1
|
Silva V, Silva A, Barbero R, Romero M, del Campo R, Caniça M, Cordeiro R, Igrejas G, Poeta P. Resistome, Virulome, and Clonal Variation in Methicillin-Resistant Staphylococcus aureus (MRSA) in Healthy Swine Populations: A Cross-Sectional Study. Genes (Basel) 2024; 15:532. [PMID: 38790161 PMCID: PMC11121583 DOI: 10.3390/genes15050532] [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: 03/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
This cross-sectional study investigates the methicillin-resistant Staphylococcus aureus (MRSA): its prevalence, antimicrobial resistance, and molecular characteristics in healthy swine populations in central Portugal. A total of 213 samples were collected from pigs on twelve farms, and MRSA prevalence was assessed using selective agar plates and confirmed via molecular methods. Antimicrobial susceptibility testing and whole genome sequencing (WGS) were performed to characterize resistance profiles and genetic determinants. Among the 107 MRSA-positive samples (83.1% prevalence), fattening pigs and breeding sows exhibited notably high carriage rates. The genome of 20 isolates revealed the predominance of the ST398 clonal complex, with diverse spa types identified. Antimicrobial susceptibility testing demonstrated resistance to multiple antimicrobial agents, including penicillin, cefoxitin, and tetracycline. WGS analysis identified a diverse array of resistance genes, highlighting the genetic basis of antimicrobial resistance. Moreover, virulence gene profiling revealed the presence of genes associated with pathogenicity. These findings underscore the significant prevalence of MRSA in swine populations and emphasize the need for enhanced surveillance and control measures to mitigate zoonotic transmission risks. Implementation of prudent antimicrobial use practices and targeted intervention strategies is essential to reducing MRSA prevalence and safeguarding public health. Continued research efforts are warranted to elucidate transmission dynamics and virulence potential, ultimately ensuring food safety and public health protection.
Collapse
Affiliation(s)
- Vanessa Silva
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Adriana Silva
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Raquel Barbero
- Department of Microbiology, University Hospital Ramón y Cajal and IRYCIS, 28034 Madrid, Spain (M.R.); (R.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28034 Madrid, Spain
| | - Mario Romero
- Department of Microbiology, University Hospital Ramón y Cajal and IRYCIS, 28034 Madrid, Spain (M.R.); (R.d.C.)
| | - Rosa del Campo
- Department of Microbiology, University Hospital Ramón y Cajal and IRYCIS, 28034 Madrid, Spain (M.R.); (R.d.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28034 Madrid, Spain
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Rui Cordeiro
- Intergados, SA, Av. de Olivença, S/N, 2870-108 Montijo, Portugal
| | - Gilberto Igrejas
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Patricia Poeta
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| |
Collapse
|
2
|
Zeggay A, Atchon A, Valot B, Hocquet D, Bertrand X, Bouiller K. Genome Analysis of Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus ST398 Strains Isolated from Patients with Invasive Infection. Microorganisms 2023; 11:1446. [PMID: 37374948 DOI: 10.3390/microorganisms11061446] [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: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Using genomic data, we determined the origin of MRSA ST398 isolates responsible for invasive infection in patients with no known livestock contact. METHODS We sequenced the genome of seven MSSA and four MRSA ST398 isolates from patients with invasive infections between 2013 and 2017, using the Illumina technique. Prophage-associated virulence genes and resistance genes were identified. To determine the origin of the isolates, their genome sequences were included in phylogenetic analysis also encompassing the ST398 genomes available on NCBI. RESULTS All isolates carried the φSa3 prophage, but with variations in the immune evasion cluster: type C in MRSA isolates, and type B in MSSA isolates. All MSSA belonged to the spa type t1451. MRSA strains had the same SCCmec type IVa (2B) cassette and belonged to spa types t899, t4132, t1939 and t2922. All MRSA harbored the tetracycline resistance gene, tet(M). Phylogenetic analysis revealed that MSSA isolates belonged to a cluster of human-associated isolates, while MRSA isolates belonged to a cluster containing livestock-associated MRSA. CONCLUSION We showed that the clinical isolates MRSA and MSSA ST398 have different origins. An acquisition of virulence genes by livestock-associated MRSA isolates allows them to induce an invasive infection in human.
Collapse
Affiliation(s)
- Abdeljallil Zeggay
- CHU Besançon, Maladies Infectieuses et Tropicales, 25000 Besançon, France
| | - Alban Atchon
- UMR-CNRS 6249 Chrono-Environnement, Université de Franche-Comté, 25000 Besançon, France
- Bioinformatique et Big Data Au Service de La Santé, UFR Santé, Université de Franche-Comté, 25000 Besançon, France
| | - Benoit Valot
- UMR-CNRS 6249 Chrono-Environnement, Université de Franche-Comté, 25000 Besançon, France
- Bioinformatique et Big Data Au Service de La Santé, UFR Santé, Université de Franche-Comté, 25000 Besançon, France
| | - Didier Hocquet
- UMR-CNRS 6249 Chrono-Environnement, Université de Franche-Comté, 25000 Besançon, France
- Bioinformatique et Big Data Au Service de La Santé, UFR Santé, Université de Franche-Comté, 25000 Besançon, France
- CHU Besançon, Hygiène Hospitalière, 25000 Besançon, France
| | - Xavier Bertrand
- UMR-CNRS 6249 Chrono-Environnement, Université de Franche-Comté, 25000 Besançon, France
- CHU Besançon, Hygiène Hospitalière, 25000 Besançon, France
| | - Kevin Bouiller
- CHU Besançon, Maladies Infectieuses et Tropicales, 25000 Besançon, France
- UMR-CNRS 6249 Chrono-Environnement, Université de Franche-Comté, 25000 Besançon, France
| |
Collapse
|
3
|
Aguglia E, Chines E, Stefani S, Cafiso V. New Antimicrobial Resistance Strategies: An Adaptive Resistance Network Conferring Reduced Glycopeptide Susceptibility in VISA. Antibiotics (Basel) 2023; 12:antibiotics12040783. [PMID: 37107145 PMCID: PMC10135003 DOI: 10.3390/antibiotics12040783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Background: Vancomycin-intermediate Staphylococcus aureus (VISA) emerges typically in the healthcare-associated methicillin-resistant S. aureus and more rarely in community-acquired S. aureus (CA-MRSA). VISA is a serious concern for public health due to its association with persistent infections, the failure of vancomycin treatment, and poor clinical outcomes. Currently, the burden of VISA is somewhat high, even though vancomycin is the mainstay treatment for severe MRSA infections. The molecular mechanisms of reduced glycopeptide susceptibility in S. aureus are constantly under investigation but have still not yet been fully characterized. Methods: Our goal was to investigate the reduced glycopeptide susceptibility mechanisms emerging in a VISA CA-MRSA versus its vancomycin-susceptible (VSSA) CA-MRSA parents in a hospitalized patient undergoing glycopeptide treatment. Comparative integrated omics, Illumina MiSeq whole-genome sequencing (WGS), RNA-Seq, and bioinformatics were performed. Results: Through a comparison of VISA CA-MRSA vs. its VSSA CA-MRSA parent, mutational and transcriptomic adaptations were found in a pool of genes involved, directly or indirectly, in the biosynthesis of the glycopeptide target conferring or supporting the VISA phenotype, and its cross-resistance with daptomycin. This pool included key genes responsible for the biosynthesis of the peptidoglycan precursors, i.e., D-Ala, the D-Ala-D-Ala dipeptide termini of the pentapeptide, and its incorporation in the nascent pentapeptide, as key targets of the glycopeptide resistance. Furthermore, accessory glycopeptide-target genes involved in the pathways corroborated the key adaptations, and thus, supported the acquisition of the VISA phenotype i.e., transporters, nucleotide metabolism genes, and transcriptional regulators. Finally, transcriptional changes were also found in computationally predicted cis-acting small antisense RNA triggering genes related both to the key or accessory adaptive pathways. Conclusion: Our investigation describes an adaptive resistance pathway acquired under antimicrobial therapy conferring reduced glycopeptide susceptibility in a VISA CA-MRSA due to a comprehensive network of mutational and transcriptional adaptations in genes involved in pathways responsible for the biosynthesis of glycopeptide's target or supporters of the key resistance path.
