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Kwit R, Zając M, Śmiałowska-Węglińska A, Skarżyńska M, Bomba A, Lalak A, Skrzypiec E, Wojdat D, Koza W, Mikos-Wojewoda E, Pasim P, Skóra M, Polak M, Wiącek J, Wasyl D. Prevalence of Enterococcus spp. and the Whole-Genome Characteristics of Enterococcus faecium and Enterococcus faecalis Strains Isolated from Free-Living Birds in Poland. Pathogens 2023; 12:836. [PMID: 37375526 DOI: 10.3390/pathogens12060836] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Enterococci as opportunistic bacteria are important for human health. Due to the prevalence and ease of acquisition and transfer of their genes, they are an excellent indicator of environmental contamination and the spread of antimicrobial resistance. The aim of the study was to assess the prevalence of Enterococcus spp. in wild birds in Poland, determination of antimicrobial susceptibility and WGS analysis of Enterococcus (E.) faecium and E. faecalis. For this purpose, 138 samples from various species of free-living birds were tested, with 66.7% positive results. Fourteen species were detected, with E. faecalis being the most common, followed by E. casseliflavus and E. hirae. In antimicrobial susceptibility testing, 10.0% of E. faecalis and 50.0% of E. faecium showed resistance to one antimicrobial agent, in addition the MDR phenotype which was found in one E. faecium. The most common resistance phenotype included tetracycline and quinupristin/dalfopristin. The WGS analysis confirmed the significant advantage of the virulence gene diversity of E. faecalis strains over E. faecium. In addition, plasmid replicons were found in 42.0% of E. faecalis and 80.0% of E. faecium. The obtained results confirm free-living birds can be a reservoir of Enterococcus spp. with a considerable zoonotic potential.
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Affiliation(s)
- Renata Kwit
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Magdalena Zając
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | | | - Magdalena Skarżyńska
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Arkadiusz Bomba
- Department of Omic Analyses, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Anna Lalak
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Ewelina Skrzypiec
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Dominika Wojdat
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Weronika Koza
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Emilia Mikos-Wojewoda
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Paulina Pasim
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Milena Skóra
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
| | - Marcin Polak
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Sklodowska University (UMCS), 20-033 Lublin, Poland
| | - Jarosław Wiącek
- Department of Zoology and Nature Protection, Institute of Biological Sciences, Maria Curie-Sklodowska University (UMCS), 20-033 Lublin, Poland
| | - Dariusz Wasyl
- Department of Microbiology, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
- Department of Omic Analyses, National Veterinary Research Institute (PIWet), 24-100 Pulawy, Poland
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2
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Caneschi A, Bardhi A, Barbarossa A, Zaghini A. The Use of Antibiotics and Antimicrobial Resistance in Veterinary Medicine, a Complex Phenomenon: A Narrative Review. Antibiotics (Basel) 2023; 12:antibiotics12030487. [PMID: 36978354 PMCID: PMC10044628 DOI: 10.3390/antibiotics12030487] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
As warned by Sir Alexander Fleming in his Nobel Prize address: “the use of antimicrobials can, and will, lead to resistance”. Antimicrobial resistance (AMR) has recently increased due to the overuse and misuse of antibiotics, and their use in animals (food-producing and companion) has also resulted in the selection and transmission of resistant bacteria. The epidemiology of resistance is complex, and factors other than the overall quantity of antibiotics consumed may influence it. Nowadays, AMR has a serious impact on society, both economically and in terms of healthcare. This narrative review aimed to provide a scenario of the state of the AMR phenomenon in veterinary medicine related to the use of antibiotics in different animal species; the impact that it can have on animals, as well as humans and the environment, was considered. Providing some particular instances, the authors tried to explain the vastness of the phenomenon of AMR in veterinary medicine due to many and diverse aspects that cannot always be controlled. The veterinarian is the main reference point here and has a high responsibility towards the human–animal–environment triad. Sharing such a burden with human medicine and cooperating together for the same purpose (fighting and containing AMR) represents an effective example of the application of the One Health approach.
