1 Université Libre de Bruxelles (ULB) - Faculté de Médecine
Universiteit Gent (Ugent) – Faculteit Diergeneeskunde
Molecular Epidemiology of
Livestock-associated Staphylococcus aureus in Animal and Human Populations in Belgium
Stien Vandendriessche
Reference Laboratory for Staphylococci – MRSA, Hopital Erasme, Faculty of Medicine, ULB Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ugent
Thesis submitted in fulfilment of the requirements for the degree of Doctor (PhD) in Biomedical Sciences (ULB) – Veterinary Sciences (Ugent)
2012
Promoters: Prof. dr. Marc Struelens (ULB), Prof. dr. Freddy Haesebrouck (UGent) Co-promoter: Prof. dr. Olivier Denis (ULB)
2 TABLE OF CONTENTS
List of Tables... iii
List of Figures... iv
List of Abbreviations... v
1. Summary ……….. 3
2. Introduction - Review of the literature……… 5
2.1. Microbiology of Staphylococcus aureus………... 7
2.1.1. Taxonomy………. 7
2.1.2. Genome composition……….. 7
2.1.2.1. Core genome………. 9
2.1.2.2. Mobile genetic elements……… 10
2.1.2.2.1. Bacteriophages……….. 11
2.1.2.2.2. Staphylococcal pathogenicity islands (SaPi)……….. 11
2.1.2.2.3. Genomic islands (GI)……….. 11
2.1.2.2.4. Plasmids………. 12
2.1.2.2.5. Insertion sequences ……… 12
2.1.2.2.6. Transposons ……… 12
2.1.2.2.7. Staphylococcal cassette chromosome (SCC) elements…. 13 2.1.3. Pathogenicity……….. 17
2.1.3.1. Virulence factors ………... 17
2.1.3.2. Regulation of virulence……….. 19
2.1.4. Antibiotic resistance determinants……… 21
2.1.4.1. β-lactams………. 21
2.1.4.2. Glycopeptides……….. 25
2.1.4.3. Macrolides, Lincosamides and Streptogramins ………. 26
2.1.4.4. Oxazolidinones……… 29
2.1.4.5. Aminoglycosides (including aminocyclitols)……… 29
2.1.4.6. Tetracyclines……… 30
2.1.4.7. Fluoroquinolones……….. 31
2.1.4.8. Sulfonamides and trimethoprim……….. 31
2.1.4.9. Other antimicrobial agents ...………. 32
2.1.4.9.1. Phenicols……… 32
2.1.4.9.2. Pleuromutilins……… 33
2.1.4.9.3. Mupirocin……….. 33
2.1.4.9.4. Fusidic acid……… 33
2.1.4.9.5. Rifampicin……….. 33
2.1.4.9.6. Resistance to heavy metals……….. 34
2.2. Identification and typing of Staphylococcus aureus………... 35
2.2.1. Detection, identification and antimicrobial susceptibility testing….. 35
2.2.2. Molecular Typing………... 36
2.2.2.1. Pulsed-field gel electrophoresis……….. 37
2.2.2.2. spa typing………. 39
3
2.2.2.3. Multi-locus sequence typing………. 40
2.2.2.4. SCCmec typing……… 41
2.3. Epidemiology of Staphylococcus aureus……….… 47
2.3.1. Ecology and clinical manifestations ………...……….. 43
2.3.1.1. In humans... 43
2.3.1.2. In animals... 43
2.3.2. Population structure of S. aureus in humans and animals... 46
2.3.3. Molecular epidemiology of methicillin-resistant S. aureus in humans 51 2.3.3.1. Healthcare-associated MRSA (HA-MRSA)... 51
2.3.3.2. Community-associated MRSA (CA-MRSA)... 54
2.3.3.3. Livestock-associated MRSA (LA-MRSA)... 57
2.3.3.3.1. In humans... 59
2.3.3.3.2. In animals... 59
3. Objectives... 65
4. Materials and Methods... 69
5. Results... 71
5.1. Prevalence and genetic diversity of methicillin-resistant Staphylococcus aureus carried by humans and animals across livestock production sectors... 73
5.2. Large variation of methicillin-susceptible Staphylococcus aureus genotypes (MSSA) in humans and animals on livestock farms and loss of SCCmec DNA in porcine MSSA CC398 due to recombination.... 89
5.3. Previous healthcare exposure is the main antecedent for methicillin- resistant Staphylococcus aureus carriage on hospital admission in Belgium 111 5.4. Methicillin-susceptible Staphylococcus aureus ST398-t571 harbouring the macrolide, lincosamide, streptogramin B resistance gene erm(T) in Belgian hospitals... 135
6. General discussion... 151
7. Conclusions and perspectives... 169
8. Reference List... 173
9. Thèse annexe... 213
Acknowledgements... 215
Curriculum vitae... 217
