, feed efficiency, and health are affected by the composition of the gut microbiota, which in turn is influenced by diet. In this study, we therefore assessed how diet composition can affect the broiler jejunal gut microbiota. A total of 96 broiler chickens were divided into four diet groups: control, coated butyrate supplementation, medium-chain fatty acid supplementation, or a high-fibre low-protein content. Diet groups were sub-divided into age groups (4, 12 and 33 days of age) resulting in groups of 8 broilers per diet per age. The jejunum content was used for metagenomic shotgun sequencing to determine the microbiota taxonomic composition at species level. The composed diets resulted in a total of 104 differentially abundant bacterial species. Most notably were the butyrate-induced changes in the jejunal microbiota of broilers 4 days post-hatch, resulting in the reduced relative abundance of mainly Enterococcus faecium (-1.8 l2fc, Padj = 9.9E-05) and the opportunistic pathogen Enterococcus hirae (-2.9 l2fc, Padj = 2.7E-08), when compared to the control diet. This effect takes place during early broiler development, which is critical for broiler health, thus exemplifying the importance of how diet can influence the microbiota composition in relation to broiler health. Future studies should therefore elucidate how diet can be used to promote a beneficial microbiota in the early stages of broiler development.
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Affiliation(s)
- Paul B Stege
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands.
| | - Dirkjan Schokker
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Frank Harders
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Soumya K Kar
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Norbert Stockhofe
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Vera Perricone
- Department of Veterinary Medicine and Animal Science, University of Milan, Milan, Italy
| | - Johanna M J Rebel
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
| | - Ingrid C de Jong
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Alex Bossers
- Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, Netherlands
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2
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Wei Y, Palacios Araya D, Palmer KL. Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01058-6. [PMID: 38890478 DOI: 10.1038/s41579-024-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
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Affiliation(s)
- Yahan Wei
- School of Podiatric Medicine, The University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA.
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3
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Mallawaarachchi S, Tonkin-Hill G, Pöntinen A, Calland J, Gladstone R, Arredondo-Alonso S, MacAlasdair N, Thorpe H, Top J, Sheppard S, Balding D, Croucher N, Corander J. Detecting co-selection through excess linkage disequilibrium in bacterial genomes. NAR Genom Bioinform 2024; 6:lqae061. [PMID: 38846349 PMCID: PMC11155488 DOI: 10.1093/nargab/lqae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/15/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Population genomics has revolutionized our ability to study bacterial evolution by enabling data-driven discovery of the genetic architecture of trait variation. Genome-wide association studies (GWAS) have more recently become accompanied by genome-wide epistasis and co-selection (GWES) analysis, which offers a phenotype-free approach to generating hypotheses about selective processes that simultaneously impact multiple loci across the genome. However, existing GWES methods only consider associations between distant pairs of loci within the genome due to the strong impact of linkage-disequilibrium (LD) over short distances. Based on the general functional organisation of genomes it is nevertheless expected that majority of co-selection and epistasis will act within relatively short genomic proximity, on co-variation occurring within genes and their promoter regions, and within operons. Here, we introduce LDWeaver, which enables an exhaustive GWES across both short- and long-range LD, to disentangle likely neutral co-variation from selection. We demonstrate the ability of LDWeaver to efficiently generate hypotheses about co-selection using large genomic surveys of multiple major human bacterial pathogen species and validate several findings using functional annotation and phenotypic measurements. Our approach will facilitate the study of bacterial evolution in the light of rapidly expanding population genomic data.
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Affiliation(s)
| | | | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Jessica K Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Harry A Thorpe
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Janetta Top
- Department of Medical Microbiology, UMC Utrecht, Utrecht, The Netherlands
| | - Samuel K Sheppard
- Ineos Oxford Institute of Antimicrobial Research, Department of Biology, University of Oxford, Oxford, United Kingdom
| | - David Balding
- Melbourne Integrative Genomics, School of BioSciences and School of Mathematics & Statistics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Croucher
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, United Kingdom
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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4
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Wagner TM, Pöntinen AK, Fenzel CK, Engi D, Janice J, Almeida-Santos AC, Tedim AP, Freitas AR, Peixe L, van Schaik W, Johannessen M, Hegstad K. Interactions between commensal Enterococcus faecium and Enterococcus lactis and clinical isolates of Enterococcus faecium. FEMS MICROBES 2024; 5:xtae009. [PMID: 38606354 PMCID: PMC11008740 DOI: 10.1093/femsmc/xtae009] [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: 12/18/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024] Open
Abstract
Enterococcus faecium (Efm) is a versatile pathogen, responsible for multidrug-resistant infections, especially in hospitalized immunocompromised patients. Its population structure has been characterized by diverse clades (A1, A2, and B (reclassified as E. lactis (Ela)), adapted to different environments, and distinguished by their resistomes and virulomes. These features only partially explain the predominance of clade A1 strains in nosocomial infections. We investigated in vitro interaction of 50 clinical isolates (clade A1 Efm) against 75 commensal faecal isolates from healthy humans (25 clade A2 Efm and 50 Ela). Only 36% of the commensal isolates inhibited clinical isolates, while 76% of the clinical isolates inhibited commensal isolates. The most apparent overall differences in inhibition patterns were presented between clades. The inhibitory activity was mainly mediated by secreted, proteinaceous, heat-stable compounds, likely indicating an involvement of bacteriocins. A custom-made database targeting 76 Bacillota bacteriocins was used to reveal bacteriocins in the genomes. Our systematic screening of the interactions between nosocomial and commensal Efm and Ela on a large scale suggests that, in a clinical setting, nosocomial strains not only have an advantage over commensal strains due to their possession of AMR genes, virulence factors, and resilience but also inhibit the growth of commensal strains.