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Affiliation(s)
| | - Anisa Bardhi
- Correspondence: (A.B.); (A.B.); Tel.: +39-051-2097-500 (Andrea Barbarossa)
| | - Andrea Barbarossa
- Correspondence: (A.B.); (A.B.); Tel.: +39-051-2097-500 (Andrea Barbarossa)
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3
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Mencía-Ares O, Borowiak M, Argüello H, Cobo-Díaz JF, Malorny B, Álvarez-Ordóñez A, Carvajal A, Deneke C. Genomic Insights into the Mobilome and Resistome of Sentinel Microorganisms Originating from Farms of Two Different Swine Production Systems. Microbiol Spectr 2022; 10:e0289622. [PMID: 36377950 PMCID: PMC9769681 DOI: 10.1128/spectrum.02896-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a threat to public health due to long-term antimicrobial use (AMU), which promotes the bacterial acquisition of antimicrobial resistance determinants (ARDs). Within food-producing animals, organic and extensive Iberian swine production is based on sustainable and eco-friendly management systems, providing an excellent opportunity to evaluate how sustained differences in AMU impact the development and spread of AMR. Here, through a whole-genome sequencing approach, we provide an in-depth characterization of the resistome and mobilome and their interaction in 466 sentinel bacteria, namely, Escherichia coli, Enterococcus spp., Campylobacter coli, and Staphylococcus spp., recovered from 37 intensive and organic-extensive pig farms. Both ARDs and mobile genetic elements (MGEs) were primarily taxon-associated, with higher similarities among bacteria which were closely phylogenetically related. E. coli exhibited the most diverse resistome and mobilome, with 85.4% mobilizable ARDs, 50.3% of which were plasmid-associated. Staphylococcus spp. exhibited a broad repertoire of ARDs and MGEs, with 52.3% of its resistome being mobilizable. Although Enterococcus spp. carried the highest number of ARDs per isolate and its plasmidome was similar in size to that of E. coli, 43.7% of its resistome was mobilizable. A narrow spectrum of ARDs constituted the C. coli resistome, with point mutations as its main AMR driver. A constrained AMU, as observed in organic-extensive herds, determined a reduction in the quantitative composition of the resistome and the complexity of the resistome-mobilome interaction. These results demonstrate taxon-associated AMR-MGE interactions and evidence that responsible AMU can contribute to reducing AMR pressure in the food chain. IMPORTANCE This study provides the first integral genomic characterization of the resistome and mobilome of sentinel microorganisms for antimicrobial resistance (AMR) surveillance from two different swine production systems. Relevant differences were observed among taxa in the resistomes and mobilomes they harbored, revealing their distinctive risk in AMR dissemination and spread. Thus, Escherichia coli and, to a lesser extent, Staphylococcus spp. constituted the main reservoirs of mobilizable antimicrobial resistance genes, which were predominantly plasmid-associated; in contrast to Campylobacter coli, whose resistome was mainly determined by point mutations. The reduced complexity of mobilome-resistome interaction in Enterococcus spp. suggested its limited role in AMR dissemination from swine farms. The significant differences in antimicrobial use among the studied farms allowed us to assess the suitability of whole-genome sequencing as a rapid and efficient technique for the assessment of mid- to long-term on-farm interventions for the reduction of antimicrobial use and the evaluation of AMR status.
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Affiliation(s)
- Oscar Mencía-Ares
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Héctor Argüello
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - José Francisco Cobo-Díaz
- Department of Food Hygiene and Technology, Veterinary Faculty, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Veterinary Faculty, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Ana Carvajal
- Department of Animal Health, Veterinary Faculty, Universidad de León, León, Spain
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Cabal A, Rab G, Daza-Prieto B, Stöger A, Peischl N, Chakeri A, Mo SS, Bock H, Fuchs K, Sucher J, Rathammer K, Hasenberger P, Stadtbauer S, Caniça M, Strauß P, Allerberger F, Wögerbauer M, Ruppitsch W. Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria. Int J Mol Sci 2022; 23:ijms231911276. [PMID: 36232576 PMCID: PMC9570485 DOI: 10.3390/ijms231911276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.