Collapse
Affiliation(s)
- Elvira Aguglia
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Eleonora Chines
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Viviana Cafiso
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| |
Collapse
|
4
|
Salgueiro V, Manageiro V, Bandarra NM, Ferreira E, Clemente L, Caniça M. First comparative genomic characterization of the MSSA ST398 lineage detected in aquaculture and other reservoirs. Front Microbiol 2023; 14:1035547. [PMID: 36970692 PMCID: PMC10030524 DOI: 10.3389/fmicb.2023.1035547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Staphylococcus aureus ST398 can cause diseases in several different animals. In this study we analyzed ten S. aureus ST398 previously collected in three different reservoirs in Portugal (humans, gilthead seabream from aquaculture and dolphin from a zoo). Strains tested against sixteen antibiotics, by disk diffusion or minimum inhibitory concentration, showed decreased susceptibility to benzylpenicillin (all strains from gilthead seabream and dolphin) and to erythromycin with an iMLSB phenotype (nine strains), and susceptibility to cefoxitin (methicillin-susceptible S. aureus, MSSA). All strains from aquaculture belonged to the same spa type, t2383, whereas strains from the dolphin and humans belonged to spa type t571. A more detailed analysis using single nucleotide polymorphisms (SNPs)-based tree and a heat map, showed that all strains from aquaculture origin were highly related with each other and the strains from dolphin and humans were more distinct, although they were very similar in ARG, VF and MGE content. Mutations F3I and A100V in glpT gene and D278E and E291D in murA gene were identified in nine fosfomycin susceptible strains. The blaZ gene was also detected in six of the seven animal strains. The study of the genetic environment of erm(T)-type (found in nine S. aureus strains) allowed the identification of MGE (rep13-type plasmids and IS431R-type), presumably involved in the mobilization of this gene. All strains showed genes encoding efflux pumps from major facilitator superfamily (e.g., arlR, lmrS-type and norA/B-type), ATP-binding cassettes (ABC; mgrA) and multidrug and toxic compound extrusion (MATE; mepA/R-type) families, all associated to decreased susceptibility to antibiotics/disinfectants. Moreover, genes related with tolerance to heavy metals (cadD), and several VF (e.g., scn, aur, hlgA/B/C and hlb) were also identified. Insertion sequences, prophages, and plasmids made up the mobilome, some of them associated with ARG, VF and genes related with tolerance to heavy metals. This study highlights that S. aureus ST398 can be a reservoir of several ARG, heavy metals resistance genes and VF, which are essential in the adaption and survival of the bacterium in the different environments and an active agent in its dissemination. It makes an important contribution to understanding the extent of the spread of antimicrobial resistance, as well as the virulome, mobilome and resistome of this dangerous lineage.
Collapse
Affiliation(s)
- Vanessa Salgueiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Lisbon, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Lisbon, Portugal
| | - Narcisa M. Bandarra
- Division of Aquaculture, Upgrading and Bioprospecting, Portuguese Institute for the Sea and Atmosphere, IPMA, Lisbon, Portugal
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Eugénia Ferreira
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Lisbon, Portugal
| | - Lurdes Clemente
- INIAV–Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Lisbon, Portugal
- CIISA, Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- *Correspondence: Manuela Caniça,
| |
Collapse
|
5
|
Bouiller K, Zeggay A, Gbaguidi-Haore H, Hocquet D, Chirouze C, Bertrand X. Epidemiology and risk factors of nasal carriage of Staphylococcus aureus CC398 in two distinct cohorts in France. Front Microbiol 2022; 13:1068420. [PMID: 36605518 PMCID: PMC9807596 DOI: 10.3389/fmicb.2022.1068420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background We aimed to determine the prevalence and factors associated with nasal carriage of Staphylococcus aureus CC398 in the community and among hospitalized patients. Methods We conducted a prospective cohort study in a French university hospital and a cross-sectional study in the surrounding region. Results From June 2019 to July 2020, 591 healthy blood donors (HBDs) and 647 hospitalized patients (HPs) were included. S. aureus CC398 was more prevalent in HBDs than in HPs (7.3% [5.3-9.7] vs. 3.8% [2.4-5.5], p = 0.006). Among S. aureus nasal carriers, the prevalence of CC398 isolates was 24.6% in HBDs and 18.3% in HPs (p = 0.19). No MRSA belonged to CC398. In multivariate analysis, prior antibiotic intake in the past year (OR 3.11 [1.37-7.06]) and active smoking (OR 3.01 [1.00-9.05]) were associated with S. aureus CC398 nasal carriage in the HBD cohort. A history of neurological disease was associated with nasal carriage (OR = 5.43 [1.21-24.2]), whereas an age between 82 and 90 years (OR 0.11 [0.02-0.54]) and diabetes (OR 0.18 [0.04-0.85]) were protective factors in the HP cohort. Contact with livestock was not a risk factor in either cohort. Conclusion The prevalence of MSSA CC398 was higher in the community than hospitalized patients. Factors associated with nasal carriage of MSSA CC398 were primarily related to general preconditions. No environmental sources of exposure were identified.
Collapse
Affiliation(s)
- Kevin Bouiller
- Service de Maladies Infectieuses et Tropicales – CHU Besancon, Besancon, France,UMR-CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France,*Correspondence: Kevin Bouiller,
| | - Abdeljalil Zeggay
- Service de Maladies Infectieuses et Tropicales – CHU Besancon, Besancon, France
| | - Houssein Gbaguidi-Haore
- UMR-CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France,Service d’Hygiène Hospitalière – CHU Besancon, Besancon, France
| | - Didier Hocquet
- UMR-CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France,Service d’Hygiène Hospitalière – CHU Besancon, Besancon, France
| | - Catherine Chirouze
- Service de Maladies Infectieuses et Tropicales – CHU Besancon, Besancon, France,UMR-CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France
| | - Xavier Bertrand
- UMR-CNRS 6249 Chrono-environnement, Université Bourgogne Franche-Comté, Besançon, France,Service d’Hygiène Hospitalière – CHU Besancon, Besancon, France
| |
Collapse
|
6
|
Silva V, Monteiro A, Pereira JE, Maltez L, Igrejas G, Poeta P. MRSA in Humans, Pets and Livestock in Portugal: Where We Came from and Where We Are Going. Pathogens 2022; 11:1110. [PMID: 36297167 PMCID: PMC9608539 DOI: 10.3390/pathogens11101110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 09/10/2023] Open
Abstract
Over the years, molecular typing of methicillin-resistant S. aureus (MRSA) has allowed for the identification of endemic MRSA strains and pathogenic strains. After reaching a peak of predominance in a given geographic region, MRSA strains are usually replaced by a new strain. This process is called clonal replacement and is observed worldwide. The worldwide spread of hospital-associated MRSA (HA-MRSA), community-associated MRSA (CA-MRSA) and livestock-associated MRSA (LA-MRSA) clones over the last few decades has allowed this microorganism to be currently considered a pandemic. In Portugal, most HA-MRSA infections are associated with EMRSA-15 (S22-IV), New York/Japan (ST5-II) and Iberian (ST247-I) clones. Regarding the strains found in the community, many of them are frequently associated with the hospital environment, namely the Pediatric, Brazilian and Iberian clones. On the other hand, a strain that is typically found in animals, MRSA clonal complex (CC) 398, has been described in humans as colonizing and causing infections. The ST398 clone is found across all animal species, particularly in farm animals where the economic impact of LA-MRSA infections can have disastrous consequences for industries. In contrast, the EMRSA-15 clone seems to be more related to companion animals. The objective of this review is to better understand the MRSA epidemiology because it is, undoubtedly, an important public health concern that requires more attention, in order to achieve an effective response in all sectors.
Collapse
Affiliation(s)
- Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
| | - Andreia Monteiro
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eduardo Pereira
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Luís Maltez
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Caparica, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| |
Collapse
|
7
|
van der Mee-Marquet N, Dos Santos S, Diene SM, Duflot I, Mereghetti L, Valentin AS, François P. Strong Biofilm Formation and Low Cloxacillin Susceptibility in Biofilm-Growing CC398 Staphylococcus aureus Responsible for Bacteremia in French Intensive Care Units, 2021. Microorganisms 2022; 10:microorganisms10091857. [PMID: 36144459 PMCID: PMC9504214 DOI: 10.3390/microorganisms10091857] [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] [Received: 08/16/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
A prospective 3-month study carried out in 267 ICUs revealed an S. aureus nosocomial bacteremia in one admitted patient out of 110 in adult and pediatric sectors, and in one out of 230 newborns; 242 S. aureus bacteremias occurred during the study, including 7.9% MRSA-bacteremias. In one ICU out of ten, the molecular characteristics, antimicrobial susceptibility profiles and biofilm production of the strains responsible for S. aureus bacteremia were studied. Of the 53 strains studied, 9.4% were MRSA and 52.8% were resistant to erythromycin. MLST showed the predominance of CC398 (37.7% of the strains) followed by CC8 (17.0%), CC45 (13.2%) and CC30 (9.4%). The lukF/S genes were absent from our isolates and tst-1 was found in 9.4% of the strains. Under static conditions and without exposure to glucose, biofilm production was rare (9.4% of the strains, without any CC398). The percentage increased to 62.3% for strains grown in broth supplemented with 1% glucose (including 7 out of 9 CC8 and 17 out of the 20 CC398). Further study of the CC398, including whole genome sequencing, revealed (1) highly frequent patient death within seven days after CC398 bacteremia diagnosis (47.4%), (2) 95.0% of the strains producing biofilm when exposed to sub-inhibitory concentrations of cloxacillin, (3) a stronger biofilm production following exposure to cloxacillin than that observed in broth supplemented with glucose only (p < 0.001), (4) a high minimum biofilm eradication concentration of cloxacillin (128 mg/L) indicating a low cloxacillin susceptibility of biofilm-growing CC398, (5) 95.0% of the strains carrying a ϕSa-3 like prophage and its particular evasion cluster (i.e., yielding chp and scin genes), and (6) 30.0% of the strains carrying a ϕMR11-like prophage and yielding a higher ability to produce biofilm. Our results provide evidence that active surveillance is required to avoid spreading of this virulent staphylococcal clone.
