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Dar MS, Ahmad M, Yetoo NUN, Bhatt B, Bhat SN, Altaf H, Rafiqee S, Nabi A, Mohiddin FA, Gaafar ARZ, Mansoor S, Shah MD, Mushtaq M. Genetic footprint of population diversity and genetic structure of Venturia inaequalis infecting apple (Malus × domestica Borkh.). 3 Biotech 2023; 13:273. [PMID: 37449250 PMCID: PMC10335993 DOI: 10.1007/s13205-023-03672-2] [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: 02/18/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Apple scab instigated by Venturia inaequalis impels remarkable losses to apple fruit production. In an effort to comprehend the key mechanisms of evolutionary potential defining V. inaequalis population, 132 isolates of V. inaequalis from five commercial apple orchards were collected and assayed using 14 microsatellite markers. The average diversity was observed within the individuals of populations based on the Shannon-Wieners index (I) and observed heterozygosity (Ho) was average but considerably lower than expected heterozygosity (He). The genetic differentiation based on FST values was revealed as an average measure of divergence between populations and had varying proportions of gene flow and migration among themselves. Analysis of Molecular Variance (AMOVA) revealed that variance (94%) was dispersed across individuals with a significant (6%) variation between populations from different regions. To examine host specialization within the V. inaequalis population, the assignment approach based on K-means of clustering (an unsupervised machine learning approach), revealed that the clustering method supported three clusters at (K = 3) and three major clusters were also observed in Principle Component Analysis (PCA). Additionally, Nei's genetic distance values, pairwise estimates of genetic differentiation, dendrogram using the neighbor-joining and PCoA revealed the random distribution of V. Inaequalis isolates that depicted a high proportion of genotypic diversity within populations and population genetic structure. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03672-2.
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Affiliation(s)
- Mohammad Saleem Dar
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-Kashmir, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Mushtaq Ahmad
- Division of Plant Pathology, Faculty of Horticulture, SKUAST-Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190025 India
| | - Nakeeb-Un-Nisa Yetoo
- Division of Genetics and Plant Breeding, FoA, SKUAST-K, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Bhagyshree Bhatt
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229 India
| | - Suhail Nazir Bhat
- Division of Fruit Science, Faculty of Horticulture, SKUAST-Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190025 India
| | - Heena Altaf
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-Kashmir, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Sumira Rafiqee
- Division of Genetics and Plant Breeding, FoA, SKUAST-K, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - Asha Nabi
- Division of Plant Pathology, Faculty of Agriculture, SKUAST-Kashmir, Wadura, Sopore, Jammu and Kashmir 193201 India
| | - F. A. Mohiddin
- Mountain Research Centre for Field Crops, SKUAST-Kashmir, Khudwani, Kulgam, Jammu and Kashmir 192101 India
| | - Abdel-Rhman Z. Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
| | - Mehraj D. Shah
- Division of Plant Pathology, Faculty of Horticulture, SKUAST-Kashmir, Shalimar, Srinagar, Jammu and Kashmir 190025 India
| | - Muntazir Mushtaq
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229 India
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Pervasive Listeria monocytogenes Is Common in the Norwegian Food System and Is Associated with Increased Prevalence of Stress Survival and Resistance Determinants. Appl Environ Microbiol 2022; 88:e0086122. [PMID: 36005805 PMCID: PMC9499026 DOI: 10.1128/aem.00861-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To investigate the diversity, distribution, persistence, and prevalence of stress survival and resistance genes of Listeria monocytogenes clones dominating in food processing environments in Norway, genome sequences from 769 L. monocytogenes isolates from food industry environments, foods, and raw materials (512 of which were sequenced in the present study) were subjected to whole-genome multilocus sequence typing (wgMLST), single-nucleotide