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Affiliation(s)
- Adriana Cabal
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Correspondence:
| | - Gerhard Rab
- Institute of Hydraulic Engineering and Water Resources Management, Technical University of Vienna, 1040 Vienna, Austria
- Institute for Land and Water Management Research, Federal Agency for Water Management, 3252 Petzenkirchen, Austria
| | - Beatriz Daza-Prieto
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Institute of Chemical, Environmental and Bioscience Engineering, 1060 Vienna, Austria
| | - Anna Stöger
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Nadine Peischl
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Ali Chakeri
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Center for Public Health, Medical University Vienna, 1090 Vienna, Austria
| | - Solveig Sølverød Mo
- Section for Food Safety and Animal Health Research, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, 1433 Ås, Norway
| | - Harald Bock
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Klemens Fuchs
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Jasmin Sucher
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Krista Rathammer
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | | | - Silke Stadtbauer
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Peter Strauß
- Institute for Land and Water Management Research, Federal Agency for Water Management, 3252 Petzenkirchen, Austria
| | | | | | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, 1096 Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
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5
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Antimicrobial-Resistant Enterococcus spp. in Wild Avifauna from Central Italy. Antibiotics (Basel) 2022; 11:antibiotics11070852. [PMID: 35884106 PMCID: PMC9311988 DOI: 10.3390/antibiotics11070852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/16/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Bacteria of the genus Enterococcus are opportunistic pathogens, part of the normal intestinal microflora of animals, able to acquire and transfer antimicrobial resistance genes. The aim of this study was to evaluate the possible role of wild avifauna as a source of antimicrobial-resistant enterococci. To assess this purpose, 103 Enterococcus spp. strains were isolated from the feces of wild birds of different species; they were tested for antimicrobial resistance against 21 molecules, vancomycin resistance, and high-level aminoglycosides resistance (HLAR). Furthermore, genes responsible for vancomycin, tetracycline, and HLAR were searched. E. faecium was the most frequently detected species (60.20% of isolates), followed by E. faecalis (34.95% of isolates). Overall, 99.02% of the isolated enterococci were classified as multidrug-resistant, with 19.41% extensively drug-resistant, and 2.91% possible pan drug-resistant strains. Most of the isolates were susceptible to amoxicillin/clavulanic acid (77.67%) and ampicillin (75.73%), with only 5.83% of isolates showing an ampicillin MIC ≥ 64 mg/L. HLAR was detected in 35.92% of isolates, mainly associated with the genes ant(6)-Ia and aac(6′)-Ie-aph(2″)-Ia. Few strains (4.85%) were resistant to vancomycin, and the genes vanA and vanB were not detected. A percentage of 54.37% of isolates showed resistance to tetracycline; tet(M) was the most frequently detected gene in these strains. Wild birds may contribute to the spreading of antimicrobial-resistant enterococci, which can affect other animals and humans. Constant monitoring is essential to face up to the evolving antimicrobial resistance issue, and monitoring programs should include wild avifauna, too.
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6
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Nielsen SS, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortázar C, Herskin M, Michel V, Miranda Chueca MÁ, Padalino B, Pasquali P, Roberts HC, Spoolder H, Ståhl K, Velarde A, Viltrop A, Winckler C, Baldinelli F, Broglia A, Kohnle L, Alvarez J. Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Enterococcus faecalis in poultry. EFSA J 2022; 20:e07127. [PMID: 35228848 PMCID: PMC8859914 DOI: 10.2903/j.efsa.2022.7127] [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] [Indexed: 12/15/2022] Open
Abstract
Enterococcus faecalis (E. faecalis) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for poultry in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. faecalis can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33-66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 0-5%, 5-10% and 1-10% probability of meeting the criteria, respectively) and the AHAW Panel is uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-66% and 33-66% probability of meeting the criteria, respectively). The animal species to be listed for AMR E. faecalis according to Article 8 criteria are mostly birds of the orders Galliformes and Anseriformes, but also mammals and reptiles can serve as reservoirs.
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Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021; 34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution is the hallmark of life. Descriptions of the evolution of microorganisms have provided a wealth of information, but knowledge regarding "what happened" has precluded a deeper understanding of "how" evolution has proceeded, as in the case of antimicrobial resistance. The difficulty in answering the "how" question lies in the multihierarchical dimensions of evolutionary processes, nested in complex networks, encompassing all units of selection, from genes to communities and ecosystems. At the simplest ontological level (as resistance genes), evolution proceeds by random (mutation and drift) and directional (natural selection) processes; however, sequential pathways of adaptive variation can occasionally be observed, and under fixed circumstances (particular fitness landscapes), evolution is predictable. At the highest level (such as that of plasmids, clones, species, microbiotas), the systems' degrees of freedom increase dramatically, related to the variable dispersal, fragmentation, relatedness, or coalescence of bacterial populations, depending on heterogeneous and changing niches and selective gradients in complex environments. Evolutionary trajectories of antibiotic resistance find their way in these changing landscapes subjected to random variations, becoming highly entropic and therefore unpredictable. However, experimental, phylogenetic, and ecogenetic analyses reveal preferential frequented paths (highways) where antibiotic resistance flows and propagates, allowing some understanding of evolutionary dynamics, modeling and designing interventions. Studies on antibiotic resistance have an applied aspect in improving individual health, One Health, and Global Health, as well as an academic value for understanding evolution. Most importantly, they have a heuristic significance as a model to reduce the negative influence of anthropogenic effects on the environment.