Collapse
Affiliation(s)
- Nathalie van der Mee-Marquet
- Centre d’Appui pour la Prévention des Infections Associées aux Soins (CPias) de la Région Centre Val de Loire, Hôpital Bretonneau, Centre Hospitalier Régional Universitaire, 37044 Tours, France
- Correspondence:
| | - Sandra Dos Santos
- Centre d’Appui pour la Prévention des Infections Associées aux Soins (CPias) de la Région Centre Val de Loire, Hôpital Bretonneau, Centre Hospitalier Régional Universitaire, 37044 Tours, France
| | - Seydina M. Diene
- Faculté de Pharmacie, Microbes Evolution Phylogeny and Infections, IHU-Méditerranée Infection, Aix-Marseille Université, 13005 Marseille, France
| | - Isabelle Duflot
- Centre d’Appui pour la Prévention des Infections Associées aux Soins (CPias) de la Région Centre Val de Loire, Hôpital Bretonneau, Centre Hospitalier Régional Universitaire, 37044 Tours, France
| | - Laurent Mereghetti
- Service de Bactériologie, Virologie et Hygiène, Hôpital Trousseau, Centre Hospitalier Régional Universitaire, 37044 Tours, France
| | - Anne-Sophie Valentin
- Centre d’Appui pour la Prévention des Infections Associées aux Soins (CPias) de la Région Centre Val de Loire, Hôpital Bretonneau, Centre Hospitalier Régional Universitaire, 37044 Tours, France
| | - Patrice François
- Department of Medicine, University of Geneva Hospitals, 1205 Geneva, Switzerland
| | | |
Collapse
|
8
|
Balancing the Virulence and Antimicrobial Resistance in VISA DAP-R CA-MRSA Superbug. Antibiotics (Basel) 2022; 11:antibiotics11091159. [PMID: 36139939 PMCID: PMC9495084 DOI: 10.3390/antibiotics11091159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Methicillin-resistant Staphylococcus aureus (MRSA) with intermediate resistance to Vancomycin (VISA) is reported worldwide. These strains frequently emerge among hospital-associated (HA)-MRSA and rarely within community-acquired (CA)-MRSA. Here, the genomic and transcriptomic adaptations distinguishing VISA daptomycin resistant (DAP-R) CA-MRSA, which emerged in a hospitalized patient under glycopeptide treatment, were explored. Methods: Whole-genome sequencing, RNA-Seq and bioinformatics were carried out. Results: Our CA-MRSA clustered in the USA400 lineage showing additional antimicrobial resistance (AMR) versus DAP and glycopeptides. Resistomics revealed adaptations related to glycopeptide, daptomycin and rifampin resistance (mprF nsSNPS and overexpression of glycopeptide and daptomycin-resistance related genes). Similar changes were detected in virulence traits (agrA HI-nsSNPs and toxin gene underexpression), in which a decrease was observed despite the abundance of virulence-related genes. Our results predicted a balance in adaptations, decreasing the virulence and biological costs to support the co-occurrence of extensive AMR in a hypervirulent genomic background. Conclusion: Our data show that VISA DAP-R CA-MRSA shifts the potential hypervirulent behavior of CA-MRSA towards the acquisition and maintenance of extensive AMR, by a decrease in virulence and biological costs mediated by a “compensatory modulatory mutation” silencing the Agr quorum-sensing cascade.
Collapse
|
9
|
Silva V, Caniça M, Manageiro V, Vieira-Pinto M, Pereira JE, Maltez L, Poeta P, Igrejas G. Antimicrobial Resistance and Molecular Epidemiology of Staphylococcus aureus from Hunters and Hunting Dogs. Pathogens 2022; 11:548. [PMID: 35631069 PMCID: PMC9143024 DOI: 10.3390/pathogens11050548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/30/2022] Open
Abstract
Several studies have showed that a dog-to-human transmission of Staphylococcus aureus occurs. Hunting dogs do not have as much contact with their owners as dogs that live in the same household as the owners; however, these dogs have contact with their owners during hunting activities as well as when hunting game; therefore, we aimed to isolate S. aureus from hunters and their hunting dogs to investigate a possible S. aureus transmission. Nose and mouth samples were collected from 30 hunters and their 78 hunting dogs for staphylococcal isolation. The species identification was performed using MALDI-TOF. The antimicrobial susceptibility profiles were accessed using the Kirby-Bauer method and respective antimicrobial resistance genes were investigated by PCR. Multilocus sequence typing (MLST) and spa- and agr-typing was performed in all S. aureus isolates. S. aureus were detected in 10 (30%) human samples and in 11 (15.4%) dog samples of which 11 and 5 were methicillin-resistant S. aureus (MRSA). Other staphylococci were identified, particularly, S. pseudintermedius. Most S. aureus isolates were resistant to penicillin, erythromycin, and tetracycline. Evidence of a possible transmission of S. aureus between human and dogs was detected in three hunters and their dogs. S. aureus isolates were ascribed to 10 STs and 9 spa-types. A moderate colonization of S. aureus in hunting dogs and their owners was detected in this study. A few dog-to-dog and dog-to-human possible transmissions were identified.
Collapse
Affiliation(s)
- Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (J.E.P.); (L.M.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal; (M.C.); (V.M.)
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal; (M.C.); (V.M.)
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
| | - Madalena Vieira-Pinto
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - José Eduardo Pereira
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (J.E.P.); (L.M.)
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Luís Maltez
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (J.E.P.); (L.M.)
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (J.E.P.); (L.M.)
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| |
Collapse
|
10
|
Laumay F, Benchetrit H, Corvaglia AR, van der Mee-Marquet N, François P. The Staphylococcus aureus CC398 Lineage: An Evolution Driven by the Acquisition of Prophages and Other Mobile Genetic Elements. Genes (Basel) 2021; 12:genes12111752. [PMID: 34828356 PMCID: PMC8623586 DOI: 10.3390/genes12111752] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/31/2022] Open
Abstract
Among clinically relevant lineages of Staphylococcus aureus, the lineage or clonal complex 398 (CC398) is of particular interest. Strains from this lineage were only described as livestock colonizers until 2007. Progressively, cases of infection were reported in humans in contact with farm animals, and now, CC398 isolates are increasingly identified as the cause of severe infections even in patients without any contact with animals. These observations suggest that CC398 isolates have spread not only in the community but also in the hospital setting. In addition, several recent studies have reported that CC398 strains are evolving towards increased virulence and antibiotic resistance. Identification of the origin and emergence of this clonal complex could probably benefit future large-scale studies that aim to detect sources of contamination and infection. Current evidence indicates that the evolution of CC398 strains towards these phenotypes has been driven by the acquisition of prophages and other mobile genetic elements. In this short review, we summarize the main knowledge of this major lineage of S. aureus that has become predominant in the human clinic worldwide within a single decade.
Collapse
Affiliation(s)
- Floriane Laumay
- Genomic Research Laboratory, Service of Infectious Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland; (F.L.); (A.-R.C.)
- Institut des Agents Infectieux, Centre de Biologie du Nord, Hospices Civils de Lyon, F-69003 Lyon, France
| | - Hugo Benchetrit
- UFR de Chimie et de Biologie, Faculté des Sciences, Université Grenoble Alpes, 38000 Grenoble, France;
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland; (F.L.); (A.-R.C.)
- Geneva Centre for Emerging Viral Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | | | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Faculty of Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland; (F.L.); (A.-R.C.)
- Correspondence:
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Abril AG, Carrera M, Böhme K, Barros-Velázquez J, Cañas B, Rama JLR, Villa TG, Calo-Mata P. Proteomic Characterization of Bacteriophage Peptides from the Mastitis Producer Staphylococcus aureus by LC-ESI-MS/MS and the Bacteriophage Phylogenomic Analysis. Foods 2021; 10:799. [PMID: 33917943 PMCID: PMC8068337 DOI: 10.3390/foods10040799] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/28/2021] [Accepted: 04/06/2021] [Indexed: 01/21/2023] Open
Abstract
The present work describes LC-ESI-MS/MS MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) analyses of tryptic digestion peptides from phages that infect mastitis-causing Staphylococcus aureus isolated from dairy products. A total of 1933 nonredundant peptides belonging to 1282 proteins were identified and analyzed. Among them, 79 staphylococcal peptides from phages were confirmed. These peptides belong to proteins such as phage repressors, structural phage proteins, uncharacterized phage proteins and complement inhibitors. Moreover, eighteen of the phage origin peptides found were specific to S. aureus strains. These diagnostic peptides could be useful for the identification and characterization of S. aureus strains that cause mastitis. Furthermore, a study of bacteriophage phylogeny and the relationship among the identified phage peptides and the bacteria they infect was also performed. The results show the specific peptides that are present in closely related phages and the existing links between bacteriophage phylogeny and the respective Staphylococcus spp. infected.