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Affiliation(s)
- Theresa Maria Wagner
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- Department of Biostatistics, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
| | - Carolin Kornelia Fenzel
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Daniel Engi
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Jessin Janice
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Ana C Almeida-Santos
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CiberES CB22/06/00035), 28029 Madrid, Spain
| | - Ana R Freitas
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 1H- TOXRUN – One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, 4584-116 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mona Johannessen
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kristin Hegstad
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
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5
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Heim AVBT, Janice J, Bjørnholt JV, Lunestad BT, Hegstad K, Svanevik CS. Genomic insights into Enterococcus faecium isolates from marine bivalves highlight One Health concerns and healthcare linkages. Microb Genom 2023; 9:001154. [PMID: 38085805 PMCID: PMC10763502 DOI: 10.1099/mgen.0.001154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Enterococci, especially Enterococcus faecium, are one of today's leading causes of multidrug-resistant infections in hospital settings. The marine environment may harbour enterococci, but its role as an evolutionary niche and as a vector for the spread of enterococci is sparsely investigated. Hence, by applying enterococci in bivalves as a sentinel tool, this study aimed to describe the prevalence of enterocooci along the Norwegian coast and in addition the phylogeny of E. faecium in particular. Enterococci in batch samples of marine bivalves, harvested from 86 different locations, were quantitatively examined by a culture-dependent most probable number (MPN) method. Isolates were identified by MALDI-TOF-MS prior to antimicrobial susceptibility testing by broth microdilution. In-detail analyses of a representative selection of E. faecium isolates (n=148) were done by Illumina whole-genome sequencing, and assembled genomes were compared to closed E. faecium genomes in the public databases and to genomes from commensal and clinical isolates from Norway. Diversity among E. faecium within the same batch sample of bivalves was also explored. Enterococci were detected in 287 of the 471 examined bivalve samples, but in low concentrations with a median value of <18 MPN /100 g. From positive samples, 479 isolates of enterococci were identified belonging to ten different species, where E. faecium (n=247), Enterococcus hirae (n=114) and Enterococcus faecalis (n=66) were most frequently found. Resistance towards one or more antimicrobial agents was observed in 197 isolates (41 %), none of the isolates showed acquired resistance to vancomycin or linezolid. Phylogenetic analyses revealed high diversity among the E. faecium isolates and showed that the marine niche is dominated by strains from the non-clinical setting belonging to clade A2 (n=85) and B (E. lactis) (n=60). Only three isolates belonged to the hospital-associated clade A1 (ST80 and ST117). Two of these clustered with one isolate from a hospitalized patient and one from a non-hospitalized person. This study demonstrated a high prevalence, but low concentrations of enterococci in bivalves, and low levels of antimicrobial resistance. E. faecium genomes showed high population diversity and that very few E. faecium isolates in bivalves may have arisen from the human healthcare system. A systematic surveillance of target micro-organisms applying methods examining multiple isolates from the same bivalve sample provides important data to assess the enterococcal phylogeny, antimicrobial resistance and the level of faecal pollution in the marine environment.
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Affiliation(s)
| | - Jessin Janice
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway (UNN), N-9038 Tromsø, Norway
| | - Jørgen Vildershøj Bjørnholt
- Department of Clinical Microbiology, Oslo University Hospital, Oslo, Norway. PO box 4950 Nydalen 0424 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo (UiO), Oslo, Norway. PO box 1171 - Blindern, 0318 Oslo, Norway
| | | | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, University Hospital of North Norway (UNN), N-9038 Tromsø, Norway
- Research Group for Host-Microbe Interactions, UiT the Arctic University of Norway, PO box 6050 Langnes, N-9037 Tromsø, Norway
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6
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da Silva RA, Wong JJ, Antypas H, Choo PY, Goh K, Jolly S, Liang C, Tay Kwan Sing L, Veleba M, Hu G, Chen J, Kline KA. Mitoxantrone targets both host and bacteria to overcome vancomycin resistance in Enterococcus faecalis. SCIENCE ADVANCES 2023; 9:eadd9280. [PMID: 36812322 PMCID: PMC9946351 DOI: 10.1126/sciadv.add9280] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance critically limits treatment options for infection caused by opportunistic pathogens such as enterococci. Here, we investigate the antibiotic and immunological activity of the anticancer agent mitoxantrone (MTX) in vitro and in vivo against vancomycin-resistant Enterococcus faecalis (VRE). We show that, in vitro, MTX is a potent antibiotic against Gram-positive bacteria through induction of reactive oxygen species and DNA damage. MTX also synergizes with vancomycin against VRE, rendering the resistant strains more permeable to MTX. In a murine wound infection model, single-dose MTX treatment effectively reduces VRE numbers, with further reduction when combined with vancomycin. Multiple MTX treatments accelerate wound closure. MTX also promotes macrophage recruitment and proinflammatory cytokine induction at the wound site and augments intracellular bacterial killing in macrophages by up-regulating the expression of lysosomal enzymes. These results show that MTX represents a promising bacterium- and host-targeted therapeutic for overcoming vancomycin resistance.