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Affiliation(s)
- F. Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. L. Martínez
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - V. F. Lanza
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Central Bioinformatics Unit, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - J. Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - J. C. Galán
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - A. San Millán
- National Center for Biotechnology (CNB-CSIC), Madrid, Spain
| | - R. Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - T. M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Network Center for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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8
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Pöntinen AK, Top J, Arredondo-Alonso S, Tonkin-Hill G, Freitas AR, Novais C, Gladstone RA, Pesonen M, Meneses R, Pesonen H, Lees JA, Jamrozy D, Bentley SD, Lanza VF, Torres C, Peixe L, Coque TM, Parkhill J, Schürch AC, Willems RJL, Corander J. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nat Commun 2021; 12:1523. [PMID: 33750782 PMCID: PMC7943827 DOI: 10.1038/s41467-021-21749-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/05/2021] [Indexed: 12/20/2022] Open
Abstract
Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the "modern hospital" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.
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Affiliation(s)
- Anna K Pöntinen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sergio Arredondo-Alonso
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Rebecca A Gladstone
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Maiju Pesonen
- Oslo Centre for Biostatistics and Epidemiology (OCBE), Oslo University Hospital Research Support Services, Oslo, Norway
| | - Rodrigo Meneses
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henri Pesonen
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Dorota Jamrozy
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Carmen Torres
- Department of Food and Agriculture, Area of Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Luisa Peixe
- UCIBIO/REQUIMTE, Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research Ramón y Cajal University Hospital, Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Julian Parkhill
- Wellcome Sanger Institute, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Anita C Schürch
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, 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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9
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Saralegui C, Ponce-Alonso M, Pérez-Viso B, Moles Alegre L, Escribano E, Lázaro-Perona F, Lanza VF, de Pipaón MS, Rodríguez JM, Baquero F, Del Campo R. Genomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species. Front Microbiol 2020; 11:451. [PMID: 32296400 PMCID: PMC7136904 DOI: 10.3389/fmicb.2020.00451] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
The first documented nosocomial outbreak caused by Serratia marcescens in Spain occurred in 1969 at the neonatal intensive care unit (NICU) of the tertiary La Paz Children's Hospital in Madrid, Spain, and based on the available phenotyping techniques at this time, it was considered as a monoclonal outbreak. Only 47 years later, another S. marcescens outbreak of an equivalent dimension occurred at the same NICU. The aim of the present study was to study isolates from these historical and contemporary outbreaks by phenotypic analysis and whole-genome sequencing techniques and to position these strains along with 444 publicly available S. marcescens genomes, separately comparing core genome and accessory genome contents. Clades inferred by both approaches showed high correlation, indicating that core and accessory genomes seem to evolve in the same manner for S. marcescens. Nine S. marcescens clusters were identified, and isolates were grouped in two of them according to sampling year. One exception was isolate 13F-69, the most genetically distant strain, located in a different cluster. Categorical functions in the annotated accessory genes of both collections were preserved among all isolates. No significant differences in frequency of insertion sequences in historical (0.18-0.20)-excluding the outlier strain-versus contemporary isolates (0.11-0.19) were found despite the expected resting effect. The most dissimilar isolate, 13F-69, contains a highly preserved plasmid previously described in Bordetella bronchiseptica. This strain exhibited a few antibiotic resistance genes not resulting in a resistant phenotype, suggesting the value of gene down expression in adaptation to long-term starvation.
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Affiliation(s)
- Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
| | - Manuel Ponce-Alonso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
| | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Laura Moles Alegre
- Unidad de Esclerosis Múltiple, Instituto de Investigación Sanitaria Biodonostia, Donostia-San Sebastián, Spain
| | - Esperanza Escribano
- Servicio de Neonatología, Hospital Universitario La Paz, and Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Val F Lanza
- Unidad de Bioinformática del IRYCIS, Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - Miguel Sáenz de Pipaón
- Servicio de Neonatología, Hospital Universitario La Paz, and Universidad Autónoma de Madrid, Madrid, Spain
| | - Juan Miguel Rodríguez
- Departamento de Nutrición y Ciencia de los Alimentos, Universidad Complutense de Madrid, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain
| | - Rosa Del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,Red Española de Investigación en Patología Infecciosa, Madrid, Spain
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