Collapse
Affiliation(s)
- Ana G. Abril
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Mónica Carrera
- Department of Food Technology, Spanish National Research Council, Marine Research Institute, 36208 Vigo, Spain
| | - Karola Böhme
- Agroalimentary Technological Center of Lugo, 27002 Lugo, Spain;
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| | - Benito Cañas
- Department of Analytical Chemistry, Complutense University of Madrid, 28040 Madrid, Spain;
| | - José-Luis R. Rama
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Tomás G. Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain; (A.G.A.); (J.-L.R.R.); (T.G.V.)
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, 27002 Lugo, Spain;
| |
Collapse
|
13
|
Cafiso V, Lo Verde F, Zega A, Pigola G, Rostagno R, Borrè S, Stefani S. Genomic Characterization of a New Biofilm-Forming and Adhesive ST398 Human-Adapted MSSA Lineage Causing Septic Knee Arthritis Following Surgical Reconstruction. Microorganisms 2021; 9:microorganisms9020305. [PMID: 33540689 PMCID: PMC7913009 DOI: 10.3390/microorganisms9020305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 01/04/2023] Open
Abstract
Methicillin-susceptible (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) is a pathogen commonly found in bone and joint infections, including septic arthritis. S. aureus virulence and the frailty of affected patients can cause several complications; a prompt and specific antibiotic treatment can positively affect the outcome of patients. We carried out an in-depth genomic characterization by Illumina whole genome sequencing and bioinformatics of two biofilm-producing M1 and M2 ST398 MSSA causing septic knee arthritis not-responding to antimicrobial therapy. The strains were characterized for antibiotic resistance, biofilm and adhesive properties as well as genomics, single nucleotide polymorphism phylogeny, resistomics and virulomics. Our results showed that M1 and M2 MSSA were ST398-t1451-agrI-Cap5, susceptible to cefoxitin and resistant to erythromycin and clindamycin, traits consistent with the lack of the SCCmec-locus and the presence of the sole blaZ and ermT. Furthermore, M1 and M2 were biofilm-producing and largely potentially adhesive strains, as indicated by the adhesion gene profile. Our data characterized a new human-adapted ST398 MSSA lineage, representing a "fusion" between the human-animal independent ST398 and the Livestock Associated (LA) ST398 lineages, forming biofilm and genomically predicted high adhesive, characterized by different genomic adaptation conferring a great ability to adhere to the host's extracellular matrix causing septic knee arthritis.
Collapse
Affiliation(s)
- Viviana Cafiso
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (F.L.V.); (A.Z.); (G.P.); (S.S.)
- Correspondence:
| | - Flavia Lo Verde
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (F.L.V.); (A.Z.); (G.P.); (S.S.)
| | - Alessandra Zega
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (F.L.V.); (A.Z.); (G.P.); (S.S.)
| | - Giuseppe Pigola
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (F.L.V.); (A.Z.); (G.P.); (S.S.)
| | - Roberto Rostagno
- Infectious Diseases Department of Sant’Andrea Hospital Vercelli, 13100 Vercelli, Italy; (R.R.); (S.B.)
| | - Silvio Borrè
- Infectious Diseases Department of Sant’Andrea Hospital Vercelli, 13100 Vercelli, Italy; (R.R.); (S.B.)
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (F.L.V.); (A.Z.); (G.P.); (S.S.)
| |
Collapse
|
14
|
Son B, Kong M, Lee Y, Ryu S. Development of a Novel Chimeric Endolysin, Lys109 With Enhanced Lytic Activity Against Staphylococcus aureus. Front Microbiol 2021; 11:615887. [PMID: 33519773 PMCID: PMC7843465 DOI: 10.3389/fmicb.2020.615887] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/16/2020] [Indexed: 01/21/2023] Open
Abstract
As the incidence of antibiotic-resistant bacteria has become increased, phage endolysins are believed as one of the promising alternatives to antibiotics. However, the discovery of potent endolysin is still challenging because it is labor intensive and difficult to obtain a soluble form with high lytic activity. In this respect, the modular structures of Gram-positive endolysins can provide an opportunity to develop novel endolysins by domain rearrangement. In this study, a random domain swapping library of four different endolysins from phages infecting Staphylococcus aureus was constructed and screened to obtain engineered endolysins. The novel chimeric endolysin, Lys109 was selected and characterized for its staphylolytic activity. Lys109 exhibited greater bacterial cell lytic activity than its parental endolysins against staphylococcal planktonic cells and biofilms, showing highly improved activity in eliminating S. aureus from milk and on the surface of stainless steel. These results demonstrate that a novel chimeric endolysin with higher activity and solubility can be developed by random domain swapping and that this chimeric endolysin has a great potential as an antimicrobial agent.
Collapse
Affiliation(s)
- Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Minsuk Kong
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul, South Korea
| | - Yoona Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Center for Food and Bioconvergence, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| |
Collapse
|
15
|
Ingmer H, Gerlach D, Wolz C. Temperate Phages of Staphylococcus aureus. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0058-2018. [PMID: 31562736 PMCID: PMC10921950 DOI: 10.1128/microbiolspec.gpp3-0058-2018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Indexed: 12/22/2022] Open
Abstract
Most Staphylococcus aureus isolates carry multiple bacteriophages in their genome, which provide the pathogen with traits important for niche adaptation. Such temperate S. aureus phages often encode a variety of accessory factors that influence virulence, immune evasion and host preference of the bacterial lysogen. Moreover, transducing phages are primary vehicles for horizontal gene transfer. Wall teichoic acid (WTA) acts as a common phage receptor for staphylococcal phages and structural variations of WTA govern phage-host specificity thereby shaping gene transfer across clonal lineages and even species. Thus, bacteriophages are central for the success of S. aureus as a human pathogen.
Collapse
Affiliation(s)
- Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David Gerlach
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| |
Collapse
|
16
|
Sun L, Chen Y, Wang D, Wang H, Wu D, Shi K, Yan P, Yu Y. Surgical Site Infections Caused by Highly Virulent Methicillin-Resistant Staphylococcus aureus Sequence Type 398, China. Emerg Infect Dis 2019; 25:157-160. [PMID: 30561317 PMCID: PMC6302609 DOI: 10.3201/eid2501.171862] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We identified 2 methicillin-resistant Staphylococcus aureus strains of sequence type 398 from surgical site infections in China. Genetic analysis and clinical data from these strains suggested that they were human-related but sporadic. Hemolysis analysis and mouse-skin infection models indicated a high virulence potential for these strains.
Collapse
|
17
|
Aerts M, Battisti A, Hendriksen R, Kempf I, Teale C, Tenhagen BA, Veldman K, Wasyl D, Guerra B, Liébana E, Thomas-López D, Belœil PA. Technical specifications on harmonised monitoring of antimicrobial resistance in zoonotic and indicator bacteria from food-producing animals and food. EFSA J 2019; 17:e05709. [PMID: 32626332 PMCID: PMC7009308 DOI: 10.2903/j.efsa.2019.5709] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Proposals to update the harmonised monitoring and reporting of antimicrobial resistance (AMR) from a public health perspective in Salmonella, Campylobacter coli, Campylobacter jejuni, Escherichia coli, Enterococcus faecalis, Enterococcus faecium and methicillin-resistant Staphylococcus aureus (MRSA) from food-producing animals and derived meat in the EU are presented in this report, accounting for recent trends in AMR, data collection needs and new scientific developments. Phenotypic monitoring of AMR in bacterial isolates, using microdilution methods for testing susceptibility and interpreting resistance using epidemiological cut-off values is reinforced, including further characterisation of those isolates of E. coli and Salmonella showing resistance to extended-spectrum cephalosporins and carbapenems, as well as the specific monitoring of ESBL/AmpC/carbapenemase-producing E. coli. Combinations of bacterial species, food-producing animals and meat, as well as antimicrobial panels have been reviewed and adapted, where deemed necessary. Considering differing sample sizes, numerical simulations have been performed to evaluate the related statistical power available for assessing occurrence and temporal trends in resistance, with a predetermined accuracy, to support the choice of harmonised sample size. Randomised sampling procedures, based on a generic proportionate stratified sampling process, have been reviewed and reinforced. Proposals to improve the harmonisation of monitoring of prevalence, genetic diversity and AMR in MRSA are presented. It is suggested to complement routine monitoring with specific cross-sectional surveys on MRSA in pigs and on AMR in bacteria from seafood and the environment. Whole genome sequencing (WGS) of isolates obtained from the specific monitoring of ESBL/AmpC/carbapenemase-producing E. coli is strongly advocated to be implemented, on a voluntary basis, over the validity period of the next legislation, with possible mandatory implementation by the end of the period; the gene sequences encoding for ESBL/AmpC/carbapenemases being reported to EFSA. Harmonised protocols for WGS analysis/interpretation and external quality assurance programmes are planned to be provided by the EU-Reference Laboratory on AMR.