polymorphism (SNP), and comparative genomic analyses. The data set comprised isolates from nine meat and six salmon processing facilities in Norway collected over a period of three decades. The most prevalent clonal complex (CC) was CC121, found in 10 factories, followed by CC7, CC8, and CC9, found in 7 factories each. Overall, 72% of the isolates were classified as persistent, showing 20 or fewer wgMLST allelic differences toward an isolate found in the same factory in a different calendar year. Moreover, over half of the isolates (56%) showed this level of genetic similarity toward an isolate collected from a different food processing facility. These were designated as pervasive strains, defined as clusters with the same level of genetic similarity as persistent strains but isolated from different factories. The prevalence of genetic determinants associated with increased survival in food processing environments, including heavy metal and biocide resistance determinants, stress response genes, and inlA truncation mutations, showed a highly significant increase among pervasive isolates but not among persistent isolates. Furthermore, these genes were significantly more prevalent among the isolates from food processing environments compared to in isolates from natural and rural environments (n = 218) and clinical isolates (n = 111) from Norway. IMPORTANCEListeria monocytogenes can persist in food processing environments for months to decades and spread through the food system by, e.g., contaminated raw materials. Knowledge of the distribution and diversity of L. monocytogenes is important in outbreak investigations and is essential to effectively track and control this pathogen in the food system. The present study presents a comprehensive overview of the prevalence of persistent clones and of the diversity of L. monocytogenes in Norwegian food processing facilities. The results demonstrate extensive spread of highly similar strains throughout the Norwegian food system, in that 56% of the 769 collected isolates from food processing factories belonged to clusters of L. monocytogenes identified in more than one facility. These strains were associated with an overall increase in the prevalence of plasmids and determinants of heavy metal and biocide resistance, as well as other genetic elements associated with stress survival mechanisms and persistence.
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Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. THE ISME JOURNAL 2021; 15:1523-1538. [PMID: 33408365 PMCID: PMC8115253 DOI: 10.1038/s41396-020-00867-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
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Affiliation(s)
- Gabrielle L Harrow
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Caroline Colijn
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK.
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Sipola A, Marttinen P, Corander J. Bacmeta: simulator for genomic evolution in bacterial metapopulations. Bioinformatics 2019; 34:2308-2310. [PMID: 29474733 DOI: 10.1093/bioinformatics/bty093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/20/2018] [Indexed: 12/25/2022] Open
Abstract
Summary The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and micro-epidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population and ultimately the whole metapopulation, is efficiently simulated using C++ objects and detailed metadata from each level can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g. large-scale simulations and likelihood-free inference. Availability and implementation Bacmeta is implemented with C++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Aleksi Sipola
- Department of Mathematics and Statistics, University of Helsinki, Finland.,Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Finland
| | - Pekka Marttinen
- Department of Computer Science, Helsinki Institute for Information Technology HIIT, Aalto University, Finland
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Finland.,Department of Biostatistics, University of Oslo, Norway
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León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environ Microbiol 2019; 21:3046-3062. [PMID: 31162871 DOI: 10.1111/1462-2920.14702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 05/20/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
Abstract
Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.