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Affiliation(s)
- Ronni A. G. da Silva
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jun Jie Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore, Singapore
| | - Haris Antypas
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Pei Yi Choo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Karlyn Goh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Shreya Jolly
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Cui Liang
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
| | - Leona Tay Kwan Sing
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
| | - Mark Veleba
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Guangan Hu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jianzhu Chen
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kimberly A. Kline
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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7
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Udaondo Z, Abram KZ, Kothari A, Jun SR. Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia. Microb Genom 2022; 8. [PMID: 35921144 PMCID: PMC9484755 DOI: 10.1099/mgen.0.000855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in the dissemination and modification of the antibiotic-resistant phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over 5 days from an inpatient with prolonged bacteraemia. Isolates from both species harboured similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype–phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium, offering a new paradigm for the study of daptomycin resistance and novel insights into its dissemination. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.
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Affiliation(s)
- Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Kaleb Z Abram
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Atul Kothari
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA.,Arkansas Dept of Health, Healthcare Associated Infections and Outbreak Response Sections, Little Rock, AR 72205, USA
| | - Se-Ran Jun
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
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8
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Gargis AS, Spicer LM, Kent AG, Zhu W, Campbell D, McAllister G, Ewing TO, Albrecht V, Stevens VA, Sheth M, Padilla J, Batra D, Johnson JK, Halpin AL, Rasheed JK, Elkins CA, Karlsson M, Lutgring JD. Sentinel Surveillance Reveals Emerging Daptomycin-Resistant ST736 Enterococcus faecium and Multiple Mechanisms of Linezolid Resistance in Enterococci in the United States. Front Microbiol 2022; 12:807398. [PMID: 35178041 PMCID: PMC8846945 DOI: 10.3389/fmicb.2021.807398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/09/2021] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecalis and faecium with resistance to daptomycin and/or linezolid are emerging globally. We present the genomic characterization of daptomycin- and linezolid-resistant E. faecalis and E. faecium surveillance isolates from the United States, 2013–2016. Daptomycin resistance was low among E. faecalis (2/364, 0.5%) and E. faecium (17/344, 5%). The majority (71%, 12/17) of daptomycin-resistant E. faecium isolates belonged to the emerging ST736 clone and contained mutations in liaFSR and cls previously associated with resistance. However, 1/2 E. faecalis and 3/17 E. faecium did not contain these mutations previously associated with daptomycin resistance. Linezolid resistance was rare among E. faecalis (1/364, 0.3%) and E. faecium (2/344, 0.6%). These two E. faecium isolates, one of which was also resistant to daptomycin and vancomycin, contained the 23S rRNA nucleotide mutation (G2576T) associated with linezolid resistance. Long-read sequencing revealed the linezolid-resistant E. faecalis isolate contained chromosomal- and plasmid-encoded copies of optrA. The chromosomal optrA was located on the recently described Tn6674 multiresistance transposon. The second copy of optrA was encoded on an ∼65 kb mosaic plasmid, with component regions sharing high sequence identity to optrA-encoding multiresistance plasmids of animal origin. The optrA-encoding plasmid contained open reading frames predicted to encode proteins associated with a pheromone-responsive plasmid transfer system, and filter mating experiments confirmed the plasmid was conjugative. Continued surveillance of enterococci is necessary to assess the prevalence and trends of daptomycin and linezolid resistance in the United States, characterize resistance mechanisms and how they transfer, and monitor for emerging sequence types associated with resistance.
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Affiliation(s)
- Amy S Gargis
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Lori M Spicer
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States.,Goldbelt C6, LLC, Chesapeake, VA, United States
| | - Alyssa G Kent
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States.,Goldbelt C6, LLC, Chesapeake, VA, United States
| | - Wenming Zhu
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Davina Campbell
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Thomas O Ewing
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States.,Goldbelt C6, LLC, Chesapeake, VA, United States
| | - Valerie Albrecht
- Office of the Director, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Valerie A Stevens
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jasmine Padilla
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States.,ASRT Incorporated, Atlanta, GA, United States
| | - Dhwani Batra
- Biotechnology Core Facility Branch, Division of Scientific Resources, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - J Kamile Rasheed
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Maria Karlsson
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Joseph D Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
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9
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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