Collapse
|
18
|
Laumay F, Corvaglia AR, Diene SM, Girard M, Oechslin F, van der Mee-Marquet N, Entenza JM, François P. Temperate Prophages Increase Bacterial Adhesin Expression and Virulence in an Experimental Model of Endocarditis Due to Staphylococcus aureus From the CC398 Lineage. Front Microbiol 2019; 10:742. [PMID: 31105650 PMCID: PMC6492496 DOI: 10.3389/fmicb.2019.00742] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/25/2019] [Indexed: 01/13/2023] Open
Abstract
Until 2007, Staphylococcus aureus from clonal complex 398 (CC398) was exclusively associated with livestock species and companion animals. Recently, several studies described the emergence of S. aureus CC398 as etiologies of severe infections in humans living in an animal-free environment. Recent sequencing efforts showed that the mobile genetic elements found in CC398 isolates were specific for each population and enabled differentiation of strains responsible for asymptomatic colonization from strains involved in bloodstream infections. We mobilized prophages from a human CC398 isolate and introduced them into two naïve ancestral isolates devoid of prophages that exclusively colonize animals. These lysogenized ancestral CC398 isolates acquired features related to virulence, such as an increased capacity to adhere to human extracellular matrix proteins and the ability to invade and survive within non-phagocytic cells. Pathogenicity of several clinical isolates from the CC398 lineage as well as ancestral and in vitro lysogenized ancestral counterparts was assessed in a model of infectious endocarditis in rats. Natural and artificial lysogens were not only more invasive than their prophage-free parent but also showed an increased capacity to multiply within aortic vegetations. This study identified prophages as mediators of bacterial virulence in a model of infectious endocarditis, probably through promotion of interaction with extracellular matrix components. Further studies are needed to identify mechanisms leading to promotion of intrinsic virulence.
Collapse
Affiliation(s)
- Floriane Laumay
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Anna-Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Seydina M Diene
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine et de Pharmacie, Aix-Marseille University, Marseille, France
| | - Myriam Girard
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| | - Frank Oechslin
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - José Manuel Entenza
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Medical University Center, Geneva University Hospitals, Geneva, Switzerland
| |
Collapse
|
19
|
Andreoni F, Toyofuku M, Menzi C, Kalawong R, Mairpady Shambat S, François P, Zinkernagel AS, Eberl L. Antibiotics Stimulate Formation of Vesicles in Staphylococcus aureus in both Phage-Dependent and -Independent Fashions and via Different Routes. Antimicrob Agents Chemother 2019; 63:e01439-18. [PMID: 30509943 PMCID: PMC6355553 DOI: 10.1128/aac.01439-18] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/18/2018] [Indexed: 12/29/2022] Open
Abstract
Bacterial membrane vesicle research has so far focused mainly on Gram-negative bacteria. Only recently have Gram-positive bacteria been demonstrated to produce and release extracellular membrane vesicles (MVs) that contribute to bacterial virulence. Although treatment of bacteria with antibiotics is a well-established trigger of bacterial MV formation, the underlying mechanisms are poorly understood. In this study, we show that antibiotics can induce MVs through different routes in the important human pathogen Staphylococcus aureus DNA-damaging agents and antibiotics inducing the SOS response triggered vesicle formation in lysogenic strains of S. aureus but not in their phage-devoid counterparts. The β-lactam antibiotics flucloxacillin and ceftaroline increased vesicle formation in a prophage-independent manner by weakening the peptidoglycan layer. We present evidence that the amount of DNA associated with MVs formed by phage lysis is greater than that for MVs formed by β-lactam antibiotic-induced blebbing. The purified MVs derived from S. aureus protected the bacteria from challenge with daptomycin, a membrane-targeting antibiotic, both in vitro and ex vivo in whole blood. In addition, the MVs protected S. aureus from killing in whole blood, indicating that antibiotic-induced MVs function as a decoy and thereby contribute to the survival of the bacterium.
Collapse
Affiliation(s)
- Federica Andreoni
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Masanori Toyofuku
- Department of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Carmen Menzi
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ratchara Kalawong
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrice François
- Laboratoire de Recherche Génomique, Service des Maladies Infectieuses, Centre Médical Universitaire, Geneva, Switzerland
| | - Annelies S Zinkernagel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
20
|
High prevalence of spa type t571 among methicillin-susceptible Staphylococcus aureus from bacteremic patients in a French University Hospital. PLoS One 2018; 13:e0204977. [PMID: 30300375 PMCID: PMC6177137 DOI: 10.1371/journal.pone.0204977] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/04/2018] [Indexed: 12/13/2022] Open
Abstract
Staphylococcus aureus bacteremia is one of the most frequent severe bacterial infections worldwide, with an associated mortality of about 20–40% in developed countries. In 2013, we noted an increase in this infection in the teaching hospital in Grenoble, France, compared to 2012. The mean incidence of S. aureus bacteremia was 0.28 per 1,000 patient-days in 2012 and 0.35 per 1,000 patient-days in 2013. This trend was confirmed in 2014 (0.35 per 1,000 patient-days). In the present work we aimed to study the population of patients presenting with S. aureus bacteremia in 2013 and to genotype the corresponding S. aureus strains in order to identify a successful and/or virulent genotype to design a specific infection control program. One hundred ninety-one S. aureus isolates (including 9 methicillin-resistant) out of 199 corresponding cases of bacteremia were characterized with the spa typing method. Among 108 spa types, t571, t002, t008 and t084 were the most prevalent. Although not widely prevalent, t571 was the most frequently identified clone (8.4% of all isolates). Spa type t571 has been described in previous studies as belonging to the clonal complex CC398, which is consistent with the recent emergence of methicillin-susceptible S. aureus CC398 reported in blood cultures in Europe.
Collapse
|
21
|
Prevalence and Genomic Structure of Bacteriophage phi3 in Human-Derived Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates from 2000 to 2015. J Clin Microbiol 2018; 56:JCM.00140-18. [PMID: 29976589 DOI: 10.1128/jcm.00140-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/26/2018] [Indexed: 02/04/2023] Open
Abstract
Whereas the emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex 398 (CC398) in animal husbandry and its transmission to humans are well documented, less is known about factors driving the epidemic spread of this zoonotic lineage within the human population. One factor could be the bacteriophage phi3, which is rarely detected in S. aureus isolates from animals but commonly found among isolates from humans, including those of the human-adapted methicillin-susceptible S. aureus (MSSA) CC398 clade. The proportion of phi3-carrying MRSA spa-CC011 isolates, which constitute presumptively LA-MRSA within the multilocus sequence type (MLST) clonal complex 398, was systematically assessed for a period of 16 years to investigate the role of phi3 in the adaptation process of LA-MRSA to the human host. For this purpose, 632 MRSA spa-CC011 isolates from patients of a university hospital located in a pig farming-dense area in Germany were analyzed. Livestock-associated acquisition of MRSA spa-CC011 was previously reported as having increased from 1.8% in 2000 to 29.4% in 2014 in MRSA-positive patients admitted to this hospital. However, in this study, the proportion of phi3-carrying isolates rose only from 1.1% (2000 to 2006) to 3.9% (2007 to 2015). Characterization of the phi3 genomes revealed 12 different phage types ranging in size from 40,712 kb up to 44,003 kb, with four hitherto unknown integration sites (genes or intergenic regions) and several modified bacterial attachment (attB) sites. In contrast to the MSSA CC398 clade, phi3 acquisition seems to be no major driver for the readaptation of MRSA spa-CC011 to the human host.