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Affiliation(s)
- Ricardo León-Sampedro
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rosa Del Campo
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Health Institute Carlos III, Madrid, Spain
| | - Mercedes Rodriguez-Baños
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - María José Pozuelo
- Department of Biology, Pharmacy Faculty, University San Pablo-CEU, Boadilla del Monte, Spain
| | - Carlos Francés-Cuesta
- Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Ana P Tedim
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Fernando González Candelas
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Fernando Baquero
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
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Metapopulation Model from Pathogen's Perspective: A Versatile Framework to Quantify Pathogen Transfer and Circulation between Environment and Hosts. Sci Rep 2019; 9:1694. [PMID: 30737423 PMCID: PMC6368549 DOI: 10.1038/s41598-018-37938-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023] Open
Abstract
Metapopulation models have been primarily explored in infectious disease epidemiology to study host subpopulation movements and between-host contact structures. They also have the potential to investigate environmental pathogen transferring. In this study, we demonstrate that metapopulation models serve as an ideal modeling framework to characterize and quantify pathogen transfer between environment and hosts. It therefore unifies host, pathogen, and environment, collectively known as the epidemiological triad, a fundamental concept in epidemiology. We develop a customizable and generalized pathogen-transferring model where pathogens dwell in and transferring (via contact) between environment and hosts. We analyze three specific case studies: pure pathogen transferring without pathogen demography, source-sink dynamics, and pathogen control via external disinfection. We demonstrate how pathogens circulate in the system between environment and hosts, as well as evaluate different controlling efforts for healthcare-associated infections (HAIs). For pure pathogen transferring, system equilibria can be derived analytically to explicitly quantify long-term pathogen distribution in the system. For source-sink dynamics and pathogen control via disinfection, we demonstrate that complete eradication of pathogens can be achieved, but the rates of converging to system equilibria differ based on specific model parameterization. Direct host-host pathogen transferring and within-host dynamics can be future directions of this modeling framework by adding specific modules.
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Update on prevalence and mechanisms of resistance to linezolid, tigecycline and daptomycin in enterococci in Europe: Towards a common nomenclature. Drug Resist Updat 2018; 40:25-39. [DOI: 10.1016/j.drup.2018.10.002] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 08/10/2018] [Accepted: 10/30/2018] [Indexed: 01/04/2023]
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Meng JW, He DC, Zhu W, Yang LN, Wu EJ, Xie JH, Shang LP, Zhan J. Human-Mediated Gene Flow Contributes to Metapopulation Genetic Structure of the Pathogenic Fungus Alternaria alternata from Potato. FRONTIERS IN PLANT SCIENCE 2018; 9:198. [PMID: 29497439 PMCID: PMC5818430 DOI: 10.3389/fpls.2018.00198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 02/01/2018] [Indexed: 06/01/2023]
Abstract
Metapopulation structure generated by recurrent extinctions and recolonizations plays an important role in the evolution of species but is rarely considered in agricultural systems. In this study, generation and mechanism of metapopulation structure were investigated by microsatellite assaying 725 isolates of Alternaria alternata sampled from potato hosts at 16 locations across China. We found a single major cluster, no isolate-geography associations and no bottlenecks in the A. alternata isolates, suggesting a metapopulation genetic structure of the pathogen. We also found weak isolation-by-distance, lower among than within cropping region population differentiation, concordant moving directions of potato products and net gene flow and the highest gene diversity in the region with the most potato imports. These results indicate that in addition to natural dispersal, human-mediated gene flow also contributes to the generation and dynamics of the metapopulation genetic structure of A. alternata in China. Metapopulation structure increases the adaptive capacity of the plant pathogen as a result of enhanced genetic variation and reduced population fragmentation. Consequently, rigid quarantine regulations may be required to reduce population connectivity and the evolutionary potential of A. alternata and other pathogens with a similar population dynamics for a sustainable plant disease management.
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Affiliation(s)
- Jing-Wen Meng
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dun-Chun He
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen Zhu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Na Yang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - E-Jiao Wu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jia-Hui Xie
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Ping Shang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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9
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Guzman Prieto AM, van Schaik W, Rogers MRC, Coque TM, Baquero F, Corander J, Willems RJL. Global Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones? Front Microbiol 2016; 7:788. [PMID: 27303380 PMCID: PMC4880559 DOI: 10.3389/fmicb.2016.00788] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/09/2016] [Indexed: 12/13/2022] Open
Abstract
Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis.
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Affiliation(s)
- Ana M Guzman Prieto
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Malbert R C Rogers
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
| | - Teresa M Coque
- Hospital Universitario Ramon y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; CIBER Epidemiología y Salud PúblicaMadrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana Asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Fernando Baquero
- Hospital Universitario Ramon y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; CIBER Epidemiología y Salud PúblicaMadrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana Asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki Helsinki, Finland
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht Utrecht, Netherlands
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