Collapse
|
22
|
Willcocks SJ, Stabler RA, Atkins HS, Oyston PF, Wren BW. High-throughput analysis of Yersinia pseudotuberculosis gene essentiality in optimised in vitro conditions, and implications for the speciation of Yersinia pestis. BMC Microbiol 2018; 18:46. [PMID: 29855259 PMCID: PMC5984423 DOI: 10.1186/s12866-018-1189-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 05/18/2018] [Indexed: 12/12/2022] Open
Abstract
Background Yersinia pseudotuberculosis is a zoonotic pathogen, causing mild gastrointestinal infection in humans. From this comparatively benign pathogenic species emerged the highly virulent plague bacillus, Yersinia pestis, which has experienced significant genetic divergence in a relatively short time span. Much of our knowledge of Yersinia spp. evolution stems from genomic comparison and gene expression studies. Here we apply transposon-directed insertion site sequencing (TraDIS) to describe the essential gene set of Y. pseudotuberculosis IP32953 in optimised in vitro growth conditions, and contrast these with the published essential genes of Y. pestis. Results The essential genes of an organism are the core genetic elements required for basic survival processes in a given growth condition, and are therefore attractive targets for antimicrobials. One such gene we identified is yptb3665, which encodes a peptide deformylase, and here we report for the first time, the sensitivity of Y. pseudotuberculosis to actinonin, a deformylase inhibitor. Comparison of the essential genes of Y. pseudotuberculosis with those of Y. pestis revealed the genes whose importance are shared by both species, as well as genes that were differentially required for growth. In particular, we find that the two species uniquely rely upon different iron acquisition and respiratory metabolic pathways under similar in vitro conditions. Conclusions The discovery of uniquely essential genes between the closely related Yersinia spp. represent some of the fundamental, species-defining points of divergence that arose during the evolution of Y. pestis from its ancestor. Furthermore, the shared essential genes represent ideal candidates for the development of novel antimicrobials against both species. Electronic supplementary material The online version of this article (10.1186/s12866-018-1189-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Samuel J Willcocks
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Richard A Stabler
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Helen S Atkins
- Microbiology, CBR Division, DSTL Porton Down, Salisbury, SP4 0JQ, UK
| | - Petra F Oyston
- Microbiology, CBR Division, DSTL Porton Down, Salisbury, SP4 0JQ, UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| |
Collapse
|
23
|
Argudín MA, Deplano A, Vandendriessche S, Dodémont M, Nonhoff C, Denis O, Roisin S. CC398 Staphylococcus aureus subpopulations in Belgian patients. Eur J Clin Microbiol Infect Dis 2018; 37:911-916. [PMID: 29450768 DOI: 10.1007/s10096-018-3205-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/29/2018] [Indexed: 10/18/2022]
Abstract
Studies based on genome-wide single nucleotide polymorphisms (SNPs) supported the existence of two subpopulations in clonal complex (CC) 398 Staphylococcus aureus: an ancestral human-adapted clade (HC) and an animal-associated clade (AC). In this study, we have investigated the occurrence of genetic markers that allow discrimination of these subpopulations among CC398 isolates collected during 2014 to 2016 from human patients in Belgium. A collection of isolates was investigated by means of spa-typing and 16S-mecA-nuc PCR. CC398 isolates were classified as belonging to the human or the animal clade by using a canonical SNPs PCR and further studied by antimicrobial susceptibility and the presence of toxins, immune evasion cluster (IEC), and resistance genes. A total of 124 (7.8%) human isolates belonged to CC398. They were grouped into HC (n = 58) or AC (n = 66). The genes erm(T), pvl, chp, and scn were predominantly found in HC-CC398, while AC-CC398 isolates carried more frequently than the mecA, erm(C), tet(K), tet(M), and tet(L) genes. Different combinations of gene profiles were observed according to the clade. CC398 isolates from Belgian patients belonged to different subpopulations including typical HC and AC-isolates. Few HC-strains with mecA and AC-isolates harboring IEC were found. CC398 isolates from Belgian patients belonged to different subpopulations including typical HC and AC-isolates, as well as new emerging subpopulations that underline the ability of this lineage to acquire resistance and virulence genes. Further research is needed to evaluate the emergence of these subpopulations in the clinical setting.
Collapse
Affiliation(s)
- M Angeles Argudín
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium.
| | - A Deplano
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - S Vandendriessche
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - M Dodémont
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - C Nonhoff
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| | - O Denis
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium.,Ecole de Santé Publique, Université Libre de Bruxelles, Bruxelles, Belgium
| | - S Roisin
- National Reference Centre-Staphylococcus aureus, Department of Microbiology, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070, Brussels, Belgium
| |
Collapse
|
24
|
Kraushaar B, Hammerl JA, Kienöl M, Heinig ML, Sperling N, Dinh Thanh M, Reetz J, Jäckel C, Fetsch A, Hertwig S. Acquisition of virulence factors in livestock-associated MRSA: Lysogenic conversion of CC398 strains by virulence gene-containing phages. Sci Rep 2017; 7:2004. [PMID: 28515479 PMCID: PMC5435737 DOI: 10.1038/s41598-017-02175-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/07/2017] [Indexed: 11/25/2022] Open
Abstract
Staphylococcus aureus MRSA strains belonging to the clonal complex 398 (CC398) are highly prevalent in livestock and companion animals but may also cause serious infections in humans. CC398 strains in livestock usually do not possess well-known virulence factors that can be frequently found in other MRSA sequence types (ST). Since many staphylococcal virulence genes are residing on the genomes of temperate phages, the question arises why livestock-associated (LA-) CC398 strains are only rarely infected by those phages. We isolated and characterized four temperate phages (P240, P282, P630 and P1105) containing genes of the immune evasion cluster (IEC) and/or for the Panton-Valentine leucocidin (PVL). Sequence analysis of the phage genomes showed that they are closely related to known phages and that the DNA region encoding lysis proteins, virulence factors and the integrase exhibits numerous DNA repeats which may facilitate genomic rearrangements. All phages lysed and lysogenized LA-CC398 strains. Integration of IEC phage P282 was detected at ten sites of the hosts' chromosome. The prophages were stably inherited in LA-CC398 and enterotoxin A, staphylokinase and PVL toxin were produced. The data demonstrate that lysogenic conversion of LA-CC398 strains by virulence-associated phages may occur and that new pathotypes may emerge by this mechanism.
Collapse
Affiliation(s)
- Britta Kraushaar
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Jens Andre Hammerl
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Marina Kienöl
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Marie Luise Heinig
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Nina Sperling
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Mai Dinh Thanh
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Jochen Reetz
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Claudia Jäckel
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Alexandra Fetsch
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Stefan Hertwig
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany.
| |
Collapse
|
25
|
Diene SM, Corvaglia AR, François P, van der Mee-Marquet N. Prophages and adaptation of Staphylococcus aureus ST398 to the human clinic. BMC Genomics 2017; 18:133. [PMID: 28166723 PMCID: PMC5294865 DOI: 10.1186/s12864-017-3516-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/26/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND It has been suggested that prophages in the ST398 S. aureus clone are responsible for expanding ST398's spectrum of action and increasing its ability to cause human infections. We carried out the first characterization of the various prophages carried by 76 ST398 bloodstream infection (BSI) isolates obtained over 9 years of observation. RESULTS Whole-genome sequencing of 22 representative isolates showed (1) the presence of the φ3-prophage and diverse genetic features typical of animal-associated isolates (i.e., SCCmec XI element, Tn916 transposon and non φ3-prophages) in a majority of BSI isolates, (2) one BSI isolate devoid of the φ3-prophage but otherwise similar to an animal-infecting isolate, (3) 35 prophages carrying numerous genes previously associated with virulence or immune evasion in animal models of staphylococcal infections. The analysis of prophage content in all 76 BSI isolates showed an increasing prevalence of polylysogeny over time. Overall, over the course of the last 10 years, the BSI isolates appear to have acquired increasing numbers of genetic features previously shown to contribute to bacterial adaptation and virulence in animal models of staphylococcal infections. CONCLUSIONS We hypothesize that lysogeny has played a significant role in increasing the ability of the ST398 clone to cause infections in humans. Our findings highlight the risk that the ST398 lineage will increase its threat to public health by continuing to acquire virulence and/or multiple antibiotic-resistance genes from hospital-associated clones of Staphylococcus aureus.
Collapse
Affiliation(s)
- Seydina M Diene
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Anna Rita Corvaglia
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | - Nathalie van der Mee-Marquet
- Département de Microbiologie, Centre Hospitalier Régional Universitaire, and UMR 1282 Infectiologie Santé Publique, Université François-Rabelais, Tours, France
| | | |
Collapse
|
26
|
Gonçalves da Silva A, Baines SL, Carter GP, Heffernan H, French NP, Ren X, Seemann T, Bulach D, Kwong J, Stinear TP, Howden BP, Williamson DA. A phylogenomic framework for assessing the global emergence and evolution of clonal complex 398 methicillin-resistant Staphylococcus aureus. Microb Genom 2017; 3:e000105. [PMID: 28348878 PMCID: PMC5361625 DOI: 10.1099/mgen.0.000105] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Distinct clones of methicillin-resistant Staphylococcus aureus (MRSA) have emerged as important causes of infection in individuals who have exposure to livestock (livestock-associated MRSA; LA-MRSA). Clonal complex 398 (CC398) is the most prevalent LA-MRSA clone, and has been reported from several geographical settings, including Europe, the Americas and Asia. To understand the factors contributing to the global dissemination of this clone, we analysed CC398 MRSA isolates from New Zealand (NZ), a geographically isolated country with an economy strongly dependent on livestock farming. We supplemented the NZ CC398 MRSA collection with global datasets of CC398 MRSA and CC398 methicillin-susceptible S. aureus. Here, we demonstrate multiple sporadic incursions of CC398 MRSA into NZ, as well as recent importation and spread of a swine-associated clade related to the European LA-MRSA lineage. Within a larger global phylogenomic framework, Bayesian modelling suggested that this NZ clade emerged in the late 2000s, with a probable origin in swine from Western Europe. Elucidating the factors responsible for the incursion and spread of LA-MRSA in geographically distant regions, such as NZ, provides important insights into global pathways of S. aureus transmission, and will inform strategies to control importation and spread.
Collapse
Affiliation(s)
- Anders Gonçalves da Silva
- 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.,2Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sarah L Baines
- 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Glen P Carter
- 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Helen Heffernan
- 3Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nigel P French
- 4Infectious Disease Research Centre, Massey University, Palmerston North, New Zealand
| | - Xiaoyun Ren
- 3Institute of Environmental Science and Research, Wellington, New Zealand
| | - Torsten Seemann
- 2Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.,5Victorian Life Sciences Computation Initiative, Melbourne, Australia
| | - Dieter Bulach
- 2Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.,5Victorian Life Sciences Computation Initiative, Melbourne, Australia
| | - Jason Kwong
- 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Timothy P Stinear
- 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.,2Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Deborah A Williamson
- 1Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.,2Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| |
Collapse
|
27
|
Ballhausen B, Kriegeskorte A, van Alen S, Jung P, Köck R, Peters G, Bischoff M, Becker K. The pathogenicity and host adaptation of livestock-associated MRSA CC398. Vet Microbiol 2016; 200:39-45. [PMID: 27236228 DOI: 10.1016/j.vetmic.2016.05.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 05/10/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
Abstract
The presence of methicillin-resistant Staphylococcus aureus (MRSA) CC398 in livestock and their transmission to humans followed by their introduction into hospitals led to a significant burden for the human healthcare system, especially in regions with a high density of livestock breeding. The CC398 lineage made two host changes in its evolutionary history: From humans to pigs and other livestock-associated animals and back to the human host. These adaptation processes are mirrored by changes of the equipment with virulence factors necessary for successful host change. Here, we consider these factors and their special role during human colonization and infection. Host adaptation of S. aureus CC398 is accompanied by genetic changes that are mainly driven by exchanges of mobile genetic elements. So far, it is not clear, which virulence or adhesion factors are important for S. aureus CC398 in host interaction. Among human and animal-derived MRSA CC398 virulence factors, e.g. (entero-) toxins, were rarely found. Overall, this review provides a comprehensive overview on the emerging S. aureus lineage CC398 by summarizing current knowledge from microbiological, molecular and cellular interaction studies in relation to clinical and epidemiological perspectives.
Collapse
Affiliation(s)
- Britta Ballhausen
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany
| | - André Kriegeskorte
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany
| | - Sarah van Alen
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany
| | - Philipp Jung
- Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, Homburg, Saar, Germany
| | - Robin Köck
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, University of Saarland Hospital, Homburg, Saar, Germany
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital of Münster, Münster, Germany.
| |
Collapse
|
28
|
Bouiller K, Gbaguidi-Haore H, Hocquet D, Cholley P, Bertrand X, Chirouze C. Clonal complex 398 methicillin-susceptible Staphylococcus aureus bloodstream infections are associated with high mortality. Clin Microbiol Infect 2016; 22:451-5. [PMID: 26851655 DOI: 10.1016/j.cmi.2016.01.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/21/2016] [Accepted: 01/22/2016] [Indexed: 11/25/2022]
Abstract
Within the last decade, methicillin-resistant Staphylococcus aureus belonging to clonal complex 398 (CC398) has become a worldwide threat associated with livestock. More recently, methicillin-susceptible S. aureus (MSSA) belonging to CC398 have been increasingly reported as a cause of invasive infections in patients without livestock contact. We investigated risk factors associated with CC398 bloodstream infections (BSIs) compared with non-CC398 BSIs with a case-control study in a French university Hospital. From January 2010 to December 2014, nonduplicate Staphylococcus aureus (SA) isolates responsible for BSIs in adult patient were typed to identify those belonging to CC398. Each adult patient with a CC398 SA BSI (cases) was matched with 2 non-CC398 SA BSI controls randomly selected on the basis of the time at risk, the unit of hospitalization and susceptibility to methicillin. We retrospectively extracted the clinical information from electronic medical records and used conditional logistic regression for univariate and multivariate analyses. We identified 67 CC398 isolates among the 770 SA responsible for BSI in adult patients. All CC398 isolates were susceptible to methicillin. The proportion of CC398 among MSSA increased steadily from 4.6% in 2010 to 15.1% in 2013 and then stabilized at 13.8% in 2014. Factors significantly associated with CC398 MSSA BSIs were healthcare-associated infection (odds ratio (OR) 3.02, 95% confidence interval (CI) 1.19-7.63), history of neurologic disease (OR 2.51, 95% CI 1.13-5.65) and 30-day mortality (OR 2.44, 95% CI 1.23-4.85).
Collapse
Affiliation(s)
- K Bouiller
- Maladies infectieuses, Centre Hospitalier Régional Universitaire, Besançon, France.
| | - H Gbaguidi-Haore
- Hygiène hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université Bourgogne Franche-Comté/CNRS, Besançon, France
| | - D Hocquet
- Hygiène hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université Bourgogne Franche-Comté/CNRS, Besançon, France
| | - P Cholley
- Hygiène hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université Bourgogne Franche-Comté/CNRS, Besançon, France
| | - X Bertrand
- Hygiène hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université Bourgogne Franche-Comté/CNRS, Besançon, France
| | - C Chirouze
- Maladies infectieuses, Centre Hospitalier Régional Universitaire, Besançon, France; Hygiène hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France; UMR 6249 Chrono-environnement, Université Bourgogne Franche-Comté/CNRS, Besançon, France
| |
Collapse
|
29
|
Varga M, Pantu˚ček R, Ru˚žičková V, Doškarˇ J. Molecular characterization of a new efficiently transducing bacteriophage identified in meticillin-resistant Staphylococcus aureus. J Gen Virol 2016; 97:258-268. [DOI: 10.1099/jgv.0.000329] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Marian Varga
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
| | - Roman Pantu˚ček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
| | - Vladislava Ru˚žičková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
| | - Jirˇí Doškarˇ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlárˇská 2, 611 37 Brno, Czech Republic
| |
Collapse
|
30
|
Von Dach E, Diene SM, Fankhauser C, Schrenzel J, Harbarth S, François P. Comparative Genomics of Community-Associated Methicillin-Resistant Staphylococcus aureus Shows the Emergence of Clone ST8-USA300 in Geneva, Switzerland. J Infect Dis 2015; 213:1370-9. [PMID: 26464204 DOI: 10.1093/infdis/jiv489] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/18/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Previous investigations of community-associated methicillin-resistant Staphylococcus aureus(CA-MRSA) isolates have revealed a wide diversity of genetic backgrounds, with only sporadic occurrence of ST8-USA300, in Geneva, Switzerland. We conducted a molecular epidemiologic analysis to identify the origin of a sudden increase of ST8 PVL-positive isolates in Geneva during 2013. METHODS On the basis of prospective CA-MRSA surveillance, we collected colonizing and infecting ST8-USA300 isolates and compared them to non-ST8 CA-MRSA isolates. Whole-genome sequencing (WGS) was performed for each isolate of this collection, and discriminating molecular features were linked to patient data. RESULTS In 2013, 22 isolates with the ST8-USA300 profile were identified among 46 cases of CA-MRSA. WGS revealed 2 groups of strains that differed by the type of the SCCmec IV element encoded and whether they harbored an arginine catabolism mobile element (ACME) locus. ACME-negative strains were mainly isolated from patients traveling in or originating from South America. Single-nucleotide polymorphism positions in isolate groups were used to infer their common ancestor, determine their geographical origin, and trace their relatedness. CONCLUSIONS WGS allowed the identification of transmission events and revealed that the increased prevalence of USA300 CA-MRSA isolates resulted from multiple importation events from the Americas but not from local clonal expansion of a successful clone.
Collapse
Affiliation(s)
- Elodie Von Dach
- Infection Control Program, Geneva University Hospitals Faculty of Medicine, University of Geneva, Switzerland
| | - Seydina M Diene
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals Faculty of Medicine, University of Geneva, Switzerland
| | - Carolina Fankhauser
- Infection Control Program, Geneva University Hospitals Faculty of Medicine, University of Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals Faculty of Medicine, University of Geneva, Switzerland
| | - Stephan Harbarth
- Infection Control Program, Geneva University Hospitals Faculty of Medicine, University of Geneva, Switzerland
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals Faculty of Medicine, University of Geneva, Switzerland
| |
Collapse
|
31
|
Botka T, Růžičková V, Konečná H, Pantůček R, Rychlík I, Zdráhal Z, Petráš P, Doškař J. Complete genome analysis of two new bacteriophages isolated from impetigo strains of Staphylococcus aureus. Virus Genes 2015; 51:122-31. [PMID: 26135320 DOI: 10.1007/s11262-015-1223-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/23/2015] [Indexed: 11/26/2022]
Abstract
Exfoliative toxin A (ETA)-coding temperate bacteriophages are leading contributors to the toxic phenotype of impetigo strains of Staphylococcus aureus. Two distinct eta gene-positive bacteriophages isolated from S. aureus strains which recently caused massive outbreaks of pemphigus neonatorum in Czech maternity hospitals were characterized. The phages, designated ϕB166 and ϕB236, were able to transfer the eta gene into a prophageless S. aureus strain which afterwards converted into an ETA producer. Complete phage genome sequences were determined, and a comparative analysis of five designed genomic regions revealed major variances between them. They differed in the genome size, number of open reading frames, genome architecture, and virion protein patterns. Their high mutual sequence similarity was detected only in the terminal regions of the genome. When compared with the so far described eta phage genomes, noticeable differences were found. Thus, both phages represent two new lineages of as yet not characterized bacteriophages of the Siphoviridae family having impact on pathogenicity of impetigo strains of S. aureus.
Collapse
Affiliation(s)
- Tibor Botka
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37, Brno, Czech Republic
| | | | | | | | | | | | | | | |
Collapse
|
32
|
van der Mee-Marquet NL, Corvaglia A, Haenni M, Bertrand X, Franck JB, Kluytmans J, Girard M, Quentin R, François P. Emergence of a novel subpopulation of CC398 Staphylococcus aureus infecting animals is a serious hazard for humans. Front Microbiol 2014; 5:652. [PMID: 25538688 PMCID: PMC4257084 DOI: 10.3389/fmicb.2014.00652] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/12/2014] [Indexed: 11/17/2022] Open
Abstract
Until recently, Staphylococcus aureus from clonal complex (CC)398 were mostly described as colonizing asymptomatic raised pigs and pig-farmers. Currently, the epidemiology of the CC398 lineage is becoming more complex. CC398 human-adapted isolates are increasingly being identified in bloodstream infections in humans living in animal-free environments. In addition, CC398 isolates are increasingly responsible for invasive infections in various animals. CC398 isolates that colonize asymptomatic pigs and the isolates that infect humans living in animal-free environments (human-adapted isolates) both lack several clinically important S. aureus–associated virulence factors but differ on the basis of their prophage content. Recent findings have provided insight into the influence of a φMR11-like helper prophage on the ability of CC398 isolates to infect humans. To assess the recent spread of the CC398 lineage to various animal species and to investigate the links between the φMR11-like prophage and the emergence of CC398 isolates infecting animals, we studied 277 isolates causing infections in unrelated animals. The prevalence of CC398 isolates increased significantly between 2007 and 2013 (p < 0.001); 31.8% of the animal isolates harbored the φMR11-like prophage. High-density DNA microarray experiments with 37 representative infected-animal isolates positive for φMR11-like DNA established that most infected-animal isolates carried many genetic elements related to antimicrobial resistance and virulence genes, and a φ3 prophage encoding immune-modulating proteins and associated with animal-to-human jumps. Our findings suggest recent clonal expansion and dissemination of a new subpopulation of CC398 isolates, responsible for invasive infections in various animals, with a considerable potential to colonize and infect humans, probably greater than that of human-adapted CC398 isolates, justifying active surveillance.
Collapse
Affiliation(s)
- Nathalie L van der Mee-Marquet
- Service de Bactériologie et Hygiène, Centre Hospitalier Régional Universitaire Tours, France ; UMR 1282, Infectiologie et Santé Publique, Université Francois Rabelais Tours, France
| | - Anna Corvaglia
- Genomic Research Laboratory, University of Geneva Hospitals Geneva, Switzerland
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Agence Nationale de Sécurité Sanitaire (Anses) Lyon, France
| | - Xavier Bertrand
- Service d'Hygiène, Centre Hospitalier Universitaire Besançon, France ; UMR 6249 Chrono-environnement, Université de Franche-Comté Besançon, France
| | - Jean-Baptiste Franck
- Service de Bactériologie et Hygiène, Centre Hospitalier Régional Universitaire Tours, France
| | - Jan Kluytmans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda and VU University Medical Center Amsterdam, Netherlands
| | - Myriam Girard
- Genomic Research Laboratory, University of Geneva Hospitals Geneva, Switzerland
| | - Roland Quentin
- Service de Bactériologie et Hygiène, Centre Hospitalier Régional Universitaire Tours, France
| | - Patrice François
- Genomic Research Laboratory, University of Geneva Hospitals Geneva, Switzerland
| |
Collapse
|
33
|
Chlebowicz MA, Mašlaňová I, Kuntová L, Grundmann H, Pantůček R, Doškař J, van Dijl JM, Buist G. The Staphylococcal Cassette Chromosome mec type V from Staphylococcus aureus ST398 is packaged into bacteriophage capsids. Int J Med Microbiol 2014; 304:764-74. [DOI: 10.1016/j.ijmm.2014.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/27/2014] [Accepted: 05/25/2014] [Indexed: 11/24/2022] Open
|
34
|
Wendlandt S, Feßler AT, Kadlec K, van Duijkeren E, Schwarz S. Identification of the novel spectinomycin resistance gene spd in a different plasmid background among methicillin-resistant Staphylococcus aureus CC398 and methicillin-susceptible S. aureus ST433. J Antimicrob Chemother 2014; 69:2000-3. [PMID: 24648508 DOI: 10.1093/jac/dku067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sarah Wendlandt
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Andrea T Feßler
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Kristina Kadlec
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Engeline van Duijkeren
- Centre for Infectious Disease Control Netherlands (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Stefan Schwarz
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| |
Collapse
|
35
|
Genome Sequences of Sequence Type 45 (ST45) Persistent Methicillin-Resistant Staphylococcus aureus (MRSA) Bacteremia Strain 300-169 and ST45 Resolving MRSA Bacteremia Strain 301-188. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00174-14. [PMID: 24625873 PMCID: PMC3953194 DOI: 10.1128/genomea.00174-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Persistent methicillin-resistant Staphylococcus aureus (MRSA) bacteremia (positive blood cultures after ≥7 days) represents a challenging subset of invasive MRSA infections. The comparison of genome sequences of persistent (300-169) and resolving (301-188) MRSA bacteremia isolates with similar genetic background (sequence type 45 [ST45]) will help us to better understand underlying mechanisms of persistent MRSA bacteremia.
Collapse
|
36
|
Brisse S, Brehony C, Conceição T, Cubero M, Glasner C, Le Gouil M, Renvoisé A, Sheppard S, Weinert LA. Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference. Res Microbiol 2014; 165:140-53. [PMID: 24486597 PMCID: PMC7126388 DOI: 10.1016/j.resmic.2014.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sylvain Brisse
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France; CNRS, UMR3525, Paris, France.
| | - Carina Brehony
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Teresa Conceição
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa (UNL), Oeiras, Portugal
| | - Meritxell Cubero
- Microbiology Department, Hospital Universitari de Bellvitge-University of Barcelona-IDIBELL, Barcelona, Spain; CIBER de Enfermedades Respiratorias, ISCIII, Madrid, Spain
| | - Corinna Glasner
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Meriadeg Le Gouil
- Institut Pasteur, Environment and Infectious Risks unit, Paris, France
| | - Aurélie Renvoisé
- AP-HP, Hôpital Pitié-Salpêtrière, Bactériologie-Hygiène, F-75013, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, U1135, Centre for Immunology and Microbial Infections, team 13, F-75013, Paris, France; INSERM, U1135, Centre for Immunology and Microbial Infections, team 13, F-75013, Paris, France
| | | | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
37
|
Whole-Genome Sequences of Staphylococcus aureus ST398 Strains of Animal Origin. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00689-13. [PMID: 24072856 PMCID: PMC3784776 DOI: 10.1128/genomea.00689-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Staphylococcus aureus sequence type 398 (ST398) was originally associated with animal infections. We announce the complete genome sequences of two ST398 methicillin-susceptible S. aureus strains from the livestock environment. These genome sequences assist in the characterization of interesting ST398 features relying on host tropism and epidemiological settings.
Collapse
|
38
|
Whole-Genome Sequences of Two Staphylococcus aureus ST398 Strains of Human Origin, S94 and S100. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00691-13. [PMID: 23990587 PMCID: PMC3757448 DOI: 10.1128/genomea.00691-13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Sequence type 398 (ST398) Staphylococcus aureus was originally associated with animal infection. We announce the complete genome sequences of two ST398 methicillin-susceptible S. aureus strains of human origin, S94 and S100. The genome sequences assist in the characterization of interesting ST398 features related to host specificities.
Collapse
|
39
|
Whole-Genome Sequence of the Ancestral Animal-Borne ST398 Staphylococcus aureus Strain S123. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00692-13. [PMID: 23990588 PMCID: PMC3757449 DOI: 10.1128/genomea.00692-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Sequence type 398 (ST398) Staphylococcus aureus was originally reported in livestock. We announce the complete genome sequence of an ST398 methicillin-susceptible S. aureus strain of animal origin, S123. The genome sequence reveals a wild-type genome that probably corresponds to an ancestral clone.
Collapse
|